CHEMICALLY MODIFIED PEPTIDES WITH IMPROVED IMMUNOGENICS

Cross Reference To Related Applications

This application claims the benefit of United States Provisional Application Nos. 60/929,125, filed June 14, 2007, 60/960,771 , filed October 12, 2007, and 61/060,978, filed June 12, 2008 (USPTO confirmation No. 8650), the entire disclosure of each of which is relied upon and incorporated by reference in its entirety.

Sequence Listing

This application contains a Sequence Listing that has been submitted via a printed paper copy, and it is incorporated by reference in its entirety.

Field of the Invention

The present invention relates to methods of preparing compositions and vaccines comprising chemically modified peptides. The invention also includes compositions and vaccines comprising chemically modified peptides.

Background

Many viruses and toxins require inactivation before they can be used as vaccines and chemical modifying agents such as formaldehyde have been widely used in vaccine production. Notable examples include, for instance, polio, tetanus, diphtheria, botulinum and anthrax vaccines. Protein modification by formaldehyde is complex and involves the chemical modification of several amino acid residues (such as arginine and lysine) and also the formation of cross-links (methylene bridges) which can lead to extensive protein aggregation (Metz et al. (2004) J. Biol Chem., 279: 6235-6243).

The use of formaldehyde for vaccine production does have its drawbacks, the most common of which is the modification of protein structure which results in a loss of immunogenic epitopes and an over all decrease in the immunogenicity of the protein (Vani et al. (2006) J. Immunol Methods . 317, 80-89). However, for some small proteins, formaldehyde has been reported to enhance the immune response through protein aggregation. For instance, it has been reported that formaldehyde treatment increases the immunogenicity and decreases the toxicity of low molecular weight Haemophilus

ducreyi cytolethal distending toxins (HdCDT) (Lagergard et al. (2007) Vaccine: 25, 3606- 14).. Problems associated with formaldehyde treatment, particularly the frequent reduction of immunogenicity and the complexity of the final product through aggregation, have led to a decline in its use, especially with the introduction of recombinant technology which provides a means of rendering harmful proteins inactive through site directed mutagenesis.

The botulinum neurotoxins (BoNTs) are a family of seven antigenically different protein toxins (serotypes A-G). These neurotoxins are extremely potent neuroparalytic agents which act primarily at the peripheral nervous system where they inhibit the release of acetylcholine at the neuromuscular junction (Niemann (1991) In Sourcebook of Bacterial Protein Toxins (Alouf, J. E. & Freer, J. H. eds.), pp. 303-348, Academic Press, London). This is mediated via highly specific zinc-dependent endopeptidase activity directed at small proteins involved in the fusion and release of synaptic vesicles. The botulinum neurotoxins are structurally similar; they have 30-40% sequence homology and, as diagrammatically shown immediately below, each neurotoxin consists of a heavy chain (100 kDa) and a light chain (50 kDa) linked by a disulphide bridge (Niemann, 1991 , as above). Despite structural similarities, antisera raised against purified neurotoxins show no cross-protection between the neurotoxin serotypes and thus necessitate the development of a separate vaccine for each serotype. In addition, within each serotype, various subtypes exist (Minton (1995) In: Current Topics in Microbiology and Immunology 195 'Clostridial Neurotoxins' (Montecucco, C, ed.) pp. 161-194, Springer, Berlin). Since these subtypes differ in their antigenic properties, the presence of these toxin variants needs to be taken into account in vaccine design to ensure adequate cross protection.

Structure of Botulinum Neurotoxins and the LH _N Fragment

Light Chain Heavy Chain

(Enzymatic) (Translocation (Binding) Domain Domain Domain

L H _N

Holotoxin I

I I s-s

LH _N L H _N

I

I I s- S

The C-terminal 50 kDa fragment (H _c fragment) is responsible for receptor-binding at the presynaptic nerve surface (Halpern & Loftus (1993) J. Biol. Chem. 268, 11188-11192); (Shone et al. (1985) Eur. J. Biochem., 151 , 75-82). The N-terminal 50 kDa portion of the heavy chain (H _N fragment) is involved in translocation of the enzymatically active light chain to within the nerve terminal (Shone et al. (1987) Eur. J. Biochem., 167, 175-180). Removal of the H _c domain from the BoNT leaves a fragment (LH _N ) consisting of the light chain and translocation domain which, although virtually non-toxic, is stable and soluble. Any residual toxicity is eliminated by double mutations in the enzymatic domain yielding a non-toxic LH _N vaccine.

Tetanus and the botulinum neurotoxin are extremely potent, bacterial neurotoxins produced by various strains of Clostridia. The botulinum neurotoxins consist of seven distinct serotypes and a separate vaccine is required for each. First generation tetanus and botulinum vaccines consist of purified or partially purified toxins treated with formaldehyde to eliminate the neurotoxic action of these protein toxins. In the case of the botulinum toxins, complete detoxification requires incubation of toxin preparations for over three weeks in order to generate the toxoid vaccine derivative. In addition, since the botulinum toxins are in the form of high molecular weight (300 - 900 kDa) protein complexes, the resulting toxoid product is an extremely heterogeneous mixture consisting of very high molecular weight species (Singh et al. (1989) Toxicon 27, 403- 410). Another disadvantage of formaldehyde treatment is that in the case of some of the botulinum toxoid serotypes (e.g., type A), several epitopes are destroyed in the prolonged toxoiding process (Hallis et al. (1993) Characterization of monoclonal antibodies to BoNT/A. In: Botulinum and Tetanus Neurotoxins, (DasGupta, B., Ed.) p 433-436, Plenum Press).

Second generation botulinum vaccines are based on non-toxic fragments of the botulinum toxins and are designed to eliminate the requirement for a detoxification step with formaldehyde. One such vaccine candidate is the LH _N fragment (light chain domain plus H _N translocation domain), which consists of the N-terminal two-thirds of the botulinum neurotoxin moiety. This fragment is a single chain polypeptide which lacks the ability of the parent neurotoxin to bind to nerve endings and in addition may contain one or more amino acid mutations within the light chain domain to render it completely

non-toxic. In addition to being non-toxic, the LH _N fragments are easy to characterize being monomeric in solution with none of the complex aggregation associated with the corresponding toxoid which is normally purified as a toxin complex. See, for instance, U.S. Patent Application Nos.: 11/717,713 and 11/077,550, which are herein incorporated by reference in their entireties.

The diversity within the BoNT family is a major problem for vaccine design and the extent of this problem is only now becoming appreciated. While it is widely recognised that the different BoNT serotypes are antigenically distinct and require separate vaccines, it is less well appreciated that antigenically different sub-types exist within each of the main BoNT serotypes (Smith et al (2005) Infect Immum, 73:5450-5457). BoNT/A, for example, is now known to contain at least 4 sub-types and a similar number of sub-types exists within the BoNT/B family. Differences in the primary structure within the various subtypes are reflected in differences in their antigenic profile, with the result that a vaccine which protects against one toxin subtype may not protect against another. Providing adequate protection against toxin sub-types is an important consideration for vaccine design.

There is therefore a need for improved botulinum and tetanus vaccines, such as vaccines having one or more of: an improved protective effect; improved stability; improved cross-serotype protection; and improved cross-subserotype protection.

In addition to the above-mentioned clostridial species, Clostridium difficile is now a major problem as a healthcare acquired infection (HCAI). The bacterium causes nosocomial, antibiotic-associated diarrhoea and pseudomembranous colitis in patients treated with broad-spectrum antibiotics. Elderly patients are most at risk from these potentially life- threatening diseases and incidents of hospital infection have increased dramatically over the last 10 years. Strains of C. difficile produce a variety of virulence factors, notable among which are several protein toxins: Toxin A, Toxin B and, in some strains, a binary toxin which is similar to Clostridium perfringens lota toxin. Toxin A is a large protein cytotoxin/enterotoxin, which plays a key role in the pathology of infection and which also appears to have some role in the gut colonisation process. Toxin B, which is primarily a cytotoxin, appears to act synergistically with Toxin A.

Antibodies to Toxins A and B have been shown to protect against Clostridium difficile associated disease and hence non-toxic fragments of either Toxin A, B, or the binary toxin have potential as vaccines or as antigens for producing therapeutic antibodies. Recombinant fragments of Clostridium difficile toxins, however, generally do not produce a strong neutralising response in animals in conjunction with an adjuvant such as aluminium hydroxide (e.g., Alhydrogel).

Again, there is therefore the need for an improved C. difficile vaccine such as a vaccine having one or more of: an improved protective effect; and improved stability.

Anthrax is an acute infectious disease in humans and animals that is caused by the bacterium Bacillus anthracis and which in some forms is lethal. Protective antigen (PA), lethal factor (LF) and edema factor (EF) are components of anthrax toxin which play a key role in mediating its biological effects and the disease. PA contains domains that bind cell receptors and which can effect the translocation of EF and LF into cells. Once inside the cell, LF and EF have lytic actions via different mechanisms. PA, EF, and LF on their own are non-toxic and are only active in combinations in which one component is PA.

Since PA is the common factor required for both the actions of LF and EF, a recombinant fragment has been assessed as a vaccine for anthrax. Recombinant PA, however, does not elicit a strong protective response against the disease and there have also been issues with its stability.

There is therefore the need for an improved anthrax vaccine, such as a vaccine having one or more of: an improved protective effect; and improved stability.

Summary of the Invention

The invention provides a method of increasing the protective effect or improving the stability of a peptide or polypeptide by chemically modifying it. In some embodiments, the increased protective effect is an improved ability to stimulate an immune response. In other embodiments, the increased protective effect may be improved cross-serotype protection. In yet other embodiments, the increased protective effect may be improved cross-subtype protection. In still other embodiments, the increased protective effect is a

combination of one, two, or three of an improved ability to stimulate an immune response, an improved cross-serotype protection, and an improved cross-subtype protection. Often, although not always, the increased protective effect of the peptide or polypeptide is associated with an increase in stability of the peptide or polypeptide.

In one embodiment, the increase in the protective effect or the improvement of the stability of a peptide is due to the formation of cross-linking or methylene bridges induced by the chemical agent. For instance, the invention includes methods of treating a Clostridium neurotoxin fragment with a chemical agent such as formaldehyde that induces the formation of methylene bridges between arginine, lysine and histidine residues.

In one embodiment, the increased protective effect of the methods and vaccine compositions of the invention is not due to polypeptide aggregation. In another embodiment, the increased protective effect is the result of little to no polypeptide aggregation. Specifically, the invention includes methods of treating a bacterial peptide with a chemical agent in such a manner that does not result in peptide aggregation or that does not result in a significant increase in peptide aggregation. For instance, the invention includes treating a Clostridium neurotoxin fragment with a chemical agent such as formaldehyde under conditions that do not result in aggregation or a significant amount of aggregation.

In one embodiment, the method involves contacting the peptide or polypeptide with a chemical modification agent for a brief period of time or for a time sufficient to obtain a desired property in the peptide or polypeptide. For instance, in some embodiments, the peptide or polypeptide is contacted with the chemical modification agent such as formaldehyde for a period of less than about 5 days, less than about 4 days, less than about 3 days, less than about 2 days, less than about 1 day, or less than about 12 hours.

In one embodiment of the invention, a chemical modification agent that induces cross- linking increases the immunogenicity and/or stability of a bacterial peptide. In another embodiment, a chemical modification agent that induces methylene bridging increases the immunogenicity and/or stability of a bacterial peptide. In one embodiment of the

invention, the chemical modification agent is formaldehyde. However, other agents may also be used. For instance, additional chemical modification agents that induce cross- linking or formation of methylene bridges, include, but are not limited to, C6-succinimidyl 4-hydrazinonicotinate acetone hydrazone, C6-succinimidyl 4-formylbenzoate, BIS- (Sulfosuccinimidyl) suberate, disuccinimidyl suberate, dimethyl suberimidate dihydrochloride, dimethyl pimelimidate 2 HCI, dimethyl adipimidate dihydrochloride, succinimidyl 4-hydrazidoterephthalate hydrochloride, and disuccinimidyl glutarate.

Irrespective of the identity of the chemical modification agent, many embodiments use the agent at a low concentration. In those embodiments, the concentration is less than about 2% (v/v or w/v based on the ratio of the modifying agent to the total reaction mixture). Alternatively, the concentration may be expressed as a molar ratio of agentpolypeptide, in which case the ratio is generally between about 3:1 and about 50:1. In addition, the temperature at which the chemical modification agent and the peptide or polypeptide are contacted may vary. In many embodiments, the contact temperature is between about 3 ⁰ C and about 45 ⁰ C.

Immunogenicity, the protective effect and/or stability of many different peptides or polypeptides can be increased by chemical modification in accordance with the methods of the invention. For example, the methods may be used to increase the protective effect of clostridial neurotoxins. Examples of such clostridial peptides and polypeptides include C. botulinum BoNT/A, C. botulinum BoNT/B, C. botulinum BoNT/E, tetanus toxin, and the different subtypes of each of the BoNT serotypes (e.g., BoNT/AI , BoNT/A2 and BoNT/A3). In various embodiments, the peptide or polypeptide is the native clostridial neurotoxin, a recombinant protein modified to render it non-toxic, or fragments, which may also have been rendered nontoxic via amino acid substitutions or deletions. In other embodiment, the clostridial neurotoxin is a fusion protein comprising a native clostridial neurotoxin, recombinant neurotoxin or neurotoxin fragment and a second polypeptide. The second polypeptide includes, for instance, a toxin (native, recombinant or fragment), a polypeptide useful for the isolation and/or isolation of the fusion protein, and/or a polypeptide useful for increasing the stability of the fusion protein.

Clostridial fragments encompassed by the methods of the present invention include, but are not limited to, the LH _N fragment of BoNT or tetanus toxin. In one embodiment, the

Clostridial peptides do not comprise a H _c fragment. Further the Clostridial polypeptides and fragments may be modified so that they are endopeptidase-negative. For instance, in one embodiment, the Clostridial peptide is a formaldehyde-treated LH _N /E fragment modified to be endopeptidase negative. In another embodiment, the Clostridial peptide is a formaldehyde-treated LH _N /A fragment modified to be endopeptidase negative. In yet another embodiment, the Clostridial peptide is a formaldehyde-treated LH _N /B fragment modified to be endopeptidase negative.

In still other embodiments, the methods are useful for increasing the immunogencity and/or stability of Clostridium difficile peptides and polypeptides, for instance, Clostridium difficile toxins or toxin fragments or toxin fusion proteins. For example, the invention includes, but is not limited to, Clostridium difficile Toxin A, Toxin B, binary toxin, or Clostridium difficile surface peptides, such as the Cwp 84 peptide.

In yet other embodiments, the methods are useful for increasing the immunogencity and/or stability of Bacillus anthracis polypeptides and peptides. Examples include lethal factor and protective antigen. Of course, there are many other peptides and polypeptides for which it is desirable to increase their protective effect, and those peptides and polypeptides are also encompassed by the invention.

The invention also provides compositions comprising chemically modified peptides and polypeptides. In some embodiments, the chemically modified peptides and polypeptides have an increased protective effect that may be measured by their improved ability to stimulate an immune response when compared to an unmodified peptide or polypeptide. In other embodiments, the increased protective effect may be measured by the ability to provide improved cross-serotype protection when compared to an unmodified peptide or polypeptide. In yet other embodiments, the increased protective effect may be measured by the ability to provide improved cross-subtype protection when compared to an unmodified peptide or polypeptide. In still other embodiments, the increased protective effect may be measured by a combination of one, two, or three of the ability to provide an improved immunogenicity, induce a protective immune response, provide an improved cross-serotype protection, and provide an improved cross-subtype protection. Often, although not always, the peptide or polypeptide may display an increase in stability compared to the unmodified peptide or polypeptide. The increased

immunogenicity and/or stability is due, at least in some embodiments, to intra-molecular cross-links, such as those comprising one or more methylene bonds. Also, in some embodiments, the peptide or polypeptide does not form aggregates.

Vaccines comprising one or more of the chemically modified peptides or polypeptides are also provided. In one embodiment, the vaccine comprises a Clostridium botulinum LH _N fragment that has been treated with formaldehyde for less than about 5 days, less than about 4 days, less than about 3 days, less than about 2 days or less than about 1 day. In one embodiment, the formaldehyde-treated LH _N fragment is modified to to be endopeptidase negative and is a LH _N /A, LH _N /B or LH _N /E fragment. The invention includes, for instance, a bivalent or trivalent vaccine comprising one or more of formaldehyde-treated, endopeptidase negative LH _N /A, LH _N /B or LH _N /E fragments.

The vaccine may further comprise one or more adjuvants. One non-limiting example of an adjuvant is aluminium hydroxide. In one embodiment, the invention includes a monovalent, bivalent or trivalent vaccine comprising one or more of formaldehyde- treated, endopeptidase negative LH _N /A, LH _N /B or LH _N /E fragments and an adjuvant.

The invention also provides methods of stimulating an immune response in a mammal, such as a human, by administering to the mammal an amount of a vaccine of the invention sufficient to stimulate an immune response. The invention includes a method of stimulating an immune response in a subject comprising administering to the subject a monovalent, bivalent or trivalent vaccine comprising one or more of formaldehyde- treated, endopeptidase negative LH _N /A, LH _N /B or LH _N /E fragments and, optionally, an adjuvant. The invention also includes, for instance, a method of stimulating an immune response in a subject comprising administering to the subject a vaccine comprising a chemically modified bacterial peptide from a BSL-3 pathogen or BSL-4 pathogen, such as B. anthracis.

In some embodiments, immune stimulation is measured by an increased protective effect compared to a vaccine comprising the unmodified form of the same peptide or polypeptide. In other embodiments, immune stimulation is measured by an increase in antibody titer that is specific for the antigen in the vaccine. In still other embodiments,

immune stimulation is measured by an increased frequency in cytotoxic T lymphocytes specific for the antigen in the vaccine.

The invention also provides methods of preventing or treating an infection in a subject comprising administering a chemically modified bacterial peptide of the invention to a subject. In one embodiment of the invention, the peptide is administered at a dose necessary to induce a protective immune response. In one embodiment, the peptide is administered at a dose necessary to produce neutralizing antibodies. The invention includes, for instance, methods of preventing or treating a Clostridium botulinum invention in a subject comprising administering to the subject a monovalent, bivalent or trivalent vaccine comprising one or more of formaldehyde-treated, endopeptidase negative LH _N /A, LH _N /B or LH _N /E fragments and, optionally, an adjuvant.

The invention also provides antisera isolated from animals that have been immunized with a vaccine of the invention. In some embodiments, the antiserum is purified to provide a monoclonal or polyclonal population of antibodies that are specific for the antigen in the vaccine. In one embodiment of the invention, the antisera is isolated from an animal administered one or more peptides of the invention, for instance, one or more of a formaldehyde-treated, endopeptidase negative LH _N /A, LH _N /B or LH _N /E fragment. In one embodiment, the isolated and purified population of monoclonal or polyclonal antibodies are from an animal administered one or more peptides of the invention, for instance, one or more of a formaldehyde-treated, endopeptidase negative LH _N /A, LH _N /B or LH _N /E fragment.

The purified polyclonal antibodies may provide improved survival when administered to an animal prior to or shortly after exposure to a toxic form of the antigen (such as an agent comprising the toxic form of the antigen) used to prepare the vaccine. The invention includes methods of preventing or treating an infection in a subject comprising administering a population of antibodies to the subject pre- or post-infection, wherein said antibodies are isolated from the antisera from animals administered one or more of the peptides of the invention. In one embodiment, the purified antibodies are specific to one or more of an endopeptidase negative LH _N /A, LH _N /B or LH _N /E fragment.

Brief Description of the Figures

Figure 1 shows an SDS-PAGE of formaldehyde-treated and control LH _N /A vaccine. Lane i : mass markers. Lane 2: control LH _N /A. Lane 3: formaldehyde-treated LH _N /A. 'D' indicates the position of the LH _N /A dimer if it is present.

Figure 2 shows an SDS-PAGE of formaldehyde-treated and control LH _N /A vaccine. Lane 1 : mass markers. Lane 2: control LH _N /A. Lane 3: formaldehyde-treated LH _N /A (0.1 mg ml ^"1 ). Lane 4: control LH _N /A. Lane 5: formaldehyde-treated LH _N /A (1.0 mg ml ^"1 ). 'D' indicates the position of the LH _N /A dimer if it is present.

Figure 3 is an SDS-PAGE gel showing the presence of intra-molecular cross-links in formaldehyde-treated L H _N /A vaccine. Lane 1 : mass markers. Lane 2: LH _N /A untreated. Lane 3: LH _N /A untreated + DTT. Lane 4: LH _N /A trypsin treated. Lane 5: LH _N /A trypsin treated + DTT. Lane 6: LH _N /A formaldehyde and trypsin treated. Lane 6: LH _N /A formaldehyde and trypsin treated +DTT.

Figure 4 is an SDS-PAGE gel of LH _N /A and B fragments under various conditions. Lane 1 : purified LH _N /A fragment. Lanes 2 and 3: LH _N /A treated with 10 μg ml ^"1 trypsin for 30 minutes at 37° C under non-reducing and reducing conditions (10 mM DTT), respectively. Lane 4: LH _N /A (1 mg ml -1 ) treated with 0.2% (v/v) formaldehyde for 24 hours at 35° C. Lane 5: purified LH _N /B. Lane 6: LH _N /B treated with 0.2% (v/v) formaldehyde for 24 hours at 35° C.

Figure 5 is a graph showing the results of ELISA and endopeptidase assays on LH _N /A and BoNT/A. Endopeptidase activities of BoNT/A (O) and LH _N /A (δ) were assessed by the cleavage of SNAP-25 (synaptosomal protein of 25kDa) bound to microtiter plates followed by detection of cleavage product using specific antibodies. ELISA of BoNT/A (•) and LH _N /A (A ) were performed using goat antibodies raised against BoNT/A toxoid.

Figure 6 is an SDS-PAGE gel showing the presence of intra-molecular cross-links in formaldehyde-treated LH _N /A vaccine. Lane 1 : LH _N /A control. Lane 2: LH _N /A (0.1 mg ml ^"1 ) treated with 0.2% (v/v) formaldehyde for 24 h at 35° C. Lanes 3 and 4: LH _N /A treated with 10 μg ml ^"1 trypsin for 30 minutes at 37° C, under non-reducing and reducing conditions (10 mM DTT), respectively. Lanes 5 and 6: LH _N /A treated with trypsin and

with 0.2% formaldehyde for 24 hours at 35° C, under non-reducing and reducing conditions, respectively.

Detailed Description of the Invention

The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited herein, including but not limited to patents, patent applications, articles, books, and treatises, are hereby expressly incorporated by reference in their entirety for any purpose. In the event that one or more of the incorporated documents or portions of documents defines a term that contradicts that term's definition in the application, the definition in this application controls.

The use of the singular includes the plural unless specifically stated otherwise. The word "a" or "an" means "at least one" unless specifically stated otherwise. The use of "or" means "and/or" unless stated otherwise. The meaning of the phrase "at least one" is equivalent to the meaning of the phrase "one or more." Furthermore, the use of the term "including," as well as other forms, such as "includes" and "included," is not limiting. Also, terms such as "element" or "component" encompass both elements or components comprising one unit and elements or components comprising more than one unit unless specifically stated otherwise.

I. Definitions

In order that the present invention may be more readily understood, certain terms are first defined. Additional definitions are set forth throughout the detailed description.

BoNT: botulinum neurotoxin. When a letter follows this designation, the letter indicates the serotype. For example, BoNT/A is botulinum neurotoxin type A.

LH _N : a fragment of a clostridial neurotoxin (botulinum or tetanus) of approximately 10OkDa which may be a single-chain or di-chain molecule comprising the light chain and the H _N domain. The latter domain represents the N-terminal 5OkDa of the neurotoxin heavy chain and is closely associated with the light chain domain in the fragment.

C. difficile Toxins A and B - large peptide toxins (approx 30OkDa) with cytotoxic and enterotoxic activity which are the principal virulence factor of the C. difficile.

C. difficile surface peptide - peptides which are expressed by the bacterium and which are presented on its outer surface. Such peptides play a role in adhesion to the gut wall. More than 29 genes with the prefix cwp (cell wall peptides) have been identified within the C. difficile genome. Examples of C. difficile surface peptides are described in Pechine et al. (2005) J. Clinical Microbiol. 43, 5018-5025, which reference is hereby incorporated by reference in its entirety.

Protective antigen (PA) - the component of anthrax toxin (approx 83 kDa) which contains the receptor-binding and translocation domains. PA binds to cell receptors and is activated by surface proteases. This allows either anthrax lethal factor or edema factor to bind and internalise within the cell. PA peptides may be modified to lack a functional binding site, thereby preventing PA from binding to either Anthrax Toxin Receptor (ATR) - see Bradley, K.A., et al (2001 ) to which native PA binds, or to native LF. By way of example, a modification made within or near to amino acid residues 315- 735, or in some embodiments within or near to residues 596-735 of Domain 4, may render PA incapable of binding to ATR. Alternatively (or in addition), the PA furin cleavage site (i.e., amino acid residues 193-196 of SEQ ID NO: 16) may be inactivated. Furin is an enzyme that activates native PA (i.e., the 83 kDa form) in vivo into the 63 kDa form by proteolytic cleavage, and thus exposes a specific binding site for which LF and EF compete in order to form LT and ET, respectively. One or more amino acid residue changes (i.e., deletion, insertion, or substitution) within or near to the furin cleavage site (RKKR) may inactivate the furin cleavage site and thereby inactivate PA. By way of example, all of residues 193-196 of native PA (i.e. SEQ ID NO: 16) may be deleted.

Lethal factor (LF) - a component of anthrax toxin containing an endopeptidase activity which can modify proteins in mammalian cells leading to cell death. LF peptides may be modified to lack a functional binding site for PA. By way of example, LF peptides may include a modification within or near to the N-terminal Domain of LF, such as within or near to amino acid residues 1-255. Particular examples include mutagenesis of the VYYEIGK (SEQ ID NOS: 17 and 18) motif of LF (residues 180-186), which renders LF unable to bind to PA. Usually, one or more of the tyrosine, isoleucine, or lysine residues

are modified to prevent binding to PA and hence formation of active toxins. Alternatively (or in addition) LF peptides may be modified to lack a functional endopeptidase activity or zinc-binding site. By way of example, LF peptides may include a modification within or near to the C-terminal Domain of LF, such as within or near to the "HEFGHAV" (SEQ ID NOS: 17 and 18) motif found around residues 719-725 of the native LF sequence.

Edema factor (EF) - a component of anthrax toxin containing an enzyme activity which can modify proteins in mammalian cells leading to cell lysis. EF peptides may be modified to lack a functional binding site for PA. By way of example, EF peptides may include a modification within or near to the N-terminal Domain of EF, such as within or near to amino acid residues 1-250 of SEQ ID NO: 21 or 22. Alternatively (or in addition), EF peptides may be modified to lack adenylyl cyclase activity e.g. by mutagenesis of histidine 351 to alanine (SEQ ID NO 22). By way of example, EF peptides may include a modification within or near to the ATP-binding site (e.g., residues 314-321 of SEQ ID NO: 21 or 22) and/or within or near to the calmodium-binding site (e.g., residues 613- 767 of SEQ ID NO: 21 or 22). Particular examples include mutagenesis of the VYYEIGK motif, which is found at residues 136-142 of EF (SEQ ID NO: 21 or 22). Mutations in this motif render EF unable to bind to PA. Usually, one or more of the tyrosine, isoleucine, or lysine residues are modified to prevent binding to PA and hence formation of active toxins.

Isolated: a molecule that is substantially free of its original environment. For instance, an isolated peptide is substantially free of material or other proteins from the cell, bacterial, or tissue source from which it was derived.

Purified: a molecule that is substantially free of its original environment and is sufficiently pure for use in pharmaceutical compositions. A substantially pure peptide, as used herein, refers to a peptide at least about 50% (w/w) pure; at least about 60% (w/w) pure; or at least about 70% (w/w) pure; or at least about 80% (w/w) pure; or at least about 85% (w/w/) pure; or at least about 90% (w/w) pure; or at least about 95% (w/w) pure; or at least about 95%, 96%, 97%, 98%, 99%, or 100% (w/w) pure.

Bacterial peptide: refers to proteins, polypeptides, peptides or fragments or variants thereof, wherein the nucleic acid encoding the peptide is derived from a bacterium. The

terms peptide, polypeptide and fragment are used interchangeably herein. The term bacterial peptide includes native peptides and recombinant peptides. The bacterial peptide of the invention can be a toxin.

In one embodiment of the invention, the bacterial peptide is a recombinant peptide or toxin fragment. Recombinant bacterial peptides include fusion proteins. For instance, the present invention includes fusion proteins comprising a first bacterial peptide fused to a second peptide, wherein the second peptide is useful for the purification and/or half- life extension of the bacterial peptide.

The peptide may be expressed by the bacterium or may be expressed by a host cell such as a non-pathogenic bacterial host cell, yeast host cell, or mammalian host cell,. The bacterial peptide of the invention can be derived from a highly pathogenic bacterium, for instance, Clostridium difficile, Clostridium botulinum, C. tetani, Bacillus anthracis or other biosafety level 3 or 4 (BSL-3 or BSL-4) pathogen.

The bacterial peptide may be a fragment of a toxin, for instance, a Clostridium LH _N fragment or other non-toxic fragment. Toxin fragments may be prepared by treating native toxins with trypsin. Toxin fragments may comprise a truncated portion of the Hc domain as disclosed in WO 2007/044382, which is herein incorporated by reference in its entirety.

Toxin fragments such as the Clostridium LH _N fragment may contain amino acid modifications. For instance, the term bacterial peptide includes LH _N fragments which have been modified to reduce endopeptidase activity and/or have been codon optimized for expression in a host system (e.g., E. coli).

In one embodiment of the invention, the bacterial peptide is a therapeutic peptide. In one embodiment of the invention, the peptide elicits a protective immune response when administered to a subject.

The bacterial peptide of the invention can be a moderate to high molecular weight protein in its native state. In one aspect of the invention, the bacterial peptide of the invention is not a low molecular weight peptide. As defined herein, a low molecular

weight protein is a protein that less than about 50 kDa. Accordingly, the bacterial peptide of the present invention includes peptides that are at least about 50 kDa, 55 kDa, 60 kDa, 65kDa, 70 kDa, 75 kDa, 80 kDa, 85 kDa, 90 kDa, 95 kDa, 100 kDa, 105 kDa, 110 kDa, 115 kDa, 120 kDa, 125 kDa, 130 kDa, 135 kDa, 140 kDa, 145 kDa, 150 kDa, 155 kDa, 160 kDa, 165 kDa, 170 kDa, 175 kDa, 180 kDa, 185 kDa, 190 kDa, 195 kDa or 200 kDa or more. Molecular weight can be determined by methods known in the art, for instance, SDS PAGE. Small molecular weight proteins that aggregate to form high molecular weight complexes are not considered to be high molecular weight peptides.

Minimally aggregated: refers to the aggregation or clumping of peptides. The term "minimally aggregated" distinguishes the chemically treated peptide (or population of peptides) of the invention from aggregated peptides that result from prolonged treatment with a chemical-modification agent (such as formaldehyde) as required for detoxification of a toxin.

A minimally aggregated peptide or polypeptide (or population of peptides or polypeptides) can be monomeric or at least predominantly monomeric. A peptide or polypeptide (or population of peptides or polypeptides) is predominantly monomeric if it is, for instance, it is greater than about 70%, 75%, 80%, 85%, 90%, 95%, or even 98% monomeric. In one embodiment, a minimally aggregated population of peptides or polypeptides is at least about 75%, 80%, 85%, 90%, 95%, or even 98% monomeric and dimeric. For instance, included in the definition of minimally aggregated peptides is a population of peptides or polypeptides comprising monomers, dimers and trimers, wherein the population of peptides or polypeptides is at least about 75%,%, 80%, 85%, 90%, 95%, or even 98% monomeric and dimeric.

A population of chemically-modified peptides of the present invention exhibit at least about 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 12 fold or 15 fold less peptide aggregation compared a population of peptides treated with a chemical-modifying agent according to traditional chemical detoxification protocols (e.g., treatment with formaldehyde up to about 25 days). For instance, the chemically- modified peptides of the invention can comprise at least about 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, or 10 fold or fewer trimers or larger complexes than

peptides treated with a chemical-modifying agent under conditions required for detoxification (e.g., treatment for a prolonged period of time such as treatment with formaldehyde for up to about 25 days).

The peptides of the invention may be partially purified, substantially purified or purified prior to determination of aggregation.

Endopeptidase negative: displays no endopeptidase activity by conventional assays. In one embodiment, a Clostridium neurotoxin or neurotoxin fragment (e.g., LH _N ) is made endopeptidase negative by modifying one or two or more amino acids by methods known in the art. Amino acid modifications that confer an endopeptidase negative phenotype, include, but are not limited to modifications at residues E224 and/or H227 for C. botulinum type A neurotoxin or fragments such as LH _N /A (see, for instance, SEQ ID NOs: 1 , 2, 3, 8 and 9 which can be modified at one or both of amino acids E224 and H227); residues E231 and/or H234 for C. botulinum type B neurotoxin or fragments such as LH _N /B (see, for instance, SEQ ID NOs: 6, 23 and 24, which can be modified at one or both of amino acids E231 and H234); and residues E213 and/or H216 for C. botulinum type E neurotoxin or fragments such as LHN/E (see, for instance, SEQ ID NOs: 4, 25, 26 and 27, which can be modified at one or both of amino acids E213 and H216. For instance, the invention includes LH _N /A comprising E224Q and/or H227Y modifications, LH _N /B comprising E231Q and/or H234Y modifications and LH _N /E comprising E213Q and/or H216Y modifications.

An example of an assay that can be used to measure the endopeptidase activity of the botulinum neurotoxins is described in detail by Hallis et al. (1996) J. Clinical Microbiol. 34:1934-1938, which is incorporated by reference. Thus, absence of detectable endopeptidase activity in the Hallis assay provides a functional definition of "endopeptidase negative."

Protease cleavage site: native proteins may comprise one or more natural protease cleavage sites (e.g., a trypsin cleavage site). For example, the clostridial neurotoxin holotoxin includes a cleavage site located between the L-chain and the H-chain. Cleavage of that site results in the formation of a di-chain molecule, wherein the L-chain and the H-chain are linked together via a disulphide bond. In some embodiments of the

invention, a protein, polypeptide, or peptide may include one, some, or all of its native cleavage sites. Examples of native protease cleavage site, and methods of inactivating them, are described elsewhere for the various proteins, polypeptides, and peptides. In some embodiments, however, it is desirable to include a non-native cleavage site, for example, to permit 'controlled' cleavage. For example, in the case of clostridial holotoxin, a non-native cleavage site may be inserted to permit controlled cleavage of the single chain molecule into its di-chain counterpart. Suitable non-native cleavage sites include those for enterokinase (DDDDK|), Factor Xa (IEGR| / IDGR|), TEV(Tobacco Etch virus) (ENLYFQ|G), thrombin (LVPR|GS), and PreScission (LEVLFCUGP), but other non-native cleavage sites may also be used. Also embraced by the term protease cleavage site is an intein, which is a self-cleaving sequence. The self-splicing reaction is controllable, for example by varying the concentration of reducing agent present.

Intra-molecular cross-linking: chemical bonding introduced within a peptide molecule such that non-contiguous peptide sequences of the same molecule become linked together. Intra-molecular cross-linking does not cross-link different peptide molecules together (this would require inter-molecular cross-linking), and there is little or no aggregation resulting in the generation of higher molecular weight species. The peptides of the present invention include at least one introduced intra-molecular bond. Intra-molecular cross-linking may be demonstrated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE), which displays peptides as bands according to molecular size. A molecule which has been intra-molecularly cross-linked by a chemical agent appears as a peptide band of similar size on SDS-PAGE to the untreated molecule. If, however the molecule is treated with a protease (e.g., trypsin) then the untreated molecule will appear as fragments on SDS-PAGE while the intra-molecularly cross- linked molecule will remain the same size as the original molecule demonstrating a change in peptide tertiary structure of the molecule such that it is no longer susceptible to digestion with the protease (e.g., trypsin) under the conditions of digestion tested. In one embodiment of the present invention, the clostridial intramolecular bond(s) crosslink the L-chain (or fragment thereof) to the H-chain (or fragment thereof).

Antibody: an immunoglobulin or fragment thereof. The term encompasses any polypeptide comprising an antigen-binding fragment or an antigen-binding domain.

Examples include, but are not limited to, polyclonal, monoclonal, monospecific, polyspecific, non-specific, humanized, human, single-chain, chimeric, synthetic, recombinant, hybrid, mutated, grafted, and in vitro generated antibodies. An antisera refers to a population of antibodies in serum that possess detectable binding, e.g., by ELISA or flow cytometry, for a particular antigen. Unless preceded by the word "intact", the term "antibody" includes antibody fragments such as Fab, F(ab') ₂ , Fv, scFv, Fd, dAb, and other antibody fragments that retain antigen-binding function. The present invention is not necessarily limited to any particular source, method of production, or other special characteristics of an antibody, unless the context makes clear that such a limitation is intended. Further, particularly when used in the context of diagnostic or therapeutic embodiments, the antibodies may be tagged with a detectable or functional label. These labels include radiolabels (e.g., ¹³¹ I or ⁹⁹ Tc), enzymatic labels (e.g., horseradish peroxidase or alkaline phosphatase), and other chemical moieties (e.g., biotin).

Specific binding: formation of a complex between two or more molecules that is relatively stable under physiologic conditions. Specific binding is characterized by a high affinity and a low to moderate capacity, as distinguished from nonspecific binding which usually has a low affinity with a moderate to high capacity. Typically, binding is considered specific when the association constant K _A is higher than 10 ⁶ M ^"1 . If necessary, nonspecific binding can be reduced without substantially affecting specific binding by varying the binding conditions. The appropriate binding conditions, such as concentration of antibodies, ionic strength of the solution, temperature, time allowed for binding, concentration of a blocking agent (e.g., serum albumin, milk casein), etc., may be optimized by a skilled artisan using routine techniques.

Effective amount: a dosage or amount that is sufficient to achieve a desired biological outcome. As used herein, a "therapeutically effective amount" refers to an amount which is effective, upon single or multiple dose administration to a subject (such as a human patient) at treating, preventing, curing, delaying, reducing the severity of, ameliorating at least one symptom of a disorder or recurring disorder, or prolonging the survival of the subject beyond that expected in the absence of such treatment.

Treatment: a therapeutic or preventative measure. A treatment may be administered to a subject already having an infection or disease, condition or symptoms associated with

an infection. When administered to a subject that already having an infection or disease, condition or symptoms associated with an infection, the therapeutic can cure, delay, reduce the severity of, or ameliorate one or more symptoms, and/or prolong the survival of a subject beyond that expected in the absence of such treatment. Alternatively, it may be administered to one who ultimately may acquire the disorder in order to prevent, cure, delay, reduce the severity of, or ameliorate one or more symptoms of a disorder or recurring disorder, or in order to prolong the survival of a subject beyond that expected in the absence of such treatment. Peptides, vaccines, pharmaceutical compositions, anti-sera and antibodies of the present invention are encompassed, for instance, by the term "treatment."

Vaccine: a composition that, when administered to an animal, stimulates an immune response against an antigen contained within the composition. A vaccine stimulates a protective immune response. The vaccines of the invention can stimulate a humoral and/or cell-mediated immune response when administered to a subject.

A vaccine of the invention can be used, for example, to protect an animal from the lethal effect of a toxin. Vaccine compositions of the invention comprise at least one chemically modified peptide and a pharmaceutically acceptable carrier, excipient, diluent and/or adjuvant. Vaccines include, for instance, monovalent (e.g., a vaccine comprising endopeptidase negative LH _N /A or LH _N /B or LH _N /E, bivalent (e.g., a vaccine comprising endopeptidase negative LH _N /A + LH _N /B or endopeptidase negative LH _N /A + LH _N /E or endopeptidase negative LH _N /B + LH _N /E) or trivalent (e.g., a vaccine comprising endopeptidase negative LH _N /A + LH _N /B + LH _N /E) compositions.

Similarly, multivalent (e.g. bivalent, or trivalent) vaccines of the present invention may include antigens from different sources, for example, a clostridial antigen (such as endopeptidase negative LH _N /A and/or LH _N /B and/or LH _N /E) in combination with an anthrax antigen (such as PA and/or LF and/or EF) and/or a C.difficile antigen (such as Toxin A peptide and/or Toxin B peptide).

Vaccines of the present invention include passive vaccines, which include corresponding antibodies that bind specifically to peptides of the present invention.

Vaccine efficacy: the ability of a vaccine to protect animals from the lethal effects of toxins. Efficacy can be measured by obtaining an ED ₅₀ value. The ED ₅₀ value is the vaccine dose that will protect animals from a pre-defined challenge dose of toxin. In one format of such an assay, animals are injected with varying doses of the vaccine and then at a defined endpoint (e.g., 28 days from the date of immunisation) are challenged with a lethal dose of toxin (e.g., 1000 mouse lethal doses (LD) 50s). The ED ₅₀ value is then calculated as the vaccine dose that protects 50% of the animals against the challenge dose of toxin. ED ₅₀ values are commonly expressed as micrograms or nanograms of peptide. The lower the ED ₅₀ value, the higher the efficacy of the vaccine. The invention includes a chemically modified peptide vaccine with an ED ₅₀ value at least about 1.5 fold, at least about 2 fold, at least about 2.5 fold, at least about 3 fold, at least about 3.5 fold, at least about 4 fold, at least about 4.5 fold, at least about 5 fold, at least about 10 fold, at least about 15 fold, at least about 20 fold, at least about 25 fold, at least about 30 fold, at least about 35 fold, at least about 40 fold, at least about 45 fold or at least about a 50 fold greater than the ED ₅₀ value of a vaccine composition comprising an untreated (i.e., not chemically modified) version of the same peptide.

II. Methods of Increasing a Protective Effect

The invention provides methods of increasing the protective effect of a peptide or polypeptide by chemically modifying it. Surprisingly, the inventors of the present invention found that treatment of peptides, including Clostridium avirulent neurotoxin fragments, with formaldehyde under conditions that resulted in minimal to no peptide aggregation increased immunogenicity of the peptides.

Protective Effect

In some embodiments, the increased protective effect is due to an improved ability to stimulate an immune response. In other embodiments, the increased protective effect is due to improved cross-serotype protection. In yet other embodiments, the increased protective effect is due to improved cross-subtype protection. In still other embodiments, the increased protective effect is a combination of one, two, or three of an improved ability to stimulate an immune response, an improved cross-serotype protection, and an improved cross-subtype protection. Often, although not always, the increased protective effect of the peptide or polypeptide results from an increase in stability.

Also, in some embodiments, the increased protective effect is not due to aggregation. That is, the peptide or polypeptide is monomeric, or at least predominantly (e.g., greater than about 70, 75, 80, 85, 90, 95, or even 98%) monomeric.

Methods of the invention comprise contacting the peptide or polypeptide with one or more chemical modification agents for a brief period of time or for a period of time sufficient to obtain a desired property in the peptide or polypeptide. In one embodiment of the invention, the peptide is contacted with at least one chemical modification agent for a period of time sufficient to obtain an increase in immunogenicity with minimal to no peptide aggregation.

Treatment with a modifying agent in accordance with the present invention is designed to give minimal aggregation and is carried out over a relatively brief incubation period, for example, when compared with the traditional toxoiding process used in first generation vaccine botulinum candidates, which required an incubation period of up to 25 days. Thus, in one embodiment of the invention a vaccine is based on a peptide (e.g. a toxin fragment), which is treated with a modifying agent (e.g. formaldehyde) at a relatively low concentration of modifying agent for a relatively brief incubation period.

Contact Period

The contact period is the time during which the chemical modification agent and the peptide or polypeptide are incubated together in a reaction mixture. The end of the contact period is generally considered the time at which the reaction is stopped, for example, by dialysis of the sample to remove the modification agent or by type of inactivation. As noted, this is generally a brief period of time. For example, the contact period may occur over a period of less than or about 144 hours, less than or about 120 hours, less than or about 96 hours, less than or about 72 hours, less than or about 60 hours, less than or about 48 hours, less than or about 36 hours, less than or about 24 hours, less than or about 18 hours, less than or about 12 hours, less than or about 6 hours, or less than or about 3 hours.

The contact period may also be within a range of time points. For example, in one embodiment, the contact period is from about 3 to about 96 hours, from about 6 to about

96 hours, from about 12 to about 96 hours, from about 18 to about 96 hours, from about 24 to about 96 hours, from about 36 to about 96 hours, from about 48 to about 96 hours, from about 60 to about 96 hours, or from about 72 to about 96 hours. In other embodiments, the contact period is from about 3 to about 72 hours, from about 6 to about 72 hours, from about 12 to about 72 hours, from about 18 to about 72 hours, from about 24 to about 72 hours, from about 36 to about 72 hours, from about 48 to about 72 hours, or from about 60 to about 72 hours. In still other embodiments, the contact period is from about 3 to about 60 hours, from about 6 to about 60 hours, from about 12 to about 60 hours, from about 18 to about 60 hours, from about 24 to about 60 hours, from about 36 to about 60 hours, or from about 48 to about 60 hours. In other embodiments, the contact period is from about 3 to about 48 hours, from about 6 to about 48 hours, from about 12 to about 48 hours, from about 18 to about 48 hours, from about 24 to about 48 hours, or from about 36 to about 48 hours. In still other embodiments, the contact period is from about 3 to about 36 hours, from about 6 to about 36 hours, from about 12 to about 36 hours, from about 18 to about 36 hours, or from about 24 to about 36 hours. In yet other embodiments, the contact period is from about 3 to about 24 hours, from about 6 to about 24 hours, from about 12 to about 24 hours, or from about 18 to about 24 hours. In some embodiments the total period of contact between the chemical modification agent and the peptide or polypeptide is less than a day, for example, the contact period is from about 3 to about 18 hours, from about 6 to about 18 hours, from about 12 to about 18 hours, from about 3 to about 12 hours, from about 6 to about 15 hours, or even from about 3 to about 6 hours.

It is also possible to measure the contact period in days. For example, the contact period can be about 5 days or less, about 4 days or less, about 3 days or less, about 2 days or less, or about a day.

As can be appreciated by a skilled artisan, the contact period may vary based on several factors, including, but not limited to, the type and concentration of the chemical modification agent used, the peptide to be treated and incubation temperature.

The contact period may also be expressed as the time period necessary to attain a particular end result. For example, the contact period may be that period of time that is necessary and sufficient to achieve intra-molecular cross-linking with minimal to no

peptide aggregation. In another embodiment, the contact period is the period of time sufficient to achieve production of intra-molecular methylene bridges with minimal to no peptide aggregation.

In another embodiment, the contact period is the period of time sufficient to achieve intra-molecular cross-linking without the modification of key epitopes which can result in loss or reduction of immunogenicity. The invention also includes a contact period that is the period of time sufficient to achieve production of intra-molecular methylene bridges without the modification of key epitopes which can result in loss or reduction of immunogenicity.

In yet another embodiment, the contact period is the period of time necessary and sufficient to achieve at least about a 1.5 fold, at least about a 2 fold, at least about a 3 fold, at least about a 4 fold, at least about a 5 fold, at least about a 10 fold, at least about a 15 fold, at least about a 20 fold, at least about a 30 fold, at least about a 40 fold or at least about a 50 fold enhancement in the efficacy of the polypeptide or peptide when used as a vaccine, compared to untreated peptide or polypeptide, as measured by an ED ₅₀ value. In yet another embodiment, the contact period is the period of time necessary and sufficient to achieve at least about a 1.5 fold, at least about a 2 fold, at least about a 3 fold, at least about a 4 fold, at least about a 5 fold, at least about a 10 fold, at least about a 20 fold, at least about a 30 fold, at least about a 40 fold or at least about a 50 fold enhancement in the efficacy of the polypeptide or peptide when used as a vaccine, compared to peptide or polypeptide treated with formaldehyde under traditional detoxification protocols (e.g., treatment with formaldehyde up to about 25 days), as measured by an ED ₅₀ value.

Chemical Modification Agents

The peptides of the present invention are treated with chemical modification agents that are capable of increasing immunogenicity. In one embodiment of the invention, the chemical modification agent induces cross-linking in the bacterial peptide. In another embodiment, the chemical modification agent induces the formation of methylene bridges in a bacterial peptide.

In certain embodiments, the chemical modification agent is formaldehyde or formalin. However, other agents may also be used. Non-limiting examples of other cross-linking agents that may be employed include C6-succinimidyl 4-hydrazinonicotinate acetone hydrazone, C6-succinimidyl 4-formylbenzoate, BιS-(Sulfosuccinimidyl) suberate, disuccinimidyl suberate, dimethyl suberimidate dihydrochloride, dimethyl pimelimidate 2 HCI, dimethyl adipimidate dihydrochloride, succinimidyl 4-hydrazidoterephthalate hydrochloride, and disuccinimidyl glutarate.

Irrespective of the identity of the chemical modification agent, many embodiments use the agent at a low concentration. In most embodiments, the concentration is less than about 2% (v/v or w/v based on the ratio of the modifying agent to the total reaction mixture). In some embodiments, the concentration is less than about 1 %, less than about 0.75%, less than about 0.5%, less than about 0.25%, or even less than about 0.1 %. Other embodiments employ a concentration range for the modifying agent. Thus, in some embodiments the modifying agent is at a concentration between about 0.05 and about 2.0%, between about 0.1 and 2.0%, between about 0.15 and 2.0%, between about 0.2 and 2.0%, between about 0.25 and 2.0%, between about 0.3 and 2.0%, between about 0.5 and 2.0%, between about 0.75 and 2.0%, or between about 1.0 and 2.0%. In other embodiments, the modifying agent is at a concentration between about 0.05 and about 1.0%, between about 0.1 and 1.0%, between about 0.15 and 1.0%, between about 0.2 and 1.0%, between about 0.25 and 1.0%, between about 0.3 and 1.0%, between about 0.5 and 1.0%, or between about 0.75 and 1.0%. In still other embodiments, the modifying agent is at a concentration between about 0.05 and about 0.75%, between about 0.1 and 0.75%, between about 0.15 and 0.75%, between about 0.2 and 0.75%, between about 0.25 and 0.75%, between about 0.3 and 0.75%, or between about 0.5 and 0.75%. In yet other embodiments, the modifying agent is at a concentration between about 0.05 and about 0.5%, between about 0.1 and 0.5%, between about 0.15 and 0.5%, between about 0.2 and 0.5%, between about 0.25 and 0.5%, or between about 0.3 and 0.5%. In some embodiments, the modifying agent is at a concentration between about 0.05 and about 0.3%, between about 0.1 and 0.3%, between about 0.15 and 0.3%, or between about 0.2 and 0.3%. In still other embodiments, the concentration of the modifying agent is between about 0.05 and about 0.25%, between about 0.1 and 0.25%, between about 0.15 and 0.25%, between about 0.2 and 0.25%, between about 0.05 and about 0.2%, between about 0.1 and 0.2%,

between about 0.15 and 0.2%, between about 0.05 and about 0.15%, between about 0.1 and 0.15%, or even between about 0.05 and about 0.1%. In certain embodiments, the concentration is about 1.0%, about 0.2%, or about 0.1 %.

Alternatively, the concentration may be expressed as a molar ratio of agentpolypeptide, in which case the ratio is generally between about 3:1 and about 50:1. Thus, in some embodiments, the modifying agent may be employed at a molar ratio of about 50:1 , about 25:1 , about 20:1 , about 15:1 , or about 10:1. In other embodiments, the molar ratio may be expressed as a range, for example, between about 3:1 and about 50:1 , between about 10:1 and about 50:1 , between about 15:1 and about 50:1 , between about 20:1 and about 50:1 , or between about 25:1 and about 50:1 , between about 3:1 and about 25:1 , between about 10:1 and about 25:1 , between about 15:1 and about 25:1 , between about 20:1 and about 25:1 , between about 3:1 and about 20:1 , between about 10:1 and about 20:1 , between about 15:1 and about 20:1 , between about 3:1 and about 15:1 , between about 10:1 and about 15:1 , or between about 3:1 and about 10:1.

As can be appreciated by a skilled artisan, the concentration of the chemical modification agent needed to modify a bacterial peptide without causing damage to the peptide can vary based on several factors, including, but not limited to, the type of chemical modification agent used, the peptide to be treated and other incubation parameters such as incubation time and temperature.

Incubation Temperature

The temperature at which the chemical modification agent and the peptide or polypeptide are contacted may vary. In many embodiments, the contact temperature is between about 3 ⁰ C and about 45 ⁰ C. Thus, the incubation temperature is typically up to about 45 ⁰ C, about 4O ⁰ C, or about 35 ⁰ C. In this regard, the minimum incubation temperature is typically higher than about 15 ⁰ C, about 2O ⁰ C, about 25 ⁰ C, and about 3O ⁰ C. The incubation temperature may also be expressed as a range, for example, between about 30 to about 37 ⁰ C, between about 20 to about 24 ⁰ C, between about 3 to about 7 ⁰ C, and between about 4 to about 37 ⁰ C. Thus, some embodiments involve an incubation temperature of between about 15 to about 45 ⁰ C, between about 20 to about 45 ⁰ C, between about 25 to about 45 ⁰ C, between about 30 to about 45 ⁰ C, between about 35 to about 45 ⁰ C, between about 37 to about 45 ⁰ C, or between about 40 to about 45 ⁰ C.

In other embodiments, the incubation temperature is a range of between about 15 to about 4O ⁰ C, between about 20 to about 4O ⁰ C, between about 25 to about 4O ⁰ C, between about 30 to about 4O ⁰ C, between about 35 to about 4O ⁰ C, or between about 37 to about 4O ⁰ C. In yet other embodiments, the incubation temperature is a range of between about 15 to about 37 ⁰ C, between about 20 to about 37 ⁰ C, between about 25 to about 37 ⁰ C, between about 30 to about 37 ⁰ C, or between about 35 to about 37 ⁰ C. For other embodiments, the incubation temperature is a range of between about 15 to about 35 ⁰ C, between about 20 to about 35 ⁰ C, between about 25 to about 35 ⁰ C, or between about 30 to about 35 ⁰ C, between about 15 to about 3O ⁰ C, between about 20 to about 3O ⁰ C, between about 25 to about 3O ⁰ C, between about 15 to about 25 ⁰ C, between about 20 to about 25 ⁰ C, or between about 15 to about 2O ⁰ C. In some embodiments, the temperature is about 35 ⁰ C, in other embodiments, it is about 4 ⁰ C.

III. Peptides and Polypeptides

The protective effect of many different bacterial peptides or polypeptides can be increased by chemical modification in accordance with the invention. For example, the methods may be used to increase the protective effect of clostridial neurotoxins. Non- limiting examples of such peptides and polypeptides include BoNT/A, BoNT/B, BoNT/E, tetanus toxin, and the different subtypes of each of the BoNT serotypes. In various embodiments, the peptide or polypeptide is the native clostridial neurotoxin, a recombinant polypeptide modified to render it nontoxic, or polypeptide fragments, which may also have been rendered nontoxic via amino acid substitutions, deletions, or insertions, such as the LH _N fragment of BoNT or tetanus toxin. The LH _N fragment can be obtained, for instance, by treating native clostridial neurotoxin with trypsin by methods known in the art. In one embodiment of the invention, the peptide or polypeptide is not a native, full length clostridial neurotoxin.

In still other embodiments, the peptides and polypeptides are Clostridium difficile toxins, such as Toxin A, Toxin B, and binary toxin, or a Clostridium difficile surface peptides, such as the Cwp 84 peptide.

In other embodiments, the polypeptides and peptides are from Bacillus anthracis, such as lethal factor, protective antigen, or edema factor.

Of course, there are many other peptides and polypeptides for which it is desirable to increase their protective effect, and those peptides and polypeptides are also encompassed by the invention.

In one embodiment, the peptide or polypeptide to be chemically modified is in a soluble or predominantly soluble form. By predominantly soluble, it is meant that the peptide or polypeptide be at least about 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or even 99% soluble..

In various embodiments, the invention utilizes polypeptides or fragments thereof that are modified. Thus, where noted, the exemplified sequences include one or more amino acid modification, insertion, or deletion relative to the native protein sequence in order to improve the polypeptide's expression characteristics and/or to render the polypeptide less toxic than the corresponding native protein. Details regarding those modifications are described elsewhere in this disclosure.

Amino acid sequences of polypeptides and peptides encompassed by the invention are presented below. The examples should not be construed to in any way limit the invention. They are presented for illustrative purposes only.

Botulinum Proteins, Polypeptides, and Fragments

Native Botulinum type A Neurotoxin (SEQ ID NO: 8):

PFVNKQFNYKDPVNGVDIAYIKI PNVGQMQ PVKAFKIHNKIWVI PERDTFTNPEEGDLNPPPEAKQVPVSY YDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTS IVRGI PFWGGSTI DTELKVI DTNCINVIQPDGS YRSEELNLVI I GPSADI IQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFA TDPAVTLAHEL IHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLY YYNKFKDIASTLNKAKS IVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTE IYTEDNFVK FFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTE INNMNFTKLKNFTGLFEFYK

IQQYYLTFNFDNEPENI S IENLSSDI I GQLELMPNIERFPNGKKYELDKYTMFHYLRAQEFEHGKSRIALT NSVNEALLNPSRVYTFFSSDYVKKVNKATEAAMFLGWVEQLVYDFTDETSEVSTTDKIAD I TI I I PYIGPA LNIGNMLYKDDFVGALI FSGAVILLEFI PE IAI PVLGTFALVSYIANKVLTVQT IDNALSKRNEKWDEVYK YIVTNWLAKVNTQI DLIRKKMKEALENQAEATKAI INYQYNQYTEEEKNNINFNIDDLSSKLNE S INKAMI NINKFLNQCSVSYLMNSMI PYGVKRLEDFDASLKDALLKYIYDNRGTL IGQVDRLKDKVNNTLSTDI PFQL SKYVDNQRLLSTFTEYIKNI INTS ILNLRYESNHLI DLSRYASKINIGSKVNFDPIDKNQIQLFNLE SSKI

EVILKNAIVYNSMYENFSTSFWIRI PKYFNS I SLNNEYT I INCMENNSGWKVSLNYGE I IWTLQDTQE IKQ RVVFKYSQMINI SDYINRWIFVTI TNNRLNNSKIYINGRLIDQKP I SNLGNIHASNNIMFKLDGCRDTHRY IWIKYFNLFDKELNEKE IKDLYDNQSNSGI LKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLK GPRGSVMTTNIYLNSSLYRGTKFI IKKYASGNKDNIVRNNDRVYINWVKNKEYRLATNASQAGVEKILSA LE I PDVGNLSQVWMKSKNDQGITNKCKMNLQDNNGNDI GFI GFHQFNNIAKLVASNWYNRQIERSSRTLG CSWEFI PVDDGWGERPL

This is but one example of a particular BoNT/A protein. Other BoNT/A proteins are known in the art and include GenBank Accession Nos: P10845.4, Q45894.3, A5HZZ9.1 , which are incorporated by reference.

In some embodiments, a protein of the invention includes the initiation methionine, whereas in other embodiments, it does not. For example, the native BoNT/A protein shown above lacks the initiation methionine, but the invention nevertheless includes those proteins that retain the initiation methionine. This can also be true for the other proteins of different types, different subtypes, and even the different species described elsewhere in the specification. Peptide variants described herein (for instance, Clostridum neurotoxins and neurotoxin fragments with modifications which confer the endopeptidase negative phenotype) reference peptide sequences with an initiation methionine to more clearly identify the location of an amino acid modification(s).

In addition to presence or absence of the initiation methionine, the various toxin proteins described in the specification can be modified to lack endopeptidase activity and/or a functional H _c binding domain. For instance, the present invention includes C. botulinum LH _N fragments (e.g., LH _N /A, LH _N /B and LH _N /E) modified to lack endopeptidase activity.

An example of a botulinum type A neurotoxin which is both endopeptidase negative and lacks a functional H _c binding domain is SEQ ID NO: 9:

PFVNKQFNYKDPVN GVDIAYIKI PNVGQMQ PVKAFKIHNKIWVI PERDTFTNPEEGDLNPPPEAKQVPVS Y YDSTYLSTDNEKDNYLKGVTKLFERI YSTDLGRMLLTS IVRGI PFWGGSTI DTELKVIDTNCINVIQPDGS YRSEELNLVI I GPSADI IQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFA TDPAVTLAHQL IYAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLY YYNKFKDIASTLNKAKS IVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTE IYTEDNFVK FFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTE INNMNFTKLKNFTGLFEFYK

IQQYYLTFNFDNEPENISIENLSSDIIGQLELMPNIERFPNGKKYELDKYTMFHYLR AQEFEHGKSRIALT NSVNEALLNPSRVYTFFSSDYVKKVNKATEAAMFLGWVEQLVYDFTDETSEVSTTDKIAD ITIIIPYIGPA LNIGNMLYKDDFVGALIFSGAVILLEFIPEIAIPVLGTFALVSYIANKVLTVQTIDNALS KRNEKWDEVYK YIVTNWLAKVNTQIDLIRKKMKEALENQAEATKAIINYQYNQYTEEEKNNINFNIDDLSS KLNESINKAMI NINKFLNQCSVSYLMNSMIPYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDKVN NTLSTDIPFQL SKYVDNQRLLSTFTEYIKNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQ IQLFNLESSKI EVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEII WTLQDTQEIKQ RVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMF KLDGCRDTHRY IWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVN NVGIRGYMYLK GPRGSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINWVKNKEYRLATNAS QAGVEKILSA LEIPDVGNLSQVWMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNLFNR QIERSSRTLG CSWEFIPVDDGWGERPL

Changes relative to the native botulinum type A neurotoxin are shown in bold.

The invention also encompasses fragments, such as the LH _N fragment, of the various botulinum neurotoxins, as well as the related tetanus toxin protein. Examples of LH _N fragments of certain subtypes of BoNT and from tetanus toxin follow:

LH _N Polypeptide Fragment of Botulinum neurotoxin subtype A ₁ (SEQ ID NO: 1):

PFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHNKIWVIPERDTFTNPEEGD LNPPPEAKQVPVSY YDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDT NCINVIQPDGS YRSEELNLVIIGPSADI IQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFA TDPAVTLAHQLIYAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFI DSLQENEFRLY YYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKML TEIYTEDNFVK FFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKL KNFTGLFEFYK

IQQYYLTFNFDNEPENISIENLSSDIIGQLELMPNIERFPNGKKYELDKYTMFHYLR AQEFEHGKSRIALT NSVNEALLNPSRVYTFFSSDYVKKVNKATEAAMFLGWVEQLVYDFTDETSEVSTTDKIAD ITIIIPYIGPA LNIGNMLYKDDFVGALIFSGAVILLEFIPEIAIPVLGTFALVSYIANKVLTVQTIDNALS KRNEKWDEVYK YIVTNWLAKVNTQIDLIRKKMKEALENQAEATKAIINYQYNQYTEEEKNNINFNIDDLSS KLNESINKAMI NINKFLNQCSVSYLMNSMIPYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDKVN NTLSTDIPFQL SKYVDNQRLLSTFTEYIK

This is but one example of a polypeptide fragment of one particular BoNTZA ₁ protein. Other BoNTZA ₁ proteins are known in the art and include GenBank Accession Nos: ZP_02612822.1, YP_001386738.1, YP_001390123.1, which are incorporated by

reference. LH _N fragments from BoNTZA ₁ proteins include fragments corresponding to the fragment shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein.

LH _N Polypeptide Fragment of Botulinum neurotoxin subtype A ₂ (SEQ ID NO: 2):

PFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGD LNPPPEAKQVPVSY YDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDT NCINVIQPDGS YRSEELNLVIIGPSADI IQFECKSFGHDVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFA TDPAVTLAHQLIYAEHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFI DSLQENEFRLY YYNKFKDVASTLNKAKSIIGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKML TEIYTEDNFVN FFKVINRKTYLNFDKAVFRINIVPDENYTIKDGFNLKGANLSTNFNGQNTEINSRNFTRL KNFTGLFEFYK

IQQYYLTFDFDNEPENISIENLSSDIIGQLEPMPNIERFPNGKKYELDKYTMFHYLR AQEFEHGDSRIILT

LNIGNMLSKGEFVEAIIFTGVVAMLEFIPEYALPVFGTFAIVSYIANKVLTVQTINN ALSKRNEKWDEVYK YTVTNWLAKVNTQIDLIREKMKKALENQAEATKAIINYQYNQYTEEEKNNINFNIDDLSS KLNESINSAMI NINKFLDQCSVSYLMNSMIPYAVKRLKDFDASVRDVLLKYIYDNRGTLVLQVDRLKDEVN NTLSADIPFQL SKYVDNKKLLSTFTEYIK

This is but one example of a polypeptide fragment of one particular BoNT/A ₂ protein. Other BoNT/A ₂ proteins are known in the art and include GenBank Accession Nos: AAX53156.1, ABC26002.1, ABY56330.1, which are incorporated by reference. LH _N fragments from BoNT/A ₂ proteins include fragments corresponding to the fragment shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity ofthe protein.

LH _N Polypeptide Fragment of Botulinum neurotoxin subtype A ₃ (SEQ ID NO: 3):

PFVNKPFNYRDPGNGVDIAYIKIPNAGQMQPVKAFKIHEGVWVIPERDTFTNPEEGD LNPPPEAKQVPVSY

YRSEELNLVITGPSADI IQFECKSFGHDVFNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGTFA TDPAVTLAHQLIYAAHRLYGIAINPNRVLKVKTNAYYEMSGLEVSFEELRTFGGNDTNFI DSLWQKKFSRD AYDNLQNIARILNEAKTIVGTTTPLQYMKNIFIRKYFLSEDASGKISVNKAAFKEFYRVL TRGFTELEFVN PFKVINRKTYLNFDKAVFRINIVPDENYTINEGFNLEGANSNGQNTEINSRNFTRLKNFT GLFEFYKLLCV RGIIPFKTKSLDEGYNKALNYLCIKVNNWDLFFSPSEDNFTNDLDKVEEITADTNIEAAE ENISSDLIQQY YLTFDFDNEPENISIENLSSDIIGQLEPMPNIERFPNGKKYELDKYTMFHYLRAQEFEHG DSRIILTNSAE

NMVSKGEFVEAILFTGVVALLEFIPEYSLPVFGTFAIVSYIANKVLTVQTINNALSK RNEKWDEVYKYTVT NWLAKVNTQIDLIREKMKKALENQAEATRAIINYQYNQYTEEEKNNINFNIDDLSSKLNR SINRAMININK FLDQCSVSYLMNSMIPYAVKRLKDFDASVRDVLLKYIYDNRGTLILQVDRLKDEVNNTLS ADIPFQLSKYV NDKKLLSTFTEYIK

This is but one example of a polypeptide fragment of one particular B0NT/A ₃ protein. Other B0NT/A ₃ proteins are known in the art and include GenBank Accession Nos: YP_001715703.1 , ACA57525.1 , which are incorporated by reference. LH _N fragments from B0NT/A ₃ proteins include fragments corresponding to the fragment shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein.

LH _N Polypeptide Fragment of Botulinum neurotoxin type B (SEQ ID NO: 6):

YYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMI INGI PYLGDRRVPLEEFNTNIASVTVNKLI S NPGEVERKKGI FANLI I FGPGPVLNENET IDI GIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGAS I FNRRGYFSDPALILMHQLIYVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGG QDPS I ITPSTD KS IYDKVLQNFRGIVDRLNKVLVC I SDPNININIYKNKFKDKYKFVEDSEGKYS IDVE SFDKLYKSLMFGF TETNIAENYKIKTRASYFSDSLPPVKIKNLLDNE IYTIEEGFNI SDKDMEKEYRGQNKAINKQAYEE I SKE HLAVYKIQMCKSVKAPGI CIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFP INELILDTDLI SKIELPSENTE SLTDFNVDVPVYEKQPAIKKI FTDENT IFQY LYSQTFPLDIRDI SLTS SFDDALLFSNKVYSFFSMDYIKTANKWEAGLFAGWVKQIVNDFVIEANKSNTM

DNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEE I IKYRYNIYSEKEKSNINI DF NDINSKLNEGINQAIDNINNFINGCSVSYLMKKMI PLAVEKLLDFDNTLKKNLLNYIDENKLYL IGSAEYE KSKVNKYLKTIMPFDLS IYTNDTI LIEMFNKYNSE

This is but one example of a polypeptide fragment of one particular BoNT/B protein. Other BoNT/B proteins are known in the art and include GenBank Accession Nos: YP_001693307.1 , ZP_02619070.1 , which are incorporated by reference. LH _N fragments from BoNT/B proteins include fragments corresponding to the fragment shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein. By way of example, two BoNT/B sequences of the present invention include:

BoNT/ B ₁ strain NCTC 7273 (SEQ ID NO: 23)

PVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKI

YYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEF NTNIASVTVNKLIS NPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVF NNVQENKGASI FNRRGYFSDPALILMHELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGG QDPSIITPSTD KSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESF DKLYKSLMFGF TETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAI NKQAYEEISKE HLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFP INELILDTDLI SKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSS FDDALLFSNKV YSFFSMDYIKTANKWEAGLFAGWVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNV GNETAKGNFE NAFEIAGASILLEFIPELLIPWGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIV AQWLSTVNTQ FYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNI NNFINGCSVSY

NKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIR VTQNQNIIFNSVFL DFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKS VFFEYNIREDI SEYINRWFFVTITNNLNNAKIYING

KLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKI QSYSEYLKDFWGNP LMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKS NSQSINDDIVR KEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQ LLFKKDEESTD EIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE

BoNT/ B ₄ strain Eklund (17b) - SEQ ID NO: 24

YYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEF NTNIASVTVNKLIS

NPGEVEQKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYV SVFNNVQENKGASI

FNRRGYFSDPALILMHELIHVLHGLYGIKVDDLPIVPNEKKFFMQSTDTIQAEELY

TFGGQDPSIISPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDK YKFVEDSEGKYSID

GQNKAINKQA YEEISKEHLA VYKIQMCKSV KVPGICIDVDNENLFFIADK NSFSDDLSKN

ERVEYNTQNNYIGNDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAI KKVTDENTIFQYLY SQTFPLNIRDISLTSSFDDALLVSSKVYSFFSMDYIKTANKWEAGLFAGWVKQIVDDFVI EANKSSTMDK

ALTKRVEKWIDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYKYNIY SEEEKSNININFND

INSKL NDGINQAMDN INDFINECSV SYLMKKMIPL AVKKLLDFDNTLKKNLLNYI DENKLYLIGS VEDEKSKVDK YLKTIIPFDLSTYTNNEILIKIFNKYNSEILNNIILNLRYRDNNLIDLSG YGAKVEVYDGVKLNDKNQFKLTSSADSKIRVTQNQNIIFNSMFLDFSVSFWIRIPKYRND DIQNYIHNEYT

ESNMDIKDIGEVIVNGEITFKLDGDVDRTQFIWMKYFSIFNTQLNQSNIKEIYKIQS YSEYLKDFWGNPLM YNKEYYMFNAGNKNSYIKLVKDSSVGEILIRSKYNQNSNYINYRNLYIGEKFIIRRKSNS QSINDDIVRKE DYIHLDFVNSNEEWRVYAYKNFKEQEQKLFLSIIYDSNEFYKTIQIKEYDEQPTYS CQLLFKKDEE

STDDIGLIGI HRFYESGVLRKKYKDYFCIS KWYLKEVKRK PYKSNLGCNW QFIPKDEGWTE

LH _N Polypeptide Fragment of Botulinum neurotoxin type E strain E185 (SEQ ID NO: 4):

PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPP TSLKNGDSSYYDPN YLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAV EIKFSNGSQHI LLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSINEFI QDPALTLMHQL IHSLHGLYGAKGITTTCIITQQQNPLITNRKGINIEEFLTFGGNDLNI ITVAQYNDIYTNLLNDYRKIASK LSKVQVSNPQLNPYKDIFQEKYGLDKDASGIYSVNINKFDDILKKLYSFTEFDLATKFQV KCRETYIGQYK YFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRI IKPITGRGLVKKI IRFCKNIVSVKGIRKSICI EINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNFNSESAPGLSDEK LNLTIQNDAYI PKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVNLTSSIDTALLEQPKIYTFFSSE FINNVNKPVQA ALFVSWIQQVLVDFTTEANQKSTVDKIADISIVVPYIGLALNIGNEAQKGNFKDALELLG AGILLEFEPEL LIPTILVFTIKSFLGSSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKR KEQMYQALQNQ VNAIKTIIESKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLM KLINEVKINKL REYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKILISYFNK FFK

This is but one example of a polypeptide fragment of one particular BoNT/E protein. Other BoNT/E proteins are known in the art and include GenBank Accession No: ZP_02950249.1 which is incorporated by reference. LH _N fragments from BoNT/E proteins include fragments corresponding to the fragment shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein. By way of example, three BoNT/E sequences of the present invention include:

LH _N /E from Beluga strain sequence (SEQ ID NO: 25)

PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPP TSLKNGDSSYYDPN YLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAV EIKFSNGSQDI LLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHRFGSIAIVTFSPEYSFRFNDNCMNEFI QDPALTLMHQL IHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTN LLADYKKIASK LSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLRTKFQV KCRQTYIGQYK YFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRI ITPITGRGLVKKIIRFCKNIVSVKGIRKSICI EINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNFNSESAPGLSDEK LNLTIQNDAYI PKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVNLTSSIDTALLEQPKIYTFFSSE FINNVNKPVQA ALFVSWIQQVLVDFTTEANQKSTVDKIADISIVVPYIGLALNIGNEAQKGNFKDALELLG AGILLEFEPEL

LIPTILVFTIKSFLGSSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQF NKRKEQMYQALQNQ VNAIKTIIESKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLM KIINEVKINKL REYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKILISYFNK FFK

BoNT/E strain E185 (SEQ ID NO: 26)

PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPP TSLKNGDSSYYDPN YLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAV EIKFSNGSQHI LLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSINEFI QDPALTLMHEL IHSLHGLYGAKGITTTCIITQQQNPLITNRKGINIEEFLTFGGNDLNIITVAQYNDIYTN LLNDYRKIASK LSKVQVSNPQLNPYKDIFQEKYGLDKDASGIYSVNINKFDDILKKLYSFTEFDLATKFQV KCRETYIGQYK YFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRI IKPITGRGLVKKIIRFCKNIVSVKGIRKSICI EINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNFNSESAPGLSDEK LNLTIQNDAYI PKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVNLTSSIDTALLEQPKIYTFFSSE FINNVNKPVQA ALFVSWIQQVLVDFTTEANQKSTVDKIADISIVVPYIGLALNIGNEAQKGNFKDALELLG AGILLEFEPEL LIPTILVFTIKSFLGSSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKR KEQMYQALQNQ VNAIKTIIESKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLM KLINEVKINKL REYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKILISYFNK FFKRIKSSSVL NMRYKNDKYVDTSGYDSNININGDVYKYPTNKNQFGIYNDKLSEVNISQNDYIIYDNKYK NFSISFWVRIP NYDNKIVNVNNEYTIINCMRDNNSGWKVSLNHNEIIWTLQDNAGINQKLAFNYGNANGIS DYINKWIFVTI TNDRLGDSKLYINGNLIDQKSILNLGNIHVSDNILFKIVNCSYTRYIGIRYFNIFDKELD ETEIQTLYSNE PNTNILKDFWGNYLLYDKEYYLLNVLKPNNFIDRRKDSTLSINNIRSTILLANRLYSGIK VKIQRVNNSST NDNLVRKNDQVYINFVASKTHLFPLYADTATTNKEKTIKISSSGNRFNQWVMNSVGNNCT MNFKNNNGNN IGLLGFKADTVVASTWYYTHMRDHTNSNGCFWNFISEEHGWQEK

BoNT/E Beluga strain (SEQ ID NO: 27)

PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPP TSLKNGDSSYYDPN YLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPDNQFHIGDASAV EIKFSNGIQDI LLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSIAIVTFSPEYSFRFNDNSMNEFI QDPALTLMHEL IHSLHGLYGAKGITTKYTITQKQNPLITNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTN LLADYKKIASK LSKVQVSNPLLNPYKDVFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQV KCRQTYIGQYK YFKLSNLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNIV SVKGIRKSICI EINNGELFFVASENSYNDDNINTPKEIDDTVTSNNNYENDLDQVILNFNSESAPGLSDEK LNLTIQNDAYI PKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVNLTSSIDTALLEQPKIYTFFSSE FINNVNKPVQA ALFVSWIQQVLVDFTTEANQKSTVDKIADISIWPYIGLALNIGNEAQKGNFKDALELLGA GILLEFEPEL LIPTILVFTIKSFLGSSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQFNKR KEQMYQALQNQ VNAIKTIIESKYNSYTLEEKNELTNKYDIKQIENELNQKVSIAMNNIDRFLTESSISYLM KLINEVKINKL REYDENVKTYLLNYIIQHGSILGESQQELNSMVTDTLNNSIPFKLSSYTDDKILISYFNK FFKRIKSSSVL

NMRYKNDKYVDTSGYDSNININGDVYKYPTNKNQFGIYNDKLSEVNI SQNDYI IYDNKYKNFS I SFWVRI P NYDNKIVNVNNEYT I INCMRDNNSGWKVSLNHNE I IWTLQDNAGINQKLAFNYGNANGI SDYINKWIFVTI TNDRLGDSKLYINGNLIDQKS ILNLGNIHVSDNILFKIVNCSYTRYI GIRYFNIFDKELDETE IQTLYNNE PNANI LKDFWGNYLLYDKEYYLLNVLKPNNFIDRRTDSTLS INNIRSTI LLANRLYSGIKVKIQRVNNS ST NDNLVRKNDQVYINFVASKTHLFPLYADTNTTNKEKTIKSSS SGNRFNQWVMNSVGNNCTMNFKNNNGNN I GMLGFKDNTLVASTWYYTHMRDNTNSNGCFWNFI SEEHGWQEK

LH _N Polypeptide Fragment of Botulinum neurotoxin type F (SEQ ID NO: 7):

PVAINSFNYNDPVNDDTILYMQIPYEEKSKKYYKAFEIMRNVWIIPERNTIGTNPSD FDPPASLKNGSSAY YDPNYLTTDAEKDRYLKTTIKLFKRINSNPAGKVLLQEISYAKPYLGNDHTPIDEFSPVT RTTSVNIKLST

ESFIADPAISLAHQLIYALHGLYGARGVTYEETIEVKQAPLMIAEKPIRLEEFLTFG GQDLNIITSAMKEK IYNNLLANYEKIATRLSEVNSAPPEYDINEYKDYFQWKYGLDKNADGSYTVNENKFNEIY KKLYSFTESDL ANKFKVKCRNTYFIKYEFLKVPNLLDDDIYTVSEGFNIGNLAVNNRGQSIKLNPKIIDSI PDKGLVEKIVK FCKSVIPRKGTKAPPRLCIRVNNSELFFVASESSYNENDINTPKEIDDTTNLNNNYRNNL DEVILDYNSQT IPQISNRTLNTLVQDNSYVPRYDSNGTSEIEEYDWDFNVFFYLHAQKVPEGETNISLTSS IDTALLEESK DIFFSSEFIDTINKPVNAALFIDWISKVIRDFTTEATQKSTVDKIADISLIVPYVGLALN IIIEAEKGNFE

NTQFNKRKEQMYQALQNQVDAIKTAIEYKYNNYTSDEKNRLESEYNINNIEEELNKK VSLAMKNIERFMTE SSISYLMKLINEAKVGKLKKY

This is but one example of a polypeptide fragment of one particular BoNT/F protein. Other BoNT/F proteins are known in the art and include GenBank Accession No: ZP_02619427.1, which is incorporated by reference. LH _N fragments from BoNT/F proteins include fragments corresponding to the fragment shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein.

Tetanus Proteins, Polypeptides, and Fragments

LH _N Polypeptide Fragment of Tetanus Toxin (SEQ ID NO: 5):

YDPNYLRTDSDKDRFLQTMVKLFNRIKNNVAGEALLDKIINAIPYLGNSYSLLDKFD TNSNSVSFNLLEQD PSGATTKSAMLTNLI IFGPGPVLNKNEVRGIVLRVDNKNYFPCRDGFGSIMQMAFCPEYVPTFDNVIENIT SLTIGKSKYFQDPALLLMHQLIYVLHGLYGMQVSSHEIIPSKQEIYMQHTYPISAEELFT FGGQDANLISI DIKNDLYEKTLNDYKAIANKLSQVTSCNDPNIDIDSYKQIYQQKYQFDKDSNGQYIVNED KFQILYNSIMY GFTEIELGKKFNIKTRLSYFSMNHDPVKIPNLLDDTIYNDTEGFNIESKDLKSEYKGQNM RVNTNAFRNVD

GSGLVSKLIGLCKKIIPPTNIRENLYNRTASLTDLGGELCIKIKNEDLTFIAEKNSF SEEPFQDEIVSYNT KNKPLNFNYSLDKIIVDYNLQSKITLPNDRTTPVTKGIPYAPEYKSNAASTIEIHNIDDN TIYQYLYAQKS PTTLQRITMTNSVDDALINSTKIYSYFPSVISKVNQGAQGILFLQWVRDIIDDFTNESSQ KTTIDKISDVS TIVPYIGPALNIVKQGYEGNFIGALETTGWLLLEYIPEITLPVIAALSIAESSTQKEKII KTIDNFLEKR YEKWIEVYKLVKAKWLGTVNTQFQKRSYQMYRSLEYQVDAIKKIIDYEYKIYSGPDKEQI ADEINNLKNKL EEKANKAMININIFMRESSRSFLVNQMINEAKKQLLEFDTQSKNILMQYIKANSKFIGIT ELKKLESKINK VFSTPIPFSYSKNLDCWVDNEEDIDV

This is but one example of a polypeptide fragment of one particular tetanus toxin protein. The amino acid sequences of tetanus toxin proteins, including native proteins, are known in the art and include GenBank Accession No: NP_783831.1 , which is incorporated by reference. LH _N fragments from tetanus toxin proteins include fragments corresponding to the fragment shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein.

C. difficile Toxin Proteins, Polypeptides, and Fragments

C. difficile Toxin A (C-terminal region) (SEQ ID NO: 10):

QSFNKMSIDFKDIKKLSLGYIMSNFKSFNSENELDRDHLGFKIIDNKTYYYDEDSKL VKGLININNSLFYF DPIEFNLVTGWQTINGKKYYFDINTGAALTSYKIINGKHFYFNNDGVMQLGVFKGPDGFE YFAPANTQNNN IEGQAIVYQSKFLTLNGKKYYFDNNSKAVTGWRIINNEKYYFNPNNAIAAVGLQVIDNNK YYFNPDTAIIS KGWQTVNGSRYYFDTDTAIAFNGYKTIDGKHFYFDSDCVVKIGVFSTSNGFEYFAPANTY NNNIEGQAIVY QSKFLTLNGKKYYFDNNSKAVTGLQTIDSKKYYFNTNTAEAATGWQTIDGKKYYFNTNTA EAATGWQTIDG KKYYFNTNTAIASTGYTIINGKHFYFNTDGIMQIGVFKGPNGFEYFAPANTDANNIEGQA ILYQNEFLTLN GKKYYFGSDSKAVTGWRIINNKKYYFNPNNAIAAIHLCTINNDKYYFSYDGILQNGYITI ERNNFYFDANN ESKMVTGVFKGPNGFEYFAPANTHNNNIEGQAIVYQNKFLTLNGKKYYFDNDSKAVTGWQ TIDGKKYYFNL NTAEAATGWQTIDGKKYYFNLNTAEAATGWQTIDGKKYYFNTNTFIASTGYTSINGKHFY FNTDGIMQIGV FKGPNGFEYFAPANTDANNIEGQAILYQNKFLTLNGKKYYFGSDSKAVTGLRTIDGKKYY FNTNTAVAVTG WQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDAN NIEGQAIRYQN RFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLPQI GVFKGSNGFEY FAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAA AGGLFEIDGVI YFFGVDGVKAPGIYG

C. difficile Toxin A (C-terminal region) (SEQ ID NO: 11 ):

TGWQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPA NTDANNIEGQAIRY QNRFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLP QIGVFKGSNGF

EYFAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPD TAMAAAGGLFE IDG VIYFFGVDGVKAPGIYG

C. difficile Toxin A (N-terminal region) (SEQ ID NO: 13):

MSLI SKEELIKLAYS IRPRENEYKTILTNLDEYNKLTTNNNENKYLQLKKLNES IDVFMNKYKTSSRNRAL SNLKKDILKEVILIKNSNTSPVEKNLHFVWIGGEVSDIALEYIKQWADINAEYNIKLWYD SEAFLVNTLKK AIVES STTEALQLLEEE IQNPQFDNMKFYKKRMEFIYDRQKRFINYYKSQINKPTVPTI DDI IKSHLVSEY NRDETVLE SYRTNSLRKINSNHGI DIRANSLFTEQELLNIYSQELLNRGNLAAASDIVRLLALKNFGGVYL DVDMLPGIHSDLFKTI SRPSS IGLDRWEMIKLEAIMKYKKYINNYTSENFDKLDQQLKDNFKLI IESKSEK SE IFSKLENLNVSDLE IKIAFALGSVINQALI SKQGSYLTNLVIEQVKNRYQFLNQHLNPAIESDNNFTDT TKIFHDSLFNSATAENSMFLTKIAPYLQVGFMPEARST I SLSGPGAYASAYYDFINLQENTIEKTLKASDL IEFKFPENNLSQLTEQE INSLWSFDQASAKYQFEKYVRDYTGGSLSED

These are but three examples of a polypeptide from one particular C. difficile toxin protein, toxin A. The amino acid sequences of C. difficile toxin A proteins, including native toxin A proteins, are known in the art and include GenBank Accession No: P16154.2, which is incorporated by reference. Fragments from C. difficile toxin proteins include fragments corresponding to the fragments shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein.

C. difficile Toxin B (C-terminal region) (SEQ ID NO: 12):

TLANKLSFNFSDKQDVPVSEIILSFTPSYYEDGLIGYDLGLVSLYNEKFYINNFGMM VSGLIYINDSLYYF KPPVNNLITGFVTVGDDKYYFNPINGGAASIGETIIDDKNYYFNQSGVLQTGVFSTEDGF KYFAPANTLDE NLEGEAIDFTGKLIIDENIYYFDDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQIGDYK YYFNSDGVMQK GFVSINDNKHYFDDSGVMKVGYTEIDGKHFYFAENGEMQIGVFNTEDGFKYFAHHNEDLG NEEGEEISYSG ILNFNNKIYYFDDSFTAWGWKDLEDGSKYYFDEDTAEAYIGLSLINDGQYYFNDDGIMQV GFVTINDKVF YFSDSGIIESGVQNIDDNYFYIDDNGIVQIGVFDTSDGYKYFAPANTVNDNIYGQAVEYS GLVRVGEDVYY

QFGYINIEDKMFYFGEDGVMQIGVFNTPDGFKYFAHQNTLDENFEGESINYTGWLDL DEKRYYFTDEYIAA TGSVIIDGEEYYFDPDTAQLVISE

C. difficile Toxin B (N-terminal region) (SEQ ID NO: 14):

MS LVNRKQLEKMANVRFRTQE DEYVAI LDALEE YHNMSENTVVEKYLKLKDINSLTDIYIDTYKKSGRNKA LKKFKEYLVTEVLELKNNNLTPVEKNLHFVWIGGQINDTAINYINQWKDVNSDYNVNVFY DSNAFLINTLK KTWE SAINDTLESFRENLNDPRFDYNKFFRKRME I IYDKQKNFINYYKAQREENPELI I DDIVKTYLSNE

YSKEIDELNTYIEESLNKITQNSGNDVRNFEEFKNGESFNLYEQELVERWNLAAASD ILRISALKEIGGMY LDVDMLPGIQPDLFESIEKPSSVTVDFWEMTKLEAIMKYKEYIPEYTSEHFDMLDEEVQS SFESVLASKSD KSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVKQIENRYKILNNSLN PAISEDNDFNT TTNTFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAYQDLLMFKE GSMNIHLIEAD LRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEGSLGED

C. difficile Toxin B Antigen (C-terminal region, residues 1756 to 2361) (SEQ ID NO: 28)

EENKVSQVKIRFVNVFKDKTLANKLSFNFSDKQDVPVSEIILSFTPSYYEDGLIGYD LGLVSLYNEKFYIN NFGMMVSGLIYINDSLYYFKPPVNNLITGFVTVGDDKYYFNPINGGAASIGETIIDDKNY YFNQSGVLQTG

LNQIGDYKYYFNSDGVMQKGFVSINDNKHYFDDSGVMKVGYTEIDGKHFYFAENGEM QIGVFNTEDGFKYF AHHNEDLGNEEGEEISYSGILNFNNKIYYFDDSFTAWGWKDLEDGSKYYFDEDTAEAYIG LSLINDGQYY FNDDGIMQVGFVTINDKVFYFSDSGIIESGVQNIDDNYFYIDDNGIVQIGVFDTSDGYKY FAPANTVNDNI YGQAVEYSGLVRVGEDVYYFGETYTIETGWIYDMENESDKYYFNPETKKACKGINLIDDI KYYFDEKGIMR TGLISFENNNYYFNENGEMQFGYINIEDKMFYFGEDGVMQIGVFNTPDGFKYFAHQNTLD ENFEGESINYT GWLDLDEKRYYFTDEYIAATGSVIIDGEEYYFDPDTAQ

These are three examples of a polypeptide from another particular C. difficile toxin protein, toxin B. The amino acid sequences of C. difficile toxin B proteins, including native toxin B proteins, are known in the art and include GenBank Accession No: P16154.2, which is incorporated by reference. Fragments from C. difficile toxin proteins include fragments corresponding to the fragments shown above, optionally including, or not, the modifications disclosed elsewhere in this specification, such as those to reduce or eliminate the toxicity of the protein.

Other C. difficile polypeptides and polypeptide fragments include: C. difficile surface peptide Cwp84 (SEQ ID NO: 15):

MRKYKSKKLSKLLALLTVCFLIVSTIPVSAENHKTLDGVETAEYSESYLQYLEDVKN GDTAKYNGVIPFPH EMEGTTLRNKGRSSLPSAYKSSVAYNPMDLGLTTPAKNQGSLNTCWSFSGMSTLEAYLKL KGYGTYDLSEE HLRWWATGGKYGWNLDDMSGSSNVTAIGYLTAWAGPKLEKDIPYNLKSEAQGATKPSNMD TAPTQFNVTDV VRLNKDKETVKNAIMQYGSVTSGYAHYSTYFNKDETAYNCTNKRAPLNHAVAIVGWDDNY SKDNFASDVKP ESNGAWLVKSSWGEFNSMKGFFWISYEDKTLLTDTDNYAMKSVSKPDSDKKMYQLEYAGL SKIMSNKVTAA NVFDFSRDSEKLDSVMFETDSVGAKYEVYYAPVVNGVPQNNSMTKLASGTVSYSGYINVP TNSYSLPKGKG AIVWIDNTANPNREKSTLAYETNIDAYYLYEAKANLGESYILQNNKFEDINTYSEFSPCN FVIKAITKTS

SGQATSGESLTGADRYETAVKVSQKGWTSSQNAVLVNGDAIVDALTATPFTAAIDSP ILLTGKDNLDSKTK AELQRLGTKKVYLIGGENSLSKNVQTQLSNMGISVERISGSDRYKTSISLAQKLNSIKSV SQVAVANGVNG LADAISVGAAAADNNMPIILTNEKSELQGADEFLNSSKITKSYIIGGTATLSSNLESKLS NPTRLAGSNRN ETNAKIIDKFYPSSDLKYAFVVKDGSKSQGDLIDGLAVGALGAKTDSPWLVGNKLDESQK NVLKSKKIET PIRVGGNGNESAFNELNTLLGK

C. difficile binary toxin fragment A (SEQ ID NO: 19):

KVCNTTYKAPIESFLKDKEKAKEWERKEAERIEQKLERSEKEALESYKKDSVEISKY SQTRNYFYDYQIEA NSREKEYKELRNAISKNKIDKPMYVYYFESPEKFAFNKVIRTENQNEISLEKFNEFKETI QNKLFKQDGFK DISLYEPGKGDEKPTPLLMHLKLPRNTGMLPYTNTNNVSTLIEQGYSIKIDKIVRIVIDG KHYIKAEASW

NALKREPIPTNLTVYRRSGPQEFGLTLTSPEYDFNKLENIDAFKSKWEGQALSYPNF ISTSIGSVNMSAFA KRKIVLRITIPKGSPGAYLSAIPGYAGEYEVLLNHGSKFKINKIDSYKDGTITKLIVDAT LIP

C. difficile binary toxin fragment B (SEQ ID NO: 20):

YTLSTDRDDVLMQVNTESTISNTLKVNMKKGKEYKVRIELQDKNLGSIDNLSSPNLY WELDGMKKIIPEEN LFLRDYSNIEKDDPFIPNNNFFDPKLMSDWEDEDLDTDNDNIPDSYERNGYTIKDLIAVK WEDSFAEQGYK KYVSNYLESNTAGDPYTDYEKASGSFDKAIKTEARDPLVAAYPIVGVGMEKLIISTNEHA STDQGKTVSRA TTNSKTESNTAGVSVNVGYQNGFTANVTTNYSHTTDNSTAVQDSNGESWNTGLSINKGES AYINANVRYYN TGTAPMYKVTPTTNLVLDGDTLSTIKAQENQIGNNLSPGDTYPKKGLSPLALNTMDQFSS RLIPINYDQLK KLDAGKQIKLETTQVSGNFGTKNSSGQIVTEGNSWSDYISQIDSISASIILDTENESYER RVTAKNLQDPE

ILIKTPTYFTNFDDYNNYPSTWSNVNTTNQDGLQGSANKLNGETKIKIPMSELKPYK RYVFSGYSKDPLTS NSIIVKIKAKEEKTDYLVPEQGYTKFSYEFETTEKDSSNIEITLIGSGTTYLDNLSITEL NSTPEILDEPE VKIPTDQEIMDAHKIYFADLNFNPSTGNTYINGMYFAPTQTNKEALDYIQKYRVEATLQY SGFKDIGTKDK EMRNYLGDPNQPKTNYVNLRSYFTGGENIMTYKKLRIYAITPDDRELLVLSVD

Anthrax Proteins, Polypeptides, and Fragments

Anthrax Protective Antigen (PA) (SEQ ID NO: 16):

MKKRKVLIPLMALSTILVSSTGNLEVIQAEVKQENRLLNESESSSQGLLGYYFSDLN FQAPMVVTSSTTGD LSIPSSELENIPSENQYFQSAIWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASN SNKIRLEKGRL YQIKIQYQRENPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQKSSNSRKKRSTSAGP TVPDRDNDGIP

VAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTSRTHTSEVHGNAEVHAS FFDIGGSVSAGFSN SNSSTVAIDHSLSLAGERTWAETMGLNTADTARLNANIRYVNTGTAPIYNVLPTTSLVLG KNQTLATIKAK ENQLSQILAPNNYYPSKNLAPIALNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYG NIATYNFENGR

VRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKE ALKIAFGFNEPNGN LQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYD RNNIAVGADES WKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQD GKTFIDFKKY NDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEIG

This is but one example of one particular anthrax protein within the scope of the invention. The amino acid sequences of PA proteins, including native proteins, from various strains of anthrax are known in the art and include, for example, GenBank Accession Nos: NP_652920.1, ZP_02937261.1, ZP_02900013.1, ZP_02880951.1 which are incorporated by reference. Various fragments, mutations, and modifications in PA to reduce its toxicity or to improve its expression characteristics are also known, such as those described elsewhere in the specification.

Anthrax Lethal Factor (LF) (SEQ ID NO: 17):

MNIKKEFIKVISMSCLVTAITLSGPVFIPLVQGAGGHGDVGMHVKEKE KNKDENKRKDEERNKTQEEHLKE

KDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQP YQKFLDVLNTIKNA SDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEA FNYMDKFNEQE INLSLEELKDQRMLARYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSL SQEEKELLKRI QIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLD IQPYDINQRLQ DTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGAD LVDSTDNTKIN RGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRN IGLEIKDVQII KQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNI VESAYLILNEW KNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSI LLHGPSKGVEL RNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFF AEAFRLMHSTD HAERLKVQKNAPKTFQFINDQIKFIINS

This is but one example of one particular anthrax protein within the scope of the invention. The amino acid sequences of LF proteins, including native proteins, from various strains of anthrax are known in the art and include, for example, GenBank Accession Nos: NP_652928.1 and ZP_02609621.1, which are incorporated by reference. Various fragments, mutations, and modifications in LF to reduce its toxicity or to improve its expression characteristics are also known, such as those described elsewhere in the specification.

An example of a lethal factor protein that has been mutated to ablate its endopeptidase activity is SEQ ID NO: 18:

MNIKKEFIKVISMSCLVTAITLSGPVFIPLVQGAGGHGDVGMHVKEKEKNKDENKRK DEERNKTQEEHLKE

KDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQP YQKFLDVLNTIKNA SDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEA FNYMDKFNEQE INLSLEELKDQRMLARYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSL SQEEKELLKRI QIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLD IQPYDINQRLQ DTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGAD LVDSTDNTKIN RGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRN IGLEIKDVQII KQSEKEYIRIDAKWPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIV ESAYLILNEW KNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSI LLHGPSKGVEL RNDSEGFIHQFGYAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFF AEAFRLMHSTD HAERLKVQKNAPKTFQFINDQIKFIINS

Changes relative to the native lethal factor are shown in bold.

Anthrax Oedema Factor Antigen (EF) (SEQ ID NO: 21):

MTRNKFIPNKFS11SFSVLLFAISSSQAIEVNAMNEHYTESDIKRNHKTEKNKTEKE KFKDSINNLVKTEF TNETLDKIQQTQDLLKKIPKDVLEIYSELGGEIYFTDIDLVEHKELQDLSEEEKNSMNSR GEKVPFASRFV FEKKRETPKLIINIKDYAINSEQSKEVYYEIGKGISLDIISKDKSLDPEFLNLIKSLSDD SDSSDLLFSQK FKEKLELNNKSIDINFIKENLTEFQHAFSLAFSYYFAPDHRTVLELYAPDMFEYMNKLEK GGFEKISESLK

DWGPVAGYIPFDQDLSKKHGQQLAVEKGNLENKKSITEHEGEIGKIPLKLDHLRIEE LKENGIILKGKKEI DNGKKYYLLESNNQVYEFRISDENNEVQYKTKEGKITVLGEKFNWRNIEVMAKNVEGVLK PLTADYDLFAL APSLTEIKKQIPQKEWDKWNTPNSLEKQKGVTNLLIKYGIERKPDSTKGTLSNWQKQMLD RLNEAVKYTG YTGGDWNHGTEQDNEEFPEKDNEIFIINPEGEFILTKNWEMTGRFIEKNITGKDYLYYFN RSYNKIAPGN

IFSQEKKRKISIFRGIQAYNEIENVLKSKQIAPEYKNYFQYLKERITNQVQLLLTHQ KSNIEFKLLYKQLN FTENETDNFEVFQKIIDEK

This is but one example of one particular anthrax protein within the scope of the invention. The amino acid sequences of EF proteins, including native proteins, from various strains of anthrax are known in the art. Various fragments, mutations, and modifications in EF to reduce its toxicity or to improve its expression characteristics are also known, such as those described elsewhere in the specification. An example of an EF protein that has been mutated to ablate its adenylyl cyclase activity is histidine 351 to alanine SEQ ID NO: 22:

Anthrax Oedema Factor Antigen (EF His351Ala) (SEQ ID NO: 22):

MTRNKFI PNKFS I I SFSVLLFAI SS SQAIEVNAMNEHYTESDIKRNHKTEKNKTEKEKFKDS INNLVKTEF TNETLDKIQQTQDLLKKI PKDVLE IYSELGGE IYFTDIDLVEHKELQDLSEEEKNSMNSRGEKVPFASRFV FEKKRETPKLI INIKDYAINSEQSKEVYYE IGKGI SLDI I SKDKSLDPEFLNLIKSLSDDSDSSDLLFSQK FKEKLELNNKS IDINFIKENLTEFQHAFSLAFSYYFAPDHRTVLELYAPDMFEYMNKLEKGGFEKI SESLK KEGVEKDRIDVLKGEKALKASGLVPEHADAFKKIARELNTYILFRPVNKLATNLIKSGVA TKGLNVAGKSS DWGPVAGYI PFDQDLSKKHGQQLAVEKGNLENKKS I TEHEGE IGKI PLKLDHLRIEELKENGI I LKGKKE I DNGKKYYLLESNNQVYEFRI SDENNEVQYKTKEGKI TVLGEKFNWRNIEVMAKNVEGVLKPLTADYDLFAL APSLTE IKKQI PQKEWDKWNTPNSLEKQKGVTNLLIKYGIERKPDSTKGTLSNWQKQMLDRLNEAVKYTG YTGGDWNHGTEQDNEEFPEKDNE IFI INPEGEFILTKNWEMTGRFIEKNI TGKDYLYYFNRSYNKIAPGN

IFSQEKKRKI S IFRGIQAYNE IENVLKSKQIAPEYKNYFQYLKERITNQVQLLLTHQKSNIEFKLLYKQLN FTENETDNFEVFQKI IDEK

In addition to the various mutations and modifications already noted, the present invention also encompasses polypeptides that are substantially homologous to a polypeptide based on any one of the SEQ ID NOS identified in this application (including fragments thereof). The term "substantially homologous" is used to denote polypeptides having at least about 70%, at least about 75%, at least about 80%, in some cases at least about 85%, in other cases at least about 90%, in yet other cases at least about 95%, and in still other cases at least about 98% or even 99% sequence identity to the other polypeptide.

Peptides disclosed in the present application likewise include peptides that are "substantially homologous" thereto, and embrace peptides having at least about 90%, in some cases at least about 95%, and in yet other cases at least about 98% or even 99%, sequence identity thereto. Exemplary peptides are provided in the present application, but unless reference is made to a specific SEQ ID NO or the discussion makes clear that only a specific sequence is intended, then the sequences exemplified in the specification are illustrative only of the various peptides, polypeptides, and proteins described in the application.

Percent sequence identity is determined by conventional methods. See, for example, Altschul et al., Bull. Math. Bio. 48: 603-16, 1986 and Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915-19, 1992. Briefly, two amino acid sequences are aligned to optimize the alignment scores using a gap opening penalty of 10, a gap extension penalty of 1 , and the "blosum 62" scoring matrix of Henikoff and Henikoff (ibid.) as shown in the following chart (amino acids are indicated by the standard one-letter codes):

A R N D C Q E G H I L K M F P S T W Y V

A 4

R-1 5

N -2 0 6

D -2 -2 1 6

C 0-3-3-39

Q-1 1 0 0-3 5

E-1 0 0 2-4 2 5

G 0 -20 -1 -3 -2 -26

H -20 1 -1 -300 -28

I -1 -3 -3 -3 -1 -3 -3 -4 -34

L -1 -2 -3 -4 -1 -2 -3 -4-324

K -1 20 -1 -3 1 1 -2 -1 -3 -25

M -1 -1 -2 -3 -1 0-2-3-2 1 2-1 5

F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0-3 0 6

P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7

S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4

T 0 -1 0-1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2-1 1 5

W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4-3-211

Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3-3-2-2 2 7

V 0-3-3 -3 -1 -2 -2 -3-3 3 1 -2 1 -1 -2 -2 0 -3 -1 4.

The percent identity is then calculated as: ([Total number of identical matches]/[length of the longer sequence plus the number of gaps introduced into the longer sequence in order to align the two sequences]) x 100.

Substantially homologous polypeptides have one or more amino acid substitutions, deletions, or additions. In many embodiments, those changes are of a minor nature, for example, involving only conservative amino acid substitutions. Conservative substitutions are those made by replacing one amino acid with another amino acid within the following groups: Basic: arginine, lysine, histidine; Acidic: glutamic acid, aspartic acid; Polar: glutamine, asparagine; Hydrophobic: leucine, isoleucine, valine; Aromatic: phenylalanine, tryptophan, tyrosine; Small: glycine, alanine, serine, threonine, methionine. Substantially homologous polypeptides also encompass those comprising other substitutions that do not significantly affect the folding or activity of the polypeptide; small deletions, typically of one to about 30 amino acids; and small amino- or carboxyl- terminal extensions, such as an amino-terminal methionine residue, a small linker peptide of up to about 20-25 residues, or an affinity tag.

In addition to the 20 standard amino acids, non-standard amino acids (such as A- hydroxyproline, 6-λ/-methyl lysine, 2-aminoisobutyric acid, isovaline and α -methyl serine) may be substituted for amino acid residues of the clostridial polypeptides of the present invention. A limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, and unnatural amino acids may be substituted for clostridial polypeptide amino acid residues. The polypeptides of the present invention can also comprise non-naturally occurring amino acid residues.

Non-naturally occurring amino acids include, without limitation, trans-3-methylproline, 2,4-methano-proline, cis-4-hydroxyproline, trans-4-hydroxy-proline, N-methylglycine, allo-threonine, methyl-threonine, hydroxy-ethylcysteine, hydroxyethylhomo-cysteine, nitro-glutamine, homoglutamine, pipecolic acid, tert-leucine, norvaline, 2- azaphenylalanine, 3-azaphenyl-alanine, 4-azaphenyl-alanine, and 4-fluorophenylalanine. Several methods are known in the art for incorporating non-naturally occurring amino acid residues into peptides. For example, an in vitro system can be employed wherein nonsense mutations are suppressed using chemically aminoacylated suppressor tRNAs. Methods for synthesizing amino acids and aminoacylating tRNA are known in the art. Transcription and translation of plasmids containing nonsense mutations can be carried out in a cell free system comprising an E. coli S30 extract and commercially available enzymes and other reagents. Peptides can be, for instance, purified by chromatography. See, for example, Robertson et al., J. Am. Chem. Soc. 113:2722, 1991 ; Ellman et al.. Methods Enzvmol. 202:301 , 1991 ; Chung et al.. Science 259:806-9, 1993; and Chung et al., Proc. Natl. Acad. Sci. USA 90:10145-9, 1993). In a second method, translation is carried out in Xenopus oocytes by microinjection of mutated mRNA and chemically aminoacylated suppressor tRNAs (Turcatti et al., J. Biol. Chem. 271 :19991-8, 1996). Within a third method, E. coli cells are cultured in the absence of a natural amino acid that is to be replaced (e.g., phenylalanine) and in the presence of the desired non-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine, 3- azaphenylalanine, 4-azaphenylalanine, or 4-fluorophenylalanine). The non-naturally occurring amino acid is incorporated into the polypeptdie in place of its natural counterpart. See, Koide et al., Biochem. 33:7470-6, 1994. Naturally occurring amino acid residues can be converted to non-naturally occurring species by in vitro chemical modification. Chemical modification can be combined with site-directed mutagenesis to

further expand the range of substitutions (Wynn and Richards, Protein Sci. 2:395-403, 1993).

Essential amino acids, such as those in the clostridial polypeptides of the present invention, can be identified according to procedures known in the art, such as site- directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, Science 244: 1081-5, 1989). Sites of biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids. See, for example, de Vos et al., Science 255:306-12, 1992: Smith et al., J. MoI. Biol. 224:899-904, 1992; Wlodaver et al., FEBS Lett. 309:59-64, 1992. The identities of essential amino acids can also be inferred from analysis of homologies with related family members of the polypeptide of interest.

Multiple amino acid substitutions can be made and tested using known methods of mutagenesis and screening, such as those disclosed by Reidhaar-Olson and Sauer (Science 241_:53-7, 1988) or Bowie and Sauer (Proc. Natl. Acad. Sci. USA 86:2152-6, 1989). Briefly, these authors disclose methods for simultaneously randomizing two or more positions in a polypeptide, selecting for functional polypeptide, and then sequencing the mutagenized polypeptides to determine the spectrum of allowable substitutions at each position. Other methods that can be used include phage display (e.g., Lowman et al., Biochem. 30:10832-7, 1991 ; Ladner et al., U.S. Patent No. 5,223,409; Huse, WIPO Publication WO 92/06204) and region-directed mutagenesis (Derbyshire et al.. Gene 46:145, 1986; Ner e. a/.. DNA 7:127, 1988).

It should be noted that reference to proteins, polypeptides, and peptides throughout the present application embraces fragments thereof unless it is clear from the context that a fragment is excluded. In particular, the present invention embraces fragments having at about 100, at least about 150, at least about 200, at least about 250, or at least about 300 contiguous amino acid residues of a peptide (including substantially homologous embodiments thereof) disclosed in the present application. The fragments may embrace at least about 200-300, often at least about 400-500, in many embodiments at least about 600-700, and in certain embodiments at least about 800 contiguous amino acids

of a polypeptide (including substantially homologous embodiments thereof) disclosed in the present application.

By way of example, one fragment of the present invention comprises an amino acid sequence having at least about 90% sequence identity, over a sequence of at least about 200 contiguous amino acids. For instance, the invention includes a fragment comprising an amino acid sequence having at least 200 contiguous amino acid residues and having at least 90% sequence identity (e.g., starting at position 350, 400, 440 or 448) with the amino acid sequence as set forth in SEQ ID NO: 8 or 9. In another embodiment, the fragment comprises an amino acid sequence having at least 200 contiguous amino acid residues and having at least 90% sequence identity (e.g., starting at position 449 or 455) with the amino acid sequence as set forth in SEQ ID NO: 8 or 9. Yet other embodiments involve a fragment comprising an amino acid sequence having at least 200 amino acid residues and having at least 90% sequence identity over the contiguous residues 348-548 of the amino acid sequence of SEQ ID NO:8 or 9.

In one embodiment of the invention, a clostridial peptide treated with a chemical modifying agent lacks a H _c region or a functional H _c region. Accordingly, said peptides are not able to bind rat synaptosomal membranes in binding assays as described in Shone et al. (1985) Eur. J. Biochem. 151 , 75-82. In one embodiment, the clostridial peptides lack the last about 50 C-terminal amino acids of a clostridial neurotoxin holotoxin. In another embodiment, the clostridial peptides lack the last about 100, the last about 150, the last about 200, the last about 250, or even the last about 300 C- terminal amino acid residues of a clostridial neurotoxin holotoxin. In one embodiment of the invention, the clostridial peptide is not a native peptide.

Alternatively, the Hc binding activity may be negated/reduced by mutagenesis. Often this involves substitution of the amino acid pair WY (tryptophan, tyrosine) with the amino acids LF (leucine, phenylalanine). By way of example, referring to BoNT/A (SEQ ID NOS: 8 and 9), modification of one or two amino acid residue mutations (W1266 to L and Y1267 to F) in the ganglioside binding pocket cause the H _c region to lose its receptor binding function. Analogous mutations may be made to non-serotype A clostridial peptides (e.g., to SEQ ID NOs: 23 and 24 for serotype B; and to SEQ ID NOs: 26 and 27 for serotype E) - by way of example, a construct based on C. botulinum B

with mutations (W1262 to L and Y1263 to F) or C. botulinum E (W1224 to L and Y1225 to F). Other mutations to the active site achieve the same ablation of H _c receptor binding activity, e.g. Y1267S in C. botulinum type A toxin (e.g., SEQ ID NO: 8) and the corresponding highly conserved residue in the other clostridial neurotoxins. Details of this and other mutations are described in Rummel et al. (2004) (Molecular Microbiol. 51 :631-634), which is hereby incorporated by reference in its entirety.

In one embodiment of the invention, the nucleic acid encoding a bacterial peptide is codon optimized for expression in a host cell. For instance, in one embodiment of the invention, a nucleic acid encoding a LH _N fragment is codon optimized for expression in a E. coli. In another embodiment, the nucleic acid encoding a LH _N fragment is codon optimized for expression in a eukaryotic cell, for instance, a yeast cell, mammalian cell or insect cell. Genes encoding polypeptides such as those described are commercially available with codon bias for any desired expression host (e.g., E. coli, Pichia pastoris).

Polypeptides are expressed from these gene using standard molecular biology methods (e.g., Sambrook et al. 1989, Molecular Cloning a Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York) and the resulting soluble expressed peptide can be purified by, for instance, a combination of hydrophobic interaction chromatography, ion exchange chromatography and ceramic hydroxyl apatite chromatography. Other chromatographic techniques well known to the art of protein purification, such size exclusion chromatography, may be used.

Methods of manipulating nucleic acids and of expressing the encoded proteins are known in the art, and include those described in Molecular Cloning, A Laboratory Manual (2nd Ed., Sambrook, Fritsch and Maniatis, Cold Spring Harbor) and Current Protocols in Molecular Biology (Eds. Aufubel, Brent, Kingston, More, Feidman, Smith and Stuhl, Greene Publ. Assoc, Wiley-lnterscience, NY, N.Y., 1992). Thus, it is possible to express a modified polypeptide by modifying a nucleic acid sequence encoding that polypeptide by replacing the codon for one amino acid with a codon for another amino acid. Techniques for making substitution and deletion mutations at predetermined sites in a nucleic acid having a known sequence are well known and include, but are not limited to, primer mutagenesis and other forms of site-directed mutagenesis.

Similarly, methods of joining two sequence fragments, such as an LH _N and an H _c fragment of a clostridial neurotoxin, and of truncating a sequence, are known in the art. These include, but are not limited to, PCR-based techniques and techniques for ligating together two or more nucleic acid sequences.

Methods of expressing proteins are known to the skilled artisan and can be practiced with no more than routine experimentation. Generally, in order to express a protein, such as a bacterial toxin or fragment thereof, a suitable host cell is transformed with a DNA sequence encoding that protein under the control of known regulatory sequences. The transformed host cells are cultured and the protein recovered and isolated from the culture medium. The isolated expressed proteins are substantially free from other proteins with which they are co-produced as well as from other contaminants.

The peptide or polypeptide to be chemically modified should generally be soluble or predominantly soluble (for instance, at least about 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or even 99% soluble). There are various ways to produce peptides or polypeptides that exhibit increased solubility. The optimal method employed depends upon the particular peptide or polypeptide. Examples of methods that can be used to produce a maximally soluble peptide or polypeptide include the use of particular buffers and/or pH during culture, and the reduction of the temperature during the fermentation process. By way of example, we refer to US 61/060,978 (filed June 12, 2008), which is incorporated by reference in its entirety. Additional examples of methods to increase solubility reduce aggregation are described in WO 2007/044382, which is incorporated by reference in its entirety.

Bacterial cells may be used as suitable hosts for expression of a bacterial toxin or fragment thereof. For example, various strains of E. coli (e.g., HB101 , MC1061 ) are well-known as host cells in the field of biotechnology. Various strains of B. subtilis, Pseudomonas, other bacilli and the like may also be used. For expression of a protein in bacterial cells, DNA encoding the propeptide is generally not necessary. Suitable cells or cell lines may also be mammalian cells, such as Chinese hamster ovary cells (CHO), the monkey kidney COS-1 cell line, or mammalian CV-1 cells. The selection of suitable mammalian host cells and methods for transformation, culturing, amplification, screening, product production and purification are known in the art. (See, e.g., Gething

and Sambrook, Nature, 293:620-625 (1981 ); Kaufman et a/., MoI Cell Biol., 5(7):1750- 1759 (1985); Howley ef a/., U.S. Patent 4,419,446.)

In some embodiments, the polypeptide or fragment thereof is expressed using a vector that contains a DNA sequence encoding the polypeptide and appropriate expression control sequences. Expression control sequences for such vectors are known to those skilled in the art and may be selected depending upon the host cells. In other embodiments, the polypeptide or fragment thereof is expressed as a fusion protein comprising the protein sequence of the polypeptide or fragment thereof and, for example, a tag to stabilize the resulting fusion protein or to simplify purification of the bacterial toxin or fragment thereof. Such tags are known in the art. Representative examples include sequences which encode a series of histidine residues, the epitope tag FLAG, the Herpes simplex glycoprotein D, beta-galactosidase, maltose binding protein, streptavidin tag or glutathione S-transferase.

IV. Compositions and Vaccines

The invention also provides compositions comprising chemically modified peptides and polypeptides.

In some embodiments, the chemically modified peptides and polypeptides have an increased protective effect that can be measured by their improved ability to stimulate an immune response when compared to an unmodified peptide or polypeptide. In other embodiments, the increased protective effect can be measured by the ability to provide improved cross-serotype protection when compared to an unmodified peptide or polypeptide. In yet other embodiments, the increased protective effect can be measured by the ability to provide improved cross-subtype protection when compared to an unmodified peptide or polypeptide. In still other embodiments, the increased protective effect can be measured by a combination of one, two, or three of the ability to provide an improved ability to stimulate an immune response, an improved cross-serotype protection, and an improved cross-subtype protection. Often, although not always, the peptide or polypeptide may display an increase in stability compared to the unmodified peptide or polypeptide. The increased stability is due, at least in some embodiments, to the intra-molecular cross-links, such as those comprising one or more methylene bonds.

Also, in some embodiments, the peptide or polypeptide does not form aggregates or forms a minimal amount of aggregates.

The invention includes, for instance, an endopeptidase negative LH _N fragment that has been treated with formaldehyde under conditions which increase the immunogenicity of the toxin fragment as compared to a fragment not treated with formaldehyde. In one embodiment of the invention, the endopeptidase negative LHN fragment is a LH _N /E fragment.

The compositions of the invention usually comprise a carrier of some type in addition to the polypeptide or peptide. Generally, the carrier is a pharmaceutically-acceptable carrier. In some embodiments, however, it may be desirable to formulate the composition with a preservative, such as thiomersal or sodium azide, to facilitate long term storage. Non-limiting examples of pharmaceutically acceptable carriers include water, saline, and phosphate-buffered saline. In some embodiments, however, the composition is in lyophilized form, in which case it may include a stabilizer, such as BSA.

Vaccines comprising a composition comprising one or more of the chemically modified peptides or polypeptides are also provided.

The active immunogenic ingredients are often mixed with carriers or excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable carriers and excipients include, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants which enhance the effectiveness of the vaccine.

The vaccine may further comprise one or more adjuvants. One non-limiting example of an adjuvant with the scope of the invention is aluminium hydroxide. Other non-limiting examples of adjuvants include but are not limited to: N-acetyl-muramyl-L-threonyl-D- isoglutamine (thr-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2- (V-Z- dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria,

monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2 % squalene/ Tween 80 emulsion.

Typically, the vaccines are prepared as injectables, either as liquid solutions or suspensions. Of course, solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The preparation may also be emulsified, or the peptide encapsulated in liposomes or microcapsules.

Vaccine administration is generally by conventional routes e.g. intravenous, subcutaneous, intraperitoneal, or mucosal routes. The administration may be by parenteral injection, for example, a subcutaneous or intramuscular injection.

The vaccines are administered in a manner compatible with the dosage formulation, and in such amount as will be prophylactically and/or therapeutically effective. The quantity to be administered, which is generally in the range of 5 micrograms to 250 micrograms of antigen per dose, depends on the subject to be treated, capacity of the subject's immune system to synthesize antibodies, and the degree of protection desired. Precise amounts of active ingredient required to be administered may depend on the judgment of the practitioner and may be particular to each subject.

The vaccine may be given in a single dose schedule, or optionally in a multiple dose schedule. A multiple dose schedule is one in which a primary course of vaccination may be with 1-6 separate doses, followed by other doses given at subsequent time intervals required to maintain and or reinforce the immune response, for example, at 1 -4 months for a second dose, and if needed, a subsequent dose(s) after several months. The dosage regimen will also, at least in part, be determined by the need of the individual and be dependent upon the judgment of the practitioner.

In addition, the vaccine containing the immunogenic antigen(s) may be administered in conjunction with other immunoregulatory agents, for example, immunoglobulins, antibiotics, interleukins (e.g., IL-2, IL-12), and/or cytokines (e.g., IFNγ).

Additional formulations which are suitable for other modes of administration include microcapsules, suppositories and, in some cases, oral formulations or formulations

suitable for distribution as aerosols. For suppositories, traditional binders and carriers may include, for example, polyalkylene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of about 0.5 % to 10 %, including for instance, about 1 %-2 %.

Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain about 10 %-95 % of active ingredient, including, for instance, about 25 %-70 % of active ingredient.

The invention also provides methods of stimulating an immune response in a mammal, such as a human, by administering to the mammal an amount of a vaccine of the invention sufficient to stimulate an immune response. In some embodiments, immune stimulation is measured by an increased protective effect compared to a vaccine comprising the unmodified form of the same peptide or polypeptide. In other embodiments, immune stimulation is measured by increases in antibody titer that is specific for the antigen in the vaccine. In still other embodiments, immune stimulation is measured by an increased frequency in cytotoxic T lymphocytes specific for the antigen in the vaccine.

Thus, one embodiment of the invention is a vaccine comprising peptides in which the peptides are treated with a chemical modifying agent to give a vaccine of much improved efficacy.

In one particular embodiment, the vaccine is based on a peptide (e.g., a botulinum toxin fragment, a tetanus toxin fragment, a C. difficile toxin or surface peptide fragment, or an anthrax toxin fragment) having intra-molecular cross-linking, which results in a vaccine of much improved efficacy. Treatment with the chemical modifying agent induces the formation of one or more intra-molecular (e.g., methylene) bonds. Since the intramolecular bond(s) are introduced by a modifying chemical, said bonds are typically absent from the corresponding native (i.e., untreated) peptide. In many embodiments, two, three, or more such bonds are formed. In this regard, the bond(s) typically,

originate from arginine and/ or lysine amino acid residues, although this is not necessarily the case. As noted, a variety of chemical modifying agents may be employed so long as the agent introduces at least one intramolecular bond (e.g., a methylene bond) into the peptide. In the case of clostridial fragments having two peptide chains (e.g., a L-chain and a H-chain in the case of a clostridial neurotoxin), the intramolecular bond(s) may form within either chain, and/ or across the chains. In some of the embodiments involving clostridial fragments, said bond(s) bridge both chains - e.g., in the case of a clostridial neurotoxin, the L-chain and H-chain are bridged by intramolecular bond(s).

In one embodiment of the invention, a vaccine is described based on an LH _N fragment of a clostridial neurotoxin (which consists of the light chain and N-terminal 50 kDa of heavy chain) in which this fragment is treated with formaldehyde to give a significantly improved vaccine.

In another embodiment of the invention, a vaccine is described comprising an extended LH _N fragment of a clostridial neurotoxin and lacking a functional H _c domain of a botulinum toxin, in which this fragment is treated with a chemical modifying agent to give a significantly improved vaccine. In this embodiment, lack of H _c functionality may be readily conferred by mutation and/or deletion of H _c amino acid residues from a clostridial neurotoxin holotoxin.

In one embodiment of the invention, a vaccine is described based on an LH _N fragment of a clostridial (e.g., botulinum) neurotoxin in which the fragment is treated with a chemical modifying agent (e.g., formaldehyde) to give a significantly improved vaccine. In a one embodiment, the clostridial neurotoxin fragment is a botulinum type A, B, or E neurotoxin fragment.

In another embodiment of the invention, a vaccine is described based on a peptide consisting of (or corresponding to) amino acid residues 2-871 of botulinum neurotoxin serotype A in which this peptide is treated with formaldehyde to give a significantly improved vaccine for botulinum type A toxin. One example of a botulinum neurotoxin serotype A polypeptide is given in SEQ ID NO: 1. Another example of a botulinum

neurotoxin serotype A polypeptide is given in SEQ ID NO: 2. Yet another example of a botulinum neurotoxin serotype A polypeptide is given in SEQ ID NO: 3.

In one embodiment of the invention, a vaccine is described based on a peptide consisting of (or corresponding to) amino acid residues 2-871 (or a fragment thereof) of botulinum neurotoxin serotype A containing 1 or 2 mutations, namely: GIu 224 to GIn and/ or His 227 to Tyr. This peptide is then treated with a modifying agent (e.g. formaldehyde) to give a significantly improved vaccine for botulinum type A toxin.

In yet another embodiment of the invention, a vaccine is described based on a peptide consisting of (or corresponding to) amino acid residues 2-871 of botulinum neurotoxin serotype E in which this peptide is treated with formaldehyde to give a significantly improved vaccine for botulinum type E toxin. One example of a botulinum neurotoxin serotype E polypeptide is given in SEQ ID NO: 4.

The above-mentioned substitution(s) described in connection with the 2-871 peptide embodiment may be introduced into any of the clostridial peptide embodiments of the present invention. In more detail, said substitution(s) (at least partially) inactivate the metalloprotease activity of the L-chain component. In this regard, simple amino acid sequence alignment of the different clostridial neurotoxin species/serotypes allows identification of the corresponding amino acid residues in clostridial neurotoxin peptides other than serotype A. Another example of a metalloprotease-inactivating mutation comprises substitution/ deletion of Glu262. Again, simple amino acid sequence alignment of the different clostridial toxin species/ serotypes allows identification of the corresponding amino acids in clostridial neurotoxin peptides other than serotype A. A yet further metalloprotease-inactivating mutation comprises modification of the HELIH (SEQ ID NO: 8) active site motif (e.g., serotype A) to an HQLIY (SEQ ID NO: 9) motif. Again, simple amino acid sequence alignment of the different clostridial toxin species/ serotypes allows identification of the corresponding amino acids in clostridial neurotoxin peptides other than serotype A. For botulinum neurotoxin serotypes B, E, F, G and tetanus neurotoxin, an identical change to the HELIH light chain motif may be made to inactivate the endopeptidase activity of the light chain. For botulinum neurotoxin serotypes C and D, the native motif is HELNH and HELTH, respectively, which, to

inactivate the endopeptidase activity, may be mutated to HQLNY and HQLTY, respectively.

In another embodiment of the invention, a vaccine for producing protective antibodies against Clostridium cZ/ff/c/Ve-associated disease is described, which comprises a surface peptide of Clostridium difficile (or a fragment thereof) or a peptide which is substantially homologous thereto. In more detail, at least one intramolecular cross-link is introduced into the surface peptide, and enhances the efficacy of a surface peptide as a vaccine and as an antigen for producing protective antibodies. Said cross-link(s) may be introduced by formaldehyde treatment or using another cross-linking reagents. Introduction of one or more intra-molecular cross-link(s) through treatment with formaldehyde or other cross-linking reagents provides antigen of improved efficacy for inducing a protective immune response compared to the untreated polypeptide.

In one embodiment of the invention, the C. difficile vaccine is based on a surface peptide such as Cwp 84 (e.g., SEQ ID NO: 15). In one embodiment, a Cwp 84 fragment treated with an agent comprises either the initial "M" or the last "K" amino acid.

In another embodiment of the invention, a vaccine is described, which comprises modified C. difficile toxin peptide. The modified peptide has one or more intramolecular cross-link(s) that have been introduced to enhance its efficacy as a vaccine and as an antigen for producing protective antibodies. Said cross-link(s) may be introduced by formaldehyde treatment or using another cross-linking reagent. In one embodiment, the peptide used as the basis for the C. difficile antigen may be a C-terminal region of Toxin A (e.g., SEQ ID NO: 10 or 11 ) or Toxin B (e.g., SEQ ID NO: 12), or may be based on a peptide sequence that is substantially homologous thereto. Alternatively, the peptide may be derived from (or be substantially homologous to) the N-terminus of Toxin A (e.g., SEQ ID NO: 13) or Toxin B (e.g., SEQ ID NO: 14). Alternatively, for a C. difficile antigen based on its binary toxin, a peptide sequence which is substantially homologous to either of the sequences in SEQ ID NO: 19 or SEQ ID NO: 20 may be employed.

In the case of fragments based on the toxin peptide sequences disclosed in SEQ ID NOS: 10, 11 and 13, the fragments include, in one embodiment, the first or last amino acid residue identified. For instance, in the case of a fragment based on the Toxin A

sequence illustrated SEQ ID NO: 13, a fragment could include the first "Q" or the last "G" amino acid residue. The same principle applies to fragments based on the other sequences.

Introduction of intra-molecular cross-links through treatment with formaldehyde or other cross-linking reagents provides antigens derived from the C. difficile factors which induce a significantly better immune response compared to the equivalent untreated polypeptide.

In another embodiment of the invention, a vaccine for producing protective antibodies against anthrax-associated disease or anthrax toxin poisoning is described. In more detail, one embodiment provides a modified anthrax protective antigen (PA) in which at least one intramolecular cross-link(s) has been introduced to enhance its efficacy as a vaccine. Said cross-link(s) may be introduced by formaldehyde treatment or by another cross-linking reagent. The peptide used as the basis for the anthrax vaccine is PA (or a fragment thereof), for instance, recombinant PA, or a peptide substantially homologous therewith. Introduction of intra-molecular cross-link(s) through treatment with formaldehyde or other cross-linking reagents overcomes the prior art problem of reduced protection or stability and provides an anthrax vaccine having enhanced efficacy or stability.

In yet another embodiment of the invention, a modified (e.g., recombinant) anthrax lethal factor is described in which at least one intramolecular cross-link(s) has been introduced to enhance its efficacy as a vaccine. Said cross-link(s) may be introduced by formaldehyde treatment or another cross-linking reagent. The peptide used as the basis for the anthrax vaccine is LF (e.g., SEQ ID NO: 17 or 18) (or a fragment thereof), or a peptide substantially homologous therewith. In some embodiments, the LF peptide may contain amino acid substitutions to ablate the endopeptidase activity of LF. For LF, the motif sequence HEFGH (SEQ ID NO: 17) is mutated to HQFGY (SEQ ID NO: 18) to eliminate endopeptidase activity.

In the case of anthrax vaccine based on PA or LF fragments, said fragments often include the first or last amino acid residue. In one embodiment, a PA fragment includes

the first "M" or last "G" illustrated in SEQ ID NO: 16. Similarly, an LF fragment may include the first "M" or the last "S" illustrated in SEQ ID NO: 17 or 18.

The above-mentioned anthrax embodiments may further comprise one or more S-layer protein. By way of example, S-layer proteins include Sap (e.g., Sap 1 ) and/ or EA1 (see Farchaus et al., (1995) J. Bacteriology, 177, pp. 2481-2489; and Mesnage et al. (1997) Molec. Microbiol. 23, pp. 1147-1155).

As discussed in the Examples that follow, studies have established that treatment of peptide preparations treated with 0.2% formaldehyde at 35 ⁰ C for 24 hours resulted in intra-molecular cross-linking. In the case of an LH _N peptide preparation of the present invention, SDS-PAGE analysis has confirmed a 97kDa monomeric fragment as a broad band (as compared to LH _N /A control preparations), and a small amount of dimeric LH _N /A molecules (<5%) - see Figs 1 and 2.

It is surprising that, under the above conditions, the modifying agent-treated vaccine displays significantly enhanced efficacy compared to control untreated samples. In the case of a type A vaccine based on formaldehyde-treated LH _N /A, the efficacy of the vaccine was increased >15 fold compared to the untreated control sample (see Tables 1 - 3). The formation of inter-molecular cross-links which would give rise to higher molecular weight aggregates does not appear to occur. This is clearly demonstrated since enhanced efficacy is observed under conditions in which inter-molecular cross- linking and the formation of aggregates does not occur (see Fig. 2). Under such conditions, ED ₅₀ values obtained were >15 fold (and hence of higher efficacy) than controls (Table 2, Test 3). The enhancement effect is therefore not mediated in the same manner as that reported previously for small peptides in which aggregation appears to be the underlying mechanism. In such cases, formaldehyde would appear to act simply as an agent to increase the overall molecular mass of smaller peptides, by aggregation, thus allowing the immune system to 'see' them more efficiently. In the case of the present invention, the enhancement in efficacy is unexpected since the untreated vaccine is already of sufficient size to be 'seen' by the immune system and does not change in overall size after treatment with formaldehyde.

For the present invention, the finding that aggregation does not have a role in the enhancement of vaccine efficacy suggests that modifying chemical treatment, through the formation of methylene bridges, results in intra-molecular cross-linking leading to the creation of a more rigid molecular structure of functional epitopes which stimulates the more efficient production of high affinity antibodies. It is well established that peptides with a flexible structure may elicit a weaker immune response than proteins which are more highly ordered in tertiary structure (Putz 2003, Hudecz 2001 , Novotny 1986).

The LH _N /A vaccine of the invention also protects against various sub-types of BoNT/A (Table 3). Single dose protection was observed for BoNT/A sub-types A ₁ , A ₂ and A ₃ . For the unmodified LH _N /A, no protection against BoNT sub-type A ₂ was observed in ED ₅₀ assessments with up to a single dose of 100 μg of native LH _N /A.

The above protection studies with clostridial neurotoxin fragments have been repeated with the C. difficile and anthrax aspects of the present invention. In this regard, the C. difficile and anthrax aspects of the present invention also demonstrate improved efficacy/protection vis-a-vis the corresponding, untreated C. difficile and anthrax peptides.

In conventional botulinum toxoid vaccines, partially purified toxins are inactivated with formaldehyde over a period up to 25 days which often results in loss of peptide epitopes and a complex, heterogeneous product containing high molecular weight aggregates. In contrast, the present invention describes the production of vaccines, which rely on a comparatively short incubation period with the modifying chemical and one in which the product contains little or no aggregation and is easy to characterise. Such properties offer significant advantages for manufacture, testing and regulatory approval of the vaccine.

The invention also provides antisera isolated from animals that have been immunized with a vaccine of the invention. In some embodiments, the antiserum is purified to provide a monoclonal or polyclonal population of antibodies that are specific for the antigen in the vaccine. Compared to an antisera produced using an unmodified polypeptide vaccine, the antisera may provide improved survival when administered to an animal prior to or shortly after exposure to a toxic form of the antigen (such as an

agent comprising the toxic form of the antigen) used to prepare the vaccine. In one embodiment, the antisera is protective against more than one serotype of BoNT. For example, the antisera may protect against BoNT/A and BoNT/B, BoNT/A and BoNT/E, BoNT/B and BoNT/E, or BoNT/A, BoNT/B, and BoNT/A. In other embodiments, the antisera is protective against one or more BoNT subtype. For example, the antisera may protect against all or some of BoNTZA ₁ , BoNT/A ₂ , and BoNT/ A ₃ .

Antibodies raised against fragments preferably have the property of recognising the full- length counterpart peptide from which they are derived. For example, an antibody raised against an LH _N /A fragment of the present invention will have common antigenic cross-reactivity with LH _N /A. Similarly, a C. difficile fragment or an anthrax fragment will have common antigenic cross-reactivity with the corresponding full-length C. difficile or anthrax peptide. Antibodies raised against toxin fragments of the invention will also neutralise the toxic activity of the corresponding full-length toxin.

Antisera can be used for the manufacture of a medicament for treating exposure to bacteria and bacterial toxins. Thus, antibody compositions, such as the isolated antisera or antibodies (monoclonal or polyclonal) purified therefrom, can be used as a passive immune serum to prevent or treat patients exposed to the wild-type toxin. For example, antisera raised in by administering a botulinum neurotoxin can be used to prevent or treat patients with botulism. In such cases, the patient is a human, including an infant, suspected of having come in contact with the toxin, or is a human, including an infant, who has had known contact with the toxin, but is not yet showing symptoms of exposure. The antibody composition can also be used in a method of treating to ameliorate symptoms in patients that are suffering from the presence of toxin in their body. When the toxin is a clostridial neurotoxin, the symptoms include diarrhea and paralysis.

Methods of preparing immune sera are known in the art. For example, a vaccine composition can be administered to an animal such as a horse or a human until a antibody response (for instance, neutralizing antibody response) to wild type toxin is generated. Neutralizing antibodies can then be harvested, purified, and administered to patients exposed to, or exhibiting symptoms of contact with, the toxin to thereby treat or prevent botulism. In some cases, the antibodies are not purified after harvesting. When the antibodies are from humans, the antibody preparation will generally be free of

viruses, such as HIV and hepatitis. Methods of preparing human antisera are known in the art, and include the methods used to prepare IVIg. The neutralizing antibodies can be administered intravenously, intramuscularly, intradermally, or subcutaneously. Antibiotic therapy can be used in conjunction. Dosages for neutralizing antibodies generally vary from about 1 mg to 1000 mg/kg. Often, they are administered at a dosage of about 50-200 mg/kg of body weight.

The invention will be further clarified by the following examples, which are intended to be purely exemplary of the invention and in no way limiting.

Examples

Example 1 : Preparation of a vaccine for botulinum Type A neurotoxin

A gene encoding amino acid residues 1-871 of LH _N /A (SEQ ID NO: #) was obtained commercially with codon bias suited to expression in E. coli. The gene also coded for the mutations GIu 224 to GIn and His 227 to Tyr. LH _N /A was expressed from this gene using standard molecular biology methods (e.g. Sambrook et al. 1989, Molecular Cloning a Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York) and the resulting soluble expressed fragment purified by a combination of hydrophobic interaction chromatography, ion exchange chromatography and ceramic hydroxyl apatite chromatography.

The purified LH _N /A fragment was dialysed against buffer (10mm Hepes buffer pH 7.4 containing 10OmM NaCI) and then the LH _N /A at a concentration of 1 mg ml ^"1 was treated with 0.2% formaldehyde (HCHO) for 24 hours at 35 ⁰ C. After incubation, the formaldehyde was removed from the mixture by dialysis.

An SDS-PAGE comparison of control LH _N /A and formaldehyde-treated LH _N /A is shown in Figure 1. Under these conditions, a small % of dimer LH _N /A can be detected (arrow D in Figure 1 ).

Example 2: Preparation of vaccines for other clostridial neurotoxins

Amino acid sequences for other polypeptides that can be used, for instance, to prepare additional vaccine peptides encompassed by the present invention are shown in SEQ ID

NOS: 4-7 and 9. The illustrated peptides form the basis of vaccines of the present invention for tetanus toxin and also other botulinum neurotoxin serotypes (e.g., B, E and F). These peptides can contain mutations to the light chain endopeptidase active site. For instance, the motif HELIH can be changed to HQLIY to ablate the enzymatic activity. Other mutations to the active site could also be used to achieve the same ablation of light chain activity, e.g. Glu262 in botulinum type A toxin and the corresponding highly conserved residue in the other clostridial neurotoxins. Details of this and other mutations are described in Montecucco et al (2001 ) (Biochem Biophys Res Comm. 288:1231-7), which is hereby incorporated by reference in its entirety.

Genes encoding peptides such as the above are commercially available with codon bias for any desired expression host (e.g. E. coli, Pichia pastoris). Peptides are expressed from these genes using standard molecular biology methods (e.g. Sambrook et al. 1989, Molecular Cloning a Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York) and the resulting soluble expressed peptide can be purified by a combination of hydrophobic interaction chromatography, ion exchange chromatography and ceramic hydroxyl apatite chromatography. Other chromatographic techniques well known to the art of protein purification, such size exclusion chromatography and/or affinity chromatography, may be used.

The purified peptide can then dialysed against buffer (10mm Hepes buffer pH 7.4 containing 10OmM NaCI) and then 0.2% formaldehyde is added and incubated for between 24 and 72 hours at 35 ⁰ C. After incubation, the formaldehyde may be removed from the mixture by dialysis.

Example 3: Preparation of fragments of the invention using other cross-linking agents

In addition to formaldehyde, other cross-linking agents may be employed to produce vaccines of the invention. Examples of other cross-linking agents that may be employed include C6-succinimidyl 4-hydrazinonicotinate acetone hydrazone, C6-succinimidyl 4- formylbenzoate, BlS-(Sulfosuccinimidyl) suberate, disuccinimidyl suberate, dimethyl suberimidate dihydrochloride, dimethyl pimelimidate 2 HCI, dimethyl adipimidate dihydrochloride, succinimidyl 4-hydrazidoterephthalate hydrochloride, and disuccinimidyl glutarate. The cross linking agent can be dissolved in a suitable solvent (e.g. water, buffer, ethanol or acetone) and then mixed with the vaccine peptide. The cross-linking

agent can be added to the peptide in a molar excess which may be between 3 - 50 fold moles of cross-linker per mole of peptide. The peptide is typically present at a concentration of between 0.1 - 5 mg/ml, and is typically incubated with the cross-linker from 1 - 24 hr at temperature between 4 - 37 ⁰ C. Exact conditions may be determined as those which provide the optimal immune response in animals (e.g. mice, guinea pigs or rabbits) (see Example 6).

Example 4: Assessment of Presence or Absence of Intra-molecular Cross-linking

LH _N /A vaccine (LH _N fragment treated with formaldehyde, e.g. at 0.2% formaldehyde for 24 hours at 35 ⁰ C) was assessed for the presence of intra-molecular cross-linking using mild proteolysis with trypsin. LH _N vaccine at a concentration of 1 mg ml ^"1 was treated with trypsin at a final concentration of 10 μg ml ^"1 in 50mm Hepes buffer containing 10OmM NaCI for 30 min at 37 ⁰ C. After the incubation period, the tryptic reaction was halted by the heating at 9O ⁰ C for 2 minutes. As a control, a sample of LH _N /A which had not been treated with formaldehyde was treated with trypsin under identical conditions. Samples were then analysed by SDS-PAGE under reducing conditions (with 2OmM dithiothreitol added) and non-reducing conditions. Under reducing conditions, the control sample of LH _N runs as two bands of molecular weight approximately 50 kDa indicating the absence of intra-molecular cross-linking to hold the tryptic cleavage products together (Fig. 3, Lane 5). In contrast, the formaldehyde treated LH _N vaccine runs as a band of 100 kDa demonstrating the presence of intra-molecular cross-linking which holds the tryptic cleavage products together (Fig. 3, Lane 7).

Example 6: Assessment of Vaccine Efficacy

Samples of vaccine adsorbed onto an adjuvant such Alhydrogel™ were diluted with buffer containing the same adjuvant to give a range of concentrations of antigen. For example, the following vaccine doses in 0.2 ml could be used: 10, 3.33, 1.11 , 0.37, 0.123, 0.041 , 0.014, and 0 μg ml ^"1 .

Doses of the vaccine were then injected into mice (10 mice per vaccine dose; 0.2 ml into each mouse by the sub-cutaneous route). At 28 days post administration, the mice were challenged with a lethal concentration of toxin (e.g. 1000 LD ₅₀ administered into the peritoneal cavity) and any deaths were recorded over a 4 day period post-challenge.

The data obtained from such tests were fit to a logistic 4 parameter curve using a statistical analysis package such as SigmaPlot™. From the analysis, the concentration of vaccine that provided protection to 50% of the animals against the challenge dose of toxin was calculated. The ED ₅ O value is usually expressed in micograms of peptide; the lower the value obtained, the more efficacious the vaccine. Tables 1 , 2, 3, and 4 summarize the results for LH _N /A. .

Table 1 : LH _N /A Vaccine Efficacy Tests (Formaldehyde-Treated & Untreated)

Approximate value due to erratic nature of the data

Table 2: LH _N /A Vaccine - Efficacy Tests (Formaldehyde (HCHO) - Treated)

Surviving Mice (of 10) at 4 days Post Challenge

Test 4 - LH _N /A was treated with formaldehyde at peptide concentration of 0.1 mg /ml to eliminate aggregation of the fragment

Table 3: Summary of ED ₅₀ Determinations on HCHO-Treated and Control LH _N /A

Example 7: Assessment of vaccine efficacy against various sub-types of BoNT/A

LH _N /A was adjusted to 1 mg ml ^"1 with Hepes/NaCI buffer, treated with HCHO (0.2% for 24 h at 35 ⁰ C) and adsorbed onto Alhydrogel (3100 μg ml ^"1 final concentration) in 1OmM Hepes pH 7.4 / 10OmM NaCI buffer (peptide concentration 100 μg ml ^"1 ).

After mixing and incubation at 4° C for 4 hours, the mixture was dialysed against the Hepes buffer to remove the formaldehyde and then diluted with buffer containing Alhydrogel to give the following concentrations of antigen of 20, 6.67, 2.22, 0.74, 0.24, 0.08, 0.027, and 0 μg per 0.2 ml dose.

At 28 days post administration, 3 test groups of mice were challenged with either BoNT/Ai, BoNT/A ₂ or B0NT/A3 (1000 LD ₅₀ i.p. in 0.5 ml). Deaths were recorded over a 4 day period post-challenge. The data, shown in Table 4, show that the vaccine protected against all three BoNT/A sub-types. Calculated ED ₅₀ values were:

A ₁ Challenge ED ₅₀ = 0.049 ± 0.007 μg

A ₂ Challenge ED ₅₀ = 0.28 ± 0.02 μg

A ₃ Challenge ED ₅₀ = 2.2 ± 0.6 μg

Table 4: Vaccine Efficacy of Formaldehyde-treated LH _N /A to BoNT/A Sub-types

Each challenge dose was 1000 LD ₅₀ of the BoNT/A subtype

In control experiments assessing the efficacy of sub-types, no protection against BoNT/ A ₂ subtype was observed in efficacy tests in which doses of up to 100 μg of native LH _N /A were administered to mouse groups. The protocol was as described in Example 6 and using 1000 LD ₅₀ of BoNT/ A ₂ as the challenge toxin.

Example 8: Detection of fragments of the invention by immunoassay

Peptide fragments of the invention bear antigenic determinants which are detectable by immunoassays. In the case of the vaccines for the clostridial neurotoxin family, one or more of these antigenic determinants is shared by the LH _N fragments of the homologous neurotoxin fragments and thus antibodies raised against the LH _N fragment also bind fragments of the invention. Immunoassays to detect the presence of fragments of the invention are conducted as follows.

Fragments of the invention are coated onto microtiter plates at concentration of 5 μg/ml in a suitable buffer such 5OmM Hepes pH 7.4 and allowed to bind at 4 ⁰ C overnight. After blocking excess protein binding sites with a blocking agent (e.g. 5% foetal bovine serum in PBS), the plate is washed with PBS containing 0.1% tween 20. Antibodies prepared in animals (e.g. rabbits) to the corresponding LH _N fragment are then added to the plate wells. Thus in the case of a test for the presence of fragments of the invention which are designed as a vaccine for BoNT/A, antibodies prepared against LH _N /A would be used. The antibody solution is applied at various dilutions, e.g. 1/1000 to 1/1000,000 dilution of the neat serum and allowed to bind for 1 hour at 37 ⁰ C. After washing with PBS/Tween20, a commercially available ant-rabbit IgG peroxidise conjugate solution is added at e.g., a 1/1000 dilution and allowed to bind for 1 hour at 37 ⁰ C. The unbound conjugate is then removed by washing with PBS/tween20 and then suitable peroxidise substrates (e.g., 3,3',5,5'-Tetramethylbenzidine and hydrogen peroxide) added. For wells coated with fragments of the invention, colour will develop which is significantly

above background levels indicating the presence of a peptide fragment containing epitopes common to the LH _N fragment. The test therefore indicates the presence peptide fragment properties consistent with fragments of the invention.

Example 9: Preparation of fragments of the invention based on clostridial neurotoxins which contain a mutated, dysfunctional Hn domain

An example of the amino acid sequence of a botulinum vaccine which has a nonfunctional Hc domain is given in SEQ ID NO: 9. This peptide contains mutations to ganglioside binding site of the H _c domain. In more detail, referring to SEQ ID NO: 9, two amino acid residue mutations (W1266 to L and Y1267 to F) in the ganglioside binding pocket cause the H _c region to lose its receptor binding function. Analogous mutations may be made to non-serotype A clostridial peptides, e.g., a construct based on botulinum B with mutations (W1262 to L and Y1263 to F) or botulinum E (W1224 to L and Y1225 to F). Other mutations to the active site achieve the same ablation of H _c receptor binding activity, e.g. Y1267S in botulinum type A toxin and the corresponding highly conserved residue in the other clostridial neurotoxins. Details of this and other mutations are described in Rummel et al (2004) (Molecular Microbiol. 51 :631-634), which is hereby incorporated by reference thereto.

Genes encoding peptides such as the above are commercially available with codon bias for any desired expression host (e.g. E. coli, Pichia pastoris). Peptides are expressed from these gene using standard molecular biology methods (e.g., Sambrook et al. 1989, Molecular Cloning a Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York) and the resulting soluble expressed peptide is purified by a combination of hydrophobic interaction chromatography, ion exchange chromatography and ceramic hydroxyl apatite chromatography. Other chromatographic techniques well known to the art of protein purification, such size exclusion chromatography, may be used.

The peptide is then dialysed against buffer (10mm Hepes buffer pH 7.4 containing 10OmM NaCI) and then 0.2% formaldehyde added and incubated for between 24 and 72 hours at 35 ⁰ C. After incubation, the formaldehyde may be removed from the mixture by dialysis.

Example 10: Assays to demonstrate that fragments of the invention do not possess a functional H _n receptor binding domain.

Clostridial neurotoxin is labelled with 125-iodine using chloramine-T and its binding to various cells assessed by standard methods such as described in Evans et al. 1986, Eur J. Biochem., 154, 409 or Wadsworth et al. 1990, Biochem. J. 268, 123). In competitive binding experiments, native clostridial neurotoxins compete for receptors present on neuronal cells or brain synaptosomes with the radiolabeled botulinum toxin, thus reducing the binding of the latter. This is measured by a reduction in bound radioactive ligand. All binding experiments are carried out in binding buffers, e.g., 5OmM HEPES pH 7.0, 3OmM NaCI, 0.25% sucrose, 0.25% bovine serum albumin. In a typical binding experiment the radiolabeled clostridial neurotoxin is held at a fixed concentration of between 1-2OnM. Reaction mixtures are prepared by mixing the radiolabeled toxin with various higher concentrations (up to 10 μM) of unlabelled neurotoxin or fragment of the invention. The reaction mixtures are then added to neuronal cells or rat brain synaptosomes and are incubated at 0-3 ⁰ C for 2hr. After this period the neuronal cells of synaptosomes are washed twice with ice-cold binding buffer and the amount of labelled clostridial neurotoxin bound to cells or synaptosomes assessed by γ-counting. In reaction mixtures which contained native neurotoxin, the peptide competes with ¹²⁵ l-labelled botulinum type A neurotoxin for neuronal cell receptors and reduces the binding of the latter. However, when a clostridial peptide of the invention is added to reaction mixture no reduction in binding of the labelled toxin occurs. This demonstrates that clostridial peptides of the invention do not contain a function H _c binding domain.

Example 11 : Vaccination by peptide/ peptide fragments of the Invention

A vaccine, represented by a peptide/ peptide fragment of the invention is prepared by current Good Manufacturing Practice. Using such practices, peptides/ peptide fragments of the invention may be bound to an adjuvant of aluminium hydroxide which is commercially available (e.g., Alhydrogel). A typical composition comprises:

A) A buffer (e.g., Hepes buffer between 5 and 20 mM and pH between 7.0 and 7.5;

B) A salt component to make the vaccine physiologically isotonic (e.g. between 100 and 15O mM NaCI);

C) An adjuvant (e.g., aluminium hydroxide at a final aluminium concentration of between 100 and 700μg per vaccine dose); and

D) A preservative (e.g., Thiomersal at 0.01 % or formaldehyde at 0.01 %).

Such vaccine compositions are administered to humans by a variety of different immunisation regimens, e.g.,

1. A singe dose (e.g., 20 μg adsorbed fragment of the invention) in 0.5 ml administered sub-cutaneously.

2. Two doses (e.g., of 10 μg adsorbed fragment of the invention) in 0.5 mis administered at 0 and 4 weeks.

3. Three doses (e.g., of 10 μg adsorbed fragment of the invention) in 0.5 mis administered at 0, 2 and 12 weeks.

These vaccination regimens confer levels of protection against exposure to the homologous serotypes of botulinum neurotoxins. An antibody response in humans is measured by standard ELISA assays such as described in Example 8.

During formulation of the fragment of the invention, other antigens may also be included in the formulation. Such antigens may include different botulinum serotype vaccines or antigens not related to the botulinum toxins.

Example 12: Generation of Clostridium difficile peptides

Amino acid sequences of a vaccine based on Clostridium difficile Toxins A and B are shown in SEQ ID NOS: 10-18 and that for the Clostridium difficile binary toxin in SEQ ID NO: 19 and 20. Genes encoding these peptides are made commercially with codon bias for any desired expression host (e.g., E. coli, Pichia pastoris). Peptides are expressed from these gene using standard molecular biology methods (e.g. Sambrook et al. 1989, Molecular Cloning a Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York) and the resulting soluble expressed peptides are purified by a combination of hydrophobic interaction chromatography, ion exchange chromatography and ceramic hydroxyl apatite chromatography. Other chromatographic techniques well known to the art of protein purification, such size exclusion chromatography and/or affinity chromatography, may be used.

If the peptides are produced in an insoluble from then the peptides may be expressed with a histidine-6 purification tag using commercially available expression vector such as pET52b and refolded by on-column refolding techniques as described by the review of Lia et al. and references contained therein (Lia M et al (2004) Protein Expression & Purification 33, 1-10), which is hereby incorporated by reference thereto.

Example 13: Treatment of C. difficile peptides to introduce intramolecular cross-links

Purified C. difficile peptides at a concentration of between 0.2 - 2 mg/ml are dialysed against a suitable buffer (e.g. 1OmM Hepes buffer pH 7.4 containing 10OmM NaCI) and then formaldehyde added at a final concentration of between 0.05 and 0.5% and incubated for between 24 and 72 hours at 35 ⁰ C. After incubation, the formaldehyde is removed from the mixture by dialysis. Conditions for the treatment with formaldehyde may vary between peptides and final conditions may be fine-tuned on the basis of outcome of protective efficacy evaluations.

As an alternative to formaldehyde, purified difficile peptides (at a concentration of between 0.1 - 5 mg/ml) are dialysed against a suitable buffer, and then reacted with a non-formaldehyde cross-linking agent, such as one of those already described. The cross linking agent is dissolved in a suitable solvent, (e.g., water, buffer, ethanol or acetone) and then mixed with the C. difficile peptide, which may be a fragment of a toxin or surface peptide. The cross-linking agent is added to the peptide in a molar excess which includes, for instance, between 3 - 50 fold moles of cross-linker per mole of peptide. The peptide is normally at a concentration of between 0.1 - 5 mg/ml and is incubated with the cross-linker from 1 - 24 hr at temperature between 4 - 37 ⁰ C. Exact conditions may be determined by those which provide the optimal immune response in animals (e.g., mice, guinea pigs or rabbits)

Example 14: Demonstration of protective efficacy of C. difficile peptides

After removing formaldehyde or other modification agent from the C. difficile peptides, the peptides are adsorbed on to aluminium hydroxide adjuvant (Alhydrogel™) and used to generate antibodies in animals such as guinea pigs, rabbits of goats. The toxin neutralizing activity of the resulting antisera is measured by cellular assays using Vero cells. In these assays, a fixed amount of either purified C. difficile Toxin A or Toxin B is

mixed with various dilutions of the antibodies, incubated for 1 h at 37 ⁰ C and then applied to vero cells growing on 24-well tissue culture plates. Both Toxin A and B possess cytotoxic activity which results in a characteristic rounding of the Vero cells over a period of 24 -48 h. In the presence of neutralising antibodies this activity is inhibited and the neutralising strength of an antibody preparation may be assessed by the dilution required to neutralise the effect of a designated quantity of either Toxin A or B.

C. difficile toxin peptides into which intramolecular cross-links have been introduced by formaldehyde or another cross-linking reagent produce antisera of higher neutralising titre compared to the corresponding control peptide which has not been treated.

Example 15: Demonstration of protective efficacy of C. difficile peptides in animals

To demonstrate the protective efficacy of C. difficile antigens in vivo, Syrian hamsters are immunised with the difficile peptide, which may be combined with an adjuvant (e.g. Alhydrogel™). Immunised animals are then administered with a broad spectrum antibiotic (e.g., clindamycin) and 12-48 h later challenged with C. difficile vegetative cells or spores by mouth. Animals are then monitored for up to 15 days for symptoms of C. difficile-associated disease. Non-immunised animals develop signs of the disease (e.g., diarrhoea, swollen abdomen, lethargy, ruffled fur) while those immunised with a protecting antigen appear normal. Lower immunising doses of C. difficile antigens into which intramolecular cross-links have been introduced by formaldehyde or another cross-linking reagent are required to incur protection compared to the corresponding control peptide which has not been treated.

Example 16: Preparation and administration of a vaccine for C. difficile

A vaccine, represented by a peptide of the invention is prepared by current Good Manufacturing Practice. Using such practices, peptides of the invention are bound to an adjuvant of aluminium hydroxide which is commercially available (e.g., Alhydrogel). A typical composition comprises:

A) The antigen which may be an intra-molecularly cross-linked fragment of a C. difficile toxin fragment or surface peptide.

B) A buffer (e.g., Hepes buffer between 5 and 20 mM and pH between 7.0 and 7.5) or alternatively if the antigen has a pi greater than 7.5, a buffer containing phosphate ions may be used (e.g., 15 mM sodium phosphate pH 6.0).

C) A salt component to make the vaccine physiologically isotonic (e.g. between 100 and 15O mM NaCI

D) An adjuvant (e.g., aluminium hydroxide at a final aluminium concentration of between 100 and 700μg per vaccine dose)

E) A preservative (e.g., Thiomersal at 0.01 % or formaldehyde at 0.01 %)

Such vaccine compositions are administered to humans by a variety of different immunisation regimens, e.g.,

1. A singe dose (e.g., 20 μg adsorbed fragment of the invention) in 0.5 ml administered sub-cutaneously

2. Two doses (e.g., of 10 μg adsorbed fragment of the invention) in 0.5 mis administered at 0 and 4 weeks

3. Three doses (e.g., of 10 μg adsorbed fragment of the invention) in 0.5 mis administered at 0, 2 and 12 weeks

These vaccination regimens confer levels of protection against exposure to C. difficile particularly when broad spectrum antibiotics are in use, e.g. in hospital environment.

During formulation of the fragment of the invention, other antigens may also be included in the formulation, e.g., a combination of difficile surface peptides and toxin fragments.

Example 17: Anthrax toxin fragment production

Amino acid sequences of vaccine peptides are shown in SEQ ID NOS: 16-18. Genes encoding these toxin fragments are commercially with codon bias for any desired expression host (e.g., E. coli, Pichia pastoris). Peptides may be expressed from these genes using standard molecular biology methods (e.g. Sambrook et al. 1989, Molecular Cloning a Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York). An example of an expression vector for use in E. coli is pET26b. The resulting soluble expressed peptide is purified by a combination of hydrophobic interaction chromatography, ion exchange chromatography and ceramic hydroxyl apatite chromatography. Other chromatographic techniques well known to the

art of protein purification, such size exclusion chromatography and/or affinity chromatography, may be used.

In order to produce an enzymically inactive form of LF, the gene is synthesised with a double mutation within the active site sequence. An inactive form of LF is shown SEQ ID NO: 18.

Example 18: Treatment of anthrax toxin fragments to introduce intramolecular crosslinks

Purified anthrax toxin components (PA or LF) at a concentration of between 0.2 - 2 mg/ml are dialysed against a suitable buffer (e.g. 1OmM Hepes buffer pH 7.4 containing 10OmM NaCI) and then formaldehyde added at a final concentration of between 0.05 and 0.5% and incubated for between 24 and 72 hours at 35 ⁰ C. After incubation, the formaldehyde is removed from the mixture by dialysis. Conditions for the treatment with formaldehyde may vary between toxin fragments and final conditions may be fine tuned on the basis of outcome of protective efficacy evaluations.

As an alternative to formaldehyde, purified anthrax toxin fragments at a concentration of between 0.1 - 5 mg/ml, are dialysed against a suitable buffer and reacted with an alternative cross-linking agent. The cross linking agent is dissolved in a suitable solvent (e.g., water, buffer, ethanol or acetone) and then mixed with the anthrax toxin fragment. The cross-linking agent is added to the peptide in a molar excess which may be between 3 - 50 fold moles of cross-linker per mole of peptide. The peptide is normally at a concentration of between 0.1 - 5 mg/ml and is incubated with the cross-linker from 1 - 24 hr at temperature between 4 - 37 ⁰ C. Exact conditions may be determined by those which provide the optimal immune response in animals (e.g., mice, guinea pigs or rabbits)

Example 19: Demonstration of protective efficacy of anthrax toxin fragments

After removing formaldehyde from the anthrax toxin or fragments, they are adsorbed on to an adjuvant (e.g. aluminium hydroxide, Alhydrogel™) and used to generate antibodies in animals such as guinea pigs, rabbits of goats. The efficacy of anthrax antigens is determined in toxin neutralising antibody (TNA) assays. In TNA assays, the ability of

antiserum to protect macrophages from anthrax toxin is assessed. Macrophages (e.g. J774A cells) are grown in 24 or 96 well plates and maintained in growth medium for 18- 24 h under appropriate incubation conditions (37 ⁰ C, 5% CO ₂ ) before testing. Various dilutions of test serum are incubated with anthrax toxin (e.g. 100ng PA ml ^"1 plus 100ng LF ml ^"1 final concentration) in buffered growth medium for 1 hr at 37 ⁰ C and then added to the macrophages. After 4 h incubation, the cells are treated with 3-[4,5-dimthylthiazol- 2-yl] 2,5-diphenyltetrazolium bromide (MTT) (e.g. 25 μl of a 5 mg ml ^"1 solution). After further incubation for 2 h, the lysed cell precipitates are dissolved by addition of a solution containing 10% sodium dodecyl sulphate and 50% dimethyl formamide. After incubation to allow solubilisation of the precipitate, the absorbance at 570 nm is measured to provide a measurement of the reduced form of the dye. The MMT reagent assay provides an estimate of the number of viable macrophage cells and hence the ability of a preparation of antiserum to protect the cells from the effects of anthrax toxin.

Anthrax toxin fragments into which intramolecular cross-links have been introduced by formaldehyde or another cross-linking reagent produce antisera of higher neutralising titre compared to the corresponding control fragment which has not been treated.

Example 20: Preparation and administration of a vaccine for Anthrax

A vaccine, represented by a peptide of the invention is prepared by current Good Manufacturing Practice. Using such practices, peptides of the invention are bound on to an adjuvant of aluminium hydroxide which is commercially available (e.g. Alhydrogel).

A typical composition comprises:

A) The antigen which may be an intra-molecularly cross-linked fragment derived from PA or LF. Alternatively combinations of antigens may be used, e.g. PA and LF in a 1 :1 mixture. In the case of LF, for instance, an enzymatically inactive derivative of the peptide can be employed.

B) A buffer (e.g. Hepes buffer between 5 and 20 mM and pH between 7.0 and 7.5) or alternatively if the antigen has a pi greater than 7.5, a buffer containing phosphate ions may be used (e.g. 15 mM sodium phosphate pH 6.0).

C) A salt component to make the vaccine physiologically isotonic (e.g. between 100 and 15O mM NaCI).

D) An adjuvant (e.g. aluminium hydroxide at a final aluminium concentration of between 100 and 700μg per vaccine dose).

E) A preservative (e.g. Thiomersal at 0.01 % or formaldehyde at 0.01 %)

Such vaccine compositions are administered to humans by a variety of different immunisation regimens, e.g.

1. A singe dose (e.g. 20 μg adsorbed fragment of the invention) in 0.5 ml administered sub-cutaneously.

2. Two doses (e.g. of 10 μg adsorbed fragment of the invention) in 0.5 mis administered at 0 and 4 weeks.

3. Three doses (e.g. of 10 μg adsorbed fragment of the invention) in 0.5 mis administered at 0, 2 and 12 weeks.

These vaccination regimens confer levels of protection against exposure to Bacillus anthracis.

Example 21 : A Bivalent Recombinant Vaccine for Botulinum Types A and B Neurotoxins

BONT/A _L BONT/A ₃ , BoNTZB ₁ and B0NT/B ₄ were purified from C. botulinum strains ATCC 3502, NCTC 2012, Okra and Eklund 17B strains, respectively using the exchange chromatography methods described in Shone CC. and H. S Tranter. 1995. Growth of Clostridia and preparation of their neurotoxins, pp 143-160. In: C. Montecucco (ed.) Current Topics in Microbiology and Immunology 195 'Clostridial Neurotoxins' , Springer, Berlin.. B0NT/A2 was obtained from Metabiologics Inc.

Expression and purification of LH _N recombinant fragments

Expression of LH _N fragments. Synthetic genes coding for BoNT/A (amino acid residues 1-871) and BoNT/B (amino acid residues 1-858) were optimised for expression in E .coli and synthesised (Geneart AG) with Ndel and Xhol restriction sites at the 5' and 3' ends, respectively to allow insertion into a pET 26b expression vector. Both LH _N sequences contained two amino acid substitutions: for LH _N /A, E224Q and H227Y; for LH _N B, E231Q, and H234Y. After transformation into E. coli ER2566, cells were inoculated into 50 ml growth medium (selected phytone, 24 g I ^"1 , bacto yeast extract, 72 g I ^"1 ; glycerol, 25 g I ^"1 ; K ₂ HPO ₄ , 2.3 g I ^"1 ; KH ₂ PO ₄ 12.5 g I ^"1 ; MgSO ₄ , 2.0 g I ^"1 ; kanamycin sulphate, 0.03 g I ^"1 , antifoam, 0.1 g I ^"1 at pH 7.3) and incubated with agitation for 16 -2O h at 37 ⁰ C. This was

then used to inoculate 500 ml growth medium which was similarly incubated and used to inoculate 4.5 I growth medium in a 5 I fermentor. The fermentor was grown at 37 ⁰ C until the OD ₆₀ O was between 15 - 20 after which the temperature was reduced to 16 ⁰ C and the culture grown for a further 16 - 29 h.

Purification of LH _N ZA. Soluble recombinant LH _N A was extracted from E. coli cell paste by resuspension with 20 mM Tris-HCI, pH 8.0, 25 mM EDTA on ice with stirring for 1 h. The suspension was passed twice through an APV1000 homogenizer (9,000 psi), clarified by microfiltration (500 kDa cutoff) and diafiltered into 20 mM Tris-HCI, pH 8.0, 25 mM EDTA. The extract was then made 1 M with (NH ₄ ) ₂ SO ₄ and applied to a Toyopearl Phenyl-650M column (10 cm [id] x 24 cm) equilibrated with 20 mM Tris-HCI, pH 8.0, 5 mM EDTA (Buffer A) and 1 M (NH ₄ ) ₂ SO ₄ . After washing with Buffer A containing 0.75 M (NH ₄ ) ₂ SO ₄ and then the LH _N A eluted from the column with Buffer A containing 0.5 M (NH ₄ ) ₂ SO ₄ . The eluate was diafiltered against 10 mM Tris-HCI, 0.1 mM EDTA pH 8.0 (Buffer B) and loaded onto a Q Sepharose column (5 cm (id) x 11.5 cm) equilibrated with Buffer B. After washing with Buffer B containing 50 mM NaCI, the LH _N /A was eluted with Buffer B containing 130 mM NaCI. and diafiltered against 10 mM sodium phosphate, pH 6.5. This solution was loaded onto a Macro-Prep Ceramic Hydroxyapatite Type I (20 μm; BioRad) column (5 cm (id) x 11.5 cm) equilibrated with 10 mM sodium phosphate, pH 6.5. After washing with 40 mM sodium phosphate, pH 6.5, LH _N A was eluted with 105 mM sodium phosphate, pH 6.5. The eluate from the hydroxyapatite column was concentrated and diafiltered against 10 mM HEPES, pH 7.4, 100 mM NaCI, filtered (0.2μm) and stored at -7O ⁰ C.

Purification of LH _N ZB. The purification process for LH _N /B was very similar to that of LH _N /A, except that it was performed at temperatures between 2 to 8 ⁰ C. After homogenization, the clarified material was loaded onto the Toyopearl phenyl-650M column as above for LH _N /A and eluted with Buffer A containing 0.7 M (NH ₄ ) ₂ SO ₄ . The remaining chromatography steps were as described for LH _N /A above except that the LH _N /B was eluted from the hydroxyapatite column with 145 mM sodium phosphate, pH 6.5.

Prior to efficacy tests, purified LH _N /A and B proteins were filtered through Mustang E filters to reduce protein-associated endotoxin levels to <1 Endotoxin Unit (EU)/mg or protein as assessed by chromogenic LAL assay.

Formulation and formaldehyde treatment

LH _N fragments were adsorbed onto Alhydrogel (Biosector 1.3) such that the final formulation contained 1OmM Hepes pH 7.4, 100 mM NaCI, Alhydrogel at 3.2 mg ml ^"1 aluminium and between 0 - 500 μg ml ^"1 LH _N fragment. Mixtures were incubated by gentle agitation for 6 h at 4 ⁰ C and stored at 4 ⁰ C until use.

LH _N fragments (1 mg ml ^"1 ) in10 mM Hepes pH 7.4 buffer containing 100 mM NaCI were made 0.2% formaldehyde by the slow addition, with stirring, of a 20% stock solution.

Mixtures were then incubated at 35 ⁰ C for 24 h and absorbed onto Alhydrogel.

Formaldehyde was removed by dialysis against 10 mM Hepes pH 7.4, 100 mM NaCI.

Determination of vaccine efficacy

The efficacy of vaccine candidates was determined using mice in which groups of 10 animals were immunised with various doses of formulated vaccine (doses in 0.2 ml were administered subcutaneously). For one-dose studies, mice were immunised on Day 0 and then challenged on Day 28 with 10 ³ MLD ₅₀ of BoNT (in 0.5 ml administered intraperitoneally). Survival of mice was monitored over 4 days post-challenge. For two- dose studies, animals were immunised on Day 0 and Day 14 and challenged on Day 28. ED ₅ O values, i.e., the vaccine dose required to protect half the animals in a group from the challenge dose, were calculated using four-parameter logistic curve analysis (SigmaPlot™).

For efficacy studies in guinea pigs, groups of 3 animals were immunised with a single dose of formulated LH _N fragment and bled 28 days post immunisation. Serum pools, combining an equal volume from each of 3 animals, were assessed for toxin neutralisation in mice. For these studies, serum diluted with PBS containing 1mg ml ^"1 BSA was mixed with BoNTZA ₁ at a final concentration of 200 LD ₅₀ ml ^"1 . After incubating for 2 h at 22 ⁰ C, 0.5 ml was injected into groups of 4 mice.

Endopeptidase and ELISA assays

Endopeptidase assay. Endopeptidase activities of LH _N fragments were measured essentially by the assay procedure described by Hallis et al. (1996) J. Clin. Microbiol. 34: 1934-1938, in which the formation of the BoNT substrate cleavage products were measured using specific antibodies in an ELISA-like assay system.

ELISA assay. For these assays, antibodies raised in goats to toxoids of the purified BoNTs were used. Purified IgG was coated onto microtiter plates a (5 μg ml ^"1 ; 100 μl/well) and incubated for 1 h at 37°C. After washing with phosphate buffered saline containing 0.1 % tween 20 (PBST), the plates were incubated for 1 h at 37 ⁰ C (150 μl/well) with blocking buffer (PBST containing 5% foetal bovine serum). After washing with PBST, test samples (BoNTs or LH _N fragments) were diluted in blocking buffer and incubated for 1 hr at 37 ⁰ C (100 μl/well). Plates were washed with PBST, incubated with 1 μg ml ^"1 biotinylated goat antibody in blocking buffer for 1 hr at 37 ⁰ C (100 μl/well), washed with PBST and then a 1/1000 dilution of a Streptavidin-horseradish peroxidase conjugate (Sigma) was added for 10 min at 37 ⁰ C. After washing with PBST, substrates 3,3',5,5'-Tetramethylbenzidine and H ₂ O ₂ were added for 10-15 min before the reaction stopped with TMB Stop Solution. Plates were read at 450 nm.

RESULTS

Expression and purification

Both LH _N /A and LH _N /B were expressed as soluble recombinant fragments and purified by a combination of hydrophobic interaction, ion exchange and hydroxyapatite chromatography. Typical yields of purified LH _N /A from three 4.5 I fermentation runs were 1.2, 1.3 and 1.4 g with overall recoveries of 62, 67 and 62%, respectively. Purity was >95% as assessed by SDS-PAGE (Figure 4). Comparable purity and yields were obtained with LH _N /B at the same scale with an average yield of 1.47 g purified fragment from three fermentation runs.

The endopeptidase activity of purified LH _N /A was assessed using an antibody-based assay system and compared with that of native, recombinant LH _N /A. At the highest concentration of LH _N A used (1.8 mg ml ^"1 ), the fragment displayed no measurable endopeptidase activity, and this was > 10 ⁷ reduced compared to the native fragment. In contrast, LH _N /A showed virtually identical reactivity in an antigen ELISA compared to the holotoxin (Figure 5). Virtually identical data were obtained for LH _N /B (not shown).

LH _N ZA formulation and efficacy evaluation

With a theoretical pi value of 5.25, LH _N /A was predicted to bind strongly to aluminium hydroxide (Alhydrogel™) at physiological pH. In the presence of 10 mM Hepes pH 7.4 and 10OmM NaCI, LH _N /A (500 μg ml ^"1 ) showed near complete binding (>99%) to Alhydrogel solution (containing 3.1 mg ml ^"1 aluminium) as assessed by protein assay of supernatant solutions after centrifugation of the protein-Alhydrogel mixture. This formulation allowed administration of doses up to 100 μg protein in mouse efficacy studies in which 0.2 ml was injected subcutaneously. Protective efficacy was assessed as an ED ₅₀ , the vaccine dose required to protect 50% of the mice in groups challenged with a BoNT dose of 10 ³ mouse LD ₅₀ . In initial studies, ED ₅₀ values were estimated after challenge with BoNTZA ₁ 28 days after administration of a single dose of vaccine (Table 5). Protection against B0NT/A1 challenge provided by the LH _N /A was found to be erratic with complete protection of mouse groups only rarely observed and at relatively high (>20 μg) doses of vaccine. ED ₅₀ values were difficult to calculate accurately and were between 2-3 μg. No protection was observed against challenge with BoNT/A ₂ subtype at the highest vaccine dose tested.

With relatively poor protection provided by the recombinant LH _N /A vaccine, several modifications to the protein were assessed. Conversion of the single chain LH _N /A to the di-chain form by trypsin treatment did not significantly improve the vaccine's efficacy and an ED ₅₀ value of 1.7 ± 0.39 μg was obtained. However, treatment with formaldehyde significantly enhanced the efficacy of LH _N /A as a vaccine. Incubation of LH _N /A (1 mg ml ^"1 ) with formaldehyde (0.2% at 35 ⁰ C) for up to 96 h led to broadening of the protein band on SDS PAGE and also the appearance of a small proportion of a higher molecular weight band consistent in size with that of an dimer of the LH _N fragment (Figure 4, lane 4). Under the above incubation conditions the appearance of HCHO-treated LH _N /A did not change significantly on SDS-PAGE after 24 h incubation so efficacy assessments were made on LH _N /A treated with 0.2% HCHO for 24h at 35 ⁰ C. Initial ED ₅₀ tests on two different batches of LH _N /A suggested that the ED ₅₀ value was below 78 ng and a third test gave an ED ₅ oθf 49 ± 7 ng against challenge with BONT/A _L AS well as providing >30 fold reduction in ED ₅₀ value, the HCHO-treated LH _N /A also afforded significantly better protection of animals at higher doses (Table 5). An even more marked enhancement in

protection against challenge with BoNTVA ₂ was observed with almost complete protection of animal immunised with vaccines doses >0.5μg.

Table 5. Single Dose Efficacy Studies of Formaldehyde-Treated LH _N /A Vaccine

In guinea-pigs, protective efficacy was also significantly enhanced, although not to the same extent as in mice. For guinea pigs immunised with a single dose (10 μg) of untreated LH _N /A, the equivalent of 800 μl pooled serum protected 50% of mice from challenge 10 ³ LD ₅₀ of BoNTZA ₁ in neutralisation tests compared to the equivalent of 200 μl serum from guinea pigs immunised with HCHO-treated LH _N /A which represents a A- fold enhancement of efficacy.

To investigate possible mechanisms of the HCHO-mediated enhancement of efficacy, LH _N /A was treated with HCHO at lower protein concentrations (0.1 mg ml ^"1 ) which minimised the production of higher molecular weight forms of the fragment (Figure 6, Lane 2). Under these conditions, which generated only traces of the dimer LH _N /A form, an ED ₅₀ Of 147 ± 13 ng was obtained which represents a statistically significant enhancement of efficacy compared to untreated controls. The efficacy enhancement

would therefore not appear to be mediated by aggregated forms of the LH _N fragment. LH _N /A cleaved by trypsin appeared as two closely running bands of approximately 5OkDa on SDS-PAGE under reducing conditions which represent the light chain and H _N fragments (Figure 6). Under similar conditions, no such dissociation of the subunits was observed after HCHO treatment which suggests a degree of intra-molecular cross- linking had occurred.

Table 6. Summary of ED ₅₀ Values for LH _N /A Efficacy Studies

Bivalent A/B vaccine formulation containing formaldehyde-treated LH _N /A and untreated LH _N /B

LH _N ZA efficacy against BoNT/A sub-types

An important consideration in vaccine design for the botulinum toxins is that they should offer protection against the principal subtypes of the relevant serotype. Both one and two-dose ED ₅₀ tests were therefore conducted in which animals were challenged with either BoNTZA ₁ , A ₂ or A ₃ toxin subtypes (Table 6). A single dose of formaldehyde- treated LH _N /A provided protection in mice against all three type A subtypes. In terms of ED ₅₀ , protective efficacy against BoNTA ₂ was reduced approximately 6-fold compared to BoNTZA ₁ and that against BoNT/A ₃ approximately 45-fold reduced. In two-dose efficacy studies, sub μM ED ₅₀ values were obtained for all three type A subtypes (Table 6).

LH _N ZB formulation and efficacy studies

LH _N /B was formulated under identical conditions as that described for LH _N /A above. Under these conditions, near complete adsorption of LH _N /B was obtained in mixtures containing 500 μg ml ^"1 LH _N /B and Alhydrogel (3.1 mg ml ^"1 Al). Efficacy data for the LH _N /B vaccine are summarised in Table 7. In single dose tests, LH _N /B displayed excellent protective efficacy with ED ₅₀ values < 0.2 μg. In view of the significant

enhancing effect of formaldehyde treatment on the efficacy LH _N /A, the effect of a similar modification of LH _N /B was assessed. Treatment of LH _N /B with 0.2% HCHO for 24 h at 35 ⁰ C was found to induce band broadening and significantly more aggregation than observed with LH _N /A with prominent bands consistent with dimer and trimer formation evident on SDS-PAGE (Figure 4, lane 6). In single dose efficacy studies, ED ₅₀ values of were obtained for untreated LH _N B and HCHO-treated LH _N /B, respectively which were not significantly different (Table 6). The efficacy of LH _N /B vaccine was also assessed against challenge with BoNT/B ₄ subtype purified from the non-proteolytic C. botulinum strain, Ekland 17B. While protection was 2 - 3 reduced compared to that against BONT/B _L ED ₅₀ values of < 1 μg were obtained after a single vaccine dose (Table 6).

Bivalent efficacy assessment

Formulations of LH _N /A and B for bivalent efficacy studies, contained final concentrations of 100 μg ml ^"1 of each vaccine candidate. For both LH _N /A and B, single dose ED ₅₀ values were obtained which were comparable to those obtained from monovalent tests (Table 6 and 7). No evidence of immunosuppression by either fragment was evident.

Table 7. Summary of ED ₅₀ Values for LH _N /B Efficacy Studies

Efficacy Test ED ₅₀ Value (μg)

B ₁ Challenge B ₄ (n _P ) Challenge

One dose (untreated) 0.14 ± 0.02 0.36 ± 0.05

One dose (HCHO-treated) 0.18 ± 0.03 n.d.

One dose (A/B) ^* 0.08 ± 0.02 n.d.

Two dose 0.08 ± 0.001 n.d

Bivalent A/B vaccine formulation containing formaldehyde-treated LH _N /A and untreated LH _N /B

Example 22: Demonstration of the enhancing effect of intramolecular cross-linking on the efficacy of LHJE vaccine

A synthetic gene encoding C. botulinum type E (strain Alaska) endopeptidase negative LH _N /E (E213Q modification) was codon-optimized for expression in E. coli. The resulting nucleic acid was cloned into a pET26b vector, expressed in E. coli ER2566 host cells and isolated as generally provided in Example 21.

LH _N /E was adjusted to 1 mg ml ^"1 with Hepes/NaCI buffer, treated with HCHO (0.2% for 24 h at 35 ⁰ C) and adsorbed onto Alhydrogel (3100 μg ml ^"1 final concentration) in 1OmM Hepes pH 7.4 / 10OmM NaCI buffer (peptide concentration 100 μg ml ^"1 ). A control sample containing unmodified LH _N /E at 1 mg ml ^"1 with Hepes/NaCI buffer was also prepared.

After mixing and incubation at 4° C for 4 hours, the control and HCHO-treated LH _N /E preparations were dialysed against the Hepes buffer to remove the formaldehyde (if present) and then diluted with buffer containing Alhydrogel to give the following concentrations of antigen per 0.2 ml:

20 6.67 2.22 0.74 0.24 0.08 0.027 0 μg per 0.2ml dose

At 28 days post administration, the control and HCHO-treated LH _N /E groups of mice were challenged with BoNT/E (1000 LD ₅₀ i.p. in 0.5 ml). Deaths were recorded over a 4 day period post-challenge.

The data, shown in Table 8, confirm a significant enhancement in protective efficacy (as shown by a lower ED ₅₀ value) in the case of LH _N /E that has been treated with formaldehyde.

Calculated ED ₅₀ values were:

LH _N /E untreated control, ED ₅₀ = 2.5 ± 0.9 μg

LH _N /E HCHO-treated, ED ₅₀ = 0.29 ± 0.01 μg

Thus there is a >8-fold enhancement of protective efficacy as a result of formaldehyde treatment.

Table 8. LH _N /E ED ₅₀ Values of both HCHO-Treated and Untreated Vaccine

Example 23: Demonstration of enhanced protective efficacy after formaldehyde treatment of a C. difficile peptide derived from the C-terminal binding domain (residues 1756 to 2361 ) of C. difficile Toxin B

A recombinant fragment of the C-terminal binding domain (residues 1756 to 2361 ) of C. difficile Toxin B (SEQ ID NO: 28) was expressed in E. coli and purified by standard chromatography methods. A 1 mg ml ^"1 solution of the peptide was treated with 0.2% formaldehyde for 24h at 35 ⁰ C.

After removing formaldehyde from the C. difficile Toxin B peptide by dialysis, the peptide was mixed with adjuvant (Titermax™) in a 1 :1 ratio and used to immunise guinea pigs using 2 doses of 20 μg given at Day 0 and Day 14. The animals were bled on Day 28 and the serum from 5 animals pooled. Guinea pigs were also immunised in an identical manner with C. difficile Toxin B peptide which had not been treated with formaldehyde.

The toxin neutralizing activities of the resulting antiserum pools were measured by cellular assays using Vero cells. In these assays, a fixed amount of purified C. difficile Toxin B was mixed with various dilutions of the antibodies, incubated for 1 h at 37 ⁰ C and then applied to Vero cells growing on 24-well tissue culture plates. Toxin B possesses cytotoxic activity which results in a characteristic rounding of the Vero cells over a period of 24 - 48 h. In the presence of neutralising antibodies this activity is inhibited and the neutralising strength of an antibody preparation may be assessed by the dilution required to neutralise the effect of a designated quantity of the Toxin B.

The C. difficile toxin peptide which had been treated with formaldehyde produced antiserum of higher neutralising titre compared to the corresponding control peptide which has not been treated. In cytotoxicity assays, the dilution of antiserum required to protect cells from the cytotoxic effects of 0.5 ng/ml of Toxin B were as follows:

Untreated control C. difficile Toxin B peptide

- no protection at x10 dilution of serum

Formaldehyde-treated C. difficile Toxin B peptide

- protection of cells at x40 dilution of serum

The treatment of the C-terminal binding domain (residues 1756 to 2361 ) of C. difficile Toxin B with formaldehyde therefore increased its protective efficacy by at least 4-fold.