# Patent

## Title
Clostridium difficile-specific antibodies and uses thereof

## Abstract

The present invention is directed to Clostridium difficile toxin-specific antibodies, compositions, and uses thereof. The anti-toxin antibodies may be specific for either TcdA or TcdB. The invention also includes methods of treating a Clostridium difficile infection, methods of capturing Clostridium difficile toxins, and methods of detecting Clostridium difficile toxins.

## Background
CROSS-REFERENCE To RELATED APPLICATIONS
This application is a national phase entry of International Patent Application PCT/CA2011/001201 filed Oct. 25, 2011, which claims the benefit of U.S. Provisional Patent Application Ser. No. 61/406,254 filed Oct. 25, 2010, the contents of both of which are incorporated herein in their entirety.


FIELD OF THE INVENTION
The present invention relates to Clostridium difficile-specific antibodies and uses thereof. More specifically, the present invention relates to Clostridium difficile toxin-specific antibodies and uses thereof.
BACKGROUND OF THE INVENTION
Clostridium difficile is a Gram-positive, anaerobic, endospore-forming gastrointestinal pathogen responsible for C. difficile-associated disease (CDAD) in humans and animals with symptoms ranging in severity from mild cases of antibiotic-associated diarrhea to fatal pseudomembranous colitis (Rupnik et al, 2009; Leffler and Lamont, 2009; Songer, 2004; Kelly et al, 1994). Each year in North America, 1-3% of hospitalized patients receiving antibiotics become infected with C. difficile, leading to thousands of deaths and over $1 billion in associated costs to the health-care system (Wilkins and Lyerly, 2003; Kyne et al, 2002; Kelly et al, 1994). C. difficile produces two primary virulence factors, toxin A (TcdA) and toxin B (TcdB), which are large (308 kDa and 269 kDa, respectively), single-subunit exotoxins composed of a catalytic, a translocation and a cell-receptor binding domain (RBD) (Jank and Aktories, 2008; Jank et al, 2007). Recently it was suggested TcdB is solely responsible for C. difficile virulence (Lyras et al, 2009), although earlier studies have shown both anti-TcdA and anti-TcdB monoclonal antibodies (mAbs) were required for full protection of hamsters from CDAD (Babcock et al, 2006; Kink and Williams, 1998) and anti-TcdA mAbs were required for protection in mice (Corthier et al, 1991).
The current approach for treating most CDAD infections involves administration of antibiotics, most commonly metronidazole or vancomycin (Leffler and Lamont, 2009). Antibiotic treatment places selection pressure on the organism, can lead to antibiotic resistance, and suppresses or eliminates beneficial commensal microbes. However, there are several other emerging challenges warranting the development of novel therapeutics. First, there is no acute CDAD treatment targeting TcdA/B. These toxins are responsible for loss of epithelial barrier function in the colon by disrupting tight junctions and increasing membrane permeability, causing diarrhea and promoting severe inflammation (Rupnik et al, 2009; Jank and Aktories, 2008). Second, hypervirulent strains of C. difficile, such as the NAP1/027 isolate, over-express TcdA and TcdB (Warny et al, 2005) and have been associated with increased mortality rates and disease severity (O'Connor et al, 2009; Pépin et al, 2005). Third, an estimated 20-25% of patients suffering from CDAD experience symptomatic relapse after the initial infection is cleared, with 45% of these patients prone to subsequent relapses (Johnson, 2009). Taken together, there is a need for non-antibiotic based reagents which target and inhibit TcdA and TcdB for CDAD therapy.
Individuals who are asymptomatic C. difficile carriers and patients who experience mild cases of CDAD tend to possess high anti-toxin A titers (Kyne et al, 2001; Kyne et al, 2000; Warny et al, 1994; Viscidi et al, 1983). Conversely, patients susceptible to relapsing C. difficile infection have low anti-TcdA immunoglobulin titers, specifically IgM, IgG2 and IgG3 isotypes (Katchar et al, 2007; Kyne et al, 2001). TcdA-neutralizing secretory IgA antibodies are also thought to play a role in regulating CDAD severity (Johal et al 2004; Kelly et al 1992). Therefore, the introduction of anti-toxin antibodies to patients suffering from severe C. difficile infection may be a therapeutically useful approach.
A limited number of animal and human studies have illustrated the effectiveness of anti-toxin Abs for treatment of CDAD. Babcock et al (2006) intravenously administered anti-TcdA and anti-TcdB mAbs to hamsters and found a significant reduction in hamster mortality in prophylactic, primary disease and relapse models when both anti-toxin mAbs were administered. A recently completed clinical trial involving these two humanized mAbs appears promising (Lowy et al, 2010). In another study, intravenous administration of anti-TcdA mAbs raised against the RBD followed by oral challenge with C. difficile resulted in protection of mice (Corthier et al, 1991). Elsewhere, a toxoid vaccine given by the intraperitoneal route to hamsters conferred protection against oral C. difficile challenge (Giannasca et al, 1999) and mice vaccinated with DNA encoding the TcdA RBD resulted in full protection from oral TcdA challenge (Gardiner et al, 2009). In humans, a number of uncontrolled studies have reported intravenous immunoglobulin (IVIG) therapy to be successful for the treatment of severe CDAD (Juang et al, 2007; Hassoun and Ibrahim, 2007; McPherson et al, 2006; Wilcox, 2004; Salcedo et al, 1997; Leung et al, 1991). IVIG involves administration of high concentrations (150-400 mg/kg) of human immunoglobulins from healthy donors which are thought to contain neutralizing anti-toxin antibodies as an estimated 60% of healthy adults have detectable TcdA- and TcdB-specific serum IgG antibodies (Viscidi et al, 1983).
Given that C. difficile toxins rely on attachment to epithelial cells for entry (Jank and Aktories, 2008; Jank et al, 2007), neutralizing the toxins within the lower gastrointestinal tract with antibodies may block the first step in CDAD pathogenesis. In animals, orally administered bovine immunoglobulin concentrate (BIC) containing TcdA and TcdB neutralizing IgGs were able to prevent hamster mortality when used as a propholyactic (Lyerly et al, 1991) and protected rats from the enterotoxic effects of TcdA in vivo (Kelly et al, 1996). Chicken IgY antibodies specific for toxin RBDs were shown to reduce hamster mortality when administered orally to infected animals (Kink and Williams, 1998). In humans, there have been limited reports on CDAD therapy with orally delivered Abs. Tjellströom et al (1993) reported the successful treatment of a 31⁄2 year old boy suffering from severe CDAD with IgA antibody orally. Warny et al (1999) and Kelly et al (1997) examined the passage of anti-toxin bovine IgG through the human gastrointestinal tract and found a significant reduction in IgG activity, likely due to proteolytic degradation within the upper gastrointestinal tract. The limited success of both oral and systemic anti-toxin immunotherapy in clinical settings has likely been hampered by the high immunoglobulin dose requirements (150-400 mg/kg), the associated costs of these doses, and a lack of published clinical data showing the effectiveness of these treatments.
Despite such advances, there remains a need in the art for a safe and effective therapeutic for treating C. difficile-associated disease as well as for sensitive and effective reagents for the detection of toxins A and B, the factors responsible for C. difficile-associated disease.
SUMMARY OF THE INVENTION
The present invention relates to Clostridium difficile-specific antibodies and uses thereof. More specifically, the present invention relates to Clostridium difficile toxin-specific antibodies and uses thereof.
The present invention provides an isolated or purified antibody or fragment thereof, comprising

    
    
        a sequence of complementarity determining region (CDR) 1 selected from GRTFNTLS (SEQ ID NO:1); GRTFSMYR (SEQ ID NO:2); GRTLSSYI (SEQ ID NO:3); GRTFSMDP (SEQ ID NO:4); IRSFSNRN (SEQ ID NO:5); and ERTFSRYP (SEQ ID NO:6);
        a sequence of CDR2 selected from VSRSGGST (SEQ ID NO:7); ITRNGSST (SEQ ID NO:8); ISRRGGNS (SEQ ID NO:9); GSSTGRTT (SEQ ID NO:10); ISWGGGST (SEQ ID NO:11); and ISSTGTST (SEQ ID NO:12); and
        a sequence of CDR3 selected from AAAATKSNTTAYRLSFDY (SEQ ID NO:13); AATSGSSYLDAAHVYDY (SEQ ID NO:14); AADGSVAGWGRRSVSVSSYDY (SEQ ID NO:15); AAAPYGANWYRDEYAY (SEQ ID NO:16); AAEFGHNIATSSDEYDY (SEQ ID NO:17); and AVNSQRTRLQDPNEYDY (SEQ ID NO:18),

wherein the antibody or fragment thereof is specific for TcdA. The isolated or purified antibody or fragment thereof as described above may be selected from the group consisting of:

        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GRTFNTLS (SEQ ID NO:1); CDR2 of VSRSGGST (SEQ ID NO:7); and CDR3 of AAAATKSNTTAYRLSFDY (SEQ ID NO:13);
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GRTFSMYR (SEQ ID NO:2); CDR2 of ITRNGSST (SEQ ID NO:8); and CDR3 of AATSGSSYLDAAHVYDY (SEQ ID NO:14);
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GRTLSSYI (SEQ ID NO:3); CDR2 of ISRRGGNS (SEQ ID NO:9); and CDR3 of AADGSVAGWGRRSVSVSSYDY (SEQ ID NO:15);
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GRTFSMDP (SEQ ID NO:4); CDR2 of GSSTGRTT (SEQ ID NO:10); and CDR3 of AAAPYGANWYRDEYAY (SEQ ID NO:16);
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of IRSFSNRN (SEQ ID NO:5); CDR2 of ISWGGGST (SEQ ID NO:11); and CDR3 of AAEFGHNIATSSDEYDY (SEQ ID NO:17); or
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of ERTFSRYP (SEQ ID NO:6); CDR2 of ISSTGTST (SEQ ID NO:12); and CDR3 of AVNSQRTRLQDPNEYDY (SEQ ID NO:18).
    
    


The isolated or purified antibody or fragment thereof described above may comprise a sequence selected from the group consisting of:








(SEQ ID NO: 34)



QVKLEESGGGLVQAGGSLRLSCAASGRTFNTLSMGWFRQAPGKEREFVAAVSRSGGST



 


YYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAATKSNTTAYRLSFDYWGQG


 


TQVTVSS;


 


(SEQ ID NO: 35)



QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVGVITRNGSSTY



 


YADSVKGRFTISRDNAKNTVYLQMNSLKPEDTALYYCAATSGSSYLDAAHVYDYWGQGT


 


QVTVSS;


 


(SEQ ID NO: 36)



QVKLEESGGGLVQPGGSLRLSCAASGRTLSSYIVAWFRQAPGKEREFVAGISRRGGNSAY



 


VESVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADGSVAGWGRRSVSVSSYDYWG


 


QGTQVTVSS;


 


(SEQ ID NO: 37)



QVQLVESGGGLAQAGGSLRLSCAASGRTFSMDPMAWFRQPPGKEREFVAAGSSTGRTT



 


YYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAPYGANWYRDEYAYWGQGT


 


QVTVSS;


 


(SEQ ID NO: 38)



QVQLVESGGGLVQAGGSLRLSCAASIRSFSNRNMGWFRQPPGKEREFVAGISWGGGST



 


RYADSVKGRFTISRDNAKKTVYLQMNSLKPEDTAVYYCAAEFGHNIATSSDEYDYWGQGT


 


QVTVSS;


 


(SEQ ID NO: 39)



QVKLEESGGGLVQAGGSLRLSCAASERTFSRYPVAWFRQAPGAEREFVAVISSTGTSTYY



 


ADSVKGRFTISRDNAKVTVYLQMNNLKREDTAVYFCAVNSQRTRLQDPNEYDYWGQGTQ


 


VTVSS;


 


(SEQ ID NO: 45)



QVKLEESGGGLVQAGGSLRLSCAASGRTFNTLSMGWFRQAPGKEREFVCAVSRSGGST



 


YYADSVKGRFTCSRDNAKNTVYLQMNSLKPEDTAVYYCAAAATKSNTTAYRLSFDYWGQ


 


GTQVTVSS;


 


(SEQ ID NO: 46)



QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVCVITRNGSSTY



 


YADSVKGRFTCSRDNAKNTVYLQMNSLKPEDTALYYCAATSGSSYLDAAHVYDYWGQGT


 


QVTVSS;


 


(SEQ ID NO: 47)



QVKLEESGGGLVQPGGSLRLSCAASGRTLSSYIVAWFRQAPGKEREFVCGISRRGGNSA



 


YVESVKGRFTCSRDNAKNTVYLQMNSLKPEDTAVYYCAADGSVAGWGRRSVSVSSYDY


 


WGQGTQVTVSS;


 


(SEQ ID NO: 48)



QVQLVESGGGLAQAGGSLRLSCAASGRTFSMDPMAWFRQPPGKEREFVCAGSSTGRTT



 


YYADSVKGRFTCSRDNAKNTVYLQMNSLKPEDTAVYYCAAAPYGANWYRDEYAYWGQG


 


TQVTVSS;


 


(SEQ ID NO: 49)



QVQLVESGGGLVQAGGSLRLSCAASIRSFSNRNMGWFRQPPGKEREFVCGISWGGGST



 


RYADSVKGRFTCSRDNAKKTVYLQMNSLKPEDTAVYYCAAEFGHNIATSSDEYDYWGQG


 


TQVTVSS;


and


 


(SEQ ID NO: 50)



QVKLEESGGGLVQAGGSLRLSCAASERTFSRYPVAWFRQAPGAEREFVCVISSTGTSTYY



 


ADSVKGRFTCSRDNAKVTVYLQMNNLKREDTAVYFCAVNSQRTRLQDPNEYDYWGQGT


 


QVTVSS,






or a sequence substantially identical thereto.

In another aspect, the present invention provides an isolated or purified antibody or fragment thereof, comprising

    
    
        a sequence of complementarity determining region (CDR) 1 selected from GNIFSINT (SEQ ID NO:19); GRTASGYG (SEQ ID NO:20); GRTFSSGV (SEQ ID NO:21); GLSRYA (SEQ ID NO:22); and GSISRIST (SEQ ID NO:23);
        a sequence of CDR2 selected from ITSGGTT (SEQ ID NO:24); ISRSGAGT (SEQ ID NO:25); ITTGGST (SEQ ID NO:26); TNWSSGNT (SEQ ID NO:27); and ISTGGTT (SEQ ID NO:28); and
        a sequence of CDR3 selected from NTVKVVGGRLDNPDY (SEQ ID NO:29); VARPTKVDRDYATRREMYNY (SEQ ID NO:30); NSVAVVGGVIKSPDY (SEQ ID NO:31); AARKLDVPSRYSQHYDY (SEQ ID NO:32); and AAGVVKWRGSLEYEY (SEQ ID NO:33),

wherein the antibody or fragment thereof is specific for TcdB. The isolated or purified antibody or fragment thereof as just described may be selected from the group consisting of:

        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GNIFSINT (SEQ ID NO:19); CDR2 of ITSGGTT (SEQ ID NO:24); and CDR3 of NTVKVVGGRLDNPDY (SEQ ID NO:29);
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GRTASGYG (SEQ ID NO:20); CDR2 of ISRSGAGT (SEQ ID NO:25); and CDR3 of VARPTKVDRDYATRREMYNY (SEQ ID NO:30);
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GRTFSSGV (SEQ ID NO:21); CDR2 of ITTGGST (SEQ ID NO:26); and CDR3 of NSVAVVGGVIKSPDY (SEQ ID NO:31);
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GLSRYA (SEQ ID NO:22); CDR2 of TNWSSGNT (SEQ ID NO:27); and CDR3 of AARKLDVPSRYSQHYDY (SEQ ID NO:32); or
        an isolated or purified antibody or fragment thereof comprising a sequence of CDR 1 of GSISRIST (SEQ ID NO:23); CDR2 of ISTGGTT (SEQ ID NO:28); and CDR3 of AAGWKVVRGSLEYEY (SEQ ID NO:33).
    
    


The isolated or purified antibody or fragment thereof as described above may comprise a sequence selected from the group consisting of:








(SEQ ID NO: 40)



QVQLVESGGGLVQPGGSLRLSCAASGNIFSINTMGWYRQAPGKQLELVAAITSGGTTSYT



 


DSVEGRFTISRDNAKNAVYLQMNSLKAEDTAVYYCNTVKVVGGRLDNPDYWGQGTQVTV


 


SS;


 


(SEQ ID NO: 41)



QVKLEESGGGLVQPGGSLRLSCAASGRTASGYGMGWFRQAPGKEREFVAAISRSGAGTL



 


NADFVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCVARPTKVDRDYATRREMYNYWG


 


QGTQVTVSS;


 


(SEQ ID NO: 42)



QVKLEESGGGLVQAGGSLRLSCSASGRTFSSGVMGWFRQAPGKQRELVAAITTGGSTSY



 


TDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNSVAVVGGVIKSPDYWGQGTQVTV


 


SS;


 


(SEQ ID NO: 43)



QVQLVESGGGSVQAGGSLRLSCAASGLSRYAMAWFRQGTGKEREFVASTNWSSGNTPY



 


ADSVKGRFIISRDNAKNTVYLQMNSLKPGDTAIYYCAARKLDVPSRYSQHYDYWGQGTQV


 


TVSS;


 


(SEQ ID NO: 44)



QVQLVESGGDLVQAGGSLRLSCAASGSISRISTMGWYRQAPGKQRELVATISTGGTTNYA



 


ESVKGRFTVSRDNAKNTMYLQMNSLKPEDTAVYYCAAGWKVVRGSLEYEYSGQGTQVTV


 


SS;


 


(SEQ ID NO: 51)



QVQLVESGGGLVQPGGSLRLSCAASGNIFSINTMGWYRQAPGKQLELVCAITSGGTTSYTDS



 


VEGRFTCSRDNAKNAVYLQMNSLKAEDTAVYYCNTVKVVGGRLDNPDYWGQGTQVTVSS,


referred to herein as B5.2m;


 


(SEQ ID NO: 52)



QVKLEESGGGLVQPGGSLRLSCAASGRTASGYGMGWFRQAPGKEREFVCAISRSGAGTLN



 


ADFVKGRFTCSRDNAKNTVYLQMNSLKPEDTAVYYCVARPTKVDRDYATRREMYNYWGQG


 


TQVTVSS,


referred to herein as B7.3m;


 


(SEQ ID NO: 53)



QVKLEESGGGLVQAGGSLRLSCSASGRTFSSGVMGWFRQAPGKQRELVCAITTGGSTSYTD



 


SVKGRFTCSRDNAKNTVYLQMNSLKPEDTAVYYCNSVAVVGGVIKSPDYWGQGTQVTVSS,


referred to herein as B13.6m;


 


(SEQ ID NO: 54)



QVQLVESGGGSVQAGGSLRLSCAASGLSRYAMAWFRQGTGKEREFVCSTNWSSGNTPYAD



 


SVKGRFICSRDNAKNTVYLQMNSLKPGDTAIYYCAARKLDVPSRYSQHYDYWGQGTQVTVS


 


S,


referred to herein as B15.3m; and


 


(SEQ ID NO: 55)



QVQLVESGGDLVQAGGSLRLSCAASGSISRISTMGWYRQAPGKQRELCATISTGGTTNYAES



 


VKGRFTCSRDNAKNTMYLQMNSLKPEDTAVYYCAAGWKVVRGSLEYEYSGQGTQVTVS,


referred to herein as B15.5m,






    
    
        or a sequence substantially identical thereto.
    
    


The isolated or purified antibody or fragment thereof as described above may be a single-domain antibody (sdAb); the sdAb may be of camelid origin.
The isolated or purified antibody or fragment thereof of as described herein may be in a multivalent display format.
The isolated or purified antibody or fragment thereof as described herein may be immobilized onto a surface.
The isolated or purified antibody or fragment thereof of the present invention may be linked to a cargo molecule; the cargo molecule may be a detectable agent, a therapeutic, a drug, a peptide, a protease, an enzyme, a carbohydrate moiety, or a cytotoxic agent; one or more liposomes loaded with a detectable agent, a therapeutic, a drug, a peptide, an enzyme, or a cytotoxic agent; or one or more nanoparticle, nanowire, nanotube, or quantum dots.
The present invention further encompasses a nucleic acid molecule encoding the isolated or purified antibody or fragment thereof as described above. The present invention also includes a vector comprising the nucleic acid molecule just described.
Also provided is a composition comprising one or more than one isolated or purified antibody or fragment thereof of the present invention and a pharmaceutically-acceptable carrier, diluent, or excipient.
The present invention further provides a method of treating a Clostridium difficile infection, comprising administering the isolated or purified antibody or fragment thereof of the present invention or the composition of described above to a subject in need thereof.
In another aspect, there is provided a method of capturing Clostridium difficile toxins, comprising contacting a sample with one or more than one isolated or purified antibody or fragment thereof of the present invention immobilized onto a surface, and allowing the toxin(s) to bind to the isolated or purified antibody or fragment thereof. The method just described may further comprise identifying the toxin by mass spectrometric methods and/or eluting the bound toxin.
The present invention additionally provides a method of detecting Clostridium difficile toxins, comprising contacting a sample with one or more than one isolated or purified antibody or fragment thereof linked to a cargo molecule, and detecting the bound antibody or fragment thereof using a suitable imaging or detection technology. The cargo molecule may be a detectable agent.
The present invention provides isolated llama single-domain antibodies (VHHs) capable of binding, detecting, capturing, and/or neutralizing C. difficile TcdA and TcdB. Without wishing to be bound by theory, VHHs targeting the toxin's receptor binding domain (RBD) may block the toxin-receptor interaction, thereby preventing toxin entry into the host cell; a critical initial step in the TcdA/B mechanism of action (Jank and Aktories, 2008). To do so, a hyperimmunized llama VHH phage display library was constructed and panned with recombinant RBD fragments. The isolated VHHs were then characterized for their ability to bind native toxins and recombinant RBD fragments and the nature and relative positioning of epitopes. In addition, the ability of VHHs to neutralize toxins in an in vitro cell cytotoxicity assay was assessed.
Several TcdA-specific VHHs capable of neutralizing TcdA in vitro through high-affinity interactions with TcdA-RBD were found. VHHs are extremely stable antigen-binding domains that are expressed at high-yields in recombinant organisms and are capable of neutralizing infectious disease-related targets (Wesolowski et al, 2009). With respect to CDAD therapy, VHHs could be administered systemically to target TcdA and TcdB as they share high sequence homology with human VH domains, thus are well-tolerated in humans (Vu et al, 1997; www.Ablynx.com). Enhanced toxin neutralizing efficacy may be obtained by increasing their blood circulation half lives, size and avidity using various techniques, including chimeric formats of anti-TcdA VHHs linked to an Fc domain, generation of bi- or tri-specific antibody fusions with two or three anti-TcdA VHHs recognizing unique epitopes, PEGylation, fusion to serum albumin, or fusion to serum albumin-specific antibody fragments. By targeting C. difficile virulence factors such as TcdA/B, selection pressure is removed from the organism, decreasing the chance of antibiotic resistance. A mutation in the RBD, which is conserved among C. difficile isolates including hypervirulent 027 ribotype strains, is unlikely to benefit the organism and in the event it does occur, the toxin may lose its ability to enter host cells. As such, anti-TcdA/B VHHs are logical agents to explore for CDAD therapy.
In order to improve the VHHs' biophysical properties, the C. difficile TcdA-specific VHHs were engineered to insert a non-canonical disulfide bond by introducing Ala/Gly54→Cys54 and Ile78→Cys78 mutations, allowing for the formation of a second, non-native disulfide bond between FR2 and FR3 in the VHH hydrophobic core. Disulfide bond formation was confirmed using a combination of proteolytic and chemical digestion coupled with MS2 to precisely identify VHH peptide fragments harboring the introduced disulfide bond. The mutant antibodies were compared to their wild-type counterparts with respect to yield, solubility, affinity for TcdA, thermal unfolding at neutral and acidic pH and protease resistance. Mutant VHHs were found to be soluble, non-aggregating monomers, possessing similar affinity constants to that of WT VHHs. SPR binding experiments revealed most mutant VHHs possessed 1- to 5-fold weaker affinity constants relative to wild-type, which is consistent with other reports in the art.
CD spectroscopy was used to compare wild-type and mutant VHH secondary structure, tertiary structure, thermal stability (Tm and Tonset), and thermal refolding efficiency (TRE). Comparisons of VHH secondary and tertiary structure with far-UV and near-UV CD spectroscopy strongly suggested structural differences between wild-type and mutants, at both neutral and acidic pH. For all mutants, peak intensity and selective peak minima shifts were observed, although the overall spectral profiles remained very similar in all wild type/mutant pairs. More specifically, mutants consistently showed rightward peak shifts in the peak range of 230 nm-235 nm (far-UV CD spectra) and around 297 nm (near-UV CD spectra) compared to wild type VHHs. Such patterns may be used as signatures that could be used to quickly identify VHHs containing a properly formed non-canonical disulfide bond, as could SDS-PAGE motility values since, compared to wild type VHHs, mutants consistently moved slower in SDS-PAGE gels. Thus, the far- and near-UV CD spectral data suggests the introduced disulfide bond changes the structure of VHHs. This is consistent with the observed perturbations in affinities and specificities and increased GI protease resistance of the mutant VHHs compared to the wild types.
CD spectroscopy thermal denaturation experiments were performed to show a profound and significant (p<0.05) increase in the Tms and Tonsets of mutant VHHs at both neutral and acidic pH. Increases in midpoint temperature of unfolding (Tm) ranging from  ̃4 to  ̃12° C. were observed for all mutants, at both neutral and acidic pH. Without wishing to be bound by theory, for the mutant VHHs with a higher thermostability gain, the non-canonical disulfide linkage may have been a better fit to overall fold. For example, A19.2m and A24.1m showed the lowest thermostability gains and this would explain why they were transformed into non-specific binders upon mutation. For A4.2m on the other hand, the non-canonical disulfide linkage seems to be a natural fit, as it increased its Tm the most (by almost 12° C.) and significantly improved GI protease resistance (with the highest increase in pepsin resistance), all without adversely affecting the KD.
Digestion of the VHHs with major gastrointestinal proteases at biologically relevant concentrations revealed a significant (p<0.05) increase in pepsin resistance for all mutants; however, increases in resistance profiles to chymotrypsin and trypsin were not as universal. Each wild-type and mutant VHH pair possessed an identical number of theoretical protease cleavage sites (data not shown); thus it seems that the added disulfide bond leads to a more compact and thermodynamically stable VHH structure, preventing pepsin and chymotrypsin from accessing proteolytic cleavage sites. VHH refolding was also examined using CD spectroscopy. While wild-type refolding was better than mutant VHH refolding at neutral pH the reverse was true under stringent conditions (acidic pH). At acidic pH, 5 of 6 mutant VHHs possessed greater refolding efficiency than wild-type after complete thermal denaturation with the majority essentially showing reversible thermal unfolding.
The introduction of the Cys54/Cys78 disulfide linkage into VHHs led to increases in both Tm and thermodynamic stability. Proteins with higher Tn, are also less likely to unfold [62]. These may be the reasons why the present mutants were more resistant to acid-induced unfolding at 37° C., supported by the higher Tonsets and pepsin resistance of the mutant VHHs. This benefit is not realized for mutants against trypsin, possibly because their cleavage sites are at hydrophilic residues (Lys or Arg), which may be in more exposed regions of the VHH, possibly located in the CDR regions. Further, these regions would not be protected by stabilizing the core of the structure. An increase in Tonset temperatures for mutants at the physiological condition representative of the stomach (pH 2.0 and 37° C.) to values significantly above 37° C. (Tonsets from 45° C.-53° C.) was observed. This indicates that the mutants should remain fully folded at 37° C. in the stomach, hence resisting pepsin degradation (and denaturation) to a higher extent than wild type VHHs, which is supported by the pepsin digestion experiments herein.
The toxin A neutralizing efficacy of the disulfide bond mutant VHHs was 3-4 fold weaker compared to the wild-type VHHs in toxin A neutralization in cell-based assays, presumably a reflection in the reduced affinities of 3 of 4 VHHs for the toxin. Under stringent conditions in vivo, the lower affinity mutants may actually be more efficacious than the higher affinity wild-type VHHs due to their greater stability.
It is presently shown that the introduction of a second disulfide bond into the hydrophobic core of a panel of llama VHHs increased thermal stability and GI protease resistance; the approach is both effective and general. While affinity, specificity, and expression yield may be reduced, the mutants comprising additional disulfide bond outperformed the wild-type VHHs under more stringent physiological conditions; this far outweighs the reductions in affinity.
Protein-based oral therapeutics have several conceived advantages over systemic administration: convenience, patience compliance, lower cost, pain-free administration, drug purity, flexibility in production source (i.e., bacterial, plant, etc.), and fewer concerns over immunogenicity. Despite the many advantages of orally administering protein therapeutics, few successes have been realized due to the destabilizing environment of the GI tract. Of the major GI proteases, pepsin is considered the primary cause of antibody degradation and hence a major obstacle facing orally-delivered antibody therapeutics. The introduction of an additional disulfide bond in the hydrophobic core of the anti-TcdA VHHs not only increased thermal stability at neutral pH, but also represents a generic strategy to increase antibody stability at low pH and impart pepsin resistance which is desirable for protein-based oral therapeutics.
Additional aspects and advantages of the present invention will be apparent in view of the following description. The detailed description and examples, while indicating preferred embodiments of the invention, are given by way of illustration only, as various changes and modifications within the scope of the invention will become apparent to those skilled in the art in light of the teachings of this invention.



BRIEF DESCRIPTION OF THE DRAWINGS
These and other features of the invention will now be described by way of example, with reference to the appended drawings, wherein:
FIG. 1 relates to the isolation of anti-TcdA/B VHHs. FIG. 1A is a schematic representation of native TcdA/B and recombinant fragments of the cell receptor-binding domain (TcdA-RBD-f1 and TcdB-RBD-f1) used for llama immunization and library panning. Numbers represent the amino acid residues of each toxin, labelled from the N-termini (1) to C-termini (2710/2366 for TcdA and TcdB, respectively). Drawings are not to scale. GT=glucosyltransferase domain; CP=cysteine protease domain; HR=hydrophobic membrane insertion domain; RBD=cell-receptor binding domain. FIG. 1B is an SDS-PAGE profile of the purified C. difficile toxins (3 μg per lane; from C. difficile strain 10463) used herein. The upper arrow shows full-length TcdA (308 kDa) and TcdB (269 kDa). FIG. 1C shows ELISA results demonstrating a total llama serum response for the recombinant RBD fragments. Serum was prepared from llama blood drawn 57 days after the initial immunization. Immune (A): immune serum against TcdA-RBD-f1; Immune (B): immune serum against TcdB-RBD-f1; Pre-Immune: pre-immune serum against TcdA-RBD-f1. FIG. 1D shows ELISA results demonstrating the llama heavy-chain IgG (HCAb) GI fraction response was specific for the recombinant RBD fragments. Serum was fractionated from llama blood drawn 84 days after the initial immunization and the GI fraction shown did not recognize PEB3 or CPS, two unrelated antigens. FIG. 1E shows the SDS-PAGE profile of purified VHHs (2 μg per lane) isolated from the hyperimmunized llama phage display library. Molecular weight markers (M) are given in kDa. NR: non-reducing.
FIG. 2 is an amino acid sequence alignment of the anti-TcdA/B VHHs isolated. Framework regions, FRs, and complementarity-determining regions, CDRs (shaded in grey), are grouped according to the IMGT numbering system (http://imgt.cines.fr/). Hallmark positions, 42, 49, 50 and 52, where VHHs can be distinguished from VH based on amino acid identity are illustrated with asterisks. VHs generally have V, G, L and W at positions 42, 49, 50 and 52, respectively; in many VHHs, the aforementioned residues are replaced with F/Y, E/Q/R, R and F/L, as shown.
FIG. 3 describes the construction, expression and functional characterization of pentameric versions of monomeric anti-TcdA VHHs. FIG. 3A is a schematic diagram of a VHH pentamer. VHH monomers expressed as fusions to the verotoxin B (VTB) subunit self-assembly into pentameric structures in E. coli. FIG. 3B shows an SDS-PAGE gel containing eluted IMAC fractions of purified VHH pentamers A5.1p and A20.1p. Molecular weight markers (M) are given in kDa. NR: non-reducing. Arrows indicate the location of purified VTB-VHH monomers. FIG. 3C shows ELISA results comparing the functional activity of VHH monomers (A5.1 and A20.1) and VHH pentamers (A5.1p and A20.1p) to wells coated with TcdA. Equimolar concentrations of monomer/pentamer were used in the assay relative to the VHH monomer. Monomer/pentamer binding was detected with rabbit anti-His6 IgG-HRP and absorbances were read at 450 nm.
FIG. 4 depicts the toxin binding characteristics of VHHs. ELISA demonstrating the anti-TcdA VHHs (FIG. 4A) and anti-TcdB VHHs (FIG. 4B) recognize native toxins and recombinant RBD fragments. Wells were coated with molar equivalent concentrations. FIG. 4C and FIG. 4D shows binding of various concentrations of VHHs to immobilized TcdA or TcdB, respectively.
FIG. 5 shows the gel filtration profiles of anti-TcdA VHHs obtained from a SuperdexTM 75 column. The single peak for all WT VHHs suggests all are non-aggregating monomeric species.
FIG. 6 shows surface plasmon resonance analysis of anti-TcdA/B VHHs. Sensorgrams of TcdA-specific VHHs A4.2, A5.1, A19.2, A20.1, A24.1 and A26.8 binding to immobilized TcdA (FIGS. 6A-F) and TcdB-RBD-f1 (FIG. 1) binding to immobilized TcdB-specific VHHs B5.2, B13.6 and B15.5 (FIGS. 6G-I) are shown. In experiments involving TcdA-specific VHHs, TcdA was immobilized on CM5-dextran chips and monomeric VHHs were passed over at concentration ranges noted on each sensorgram, giving affinity constants ranging from 2 nM to 290 nM. In experiments involving TcdB-specific VHHs, antibodies were immobilized on CM5-dextran chips and TcdB-RBD-f1 ranging in concentration from 2 μM to 200 nM was passed over, giving affinity constants ranging from 100 nM to 400 nM. Black lines represent raw data measurements and grey lines represent fitted curves. All data presented here showed acceptable fitting to a 1:1 binding model. Rate and affinity constants are shown in Table 1.
FIG. 7 shows a subset of TcdB-specific VHHs with complex binding to recombinant TcdB-RBD. Surface plasmon resonance sensorgrams for VHHs that showed binding to TcdB-RBD-f1, but whose data was non analyzable. The recombinant TcdB-RBD-f1 fragment (2 μM→200 nM) was passed over immobilized VHHs (526-1209 RUs). (A) B7.3, (B) B13.2, (C) B13.3, and (D) B15.3.
FIG. 8 shows the in vitro neutralization of TcdA cytotoxicity with anti-TcdA VHHs. Dose-response curves of TcdA (FIG. 8A) and TcdB (FIG. 8B) on monolayers of IMR-90 human lung fibroblast (HLF) cells. The percentage of cell rounding was scored from 0% to 100% of the cells affected. FIGS. 8C-E show neutralization of TcdA-induced cell rounding with VHHs at 24 h post addition of 100 ng/ml TcdA. The final concentration of VHHs in each assay well were 1000 nM (FIG. 8C), 10 nM (FIG. 8D) and 0.1 nM (FIG. 8E) and VHHs were added as singles, pairs, or triplet combinations. White bars represent single VHHs or PBS control, grey bars represent paired combinations and black bars represent triplet combinations. Combinations of VHHs (i.e., pairs and triples) increased toxin neutralizing efficacy. FIG. 8F shows representative photographs of TcdA neutralization with 1000 nM VHH were taken 24 h post toxin addition. The black bar represents 100 μm.
FIG. 9 shows results of epitope typing experiments. Anti-toxin VHHs recognize conformational (A4.2, A5.1, A20.1, A26.8) and linear (A19.2) epitopes on native C. difficile toxin and recombinant fragments of the cell receptor-binding domain. FIG. 9A shows ELISA results on TcdA treated with various temperatures for 30 min before probing with VHHs. At treatment temperatures above the TcdA midpoint unfolding temperature (Tm), binding of 4 out of 5 TcdA-specific VHHs was abolished. The dotted line represents the TcdA Tm of  ̃55° C. FIG. 9B shows Western blots (reducing/denaturing) probed with His-tagged anti-TcdA VHHs or control mouse anti-TcdA IgG (PCG-4). Binding was detected with nickel-AP or goat anti-mouse IgG-AP, respectively. Of the VHHs tested, only A19.2 recognized denatured TcdA and the secondary conjugates did not bind denatured TcdA. FIG. 9C shows Western blots (native-PAGE) probed with anti-TcdA VHHs or control PCG4. VHHs and PCG4 bound TcdA. The goat anti-mouse IgG-AP conjugates strongly cross-reacted with TcdA in the absence of PCG4.
FIG. 10 shows results of Biacore co-injection experiments, which were used to determine if pairs of VHHs could bind TcdA simultaneously. The Biacore sensorgrams in FIG. 10A and FIG. 10B of all of the possible paired combinations of A4.2, A5.1, A20.1 and A26.8, in both orientations, are shown. Dashed lines represent injection of a single VHH followed by injection of buffer. Solid lines represent co-injections of the first VHH followed by injection of a second VHH. For all experiments, 80 μl of each VHH at a concentration 20× its KD was injected over 10,287 RUs of immobilized TcdA at 40 μl/min. In general, A4.2, A5.1 and A26.8 appeared to share an overlapping epitope as no significant increase in response was found upon injection of the second species. Conversely, A20.1 appeared to bind a distinct, non-overlapping epitope.
FIG. 11 shows Biacore results indicating that a subset of VHHs bind TcdA at overlapping epitopes. The three VHHs suspected of sharing an overlapping epitope (FIG. 7) were injected alone (A4.2, A5.1, or A26.8) and as a triplet mixture (“Mix”) over immobilized TcdA. The Biacore sensorgram illustrates similar Rmax ( ̃160-200 RUs) values for individual VHHs with no increase in response upon injection of the mixed population, indicating these antibodies recognize an overlapping epitope on TcdA. If the mixture of VHHs were free to bind at non-overlapping sites, one would expect an Rmax value for the mixtures to reach the sum of all individual Rmax values (i.e.,  ̃540 RUs). In all experiments, 80 μl of VHHs were injected at 40 μl/min and used at 20× their KD concentrations.
FIG. 12 shows results of Biacore analysis, which revealed that two trisaccharides, CD-grease (CD) and LeX-AmHex (LeX), known to interact at the carbohydrate binding sites of TcdA-RBD, did not inhibit VHH binding to immobilized TcdA. All four neutralizing VHHs were tested and one representative example is shown. FIG. 12A shows the responses of A26.8 binding TcdA, CD-grease binding TcdA and co-injection of A26.8 and CD-grease. FIG. 12B shows the responses of A26.8 binding TcdA, LeX-AmHex binding TcdA and co-injection of A26.8 and LeX-AmHex. FIGS. 12C and 12D show subtraction of the response generated from either trisaccharide binding to TcdA from co-injection experiments reveals a near identical response to that of A26.8 alone, an indication that VHH binding to TcdA is not inhibited by the trisaccharides. In all experiments, VHHs were used at their KD concentrations and trisaccharides at their apparent KD (2 mM).
FIG. 13 shows Biacore results indicating VHH binding to TcdA does not impair binding of the trisaccharide CD-grease (CD), which is known to bind TcdA-RBD. FIG. 13A shows the injection of A20.1 (A, grey and dashed lines), followed by injection of A20.1 (B, dashed line) or A20.1+CD-grease (B, grey line), and finally injection of Biacore buffer (C, grey and dashed lines). FIG. 13B shows the injection of A26.8 (A, grey and dashed lines), followed by injection of A26.8 (B, dashed line) or co-injection of A26.8+CD-grease (B, grey line), and finally injection of Biacore buffer (C, grey and dashed lines). These results suggest VHH binding is not at or in the carbohydrate binding site on TcdA-RBD.
FIG. 14 shows the alignment and comparison of wild-type and mutant VHH amino acid sequences. Wild-type VHH sequences are shown with a single disulfide bond between Cys23 and Cys104. A second disulfide bond was introduced through mutation of Ala54/Gly54 and Ile78 to Cys54 and Cys78 in framework region (FR) 2 and FR3, respectively. Disulfide bonds are shown as black lines. Bolded residues illustrate the disulfide bond-linked peptides identified by nanoRPLC-ESI-MS analysis on CNBr and trypsin digested mutant VHHs. Amino acid numbering and CDR designation is based on the IMGT system.
FIG. 15A shows a non-reducing (NR) SDS-PAGE analysis and Western blot (WB) probed with an anti-His6 IgG on IMAC-purified mutant VHHs. M: molecular weight marker in kDa. FIG. 15B is a representative SDS-PAGE analysis showing mutant VHHs run slower than the corresponding wild-type VHHs under non-reducing conditions.
FIG. 16 confirms the disulfide bond formation between residues Cys54 and Cys78 by MS2. FIG. 16A shows a SDS-PAGE gel under non-reducing (NR) conditions of VHHs (3 μg per lane), which illustrates near-complete digestion with CNBr and trypsin. Untreated A5.1m was added as a control (Ctl). M: molecular weight marker in kDa. FIG. 16B shows a MaxEnt 3 deconvoluted CID-MS2 spectrum of the m/z 526.25 (3+) ion of the disulfide-linked peptide EFVCVITR (P1)-FTCSR (P2), encompassing the Cys54-Cys78 disulfide bond, from CNBr/trypsin digested A5.1m. Amino acid positions are based on the IMGT numbering system.
FIG. 17 shows the characterization of mutant anti-TcdA VHHs which possessed a second disulfide bond in the hydrophobic core that were introduced by mutation of two amino acids to cysteine. FIG. 17A shows a comparison of the Size exclusion chromatography (SEC) analysis of wild-type (WT) anti-TcdA VHHs (top) and mutant anti-TcdA VHHs (bottom) obtained from a SuperdexTM 75 column. Similar size exclusion profiles were obtained for mutant and wild-type, indicating the second disulfide bond does not promote the formation of interdomain disulfide-bonds or multimeric mutant VHHs. The elution volumes (Ves) of SEC molecular weight standards are shown with arrows and are aligned relative to the A4.2 and A4.2m chromatograms. a: ovalbumin (MW=43.0 kDa, Ve=8.90 ml); b: carbonic anhydrase (MW=30.0 kDa, Ve=9.71 ml); c: typsin inhibitor (MW=20.1 kDa, Ve=11.06 ml); d: α-lactalbumin (MW=14.4 kDa, Ve=11.97 ml); e: vitamin B (MW=1.3 kDa, Ve=18.7 ml). The equation of the line of a standard curve generated from these standards was LOG10MW=−0.1539Ve+2.9949 (r2=0.9995). From this equation the VHH apparent MWs ranged from 9.8-13.6 kDa, indicating monomeric VHHs. FIG. 17B shows surface plasmon resonance (SPR) sensorgrapms for four mutant VHHs binding to immobilized TcdA. Grey lines represent raw data measurements and black lines represent fitted curves. Kinetic and affinity constants are given in Table 4. Binding of A19.2m and A24.1m to TcdA was non-specific, and the kinetic and affinity constants could not be determined. The binding shows mutant VHHs with a second disulfide bond retain high-affinity binding to TcdA.
FIG. 18 shows far-UV CD spectra of VHHs at neutral and acidic pH. CD scans (210 nm-260 nm) were performed at 25° C. on VHHs (50 μg/mL) equilibrated for 2 h in 10 mM phosphate buffer (pH 7.3) or 10 mM phosphate buffer+50 mM HCl (pH 2.0). The spectra represent the mean residue ellipticity of 8 data accumulations collected from 2 independent experiments. Black lines: wild-type VHH; grey lines: mutant VHH.
FIG. 19 shows near-UV CD analysis of VHHs at neutral and acidic pH. CD scans (250 nm-340 nm) were performed at 25° C. on VHHs (250 μg/mL) equilibrated for 2 h in 10 mM phosphate buffer (pH 7.3) or 10 mM phosphate buffer+50 mM HCl (pH 2.0). The spectra represent the mean residue ellipticity from 8 data accumulations collected from 2 independent experiments. Black lines: wild-type VHH; grey lines: mutant VHH.
FIG. 20 shows far-UV CD scans used to determine VHH refolding efficiencies under neutral and acidic pH conditions. A5.1 is shown as a representative example. FIG. 20A shows CD spectra collected on equilibrated VHHs (50 μg/ml) at 25° C. before heat treatment (scan 1, solid lines), after exposure to 96° C. for 20 min (scan 2, dotted lines), and after cooling to 25° C. for 3 h (scan 3, dashed lines). Scans are an average of 4 data accumulations. FIG. 20B shows a summary of thermal refolding efficiencies at pH 7.3 and pH 2.0, calculated using Equation 2 and following the changes in ellipticity at 215 nm. Dots represent the mean thermal refolding efficiency (TRE) of individual VHHs from two independent experiments with 4 data accumulations in each experiment. Bars represent the mean TRE of each group of VHHs.
FIG. 21 shows results of circular dichroism analysis for the determination of WT and mutant VHH melting temperatures at neutral and acidic pH. FIG. 21A shows unfolding transition curves for all six WT and mutant anti-TcdA VHHs at neutral pH (7.3) and acidic pH (2). VHH thermal unfolding midpoint temperatures (Tms) were determined using CD spectroscopy by following antibody unfolding (50 μg/mL) at 215 nm in 10 mM phosphate buffer+/−50 mM HCl. Tm was determined for each curve by Boltzmann non-linear curve fitting analysis in GraphPad Prism. The goodness of curve fit (r2) ranged from 0.9901-0.9995. In the case of VHHs with few lower baseline data points the Tm is a minimal estimate. FIGS. 21B and 21C show a summary of the VHH Tms and Tonsets, respectively. Each dot represents individual VHH and the bar represents the mean Tn, or Tonset value in each group. P-values were determined using the unpaired two-tailed t-test The Tm values are summarized in Table 6.
FIG. 22 shows the resistance profiles of WT and mutant VHHs to the major gastrointestinal proteases pepsin, trypsin and chymotrypsin. FIG. 22A is a representative SDS-PAGE gel comparing the profiles of WT and mutant A5.1 VHH after no treatment or digestion with various ratios of pepsin for 1 h at 37° C. VHH epitope tags (“tag”), consisting of c-Myc and His6, were preferentially cleaved by all proteases (confirmed by mass spectrometry analysis—data not shown). Densitometric analysis of SDS-PAGE gels allowed for the determination of a percent of retained VHH structure, which was denoted percent resistance. FIG. 22B-D summarizes the percent resistance of WT and mutant VHHs to pepsin, trypsin, and chymotrypsin after digestion for 1 h at 37° C. using a protease concentration of 100 μg/ml (1:2.4 ratio of protease:VHH). Error bars represent the SEM obtained from 3 independent digestions for each VHH. FIG. 22E shows a summary of the VHH resistance to each protease. Dots represent the mean (n=3) protease resistance profile of each VHH relative to undigested controls and the black bars represent the median resistance of each group. P-values were determined using the unpaired two-tailed Mann-Whitney U test. WT: wild-type VHH; Mut: mutant VHH; Chymo: chymotrypsin. The percent VHH resistance to each protease is given in Table 8. In A, 1:240 and 1:24 ratios correspond to pepsin concentrations of 1 μg/ml and 10 μg/ml, respectively, in reaction mixtures.
FIG. 23 shows the correlation between VHH resistance to pepsin and thermal stability at pH 2. FIG. 23A is a graph showing linear regression between VHH pepsin resistance and VHH Tm at pH 2.0. Boxes show the wild-type (WT) and mutant (Mut) VHHs, respectively. Linear regression analysis gave a correlation coefficient of r2=0.735 and a significantly non-zero slope of the line (p=0.0004). FIG. 23B is a graph showing linear regression between wild-type VHH pepsin resistance and wild-type VHH Tonset at pH 2.0. The Tonset is defined as the temperature at which 5% of the VHH is unfolded. Linear regression analysis gave a correlation coefficient of r2=0.975 and a significantly non-zero slope of the line (p=0.0002). FIG. 23C shows SPR analysis (bottom) on mutant VHHs digested with pepsin (100 μg/ml, 1 h, 37° C.). The pepsin-treated VHHs retained their ability to bind surface-immobilized TcdA. SDS-PAGE gel (top) shows untreated (lanes 1, 3, 5, 7) and pepsin-digested (lanes 2, 4, 6, 8) VHHs used for SPR. The contents of lanes 1 thru 8 are listed in the box. Normalized koffs for pepsin treated VHHs were similar to the koff of untreated controls (box and Table 2). M: molecular weight markers in kDa; WT: wild-type VHH; Mut: mutant VHH; P: pepsin; R: reducing SDS-PAGE conditions.
FIG. 24 is a bar graph showing that mutant VHHs retain TcdA-neutralizing capacity. Confluent monolayers of IMR-90 human lung fibroblasts were incubated with TcdA or TcdA+VHHs for 24 h, and the percentage of cells rounded was scored. VHHs (wild-type (WT) or mutant (Mut)) were added as pooled mixtures of A4.2, A5.1, A20.1, and A26.8 (250 nM each) or A4.2m, A5.1m, A20.1m, and A26.8m (250 nM each).



DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to Clostridium difficile-specific antibodies and uses thereof. More specifically, the present invention relates to Clostridium difficile toxin-specific antibodies and uses thereof.
The present invention provides isolated llama single-domain antibodies (VHHs) capable of binding and neutralizing C. difficile TcdA and TcdB. Without wishing to be bound by theory, VHHs targeting the toxin's receptor binding domain (RBD) may block the toxin-receptor interaction, thereby preventing toxin entry into the host cell; this represents a critical initial step in the TcdA/B mechanism of action (Jank and Aktories, 2008).
Thus, the present invention provides an isolated or purified antibody or fragment thereof, comprising

    
    
        a sequence of complementarity determining region (CDR) 1 selected from GRTFNTLS (SEQ ID NO:1); GRTFSMYR (SEQ ID NO:2); GRTLSSYI (SEQ ID NO:3); GRTFSMDP (SEQ ID NO:4); IRSFSNRN (SEQ ID NO:5); and ERTFSRYP (SEQ ID NO:6);
        a sequence of CDR2 selected from VSRSGGST (SEQ ID NO:7); ITRNGSST (SEQ ID NO:8); ISRRGGNS (SEQ ID NO:9); GSSTGRTT (SEQ ID NO:10); ISWGGGST (SEQ ID NO:11); and ISSTGTST (SEQ ID NO:12); and
        a sequence of CDR3 selected from AAAATKSNTTAYRLSFDY (SEQ ID NO:13); AATSGSSYLDAAHVYDY (SEQ ID NO:14); AADGSVAGWGRRSVSVSSYDY (SEQ ID NO:15); AAAPYGANWYRDEYAY (SEQ ID NO:16); AAEFGHNIATSSDEYDY (SEQ ID NO:17); and AVNSQRTRLQDPNEYDY (SEQ ID NO:18),

wherein the antibody or fragment thereof is specific for TcdA. The isolated or purified antibody or fragment thereof as just described may comprise

        a sequence of CDR 1 of GRTFNTLS (SEQ ID NO:1); CDR2 of VSRSGGST (SEQ ID NO:7); and CDR3 of AAAATKSNTTAYRLSFDY (SEQ ID NO:13);
        a sequence of CDR 1 of GRTFSMYR (SEQ ID NO:2); CDR2 of ITRNGSST (SEQ ID NO:8); and CDR3 of AATSGSSYLDAAHVYDY (SEQ ID NO:14);
        a sequence of CDR 1 of GRTLSSYI (SEQ ID NO:3); CDR2 of ISRRGGNS (SEQ ID NO:9); and CDR3 of AADGSVAGWGRRSVSVSSYDY (SEQ ID NO:15);
        a sequence of CDR 1 of GRTFSMDP (SEQ ID NO:4); CDR2 of GSSTGRTT (SEQ ID NO:10); and CDR3 of AAAPYGANWYRDEYAY (SEQ ID NO:16);
        a sequence of CDR 1 of IRSFSNRN (SEQ ID NO:5); CDR2 of ISWGGGST (SEQ ID NO:11); and CDR3 of AAEFGHNIATSSDEYDY (SEQ ID NO:17); or
        a sequence of CDR 1 of ERTFSRYP (SEQ ID NO:6); CDR2 of ISSTGTST (SEQ ID NO:12); and CDR3 of AVNSQRTRLQDPNEYDY (SEQ ID NO:18).
    
    


The present invention also provides an isolated or purified antibody or fragment thereof, comprising

    
    
        a sequence of complementarity determining region (CDR) 1 selected from GNIFSINT (SEQ ID NO:19); GRTASGYG (SEQ ID NO:20); GRTFSSGV (SEQ ID NO:21); GLSRYA (SEQ ID NO:22); and GSISRIST (SEQ ID NO:23);
        a sequence of CDR2 selected from ITSGGTT (SEQ ID NO:24); ISRSGAGT (SEQ ID NO:25); ITTGGST (SEQ ID NO:26); TNWSSGNT (SEQ ID NO:27); and ISTGGTT (SEQ ID NO:28); and
        a sequence of CDR3 selected from NTVKVVGGRLDNPDY (SEQ ID NO:29); VARPTKVDRDYATRREMYNY (SEQ ID NO:30); NSVAVVGGVIKSPDY (SEQ ID NO:31); AARKLDVPSRYSQHYDY (SEQ ID NO:32); and AAGWKVVRGSLEYEY (SEQ ID NO:33),

wherein the antibody or fragment thereof is specific for TcdB. The isolated or purified antibody or fragment thereof as just described may comprise

        a sequence of CDR 1 of GNIFSINT (SEQ ID NO:19); CDR2 of ITSGGTT (SEQ ID NO:24); and CDR3 of NTVKVVGGRLDNPDY (SEQ ID NO:29);
        a sequence of CDR 1 of GRTASGYG (SEQ ID NO:20); CDR2 of ISRSGAGT (SEQ ID NO:25); and CDR3 of VARPTKVDRDYATRREMYNY (SEQ ID NO:30);
        a sequence of CDR 1 of GRTFSSGV (SEQ ID NO:21); CDR2 of ITTGGST (SEQ ID NO:26); and CDR3 of NSVAVVGGVIKSPDY (SEQ ID NO:31);
        a sequence of CDR 1 of GLSRYA (SEQ ID NO:22); CDR2 of TNWSSGNT (SEQ ID NO:27); and CDR3 of AARKLDVPSRYSQHYDY (SEQ ID NO:32); or
        a sequence of CDR 1 of GSISRIST (SEQ ID NO:23); CDR2 of ISTGGTT (SEQ ID NO:28); and CDR3 of AAGWKVVRGSLEYEY (SEQ ID NO:33).
    
    


The term “antibody”, also referred to in the art as “immunoglobulin” (Ig), used herein refers to a protein constructed from paired heavy and light polypeptide chains; various Ig isotypes exist, including IgA, IgD, IgE, IgG, and IgM. When an antibody is correctly folded, each chain folds into a number of distinct globular domains joined by more linear polypeptide sequences. For example, the immunoglobulin light chain folds into a variable (VL) and a constant (CL) domain, while the heavy chain folds into a variable (VH) and three constant (CH, CH2, CH3) domains. Interaction of the heavy and light chain variable domains (VH and VL) results in the formation of an antigen binding region (Fv). Each domain has a well-established structure familiar to those of skill in the art.
The light and heavy chain variable regions are responsible for binding the target antigen and can therefore show significant sequence diversity between antibodies. The constant regions show less sequence diversity, and are responsible for binding a number of natural proteins to elicit important biochemical events. The variable region of an antibody contains the antigen binding determinants of the molecule, and thus determines the specificity of an antibody for its target antigen. The majority of sequence variability occurs in six hypervariable regions, three each per variable heavy (VH) and light (VL) chain; the hypervariable regions combine to form the antigen-binding site, and contribute to binding and recognition of an antigenic determinant. The specificity and affinity of an antibody for its antigen is determined by the structure of the hypervariable regions, as well as their size, shape and chemistry of the surface they present to the antigen. Various schemes exist for identification of the regions of hypervariability, the two most common being those of Kabat and of Chothia and Lesk. Kabat et al (1991) define the “complementarity-determining regions” (CDR) based on sequence variability at the antigen-binding regions of the VH and VL domains. Chothia and Lesk (1987) define the “hypervariable loops” (H or L) based on the location of the structural loop regions in the VH and VL domains. As these individual schemes define CDR and hypervariable loop regions that are adjacent or overlapping, those of skill in the antibody art often utilize the terms “CDR” and “hypervariable loop” interchangeably, and they may be so used herein. For this reason, the regions forming the antigen-binding site are presently referred to herein as CDR L1, CDR L2, CDR L3, CDR H1, CDR H2, CDR H3 in the case of antibodies comprising a VH and a VL domain; or as CDR1, CDR2, CDR3 in the case of the antigen-binding regions of either a heavy chain or a light chain. The CDR/loops are referred to herein according to the IMGT numbering system (Lefranc, M.-P. et al., 2003), which was developed to facilitate comparison of variable domains. In this system, conserved amino acids (such as Cys23, Trp41, Cys104, Phe/Trp118, and a hydrophobic residue at position 89) always have the same position. Additionally, a standardized delimitation of the framework regions (FR1: positions 1 to 26; FR2: 39 to 55; FR3: 66 to 104; and FR4: 118 to 128) and of the CDR (CDR1: 27 to 38, CDR2: 56 to 65; and CDR3: 105 to 117) is provided.
An “antibody fragment” as referred to herein may include any suitable antigen-binding antibody fragment known in the art. The antibody fragment may be a naturally-occurring antibody fragment, or may be obtained by manipulation of a naturally-occurring antibody or by using recombinant methods. For example, an antibody fragment may include, but is not limited to a Fv, single-chain Fv (scFv; a molecule consisting of VL and VH connected with a peptide linker), Fab, F(ab′)2, single domain antibody (sdAb; a fragment composed of a single VL or VH), and multivalent presentations of any of these.
In a non-limiting example, the antibody fragment may be an sdAb derived from naturally-occurring sources. Heavy chain antibodies of camelid origin (Hamers-Casterman et al, 1993) lack light chains and thus their antigen binding sites consist of one domain, termed VHH. sdAb have also been observed in shark and are termed VNAR (Nuttall et al, 2003). Other sdAb may be engineered based on human Ig heavy and light chain sequences (Jespers et al, 2004; To et al, 2005). As used herein, the term “sdAb” includes those sdAb directly isolated from VH, VHH, VL, or VNAR reservoir of any origin through phage display or other technologies, sdAb derived from the aforementioned sdAb, recombinantly produced sdAb, as well as those sdAb generated through further modification of such sdAb by humanization, affinity maturation, stabilization, solubilization, e.g., camelization, or other methods of antibody engineering. Also encompassed by the present invention are homologues, derivatives, or fragments that retain the antigen-binding function and specificity of the sdAb.
A person of skill in the art would be well-acquainted with the structure of a single-domain antibody (see, for example, 3DWT, 2P42 in Protein Data Bank). An sdAb comprises a single immunoglobulin domain that retains the immunoglobulin fold; most notably, only three CDR/hypervariable loops form the antigen-binding site. However, and as would be understood by those of skill in the art, not all CDR may be required for binding the antigen. For example, and without wishing to be limiting, one, two, or three of the CDR may contribute to binding and recognition of the antigen by the sdAb of the present invention. The CDR of the sdAb or variable domain are referred to herein as CDR1, CDR2, and CDR3, and numbered as defined by Lefranc, M.-P. et al. (2003).
As previously stated, the antibody or fragment thereof may be an sdAb. The sdAb may be of camelid origin or derived from a camelid VHH, and thus may be based on camelid framework regions; alternatively, the CDR described above may be grafted onto VNAR, VHH, VH or VL framework regions. In yet another alternative, the hypervariable loops described above may be grafted onto the framework regions of other types of antibody fragments (Fv, scFv, Fab). The present embodiment further encompasses an antibody fragment that is “humanized” using any suitable method know in the art, for example, but not limited to CDR grafting and veneering. Humanization of an antibody or antibody fragment comprises replacing an amino acid in the sequence with its human counterpart, as found in the human consensus sequence, without loss of antigen-binding ability or specificity; this approach reduces immunogenicity of the antibody or fragment thereof when introduced into human subjects. In the process of CDR grafting, one or more than one of the heavy chain CDR defined herein may be fused or grafted to a human variable region (VH, or VL), or to other human antibody fragment framework regions (Fv, scFv, Fab). In such a case, the conformation of said one or more than one hypervariable loop is preserved, and the affinity and specificity of the sdAb for its target (i.e., toxins A and B) is also preserved. CDR grafting is known in the art and is described in at least the following: U.S. Pat. Nos. 6,180,370, 5,693,761, 6,054,297, 5,859,205, and European Patent No. 626390. Veneering, also referred to in the art as “variable region resurfacing”, involves humanizing solvent-exposed positions of the antibody or fragment; thus, buried non-humanized residues, which may be important for CDR conformation, are preserved while the potential for immunological reaction against solvent-exposed regions is minimized. Veneering is known in the art and is described in at least the following: U.S. Pat. Nos. 5,869,619, 5,766,886, 5,821,123, and European Patent No. 519596. Persons of skill in the art would also be amply familiar with methods of preparing such humanized antibody fragments and humanizing amino acid positions.
In a specific, non-limiting example, the antibody or fragment thereof that is specific for TcdA may comprise a sequence selected from the group consisting of:








(SEQ ID NO: 34)



QVKLEESGGGLVQAGGSLRLSCAASGRTFNTLSMGWFRQAPGKEREFVAAVSRSGGSTYY



 


ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAATKSNTTAYRLSFDYWGQGTQVT


 


VSS,


referred to herein as A4.2;


 


(SEQ ID NO: 35)



QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVGVITRNGSSTYYA



 


DSVKGRFTISRDNAKNTVYLQMNSLKPEDTALYYCAATSGSSYLDAAHVYDYWGQGTQVTVS


 


S,


referred to herein as A5.1;


 


(SEQ ID NO: 36)



QVKLEESGGGLVQPGGSLRLSCAASGRTLSSYIVAWFRQAPGKEREFVAGISRRGGNSAYV



 


ESVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADGSVAGWGRRSVSVSSYDYWGQG


 


TQVTVSS,


referred to herein as A19.2;


 


(SEQ ID NO: 37)



QVQLVESGGGLAQAGGSLRLSCAASGRTFSMDPMAWFRQPPGKEREFVAAGSSTGRTTYY



 


ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAPYGANWYRDEYAYWGQGTQVTV


 


SS,


referred to herein as A20.1;


 


(SEQ ID NO: 38)



QVQLVESGGGLVQAGGSLRLSCAASIRSFSNRNMGWFRQPPGKEREFVAGISWGGGSTRY



 


ADSVKGRFTISRDNAKKTVYLQMNSLKPEDTAVYYCAAEFGHNIATSSDEYDYWGQGTQVTV


 


SS,


referred to herein as A24.1;


and


(SEQ ID NO: 39)



QVKLEESGGGLVQAGGSLRLSCAASERTFSRYPVAWFRQAPGAEREFVAVISSTGTSTYYAD



 


SVKGRFTISRDNAKVTVYLQMNNLKREDTAVYFCAVNSORTRLQDPNEYDYWGQGTQVTVS


 


S,


referred to herein as A 26.8,






or a sequence substantially identical thereto.

In a specific, non-limiting example, the antibody or fragment thereof that is specific for TcdB may comprise a sequence selected from the group consisting of:








(SEQ ID NO: 40)



QVQLVESGGGLVQPGGSLRLSCAASGNIFSINTMGWYRQAPGKQLELVAAITSGGTTSYTDS



 


VEGRFTISRDNAKNAVYLQMNSLKAEDTAVYYCNTVKVVGGRLDNPDYWGQGTQVTVSS,


referred to herein as B5.2;


 


(SEQ ID NO: 41)



QVKLEESGGGLVQPGGSLRLSCAASGRTASGYGMGWFRQAPGKEREFVAAISRSGAGTLN



 


ADFVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCVARPTKVDRDYATRREMYNYWGQGT


 


QVTVSS,


referred to herein as B7.3;


 


(SEQ ID NO: 42)



QVKLEESGGGLVQAGGSLRLSCSASGRTFSSGVMGWFRQAPGKQRELVAAITTGGSTSYTD



 


SVKGRFTISRDNAKNIVYLQMNSLKPEDTAVYYCNSVAVVGGVIKSPDYWGQGTQVTVSS,


referred to herein as B13.6;


 


(SEQ ID NO: 43)



QVQLVESGGGSVQAGGSLRLSCAASGLSRYAMAWFRQGTGKEREFVASTNWSSGNTPYAD



 


SVKGRFIISRDNAKNTVYLQMNSLKPGDTAIYYCAARKLDVPSRYSQHYDYWGQGTQVTVSS,


referred to herein as B15.3;


and


 


(SEQ ID NO: 44)



QVQLVESGGDLVQAGGSLRLSCAASGSISRISTMGWYRQAPGKQRELVATISTGGTTNYAES



 


VKGRFTVSRDNAKNTMYLQMNSLKPEDTAVYYCAAGWKVVRGSLEYEYSGQGTQVTVSS,


referred to herein as B15.5,






or a sequence substantially identical thereto

A substantially identical sequence may comprise one or more conservative amino acid mutations. It is known in the art that one or more conservative amino acid mutations to a reference sequence may yield a mutant peptide with no substantial change in physiological, chemical, physico-chemical or functional properties compared to the reference sequence; in such a case, the reference and mutant sequences would be considered “substantially identical” polypeptides. Conservative amino acid mutation may include addition, deletion, or substitution of an amino acid; a conservative amino acid substitution is defined herein as the substitution of an amino acid residue for another amino acid residue with similar chemical properties (e.g. size, charge, or polarity).
In a non-limiting example, a conservative mutation may be an amino acid substitution. Such a conservative amino acid substitution may substitute a basic, neutral, hydrophobic, or acidic amino acid for another of the same group. By the term “basic amino acid” it is meant hydrophilic amino acids having a side chain pK value of greater than 7, which are typically positively charged at physiological pH. Basic amino acids include histidine (His or H), arginine
(Arg or R), and lysine (Lys or K). By the term “neutral amino acid” (also “polar amino acid”), it is meant hydrophilic amino acids having a side chain that is uncharged at physiological pH, but which has at least one bond in which the pair of electrons shared in common by two atoms is held more closely by one of the atoms. Polar amino acids include serine (Ser or S), threonine (Thr or T), cysteine (Cys or C), tyrosine (Tyr or Y), asparagine (Asn or N), and glutamine (Gln or Q). The term “hydrophobic amino acid” (also “non-polar amino acid”) is meant to include amino acids exhibiting a hydrophobicity of greater than zero according to the normalized consensus hydrophobicity scale of Eisenberg (1984). Hydrophobic amino acids include proline (Pro or P), isoleucine (Ile or I), phenylalanine (Phe or F), valine (Val or V), leucine (Leu or L), tryptophan (Trp or W), methionine (Met or M), alanine (Ala or A), and glycine (Gly or G). “Acidic amino acid” refers to hydrophilic amino acids having a side chain pK value of less than 7, which are typically negatively charged at physiological pH. Acidic amino acids include glutamate (Glu or E), and aspartate (Asp or D).
Sequence identity is used to evaluate the similarity of two sequences; it is determined by calculating the percent of residues that are the same when the two sequences are aligned for maximum correspondence between residue positions. Any known method may be used to calculate sequence identity; for example, computer software is available to calculate sequence identity. Without wishing to be limiting, sequence identity can be calculated by software such as NCBI BLAST2 service maintained by the Swiss Institute of Bioinformatics (and as found at http://ca.expasy.org/tools/blast/), BLAST-P, Blast-N, or FASTA-N, or any other appropriate software that is known in the art.
The substantially identical sequences of the present invention may be at least 65% identical; in another example, the substantially identical sequences may be at least 65, 70, 85, 90, 95, 96, 97, 98, 99, or 100% identical, or any percentage therebetween, at the amino acid level to sequences described herein. Importantly, the substantially identical sequences retain the activity and specificity of the reference sequence. In a non-limiting embodiment, the difference in sequence identity may be due to conservative amino acid mutation(s). By way of example only, and without wishing to be limiting in any manner, the VHHs of the present invention have between about 66% and 82% sequence identity (see Tables 5 and 6). In another non-limiting example, the present invention may be directed to an antibody or fragment thereof comprising a sequence at least 98% identical to that of the VHHs described herein.
A substantially identical sequence as defined by the present invention also includes a mutation to introduce an additional non-canonical disulfide bond. For example, and without wishing to be limiting, the non-canonical disulfide bond may be introduced between framework region (FR) 2 and FR3. In a specific, non-limiting example, the mutation may be Ala/Gly54→Cys54 and/or Val/Ile78→Cys78 mutation (based on IMGT numbering). In a further specific example, the antibody or fragment thereof that is specific for TcdA may comprise a sequence selected from the group consisting of:








(SEQ ID NO: 45)



QVKLEESGGGLVQAGGSLRLSCAASGRTFNTLSMGWFRQAPGKEREFV AVSRSGGSTYY



 


ADSVKGRFT SRDNAKNTVYLQMNSLKPEDTAVYYCAAAATKSNTTAYRLSFDYWGQGTQV


 


TVSS,


referred to herein as A4.2m;


 


(SEQ ID NO: 46)



QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFV VITRNGSSTYYA



 


DSVKGRFT SRDNAKNTVYLQMNSLKPEDTALYYCAATSGSSYLDAAHVYDYWGQGTQVTV


 


SS,


referred to herein as A5.1m;


 


(SEQ ID NO: 47)



QVKLEESGGGLVQPGGSLRLSCAASGRTLSSYIVAWFRQAPGKEREFV GISRRGGNSAYV



 


ESVKGRFT SRDNAKNTVYLQMNSLKPEDTAVYYCAADGSVAGWGRRSVSVSSYDYWGQG


 


TQVTVSS,


referred to herein as A19.2m;


 


(SEQ ID NO: 48)



QVQLVESGGGLAQAGGSLRLSCAASGRTFSMDPMAWFRQPPGKEREFV AGSSTGRTTYY



 


ADSVKGRFT SRDNAKNTVYLQMNSLKPEDTAVYYCAAAPYGANWYRDEYAYWGQGTQVT


 


VSS,


referred to herein as A20.1m;


 


(SEQ ID NO: 49)



QVQLVESGGGLVQAGGSLRLSCAASIRSFSNRNMGWFRQPPGKEREFV GISWGGGSTRY



 


ADSVKGRFT SRDNAKKTVYLQMNSLKPEDTAVYYCAAEFGHNIATSSDEYDYWGQGTQVT


 


VSS,


referred to herein as A24.1m;


 


(SEQ ID NO: 50)



QVKLEESGGGLVQAGGSLRLSCAASERTFSRYPVAWFRQAPGAEREFV VISSTGTSTYYAD



 


SVKGRFT SRDNAKVTVYLQMNNLKREDTAVYFCAVNSQRTRLQDPNEYDYWGQGTQVTV


 


SS,


referred to herein as A26.8m;


 


(SEQ ID NO: 51)



QVQLVESGGGLVQPGGSLRLSCAASGNIFSINTMGWYRQAPGKQLELV AITSGGTTSYTDS



 


VEGRFT SRDNAKNAVYLQMNSLKAEDTAVYYCNTVKVVGGRLDNPDYWGQGTQVTVSS,


referred to herein as B5.2m;


 


(SEQ ID NO: 52)



QVKLEESGGGLVQPGGSLRLSCAASGRTASGYGMGWFRQAPGKEREFV AISRSGAGTLN



 


ADFVKGRFT SRDNAKNTVYLQMNSLKPEDTAVYYCVARPTKVDRDYATRREMYNYWGQG


 


TQVTVSS,


referred to herein as B7.3m;


 


(SEQ ID NO: 53)



QVKLEESGGGLVQAGGSLRLSCSASGRTFSSGVMGWFRQAPGKQRELV AITTGGSTSYTD



 


SVKGRFT SRDNAKNTVYLQMNSLKPEDTAVYYCNSVAWGGVIKSPDYWGQGTQVTVSS,


referred to herein as B13.6m;


 


(SEQ ID NO: 54)



QVQLVESGGGSVQAGGSLRLSCAASGLSRYAMAWFRQGTGKEREFV STNWSSGNTPYAD



 


SVKGRFI SRDNAKNTVYLQMNSLKPGDTAIYYCAARKLDVPSRYSQHYDYWGQGTQVTVS


 


S,


referred to herein as B15.3m;


and


 


(SEQ ID NO: 55)



QVQLVESGGDLVQAGGSLRLSCAASGSISRISTMGWYRQAPGKQREL ATISTGGTTNYAES



 


VKGRFT SRDNAKNTMYLQMNSLKPEDTAVYYCAAGWKVVRGSLEYEYSGQGTQVTVS,


referred to herein as B15.5m,






or a sequence substantially identical thereto, with the proviso that the substantially identical sequence retains the non-canonical disulfide bond.

The isolated or purified antibody or fragment thereof of the present invention may bind to a conformational or linear epitope. A conformational epitope is formed by amino acid residues that are discontinuous in sequence, but proximal in the three-dimensional structure of the antigen. In contrast, a linear epitope (also referred to in the art as a “sequential epitope”) is recognized by its linear amino acid sequence, or primary structure. The conformational and linear epitopes of the antibodies or fragments thereof of the present invention recognize conformational and linear epitopes located in the region of TcdA responsible for cell-receptor binding.
The antibody or fragment thereof of the present invention may also comprise additional sequences to aid in expression, detection or purification of a recombinant antibody or fragment thereof. Any such sequences or tags known to those of skill in the art may be used. For example, and without wishing to be limiting, the antibody or fragment thereof may comprise a targeting or signal sequence (for example, but not limited to ompA), a detection/purification tag (for example, but not limited to c-Myc or a His6 or His6), or a combination thereof. In another example, the additional sequence may be a biotin recognition site such as that described by Cronan et al in WO 95/04069 or Voges et al in WO/2004/076670. As is also known to those of skill in the art, linker sequences may be used in conjunction with the additional sequences or tags, or may serve as a detection/purification tag.
The antibody or fragment thereof of the present invention may also be in a multivalent display format, also referred to herein as multivalent presentation. Multimerization may be achieved by any suitable method of know in the art. For example, and without wishing to be limiting in any manner, multimerization may be achieved using self-assembly molecules as described in Zhang et al (2004a; 2004b) and WO2003/046560. The described method produces pentabodies by expressing a fusion protein comprising the antibody or fragment thereof of the present invention and the pentamerization domain of the B-subunit of an AB5 toxin family (Merritt & Hol, 1995); the pentamerization domain assembles into a pentamer, through which a multivalent display of the antibody or fragment thereof is formed. Each subunit of the pentamer may be the same or different, and may have the same or different specificity. Additionally, the pentamerization domain may be linked to the antibody or antibody fragment using a linker; such a linker should be of sufficient length and appropriate composition to provide flexible attachment of the two molecules, but should not hamper the antigen-binding properties of the antibody.
Other forms of multivalent display are also encompassed by the present invention. For example, and without wishing to be limiting, the antibody or fragment thereof may be presented as a dimer, a trimer, or any other suitable oligomer. This may be achieved by methods known in the art, for example direct linking connection (Nielson et al, 2000), c-jun/Fos interaction (de Kruif & Logtenberg, 1996), “Knob into holes” interaction (Ridgway et al, 1996). Another method known in the art for multimerization is to dimerize the antibody or fragment thereof using an Fc domain, e.g., human Fc domains. The Fc domains may be selected from various classes including, but not limited to, IgG, IgM, or various subclasses including, but not limited to IgG1, IgG2, etc. In this approach, the Fc gene in inserted into a vector along with the sdAb gene to generate a sdAb-Fc fusion protein (Bell et al, 2010; Iqbal et al, 2010); the fusion protein is recombinantly expressed then purified. For example, and without wishing to be limiting in any manner, multivalent display formats may encompass chimeric formats of anti-TcdA VHHs linked to an Fc domain, or bi- or tri-specific antibody fusions with two or three anti-TcdA VHHs recognizing unique epitopes. Enhanced toxin neutralizing efficacy may also be obtained using various techniques, including PEGylation, fusion to serum albumin, or fusion to serum albumin-specific antibody fragments; these approaches increase their blood circulation half lives, size and avidity.
The present invention also encompasses nucleic acid sequences encoding the molecules as described herein. The nucleic acid sequence may be codon-optimized for expression in various micro-organisms. The present invention also encompasses vectors comprising the nucleic acids as just described. Furthermore, the invention encompasses cells comprising the nucleic acid and/or vector as described.
The present invention further encompasses the isolated or purified antibody or fragments thereof immobilized onto a surface using various methodologies; for example, and without wishing to be limiting, the antibody or fragment may be linked or coupled to the surface via His-tag coupling, biotin binding, covalent binding, adsorption, and the like. Immobilization of the antibody or fragment thereof of the present invention may be useful in various applications for capturing, purifying or isolating proteins. The solid surface may be any suitable surface, for example, but not limited to the well surface of a microtiter plate, channels of surface plasmon resonance (SPR) sensorchips, membranes, beads (such as magnetic-based or sepharose-based beads or other chromatography resin), glass, plastic, stainless steel, a film, or any other useful surface such as nanoparticles, nanowires and cantilever surfaces.
Thus, the present invention also provides a method of capturing Clostridium difficile toxins, comprising contacting a sample (such as, but not limited to C. difficile culture supernatant, human/animal intestinal/colonic fluid, or any other suitable sample) with one or more than one isolated or purified antibody or fragment thereof of the present invention. The isolated or purified antibody or fragments thereof may be immobilized onto a surface. The toxin(s) then bind to the isolated or purified antibody or fragment thereof and are thus captured. The toxins may then optionally be identified by mass spectrometric methods and/or released or eluted from their interaction with the antibody or fragment thereof; methods for releasing or eluting bound molecules are well-known to those of skill in the art (for example but not limited to heat elution steps), as are spectrometric methods capable of detecting and identifying the toxin. The isolated or purified antibody or fragment thereof of the present invention provide particularly robust affinity purification reagents due to their resistance to acidic and heat elution steps.
The invention also encompasses the antibody or fragment thereof as described above linked to a cargo molecule. The cargo molecule may be any suitable molecule. For example, and without wishing to be limiting in any manner, the cargo molecule may be a detectable agent, a therapeutic agent, a drug, a peptide, an enzyme, a protease, a carbohydrate moiety, a cytotoxic agent, one or more liposomes loaded with any of the previously recited types of cargo molecules, or one or more nanoparticle, nanowire, nanotube, or quantum dots. For example, and without wishing to be limiting in any manner, the cargo molecule may be a protease that may digest the C. difficile toxin; in a further non-limiting example, the protease may be linked to a VHH such as a mutant VHH that is protease resistant. In yet another non-limiting example, the cargo molecule may be a cytotoxic agent that may be antibacterial or toxic towards host cells “infected” with C. difficile toxins. In a further non-limiting example, the cargo molecule is a liposome, which makes the construct well-suited as a delivery agent for mucosal vaccines. The cargo molecule may be linked to the antibody or fragment thereof by any suitable method known in the art. For example, and without wishing to be limiting, the cargo molecule may be linked to the peptide by a covalent bond or ionic interaction. The linkage may be achieved through a chemical cross-linking reaction, or through fusion using recombinant DNA methodology combined with any peptide expression system, such as bacteria, yeast or mammalian cell-based systems. Methods for linking an antibody or fragment thereof to a therapeutic agent or detectable agent would be well-known to a person of skill in the art.
The present invention also encompasses an antibody or fragment thereof linked to a detectable agent. For example, the TcdA- or TcdB-specific antibody or fragment thereof may be linked to a radioisotope, a paramagnetic label, a fluorophore, an affinity label (for example biotin, avidin, etc), fused to a detectable protein-based molecule, nucleotide, quantum dot, nanoparticle, nanowire, or nanotube or any other suitable agent that may be detected by imaging methods. In a specific, non-limiting example, the antibody or fragment thereof may be linked to a fluorescent agent such as FITC or may genetically be fused to the Enhanced Green Fluorescent Protein (EGFP). The antibody or fragment thereof may be linked to the detectable agent using any method known in the art (recombinant technology, chemical conjugation, etc.).
Thus, the present invention further provides a method of detecting Clostridium difficile toxins, comprising contacting a sample (such as, but not limited to C. difficile culture supernatant, human/animal intestinal/colonic fluid, or any other suitable sample) with one or more than one isolated or purified antibody or fragment thereof of the present invention. The isolated or purified antibody or fragments thereof may be linked to a detectable agent. The toxin(s) can then be detected using detection and/or imaging technologies known in the art, such as, but not limited to mass spectrometric or immunoassay methods.
For example, and without wishing to be limiting in any manner, the isolated or purified antibody or fragment thereof linked to a detectable agent may be used in immunoassays (IA) including, but not limited to enzyme IA (EIA), ELISA, “rapid antigen capture”, “rapid chromatographic IA”, and “rapid EIA”. (For example, see Planche et al, 2008; Sloan et al, 2008; Rüssmann et al, 2007; Musher et al, 2007; Turgeon et al, 2003; Fenner et al, 2008)
The present invention also encompasses the isolated or purified antibody or fragment thereof for detection of toxins in neutralized cell toxicity assays; methods for cell toxicity assays, also referred to herein as cytotoxicity assays, are known in the art and include, but are not limited to those described by Planche et al (2008); Musher et al (2007); Turgeon et al (2003); and Fenner et al (2008). Cell cytotoxicity assays involve incubating samples (for example, but not limited to patient stool samples) with cultured cells (for example, but not limited to fibroblasts) alone, or with the addition of a neutralizing agent, in this case, the isolated or purified antibody or fragment thereof as described herein. If the presence of the neutralizing agent reduces or eliminates cell toxicity observed with the cultured cells alone, presence of the toxins in the sample is confirmed. This type of assay is the practical gold standard for CDAD detection in hospital diagnostic laboratories.
The present invention also encompasses a composition comprising one or more than one isolated or purified antibody or fragment thereof as described herein. The composition may comprise a single antibody or fragment as described above, or may be a mixture of antibodies or fragments. Furthermore, in a composition comprising a mixture of antibodies or fragments of the present invention, the antibodies may have the same specificity, or may differ in their specificities; for example, and without wishing to be limiting in any manner, the antibodies or fragments may be specific to TcdA or TcdB, or a portion of the antibodies may be specific to TcdA while the other portion is specific to TcdB.
The composition may also comprise a pharmaceutically acceptable diluent, excipient, or carrier. The diluent, excipient, or carrier may be any suitable diluent, excipient, or carrier known in the art, and must be compatible with other ingredients in the composition, with the method of delivery of the composition, and is not deleterious to the recipient of the composition. The composition may be in any suitable form; for example, the composition may be provided in suspension form, powder form (for example, but limited to lyophilised or encapsulated), capsule or tablet form. For example, and without wishing to be limiting, when the composition is provided in suspension form, the carrier may comprise water, saline, a suitable buffer, or additives to improve solubility and/or stability; reconstitution to produce the suspension is effected in a buffer at a suitable pH to ensure the viability of the antibody or fragment thereof. Dry powders may also include additives to improve stability and/or carriers to increase bulk/volume; for example, and without wishing to be limiting, the dry powder composition may comprise sucrose or trehalose. In a specific, non-limiting example, the composition may be so formulated as to deliver the antibody or fragment thereof to the gastrointestinal tract of the subject. Thus, the composition may comprise encapsulation, time-release, or other suitable technologies for delivery of the antibody or fragment thereof. It would be within the competency of a person of skill in the art to prepare suitable compositions comprising the present compounds.
The present invention also comprises a method of treating a Clostridium difficile infection, comprising administering the isolated or purified antibody or fragment thereof of the present invention, or a composition comprising the antibody or fragment thereof, to a subject in need thereof. Any suitable method of delivery may be used. For example, and without wishing to be limiting in any manner, the antibody or fragment thereof, or the composition, may be delivered systemically (orally, nasally, intravenously, etc.) or may be delivered to the gastrointestinal tract. Those of skill in the art would be familiar with such methods of delivery.
The present invention will be further illustrated in the following examples. However, it is to be understood that these examples are for illustrative purposes only and should not be used to limit the scope of the present invention in any manner.
EXAMPLE 1
Purification of Toxins and Recombinant Fragments
C. difficile-associated diseases (CDAD) are caused by two high-molecular weight toxins composed of enzymatic, translocation, and cell-receptor binding domains (RBD; FIG. 1A). TcdA and TcdB toxins were purified from natural sources, and recombinant fragments thereof were prepared.
TcdA and TcdB were isolated from Clostridium difficile strain 10463 (ATCC, Manassas, Va.) as described previously (Keel and Songer, 2007) and were stored in 50 mM Tris-HCl buffer pH 7.5 at 4° C. The SDS-PAGE profile of the purified C. difficile toxins (3 μg per lane; from strain 10463) used is shown in FIG. 1B.
Recombinant fragments of TcdA (amino acid residues 2304-2710) and TcdB (amino acid residues 2286-2366), which are fragments of the RBD, were cloned (as a BamHI-HindIII fragment for tcdA and a BamHI-EcoRI fragment for tcdB) into pTrcHisB (Invitrogen, Carlsbad, Calif.), transforming E. coli DH5aMCR. Expression was induced by IPTG, cells harvested and lysed in a French pressure cell, and proteins TcdA-RBD-f1 and TcdB-RBD-f1 purified by immobilized metal-affinity chromatography (IMAC). Recombinant RBD fragments were dialyzed into phosphate-buffered saline (PBS) pH 7.3 and stored at 4° C.
EXAMPLE 2
Llama Immunization and Serum Response
To isolate VHHs which target the RBD of toxin A (TcdA) and toxin B (TcdB), a llama was immunized with recombinant RBD fragments TcdA-RBD-f1 and TcdB-RBD-f1 (FIG. 1A) obtained in Example 1.
One male llama (Lama glama) was immunized by sub-cutaneous, lower-back injection of TcdA-RBD-f1 and TcdB-RBD-f1 antigens. On Day 1, 200 μg of each antigen diluted in PBS to 1 ml was injected with 1 ml of Freund's Complete Adjuvant (Sigma, St. Louis, Mo.). Three more injections of 100 μg of each antigen+Freund's Incomplete Adjuvant (Sigma) were performed on Days 22, 36, and 50. A final injection of 100 μg of each antigen with no adjuvant was performed on Day 77. Pre-immune blood was drawn before the first injection on Day 1 and served as a negative control. Blood (10-15 ml) was collected on Days 29, 43, 57and 84. Pre-immune and post-immune total serum was analyzed for a specific response to TcdA-RBD-f1 and TcdB-RBD-f1 by ELISA on Day 57 (see below). Llama sera from Day 84 were fractionated as previously described (Doyle et al, 2008). The resulting fractions, A1 (HCAb), A2 (HCAb), G1 (HCAb) and G2 (clgG) were analyzed for specific binding to TcdA-RBD-f1 and TcdB-RBD-f1 by ELISA. Briefly, 5 μg of TcdA-RBD-f1 or TcdB-RBD-f1 diluted in PBS was coated overnight (100 μl/well, 18 h, 4° C.) in 96 well MAXISORP plates (Nalge Nunc International, Rochester, N.Y.). Plates were blocked with bovine serum albumin (BSA), washed with PBS-T (PBS+0.05% (v/v) Tween-20), and serial dilutions of pre-immune total serum, post-immune total serum (Day 57) and fractionated serum (Day 84) applied. After incubation at room temperature for 1.5 h and washing with PBS-T, goat anti-llama IgG (1:1,000 in PBS) was added for 1 h at 37° C. After washing with PBS-T, pig anti-goat IgG-HRP conjugate (1:3,000 in PBS) was added for 1 h at 37° C. A final PBS-T wash precluded the addition of 100 μl/well TMB substrate (KPL, Gaithersburg, Md.) for 10 min. The reaction was stopped with 100 μl/well 1 M H3PO4 and read on a BioRad plate reader (Hercules, CA) at 450 nm.
An ELISA conducted on total serum from Day 57 clearly showed a specific immune response for TcdA-RBD-f1 and TcdB-RBD-f1 compared to pre-immune sera collected before immunization on Day 0 (FIG. 1C). A second ELISA performed on fractionated sera from Day 84 indicated the heavy-chain IgG (HCAb) and conventional IgG (cIgG) serum fractions recognized TcdA-RBD-f1 and TcdB-RBD-f1. For example, the G1 HCAb fraction was shown to specifically recognize both recombinant fragments and did not bind to two unrelated proteins PEB3 or CPS (FIG. 1D).
EXAMPLE 3
Library Construction and Selection of Toxin-binding VHHs
A hyperimmunized llama VHH library was constructed based on RNA isolated from the serum collected in Example 2.
Library construction and panning was performed essentially as previously described (Arbabi-Ghahroudi et al, 2009c, 2009b; Tanha et al, 2003). Total RNA was isolated from approximately 5×106 lymphocytes collected on day 84 post-immunization using the QIAAMP RNA Blood Mini Kit (QIAGEN, Mississauga, ON, Canada). About 5 μg of total RNA was used as template for first strand cDNA synthesis with oligo dT primers using the First-Strand cDNA Synthesis Kit (GE Healthcare, Baie-d'Urfé, QC, Canada). The cDNA was amplified by an equimolar mix of three variable region-specific sense primers:







MJ1:


(SEQ ID NO: 56)


5′-GCCCAGCCGGCCATGGCCSMKGTGCAGCTGGTGGAKTCTGGGGG


 


A-3′


 


MJ2:


(SEQ ID NO: 57)


5′-CAGCCGGCCATGGCCCAGGTAAAGCTGGAGGAGTCTGGGGGA-3′


 


MJ3:


(SEQ ID NO: 58)


5′-GCCCAGCCGGCCATGGCCCAGGCTCAGGTACAGCTGGTGGAGTC


 


T-3′,






and two antisense CH2-specific primers:










CH2:



(SEQ ID NO: 59)



5′-CGCCATCAAGGTACCAGTTGA-3′



 



CH2b3:



(SEQ ID NO: 60)



5′-GGTACCTGTCATCCACGGACCAGCTGA-3′.






Briefly, the PCR reaction mixture was set up in a total volume of 50 μl with the following components: 1-3 μl cDNA, 5 pmol of MJ1-3 primer mixture, 5 pmol of CH2 or CH2b3 primers, 5 μl of 10× reaction buffer, 1 μl of 10 mM dNTP, 2.5 unit of Taq DNA polymerase (Hoffmann-La Roche, Mississauga, ON, Canada). The PCR protocol consisted of an (i) initial step at 94° C. for 3 min, (ii) followed by 30 cycles of 94° C. for 1 min, 55° C. for 30 s, 72° C. for 30 s and (iii) a final extension step at 72° C. for 7 min. The amplified PCR products were run in a 2% agarose gel and two major bands were observed: a band of about 850 bp, corresponding to conventional IgG, and a second band of around 600 bp, corresponding to heavy chain antibodies. The smaller bands were cut and purified using the QIAQUICK Gel Extraction Kit (QIAGEN) and reamplified in a second PCR in a total volume of 50 μl using 1 μl of DNA template, 5 pmol of each of MJ7 primer (5′-CATGTGTAGACTCGCG GCCCAGCCGGCCATGGCC-3′ SEQ ID NO:61) and MJ8 primer (5′-CATGTGTAGATTCCTGGCCGGCCTGGCCTGAGGAGACGGTGACCTGG-3′ SEQ ID NO:62), 5 μl of 10× reaction buffer, 1 μl of 10 mM dNTP, 2.5 unit of Taq DNA polymerase. The PCR protocol consisted of (i) an initial step at 94° C. for 3 min, (ii) followed by 30 cycles of 94° C. for 30 s, 57° C. for 30 s and 72° C. for 1 min and (iii) a final extension step at 72° C. for 7 min. The amplified PCR products, ranging between 340 bp and 420 bp and corresponding to VHH fragments of heavy chain antibodies, were purified using the QIAQUICK PCR Purification Kit (QIAGEN), digested with SfiI restriction enzyme (New England BioLabs, Pickering, ON, Canada) and re-purified using the same kit.
Eighty micrograms of pMED1 phagemid (Arbabi-Ghahroudi et al, 2009c) was digested with SfiI overnight at 50° C. To minimize self-ligation, 20 units of Xhol and Pstl restriction enzymes were added and the digestion reaction was incubated for an additional 2 h at 37° C. Sixty micrograms of digested phagemid DNA was ligated with 6 μg of digested VHH fragments for 3 h at room temperature using LigaFast Rapid DNA Ligation System (Promega, Madison, Wis.) and its protocol. The ligated materials were purified using the QIAQUICK PCR Purification Kit in a final volume of 100 μl and electroporated in 5 μl portions into commercial electrocompetent TG1 E. coli cells (Stratagene, La Jolla, Calif.) as described (Arbabi-Ghahroudi et al, 2009c). The size of the library was determined (Arbabi-Ghahroudi et al, 2009c) to be 5×107. Colony-PCR and sequencing involving 20 colonies showed all tested clones had unique VHHs (Arbabi-Ghahroudi et al, 2009c). The library was grown for 2 h at 37° C., 250 rpm in the presence of 2% (w/v) glucose. The bacterial cells were pelleted, resuspended in 2×YT/Amp/Glu (2×YT medium with 100 μg/ml ampicillin and 2% (w/v) glucose) with 35% (v/v) glycerol and stored at −80° C. in small aliquots.
Panning experiments were essentially performed as described (Arbabi et al, 1997). Five milliliters of the library (1.5×108 cells) was thawed on ice and grown in 2×YT/Amp/Glu for about 2 h at 37° C. (A600=0.4-0.5). Cells were subsequently infected with 20× excess M13KO7 helper phage (New England Biolabs) for 1 h at 37° C. The culture was then centrifuged at 4° C. and infected cell pellets were resuspended in 200 ml of 2×YT/Amp with 50 μg/ml kanamycin and incubated at 37° C. and 250 rpm. The phage particles in culture supernatant were incubated with 1⁄5 volume of 20% PEG 6000/2.5M NaCl on ice for 1 h and centrifuged at 10,000 rpm for 15 min. The phage pellets were resuspended in 1.5 ml of sterile PBS, titrated and used as input phage for panning. For panning, 96-well MAXISORP plates were coated with 20 μg of TcdA-RBD-f1 or TcdB-RBD-f1 overnight at 4° C. The wells were rinsed with PBS and blocked with PBS/1% (w/v) casein for 2 h at 37° C. Approximately 1012 phage was added to the blocked wells and incubated for 2 h at 37° C. After 10× washing with PBS/0.1% (v/v) TWEEN 20, the bound phage was eluted with 0.1 M triethylamine, neutralized and mixed with exponentially growing TG1 cells. Titration of eluted phage was performed and infected bacterial cells were superinfected with M13 K07 and grown overnight at 37° C. The purified phage from the overnight culture was used as the input for the next round of panning. The panning was continued for three more rounds following the same procedure except that the amount of coated RBD-fragments was reduced to 15 μg, 10 μg and 5 μg for the second, third and fourth rounds of panning, respectively.
Individual TG1 colonies obtained after round four of panning were subjected to phage ELISA screening, essentially as described elsewhere (Doyle et al, 2008), with the exception that 5 μg/ml of toxin (TcdA and TcdB) and recombinant fragments (TcdA-RBD-f1 and TcdB-RBD-f1) were coated onto microtiter plates. All positive clones were sent for DNA sequencing. Unique clones that gave high phage ELISA signals were selected for large-scale expression and purification. Seven unique TcdA-specific and 7 unique TcdB-specific binders, all determined to be VHHs based on the presence of characteristic amino acids at positions 42, 49, 50 and 52 (FIG. 2), were selected.
EXAMPLE 4
Expression and Purification of Selected VHHs
The unique TcdA-specific and TcdB-specific binders of Example 3 were sub-cloned into expression plasmids for protein expression and purification.
Phagemid vectors containing the DNA of selected VHH clones were purified using the QIAPREP MiniPrep Kit, Of the 14 VHHs, 11 clones were PCR amplified from the pMED1 phagemid vector with either BbsI1-VHH (5′-TATGAAGACACCAGGCCCAGGTAAAGCTGGAGGAGTCT-3′ SEQ ID NO:63) or BbsI2-VHH (5′-TATGA AGACACCAGGCCCAGGTGCAGCTGGTGGAGTCT-3′ SEQ ID NO:64) sense primers and BamHI-VHH (5′-TTGTTCGGATCCTGAGGAGACGGTGACCTG-3′ SEQ ID NO:65) antisense primer. These PCR fragments were digested with BbsI and BamHI restriction enzymes and ligated into the similarly digested pSJF2H expression vector (Arbabi-Ghahroudi et al, 2009b). Three of the 14 clones contained internal BbsI or BamHI sites and were cloned into the pMED2 expression vector via digestion with SfiI. The vector pMED2 is a modified version of pSJF2H which contains SfiI restriction enzyme sites in its multiple cloning site. Since VHH sequences in pMED1 are flanked with SfiI restriction sites, no PCR amplification was required for sub-cloning. Upon ligation, all plasmids were transformed into electro-competent TG1 E. coli and selected on LB agar plates+100 μg/ml ampicillin. Colonies were screened by colony PCR for inserts and the DNA sequenced.
VHHs were expressed using the 5-day M9 minimal media method (Arbabi-Ghahroudi et al, 2009c). After induction of protein expression, cell cultures were harvested at 6,000 rpm×30 min (4° C.), the supernatant decanted, and the periplasmic contents extracted from the cell pellet. Briefly, each pellet was resuspended in 30 ml of ice-cold TES buffer (0.2 M Tris-HCl buffer pH 8.0, 20% (w/v) sucrose, 0.5 mM EDTA) and incubated on ice for 30 min. Next, 40 ml of ice-cold 1/8 TES was added, incubated an additional 30 min on ice and the slurry centrifuged at 12,000 rpm for 30 min (4° C.). The resulting supernatant was dialysed overnight into IMAC buffer A (10 mM HEPES buffer pH 7.0, 500 mM NaCl) and purified as previously described (Hussack et al, 2009). Eluted fractions were analyzed by SDS-PAGE and Western blotting before being dialysed into PBS. VHH concentrations were determined by absorbance measurements at 280 nm using theoretical MW and extinction coefficients calculated with the ExPASy ProtParam Tool (http://expasy.org/tools/protparam.html) (Pace et al, 1995).
The expression of the anti-TcdA and anti-TcdB VHH was targeted to the periplasm of TG1 E. coli and purified (FIG. 1E) with yields ranging from 1.2-72.3 mg/l bacterial culture (Table 1, Example 7).
EXAMPLE 5
Pentabody Expression and Purification
Two TcdA-specific pentameric VHHs (pentabodies) were constructed as previously described (Zhang et al, 2004b), using the vector pVT2 which contains the verotoxin B (VTB) subunit pentamerization domain. Pentabodies were expressed in TG1 E. coli, as described in Example 4, the cells were lysed and processed as previously described (Hussack et al, 2009), and proteins purified with HITRAP IMAC columns using an imidazole gradient (0-500 mM) for elution. The pentabodies were constructed base on the highest affinity anti-TcdA VHHs, A5.1 and A20.1 (FIG. 3). The resulting pentabodies are referred to hereafter as A5.1p and A20.1p.
EXAMPLE 6
Enzyme-Linked Immunosorbant Assay (ELISA)
ELISA experiments were used to characterize the binding of VHH monomers and pentamers of Examples 4 and 5, as well as their ability to recognize natural and recombinant antigen.
ELISA was used to determine if the purified anti-toxin VHH monomers recognized native TcdA or TcdB and recombinant TcdA-RBD-f1 or TcdB-RBD-f1 fragments. Equivalent molar concentrations of proteins (BSA, TcdA, TcdB, TcdA-RBD-f1, and TcdB-RBD-f1) were coated overnight in 96 well microtiter plates at 4° C. The next day, wells were blocked with 3% (w/v) skim milk diluted in PBS-T. After washing with PBS-T, purified VHHs at concentrations as high as 10 μg/ml were added to wells with the various coated antigens for 1 h at 37° C. Wells were washed with PBS-T, rabbit anti-His6 IgG conjugated with HRP (1:2,500 in PBS) added for 1 h at room temperature and the wells were washed an additional 5× with PBS-T. Rabbit anti-His6 IgG-HRP did not recognize the N-terminal His6 epitope tags on recombinant RBD fragments (data not shown). Binding was detected with TMB substrate (KPL), the reactions were stopped with 1 M H3PO4 and absorbance read at 450 nm. All conditions were performed in triplicate and the reported values are representative of two independent experiments.
ELISA demonstrated that 6 of 7 anti-TcdA VHHs recognized native TcdA and TcdA-RBD-f1 and that none of the VHHs cross-reacted with TcdB or TcdB-RBD-f1 (FIG. 4A). Of the 7 anti-TcdB VHHs tested, 4 recognized TcdB and TcdB-RBD-f1 and one clone (B5.2) also recognized TcdA (FIG. 4B). ELISA experiments were also performed by coating 5 μg/ml of TcdA in microtiter wells and serially diluting VHHs from 10 μg/ml to 1 ng/ml (FIGS. 4C-D). The remaining detection steps were performed as described above. With this ELISA, which was performed at a higher VHH concentration, a fifth VHH, B15.3, was shown to bind to TcdB.
A second ELISA was used to compare the activities of monomeric and pentameric VHHs for TcdA. TcdA (5 μg/ml) was coated overnight in 96 well microtiter plates and blocked with 3% milk, before addition of equivalent molar concentrations of VHH monomers and pentamers. VHH binding to TcdA was detected with HRP-labelled rabbit-anti-His6 IgG and TMB substrate. Binding of the pentamers to immobilized TcdA by ELISA was similar to monomeric versions of the same VHHs (FIG. 3).
EXAMPLE 7
Size Exclusion Chromatography and Surface Plasmon Resonance Analysis
The affinity of the TcdA- and TcdB-specific VHHs of Example 4 to their respective antigens was determined by surface plasmon resonance (SPR).
Size exclusion chromatography was performed on all purified VHHs using a SUPERDEX 75 size exclusion column (GE Healthcare) as previously described (To et al, 2005) under the control of an AKTA FPLC. Briefly, VHHs were applied at concentrations ranging from 0.75-1 mg/ml (≅45-60 μM) with a flow rate of 0.5 ml/min in a mobile phase that consisted of HBS-EP running buffer (10 mM HEPES, pH 7.4, 150 mM NaCl, 3 mM EDTA, and 0.005% (v/v) P20 surfactant). As expected, all were non-aggregating monomers (FIG. 5).
Fractions from the size exclusion column were then used for affinity measurements. The binding kinetics for the interaction of anti-toxin VHHs and TcdA or TcdB were determined by surface plasmon resonance using a BIACORE 3000 biosensor system (GE Healthcare). A total of 10,377 resonance units (RUs) of TcdA and 5,980 RUs of mouse IgG 13D9 control (Liu et al, 2000) were immobilized on a CM5 sensor chip (GE Healthcare). Anti-TcdA VHH affinity measurements were carried out in HBS-EP running buffer (10 mM HEPES pH 7.4, 150 mM NaCl, 3 mM EDTA and 0.005% (v/v) P20 surfactant) at a flow rate of 40 μl/min. Surfaces were regenerated by washing with either running buffer or 10 mM glycine pH 2.0. Initial attempts to immobilize TcdB directly onto a CM5 sensor chip were unsuccessful due to the toxin's low pI (theoretical pI=4.42). TcdB was therefore biotinylated with the EZ-LINK Sulfo-NHS-LC-LC-Biotin kit from Pierce (Rockford, Ill.) and 825 RUs were immobilized onto a streptavidin-coated CM5 sensor chip. However, due to the size difference of TcdB-biotin (269 kDa) compared to streptavidin (53 kDa), not all streptavidin sites were occupied and roughly 1 TcdB-biotin was immobilized for every 7 streptavidin molecules. Furthermore, no binding was observed between the anti-TcdB VHHs and immobilized TcdB-biotin. Data on the VHH-TcdB-RBD-f1 interaction was collected by immobilizing TcdB-specific VHHs onto the CM5 sensor chip (RUs ranging from 215 to 1209) and injecting TcdB-RBD-f1 at 20 μl/min. The IgG 13D9 or human single-domain antibody HVHP420 (To et al, 2005) served as controls. In all cases, data were analyzed with BIAevaluation 4.1 software (GE Healthcare).
Surface plasmon resonance (SPR) analysis revealed 6 of 7 anti-TcdA VHHs specifically bound TcdA with equilibrium dissociation constants ranging from 290 nM for A19.2 to 2 nM for A20.1 (FIG. 6). Observed VHH affinities for TcdA were strong, with four of the clones having KD values ranging from 2 to 24 nM (Table 1). The anti-TcdA VHHs isolated here are among the highest affinity proteinaceous toxin-binding single-domain antibodies characterized to date (Stewart et al, 2007; Goldman et al, 2006; Liu et al, 2007a; Hmila et al, 2008; Goldman et al, 2008; Anderson et al, 2008).
Analyzing the TcdB-binding VHHs by SPR was more challenging. Initial attempts to immobilize TcdB onto the CM5 dextran biosensor chip may have been hindered by the low theoretical pI of TcdB. An attempt to biotinylate TcdB for immobilization on a streptavidin-coated biosensor chip was equally as unsuccessful. To circumvent this problem, anti-TcdB VHHs were immobilized directly onto the CM5 dextran chips and data collected using various concentrations of TcdB-RBD-f1. Analyzable data could only be collected for 3 of 7 anti-TcdB VHHs, with affinity constants ranging from 100 nM to 400 nM (FIG. 6; Table 1). Specific binding was detected for the other 4 anti-TcdB VHHs, however, the data was non-analyzable (FIG. 7).







TABLE 1







Properties of anti-C. difficile toxin A and B VHH single-domain antibodies. 















MW

Expression


KD



VHH
(kDa) 
pla
Yield (mg/l)
kon (M−1s−1)
koff (s−1)
(nM)
Neutralizing?

















A1.3
16.75
6.71
1.4
NB
NB
NB
Nob


A4.2
15.73
8.59
31.3
6.7 × 105
1.6 × 10−2
24
Yes


A5.1
15.80
6.71
55.5
1.6 × 106
5.0 × 10−3
3
Yes


A19.2
16.01
8.61
3.8
1.4 × 104
3.9 × 10−3
290
Yes


A20.1
16.61
6.64
72.3
8.2 × 106
1.6 × 10−3
2
Yes


A24.1
16.71
6.71
8.5
6.0 × 104
1.6 × 10−2
260
Yes


A26.8
16.02
6.65
64.9
1.4 × 106
1.6 × 10−2
12
Yes


B5.2
15.11
6.04 
6.7
2.0 × 103
2.0 × 10−4
100
Nob


B7.3
16.13
8.93
1.5
NB
NB
NB
NA


B13.2
15.79
7.98
4.0
NB
NB
NB
NA


B13.3
15.62
8.00
1.6
NB
NB
NB
NA


B13.6
15.01
8.00 
3.6
2.5 × 103
1.0 × 10−3
400
Nob


B15.3
15.58
8.59
1.2
NB
NB
NB
NA


B15.5
15.23
7.18 
4.6
2.8 × 103
1.0 × 10−3
357
Nob





aTheoretical pl calculated using the ExPASy ProtParam tool (expasy.ch/tools/protparam.html).


bNot neutralizing at concentration as high as 1 μM.


NB: no binding detected by Biacore.


NA: not attempted.






EXAMPLE 8
In Vitro Toxin Neutralization Assay
The human lung fibroblast (HLF) cell cytotoxicity assay is routinely used for analyzing the presence of C. difficile toxins in biological samples (Babcock et al, 2006). The assay was used here to determine if anti-toxin VHHs of Example 4 or 5 could neutralize the cytopathic effects of TcdA and TcdB.
HLF cells (ATCC#CCL-186) were purchased from ATCC (Manassas, Va.) and maintained in Eagle's minimal medium (Invitrogen, Carlsbad, Calif.) supplemented with 10% fetal bovine serum (Invitrogen) at 37° C. with 5% CO2. Cells were seeded in sterile 96 well microtiter plates (2×104 cells 200 μl−1 well−1) for 20 h, allowing for the formation of confluent monolayers.
Initially, a dose-response experiment was conducted to find the minimum concentration of TcdA and TcdB which induced 100% HLF cell rounding after 24 h post toxin addition. To do so, 10 μl of sterile filtered TcdA or TcdB were added to wells containing confluent monolayers, giving final toxin concentrations ranging from 500 ng/ml to 0.5 ng/ml. Each concentration was performed in triplicate and the assay performed twice. HLF cells were scored visually for rounding at various time points over 24 h. For all subsequent assays, 100 ng/ml of TcdA and 20 ng/ml of TcdB were used.
For experiments involving VHHs, 20 μl of purified and sterile filtered monomeric or pentameric VHHs were added to HLF cells with 10 μl TcdA/B or 10 μl PBS. For experiments involving combinations of 2 or 3 VHHs, the concentration of each VHH was reduced by 1/2 and 1/3, respectively, giving the same final concentrations as experiments involving a single VHH. Importantly, VHHs and toxin were not pre-incubated; rather, each was added directly to HLF monolayers at time=0 h; this was more representative of in vivo scenarios and did not bias the in vitro results by pre-incubating. HLF cells containing PBS, VHH, toxin, or VHH+toxin were scored visually for cell rounding using a confocal microscope at 8 h and 24 h post antibody/toxin addition. Assays were performed in triplicate and repeated twice. Each assay was performed on fresh preparations of HLF cells (passage 3-5) and VHHs were from separate purifications. The purified TcdA and TcdB stock remained the same for all assays.
Human lung fibroblast (HLF) cytotoxicity assays were used to determine whether VHHs could neutralize TcdA- or TcdB-induced HLF cell rounding. Dose-response experiments with TcdA (FIG. 8A) and TcdB (FIG. 8B) determined the minimum toxin concentrations capable of 100% cell rounding after 24 h to be 50 ng/ml and 5 ng/ml, respectively. For all subsequent experiments, 2× this minimum concentration was used (i.e., 100 ng/ml of TcdA and 10 ng/ml of TcdB). VHHs had no effect on HLF cells when incubated in the absence of toxin A (FIG. 8F). When VHHs and TcdA were added simultaneously to HLF cells, 6 of 7 anti-TcdA VHHs inhibited TcdA-induced cell rounding in a dose-dependent manner at 8 h (data not shown) and 24 h post TcdA addition (FIG. 8C-F). The neutralizing capacity of the 4 strongest monomeric VHHs (A4.2, A5.1, A20.1 and A26.8) was similar at all concentrations tested, reflective of their close range of KD's (2-24 nM). The weakest neutralizers, A19.2 and A24.1, also possessed the weakest affinity constants of 290 and 260 nM, respectively. The non-binding A1.3 VHH did not inhibit cell rounding.
The toxin neutralizing efficacy of various combinations of VHHs was tested. All possible pair-wise and triplet combinations were tested. When various combinations of A4.2, A5.1, A20.1 and A26.8 were tested, their TcdA neutralizing efficacy was greater than any of the VHHs alone. These observations suggested the VHHs recognized distinct epitopes on TcdA, which was subsequently confirmed for A20.1 by co-injection BIACORE surface plasmon resonance (SPR) epitope mapping experiments (FIG. 10). In contrast, the other potent neutralizers appeared to bind to overlapping epitopes on TcdA. These data explain the increased neutralizing capacity seen for pairs and triplet combinations containing A20.1, but do not explain why some pairs (i.e., A5.1/A26.8) or triplet combinations (i.e., A4.2/A5.1/A26.8) show greater efficacy than the individual VHHs. The SPR data indicated a 1:1 binding stoichiometry, which is difficult to reconcile with the observation of enhanced neutralizing efficacy with mixed VHHs binding to overlapping epitopes. The binding stoichiometry determination assumes a mainly active toxin surface, which may not be the case since the toxin preparations showed breakdown products (FIG. 1B and FIG. 9B/C).
Pentabodies A5.1p and A20.1p, were also tested for toxin neutralizing efficacy. Surprisingly, the pentabodies showed similar neutralizing efficacy to their monomeric counterparts at the same concentration (data not shown). While it is possible that size effects increased the hindrance of TcdA binding to cell receptors, this effect on neutralizing potency may have been offset with a reduction in effective VHH concentration. For example, if only 1 of 5 VHH molecules could bind TcdA, the number of total VHHs available for TcdA binding would be reduced by 5-fold.
The neutralizing capacity of the anti-TcdB VHHs was also tested. None of the 3 TcdB-specific VHHs were capable of TcdB neutralization, even at a concentration of 1 μM (data not shown). It is not clear whether the VHH affinity was insufficient for neutralization, or if the epitopes these VHHs were raised against was not capable of preventing TcdB binding to fibroblast cell receptors. SPR Data was only collected for the TcdB-RBD-f1-VHH interaction; it is possible that the VHH affinities for TcdB may be considerably lower and this could account for poor neutralization.
The structure of TcdA-RBD contains 7 putative carbohydrate binding sites (Greco et al, 2006; Ho et al, 2005), which are thought to interact with epithelial cell surface receptors to mediated endocytosis (Florin and Thelestam, 1983). Due to geometric constraints, all 7 sites cannot access the cell-surface receptors simultaneously, although multiple (<7) low affinity interactions are predicted (Greco et al, 2006). As such, avidity appears to be crucial to the strength of toxin binding to its cellular receptors. It was hypothesized that pooling of neutralizing VHHs which recognized distinct epitopes on TcdA-RBD may enhance neutralizing potency through greater hindrance of toxin-cell receptor contacts. When various combinations of A4.2, A5.1, A20.1 and A26.8 were tested, their TcdA neutralizing efficacy was greater than any of the VHHs alone. These observations suggested the VHHs recognized distinct epitopes on TcdA, which was subsequently confirmed for one VHH (A20.1) by co-injection Biacore epitope mapping experiments (Example 9).
EXAMPLE 9
Epitope Mapping
To gain insight into whether the TcdA-specific VHHs recognized a linear or conformational epitope on TcdA, and whether the VHHs could bind unique, non-overlapping epitopes, a combination of Western blotting, ELISA, and SPR was used.
Western blots using both denaturing SDS-PAGE and native PAGE, and containing TcdA were probed with anti-TcdA VHHs or control anti-TcdA IgG (PCG4; Novus Biologicals, Littleton, Colo.) to determine if the VHHs recognized linear or conformational epitopes. For denaturing SDS-PAGE Western blots, TcdA (0.75 μg/lane), A4.2 VHH (1 μg/lane) and PCG4 IgG (1 μg/lane) were separated on 12.5% SDS-PAGE gels under reducing conditions and transferred to PVDF membranes at 100 V for 1 h. Membranes were blocked for 1 h with 5% (w/v) BSA diluted in PBS-T followed by probing with various VHHs (25 μg/10 ml blocking buffer) or PCG4 (10 μg/10 ml blocking buffer) for 1 h. Membranes were washed 4× in PBS-T followed by addition of either: (i) mouse anti-His6 IgG-alkaline phosphatase (AP) conjugate (Abcam, Cambridge, Mass.) diluted 1:5,000 in blocking buffer, (ii) HisDetector Nickel-AP conjugate (Mandel Scientific, Guelph, ON, Canada) diluted 1:5,000 in blocking buffer, or (iii) goat anti-mouse IgG-AP conjugate (Cederlane, Burlington, ON, Canada) diluted 1:10,000 in blocking buffer for 1 h. After a final set of 4 washes, membranes were subjected to AP substrate (BioRad, Hercules, Calif.) for 7 min, washing in dH2O and air drying. For native PAGE Western blots, TcdA, VHH and PCG4 (concentrations as above) were separated on 8% PAGE gels (without SDS) at 100 V for 2 h on ice. Next, gels were transferred to PVDF membranes at 20 V for 14 h at 4° C. Membranes were blocked, probed, washed and detected using the same protocol as for SDS-PAGE Western blots.
Only A19.2 VHH recognized TcdA run under denaturing/reducing conditions (FIG. 9B). The anti-TcdA mAb PCG4 (Lyerly et al, 1986), which was previously shown to recognize TcdA in Western blots (Ochsner et al, 2009), confirmed that TcdA was transferred to the blot. The weak signal obtained from A19.2 relative to PCG4 was likely due to the low affinity and/or lack of avidity of A19.2 for TcdA. In the absence of primary antibody, the secondary conjugates Nickel-AP and goat anti-mouse IgG-AP did not bind TcdA as expected. The VHH A4.2 and PCG4 were included to confirm the functionality of the secondary conjugates. Under non-denaturing conditions (native PAGE), VHH binding to TcdA was originally probed with anti-His6 IgG-AP and this secondary antibody was found to cross-react with TcdA in the absence of VHH (data not shown). To overcome this, the secondary antibody was replaced with Nickel-AP. Using this secondary conjugate, the VHHs A4.2, A5.1, A20.1 and A26.8 recognized native TcdA while the non-binding A1.3 essentially did not react with TcdA (FIG. 9C). The Nickel-AP secondary conjugate did not bind native TcdA in control blots. The diffuse signal and poor migration pattern of A4.2 VHH control is likely due to its high pI (theoretical pI: 8.59). To confirm the presence of TcdA on native PAGE blots, PCG4 was used as a control. Just like anti-His6 IgG-AP, the secondary antibody goat anti-mouse IgG-AP also bound TcdA in the absence of the primary probe, PCG4 in this case (FIG. 9C).
To further investigate whether the VHHs recognized linear or conformational epitopes, ELISA was performed with TcdA exposed to various temperature above and below its thermal unfolding midpoint temperature (Tm  ̃55° C.; Salnikova et al, 2008). Briefly, TcdA (5 μg/ml) was exposed to the following condition for 30 min: 4° C., 20° C., 37° C., 50° C., 60° C. or 70° C. After temperature treatment, 100 μl of TcdA was coated in 96 well microtiter plates overnight at 4° C. and the assay performed essentially as described in Example 6, except that 0.05-1 μg/ml of VHH was used. All conditions were performed in duplicate and the reported values are representative of two independent experiments.
For 4 of the 5 VHHs, A4.2, A5.1, A20.1 and A26.8, binding to TcdA was completely abolished when TcdA was heated above its Tm (FIG. 9A), confirming the above results that the VHHs recognize a conformational epitope on TcdA. A19.2 was found to bind TcdA with the same strength at all temperature, indicating that this VHH recognizes a linear epitope. The epitopes must be located in the region of TcdA responsible for cell-receptor binding, since llama immunization and library panning were both performed with TcdA-RBD-f1 and because the VHHs were shown to recognize this recombinant fragment by ELISA (FIG. 4A).
BIACORE surface plasmon resonance (SPR) co-injection experiments were also used to determine if the VHHs could bind unique, non-overlapping epitopes on TcdA. Briefly, 80 μl of the first VHH diluted in HBS-EP buffer to a concentration of 20× its KD was injected over 10,287 RUs of immobilized TcdA at 40 μl/min. Following injection of the first VHH, buffer or a second VHH (80 μl total volume, at 20×KD) was injected at 40 μl/min over the TcdA surface already saturated with the first VHH. Data were collected on all possible paired combinations of A4.2, A5.1, A20.1 and A26.8, in both orientations (i.e., each VHH acted as the first and second VHH). Data were collected and evaluated as described in Example 7.
The observation that combining anti-TcdA VHHs increased TcdA neutralizing efficacy relative to single VHHs at the same concentration (FIG. 8C-E; Example 8) suggested the antibodies recognized distinct, non-overlapping epitopes. Co-injection BIACORE SPR experiments were performed with pairs of VHHs, in both orientations, to determine if antibodies could bind TcdA simultaneously (FIG. 10). Of the paired combinations, only those involving A20.1 VHH showed a significant increase in response consistent with theoretical Rmax values ( ̃160-180 RUs) upon co-injection. This suggests that A20.1 is free to bind TcdA when A4.2, A5.1 or A26.8 are bound at saturating concentrations and also indicates the A20.1 epitope is distinct and does not hinder binding of the other three VHHs. For A4.2, A5.1 and A26.8, however, only minor changes in response were seen upon co-injection with theoretical Rmax values not reached, an indication that the VHHs were binding overlapping epitopes and hindering their binding to TcdA (FIG. 10). This was confirmed by co-injection of all three of these VHHs simultaneously (FIG. 11).
Taken together, the BIACORE SPR-based epitope mapping studies suggest A20.1 freely binds TcdA at a site that does not overlap with, or is not sterically hindered by, A4.2, A5.1 or A26.8 binding. These latter three VHHs bind at sites on TcdA that hinder freely accessible binding of the others, suggesting these antibodies share a single epitope, or bind epitopes in such close proximity to one another that it prevents unhindered interaction with TcdA. It is likely that “overlapping” VHHs recognize repeating epitopes. With mixed VHH, the spatial geometry of binding along the toxin RBD length at multiple epitope sites is such that it makes them more effective toxin neutralizers than when a single VHH is bound. Thus, despite binding an overlapping epitope, the mixture of VHH geometries would enhance steric effects (and neutralizing capacity) compared to single VHH species which presents a single geometry.
Using BIACORE SPR, inhibition of the VHH-TcdA interaction with two trisaccharides known to bind TcdA-RBD was also attempted, in order to gain insight into the TcdA epitope recognized by the VHHs. CD-grease (α-Gal-(1,3)-β-Gal-(1,4)-β-GlcNAcO(CH2)8CO2CH3; Greco et al, 2006) and Lex-AmHex (Gal-β1,4-(Fuc-α1,3)-GlcNAc-(CH2)6—NH2—HOAc; P. Zhang and C. C. Ling, unpublished) are known to interact with the carbohydrate binding pockets of TcdA-RBD (Greco et al, 2006). Briefly, 4 VHHs (i.e., A4.2, A5.1, A20.1 and A26.8) at KD concentrations were injected alone or in the presence of trisaccharide (2 mM) over immobilized TcdA ( ̃8000 RUs). The response obtained from the interaction of trisaccharide with TcdA was subtracted from response generated by VHH+trisaccharide co-injection experiments. Then, the response of each VHH to TcdA in the presence of trisaccharide was compared to the response generated by the VHH-TcdA interaction. FIG. 12 shows a representative example in which CD-grease and Lex-AmHex trisaccharides are free to bind TcdA in the presence of A26.8 VHH. We also show in FIG. 13 two examples of CD-grease binding freely to TcdA in the presence of saturating amounts of bound VHHs A20.1 (FIG. 13A) and A26.8 (FIG. 13B). Collectively, these studies indicate the VHHs are not binding to TcdA in such a way as to prevent trisaccharide binding. Therefore, the anti-TcdA VHH tested do not bind in the carbohydrate binding pocket, or sufficiently close to it, as they do not inhibit the free trisaccharide from accessing the toxin.
VHHs have long, flexible CDR3 loop regions that have been shown to form a convex paratope that can extend into clefts or active sites of protein antigens (De Genst et al, 2006). The recently solved crystal structure of TcdA-RBD was shown to contain seven carbohydrate binding pockets thought to be involved in cell receptor binding (Greco et al, 2006). The methods just described were to investigate whether TcdA neutralization was due to VHH binding in the TcdA-RBD carbohydrate-binding pocket. The binding of the neutralizing VHHs to TcdA was not inhibited in the in co-injection experiments (FIG. 12). Both CD-grease and LeX-AmHex trisaccharides were used at their predicted KD concentrations and were shown to bind immobilized TcdA by BIACORE SPR, but did not prevent VHH binding to TcdA when the trisaccharide response for TcdA was subtracted from response generated by co-injection experiments (FIG. 12). In additional BIACORE SPR experiments, both of the trisaccharides were found to be free to bind VHH-saturated TcdA (data not shown). Furthermore, VHH binding to TcdA was not inhibited in ELISA with trisaccharide concentrations as high as 10 mM (data not shown). Taken together, these data suggest the present VHHs do not inhibit free trisaccharides from accessing their binding sites on TcdA-RBD and that the VHHs are not binding at sites occupied by the trisaccharides.
EXAMPLE 10
Engineering, Expression, and Purification of Mutant VHHs
The extreme pH and protease-rich environment of the upper gastrointestinal tract is a major obstacle facing orally-administered protein therapeutics, including antibodies. For these reasons, the VHHs of Example 4 were engineered to improve biophysical properties. The methods used herein are also summarized in Hussack et al (2011).
A panel of C. difficile toxin A (TcdA)-specific VHHs were expressed with an additional disulfide bond by introducing Ala/Gly54-Cys54 and Ile78→Cys78 mutations. It was hypothesized that the addition of a disulfide bond in the hydrophobic core of a VHH antibody fragments between framework 2 (FR2) and FR3 would not only increase thermal stability at neutral pH, as previously reported (Hagihara et al, 2007; Saerens et al, 2008), but would also impart resistance to proteolytic degradation and increase antibody stability at low pH. The sequences of the mutant VHHs are shown in FIG. 14.
To construct mutant VHHs with a second internal disulfide bond, splice-overlap extension (SOE) PCR was performed essentially as described (Ho et al, 1989; Arbabi et al, 2010) using 4 primers for each VHH and two rounds of PCR. Nucleotides encoding amino acid residues at positions 54 and 78 (IMGT numbering system) were changed to Cys-coding nucleotides through primer-forced mutation. In the first PCR, two mutagenized overlapping sub-fragments were generated for each VHH. The primer pairs used for each VHH were as follows: A4.2m (BbsI-VHH and A4.2mR-Cys, A4.2mF-Cys and BamHI-VHH); A5.1m (BbsI-VHH and A5.1mRCys, A4.2mR-Cys and BamHI-VHH); A19.2m (BbsI-VHH and A19.2mR-Cys, A19.2mF-Cys and BamHI-VHH); A20.1m (A20.1 mSfiI-F and A20.1mR-Cys, A20.1mF-Cys and A20.1 mSfiI-R); A24.1m (A20.1 mSfiI-F and A24.1mR-Cys, A24.1mF-Cys and A20.1 mSfiI-R); A26.8m (BbsI-VHH and A26.8mR-Cys, A26.8mF-Cys and BamHI-VHH). Each sub-fragment was gel purified and spliced with its partner fragment in a second PCR. Briefly, 160 ng of each sub-fragment were added to a 50 μl PCR mixture containing Pfu DNA polymerase, dNTPs and reaction buffer. The reaction was placed in a thermal cycler and the two fragments were spliced together using a program consisting of a preheating step at 94° C. for 5 min and 10 cycles of 94° C. for 30 s, 55° C. for 30 s, and 72° C. for 1 min. To amplify the spliced products, the reaction was heated to 94° C. for 3 min, 5 pmol (0.5 μl) of each primer pair was added (BbsI-VHH and BamHI-VHH for A4.2m, A5.1m, A19.2m, and A26.8m; A20.1 mSfiI-F and A20.1 mSfiI-R for A20.1m and A24.1m), and 35 PCR cycles were performed exactly as described above. The resulting fragments were gel purified, digested with BbsI and BamHI (A4.2m, A5.1m, A19.2m, and A26.8) or SfiI (A20.1m and A24.1m) restriction enzymes and ligated into similarly digested expression vectors (pSJF2H or pMED2). All mutant VHHs were expressed in the same vectors as their counterpart wild-type VHHs (see Example 4). For cloning into pSJF2H, mutant VHH DNA were amplified with primers containing 5′ BbsI and 3′ BamHI restriction sites while cloning into pMED2 required amplification with primers containing both 5′ and 3′ SfiI restriction sites. The vectors were transformed into TG1 E. coli for VHH expression. Positive colonies were identified by colony-PCR and DNA sequencing, using the M13RP and M13FP primers.







TABLE 2 







Primers used for construction of disulfide mutant VHHs. aReverse and


forward primers for construction of A4.2m, A5.1m, A19.2m, and A26.8m.









Primers
Sequence (5′ → 3′)
Purpose





M13FP
GTA AAA CGA CGG CCA GT (SEQ ID NO: 66)
Screening


 


M13RP
CAG GAA ACA GCT ATG AC (SEQ ID NO: 67)
Screening


 


BbsI-VHHa
TAT GAA GAC ACC AGG CCC AGG TAA AGC TGG AGG AGT CT
Constructing



(SEQ ID NO: 63)
mutants


 


BamHI-VHHa
TTG TTC GGA TCC TGA GGA GAC GGT GAC CTG
Constructing



 (SEQ ID NO: 65)
mutants


 


A4.2mR-Cys
AGT CTG CAT AGT ATG TGC TAC CAC CAC TCC GGC TAA CAG
Constructing



CGC AAA CAA ACT C (SEQ ID NO: 68)
A4.2m


 


A4.2mF-Cys
TAG CAC ATA CTA TGC AGA CTC CGT GAA GGG CCG ATT CAC
Constructing



CTG CTC CAG AGA C (SEQ ID NO: 69)
4.2m/A5.1m


 


A5.1mR-Cys
AGT CTG CAT AGT ATG TGC TAC TAC CAT TCC GGG TAA TAA
Constructing



CGC ATA CAA ACT C (SEQ ID NO: 70)
A5.1 m


 


A19.2mR-Cys
ACT CTA CAT AGG CAC TAT TAC CAC CAC GCC GGC TAA TAC
Constructing



CGC ATA CAA ACT C (SEQ ID NO: 71)
A19.2m


 


A19.2mF-Cys
TAA TAG TGC CTA TGT AGA GTC CGT GAA GGG CCG ATT CAC
Constructing



CTG CTC CAG AGA C (SEQ ID NO: 72)
A19.2m


 


A20.1mSfiI-F
ACC GTT GCG CAG GCC CAG CCG GCC ATG GCC CAG GTA CAG C
Constructing



 (SEQ ID NO: 73)
A20.1m/A24.1m


 


A20.1mR-Cys
TGT CTG CAT AGT ATG TGG TCC GCC CCG TAG AAC TCC CCG
Constructing



CGC ATA CAA ACT C (SEQ ID NO: 74)
A20.1m


 


A20.1mF-Cys
GAC CAC ATA CTA TGC AGA CAG CGT GAA GGG CCG ATT CAC
Constructing



CTG CTC CAG AGA C (SEQ ID NO: 75)
A20.1m


 


A20.1mSfiI-R
GTT CGG ATC CCT GGC CGG CCT GGC CTG AGG AGA CGG TGA CC
Constructing



 (SEQ ID NO: 76)
A20.1m/A24.1m


 


A24.1mR-Cys
AGT CTG CAT AGC GTG TGC TAC CTC CAC CCC AGC TAA TAC
Constructing



CGC ATA CAA ACT C (SEQ ID NO: 77)
A24.1m


 


424.1mF-Cys
TAG CAC ACG CTA TGC AGA CTC CGT GAA GGG CCG ATT CAC
Constructing



CTG CTC CAG AGA C (SEQ ID NO: 78)
A24.1m


 


A26.8mR-Cys
AGT CTG CAT AGT ATG TGC TCG TAC CAG TCG AGC TAA TAA
Constructing



CGC ATA CAA ACT C (SEQ ID NO: 79)
A26.8m


 


A26.8mF-Cys
GAG CAC ATA CTA TGC AGA CTC GGT GAA GGG CCG GTT CAC
Constructing



CTG CTC CAG AGA C  (SEQ ID NO: 80)
A26.8m









Expression and purification of mutant VHHs was performed as described in Example 4, followed by dialysis into phosphate-buffered saline pH 7.3 (PBS), into distilled, deionized water (ddH2O) for mass spectrometry (MS) analysis, or into 10 mM phosphate buffer pH 7.3 for CD experiments. Soluble mutant VHHs were extracted from the periplasm of TG1 E. coli and purified by immobilized-metal affinity chromatography (IMAC) with purified yields ranging from 3-12 mg/l of bacterial culture. Non-reducing SDS-PAGE and Western blot analysis of the purified products revealed the mutant VHHs were of high purity and did not form interdomain disulfide bonds (FIG. 15A). On non-reducing SDS-PAGE gels, mutant VHHs consistently ran slower than their corresponding wild-type VHHs (FIG. 15B).
Formation of the non-canonical disulfide linkages was confirmed by mass spectrometry analysis on cyanogen bromide+trypsin digested mutant VHHs by identifying peptides containing the introduced disulfide bond. Briefly, 100 μl reactions containing 50 μg of mutant VHH (diluted in PBS), 10 μl of 1 M HCl and 40 μL of CNBr (10 mg/ml stock prepared in 1 M HCl) were digested for 14 h at ambient temperature in the dark. The next day, 100 μl of 1 M Tris-HCl, pH 8.6, and 60 μl of trypsin (100 μg/ml stock; sequencing grade, Roche, Mississauga, ON, Canada) were added directly to the CNBr reaction mixture and incubated for 2 h at 37° C. Samples were then analyzed by non-reducing SDS-PAGE to ensure digestion prior to MS analysis. An aliquot of the proteolytic digest of each VHH was re-suspended in 0.1% formic acid (aq) and analyzed by nano-flow reversed-phase HPLC mass spectrometry (nanoRPLC-ESI-MS) using a nanoAcquity UPLC system coupled to a Q-TOF ULTIMA hybrid quadrupole/TOF mass spectrometer (Waters, Milford, Mass.) with data dependent analysis (DDA). The peptides were first loaded onto a 180 μm I.D.×20 mm 5 μm SYMMETRY C18 trap (Waters), then eluted to a 100 μm I.D.×10 cm 1.7μm BEH130C18 column (Waters) using a linear gradient from 0% to 36% solvent B (ACN+0.1% formic acid) in 36 min, 36%-90% solvent B for 2 min. Solvent A was 0.1% formic acid in water. The peptide MS2 spectra were searched against the VHH protein sequences using the MASCOT database searching algorithm (Matrix Science, London, UK). The MS2 spectra of the disulphide-linked peptides were deconvoluted using the MaxEnt 3 program (Waters) for de-novo sequencing.
To precisely confirm the presence of the introduced disulfide bond, mutant VHHs were digested with CNBr and trypsin (FIG. 16A) and their digests subjected to MS2 analysis. The identification coverage of the mutant VHHs from the analysis of their CNBr/trypsin digests using nanoRPLC-ESI-MS with DDA was more than 30%. The disulfide-linked peptide ions appeared prominent in the survey scan of the DDA experiment when the proteins were digested with a combination of CNBr and trypsin. Peptide fragments linked by the engineered Cys54-Cys78 disulfide bond (shown in bold text in FIG. 14) were positively identified for all mutant VHHs by manual de-novo sequencing (Table 3). For example, the protein sequence coverage of A5.1m was 43% and a prominent ion at m/z 526.25 (3+) was sequenced as a disulfide-linked peptide EFVCVITR (P1) and FTCSR (P2) as shown (FIG. 16B, FIG. 14, Table 3). An almost complete disulfide-linked y fragment ion series was observed from one peptide with the other peptide attached as a modification via a disulfide bond, which remains intact under collision induced dissociation (CID) [59].







TABLE 3







Disulfide linkage determination of mutant VHHs by MS2 analysis. Mutant


VHHs were digested with CNBr and trypsin and the peptides analyzed by MS2.


The peptides containing the Cys54-Cys78 disulfide linkage are shown with


connecting cysteines bolded. A nearly perfect match between MWfor and


MWexp equates to the presence of the Cys54-Cys78 disulfide linkage.











VHH
CNBr/tryptic peptides
MWfor
MWexp
ΔMW















A4.2m
EFVCAVSR
FTCSR
1519.69
1519.70
−0.01



(SEQ ID NO: 81 and 87)






A5.1m
EFVCVITR
FTCSR
1575.75
1575.76
−0.01



(SEQ ID NO: 82 and 87)






A19.2m
EFVCGISR
FTCSR
1519.69
1519.64
0.05



(SEQ ID NO: 83 and 87)






A20.1m
EFVCAGSSTGR
FTCSR
1722.74
1722.84
−0.10



(SEQ ID NO: 84 and 87)






A24.1m
EFVCGISWGGGSTR
FTCSR
2064.91
2064.98
−0.07



(SEQ ID NO: 85 and 87)






A26.8m
EFVCVISSTGTSTYYADSVK
FTCSR
2766.25
2766.33
−0.08



(SEQ ID NO: 86 and 87)





MWfor: formula (expected) molecular weight (Da);


MWexp: experimental molecular weight (Da);


ΔMW = MWfor − MWexp.






EXAMPLE 11
Size Exclusion Chromatography and Affinity Measurements of Wild-Type and Mutant VHHs
Wild-type and mutant VHHs were passed over a SUPERDEX 75 (GE Healthcare) size exclusion chromatography column as described in Example 7 to determine their aggregation state. Both wild-type and mutant VHHs were determined to be non-aggregating monomers (FIGS. 5, 17A). Similar size exclusion profiles were obtained for mutant and wild-type, indicating the second disulfide bond does not promote the formation of interdomain disulfide-bonds or multimeric mutant VHHs. The elution volumes (Ves) of SEC molecular weight standards are shown with arrows in FIG. 17A and are aligned relative to the A4.2 and A4.2m chromatograms. a: ovalbumin (MW=43.0 kDa, Ve=8.90 ml); b: carbonic anhydrase (MW=30.0 kDa, Ve=9.71 ml); c: typsin inhibitor (MW=20.1 kDa, Ve=11.06 ml); d: α-lactalbumin (MW=14.4 kDa, Ve=11.97 ml); e: vitamin B (MW=1.3 kDa, Ve=18.7 ml). The equation of the line of a standard curve generated from these standards was LOG10 MW=−0.1539Ve+2.9949 (r2=0.9995). From this equation the VHH apparent MWs ranged from 9.8-13.6 kDa, indicating monomeric VHHs.
All kinetic rate and equilibrium constants of the mutants were determined as described (Example 7) using a BIACORE 3000 instrument from GE Healthcare and 10,287 RUs of immobilized TcdA. SPR analysis revealed the specific and high-affinity binding of 4 of 6 mutant VHHs to TcdA (FIG. 17B, Table 4). These four were also the strongest neutralizers (see Example 14). Two mutants (A19.2m and A24.1m) exhibited non-specific binding to reference cell proteins and as a result specific interaction data could not be generated, even at antibody concentrations as high as 3.2 μM. When compared to their wild-type counterparts, the KDs of 3 TcdA-binding mutants were reduced approximately 2-6 fold (Table 4), while the affinity of one VHH was relatively unchanged (KDs of 24 nM and 20 nM for A4.2 and A4.2m, respectively). The KD reductions were largely a result of faster koff values and to a much lesser extent influenced by slower kon values. Without wishing to be bound by theory, the Cys54-Cys78 disulfide bond may slightly distort the VHH structure leading to decreases in target binding affinities and decreases in antibody specificity.







TABLE 4







Kinetic and affinity constants of wild-type and mutant VHHs binding to TcdA.





















Fold











Wild-type
Mutant
change in














VHH
kon (M−1s−1)
koff (s−1)
KD (nM)
kon (M−1s−1) 
koff (s−1)
KD (nM)
KDa

















A4.2/A4.2m
6.7 × 105
1.6 × 10−2
24
9.3 × 105
1.9 × 10−2
20
−1.2


A5.1/A5.1m
1.6 × 106
5.0 × 10−3
3
9.5 × 105
1.6 × 10−2
17
+5.7


A19.2/A19.2m
1.4 × 104
3.9 × 10−3
290
—
—
—



A20.1/A20.1m
8.2 × 105
1.6 × 10−3
2
6.4 × 105
5.9 × 10−3
9.2
+4.6


A24.1/A24.1m
6.0 × 104
1.6 × 10−2
260
—
—
—



A26.8/A26.8m
1.4 × 106
1.6 × 10−2
12
1.0 × 106
2.8 × 10−2
28
+2.3





NB: no binding detected by Biacore, at VHH concentrations as high as 3.2 μM.


aRelative to wild-type VHH.






EXAMPLE 12
Circular Dichroism Analysis of Mutant and Wild-type VHHs
Circular dichroism (CD) experiments were used to examine VHH secondary structure, tertiary structure, thermal refolding efficiency, and thermal stability at both neutral and acidic pH.
Wild-type and mutant VHHs were analyzed by circular dichroism spectrophotometry using a Jasco J-815 Spectrophotometer (Jasco, Easton, Md.) at pH 7.3 in 10 mM phosphate buffer (PB; 1.4 g/ml Na2HPO4+0.24 g/ml KH2PO4) and at pH 2.0 (10 mM PB+50 mM HCl). For all CD experiments performed at pH 2.0, proteins were equilibrated in the above buffer for a minimum of 2 h before scanning. For far-UV CD secondary structure scans, thermal refolding, and thermal unfolding experiments, a 5 mm cuvette containing 1.5 ml of VHH at 50 μg/ml (3.2 μM; A280≅0.1) was used. In these experiments, data were collected for each sample between 190-260 nm with a 1 mm bandwidth, 20 nm/min scan speed and 0.5 nm data pitch. Raw data was smoothed using the Jasco software, exported and converted to mean residue ellipticity, [θ]. Thermal unfolding was followed at 215 nm by far-UV CD, with CD measurements taken every 2° C. from 30° C. to 96° C. with a temperature increase of 1° C./min. Mean residue ellipticities [θ] were used to calculate the fraction of protein folded (FF) which is shown in Equation 1,

FF=([θ]−[θU])/([θF]−[θU])  Equation 1

where [θF] and [θU] are the molar ellipticities of the folded (30° C.) and unfolded (96° C.) states, respectively. The thermal unfolding midpoint temperature (Tm) was obtained by plotting FF against temperature and performing sigmoidal Boltzmann curve fitting in GraphPad Prism (GraphPad Software, Inc., La Jolla, Calif.). For refolding experiments, VHHs were first scanned (190 nm-260 nm) at 25° C. (folded); heated at 96° C. for 20 min and scanned (unfolded); and equilibrated to 25° C. for 3 h before a third scan (refolded). Raw data was converted as before and thermal refolding efficiencies (TRE) were calculated at 215 nm using Equation 2,

TRE=(([θU]−[θR])/([θU]−[θF]))×100  Equation 2

where [θF] is the molar ellipticity of the folded state acquired at 25° C., [θU] is the molar ellipticity of the unfolded state acquired at 96° C., and [θR] is the molar ellipticity of the refolded state acquired at 25° C. To compare the tertiary structures of wild-type and mutant VHHs at neutral and acidic pH, near-UV CD experiments were performed in the range of 250 nm-340 nm using the conditions described above with the exception that a 10 mm cuvette containing 2 ml of protein at 250 μg/ml was used. In all cases, the ellipticity of buffer blanks were subtracted from experimental values and the reported data is the average of two independent experiments with 4 data accumulations in each.

Far-UV CD examined the VHH secondary structure, and results are shown in FIG. 18. Although the overall shape of the far-UV CD spectra from wild-type and mutant VHH pairs was similar at a given pH, spectra intensity shifts were observed for all wild-type/mutant pairs. In general, peak minima were seen at 216 nm-218 nm and at 230 nm-235 nm wavelengths but, in almost all cases, the intensity of the peak at 216 nm-218 nm was lower (decreased negative ellipticity) for mutant VHHs. Another prominent feature in the far-UV CD spectra was that mutant VHHs exhibited a near-UV shift in the peak range of 230 nm-235 nm. Wild-type VHHs possessed peak minima around 230 nm-232 nm whereas mutants displayed peak minima in this region around 232 nm-235 nm. Interestingly, A4.2/A4.2m, which had the most similar CD spectra at neutral pH of all the wild-type/mutant pairs, also had the same binding affinity for TcdA.
VHH tertiary structures were analyzed with near-UV CD spectroscopy, and results are shown in FIG. 19. Overall, the near-UV spectra profiles were similar between wild-type and mutant VHH pairs. Spectra from wild-type and mutant pairs shared nearly identical peak wavelengths; however, between 250 nm to 295 nm, the ellipticity of mutant VHHs was consistently more negative than wild-type VHHs. There were also subtle differences in peaks occurring around 297 nm, with mutant VHHs exhibiting a minor but consistent shift to the right. Three of the four wild-type/mutant pairs (A4.2/A4.2m, A5.1/A5.1m, and A20.1m/A20.1m) produced predominantly negative ellipticity, whereas the A26.8/A26.8m pair remained positive. The contributions of the second disulfide bond cannot be ruled out as a factor which may augment the contribution of aromatic residues to ellipticity (increasing negatively) of the mutants.
Thermal refolding efficiencies (TREs) of wild-type and mutant VHHs at neutral and acid pH were also determined by far-UV CD. CD scans were performed at 50 μg/ml concentrations of VHHs (3.1 μM) at 25° C. (folded), after heating to 96° C. (unfolded), and after cooling for 3 h to 25° C. (refolded). Thermal refolding efficiencies were determined as the extent to which the CD spectrum of the heated-and-cooled VHH approached that of the folded form. At pH 7.3, the TRE of wild-type VHHs was essentially 100% and significantly higher than for the mutants (FIG. 20, p=0.018, unpaired two-tailed t-test). Specifically, wild-type VHHs possessed a mean TRE of 99.7%±0.2% compared to mutant VHHs with a mean TRE of 90.0%±3.4% (FIG. 20). The ability of VHHs to refold in acidic conditions was also examined and, in general, mutants showed higher TREs at pH 2.0 (FIG. 20, Table 5). The mean TRE of wild-type VHHs in acid was 68.2%±9.4% compared to 80.6%±4.8% for mutant TREs in acid (FIG. 20). However, the mutant TREs were not significantly higher (p=0.268, unpaired two-tailed t-test). It should be noted that the TRE of 5 of 6 mutant VHHs increased in acidic conditions, with the TRE of A26.8m reaching 64.7% compared to only 25.8% for A26.8.







TABLE 5







Thermal refolding efficiencies (TREs) of wild-type and mutant


VHHs at pH 2.0. TRE (%) ± SEM (n = 8).












VHH
TRE (%)
VHH
TRE (%)















A4.2
80.0 ± 3.8
A4.2m
87.4 ± 1.6



A5.1
66.9 ± 4.2
A5.1m
87.2 ± 3.1



A19.2
78.3 ± 4.9
A19.2m
91.6 ± 1.4



A20.1
65.7 ± 2.5
A20.1m
85.9 ± 2.2



A24.1
92.7 ± 0.6
A24.1m
66.7 ± 0.3



A26.8
 25.8 ± 17.6
A26.8m
64.7 ± 2.2









Temperature-induced unfolding experiments were conducted in order to determine VHH Tms and Tonsets by following changes in VHH ellipticity at 215 nm (FIG. 21; Tables 6, 7). All VHHs exhibited sigmoidal melting curves. The wild-type VHHs have high Tms (as high as 84.7° C.)—significantly higher than those reported for other VHHs [60]. For all six VHHs, the mutants possessed higher Tm values, at both neutral and acidic pH (FIG. 21 and Table 6). At neutral pH, the Tm values of mutants ranged from 78.8° C. to 93.6° C., with one mutant, A5.1m, having a Tm 11.6° C. higher than wild-type (A5.1). The increase in mutant VHH Tms relative to wild-type ranged from 3.7° C. to 11.6° C. Overall, at neutral pH, the mean Tm±SEM was 76.2° C.±1.8° C. and 83.6° C.±2.3° C. for wild-type and mutant VHHs, respectively (FIG. 21B). At acidic pH a considerable reduction in Tm was observed for both wild-type (22.1° C. to 32.4° C.) and mutant VHHs (23.7° C. to 31.2° C.) when compared to the Tm values recorded at pH 7.3. However, at acidic pH the Tm of all six mutants was still significantly higher than the corresponding wild-type VHHs (p=0.002, unpaired two-tailed t-test). In acid, the increase in mutant VHH Tms relative to wild-type ranged from 2.1° C. to 11.6° C., which is a nearly identical spread in temperature increases to that seen at neutral pH. Overall, at pH 2.0, the mean Tm±SEM was 49.3° C.±1.2° C. and 56.6° C.±1.2° C. for wild-type and mutant VHHs, respectively (FIG. 21B). Interestingly, the highest Tm gains at both pH were seen for the four strongest neutralizers. The Tm differences between wild-type/mutant pairs are more significant at acidic pH than neutral pH. Without wishing to be bound by theory, these results (Table 6; FIG. 21) suggest the Cys54-Cys78 disulfide bond may stabilize the VHHs from acid-induced denaturation.
For example, A5.1 wild-type VHH had a Tm of 73.1° C. and 45.6° C. at neutral and acidic pH, respectively, while the A5.1 mutant (A5.1m) had a Tm of 84.7° C. and 57.2° C. at neutral and acidic pH, respectively.







TABLE 6







Comparison of wild-type (WT) and mutant (Mut) VHH thermal


unfolding midpoint temperatures (Tm) at neutral and acidic pH.










Tm (° C.) at pH 7.3
Tm (° C.) at pH 2.0













VHH
Wild-type
Mutant
ΔTm
Wild-type 
Mutant
ΔTm
















A4.2/A4.2m
 84.7*
 93.6*
8.9
52.3
62.4
10.1


A5.1/A5.1m
73.1
 84.7*
11.6
45.6
57.2
11.6


A19.2/A19.2m
75.1
78.8
3.7
53.0
55.1
2.1


A20.1/A20.1m
72.4
79.1
6.7
46.6
55.4
8.8


A24.1/A24.1m
74.6
80.1
5.5
49.4
54.6
5.2


A26.8/A26.8m
77.2
 85.3*
8.1
48.8
54.8
6.0





*Minimum estimated Tm.






Using the thermal unfolding curves, VHH Tonset temperatures were also identified; this is the temperature at which 5% of the VHH was unfolded (FIG. 21C; Table 7). The Tonset of mutant VHHs was significantly higher than wild-type VHHs at both neutral and acidic pH (p=0.027 and p=0.006, respectively, unpaired two-tailed t-test). The Tonset differences between wild-type/mutant pairs are more significant at acidic pH than neutral pH. At pH 7.3, the mean Tonset±SEM was 68.9° C.±1.8° C. and 74.9° C.±1.5° C. for wild-type and mutant VHHs, respectively. At pH 2.0, the mean Tonset±SEM was 41.2° C.±1.3° C. and 47.3° C.±1.3° C. for wild-type and mutant VHHs, respectively. Therefore, the lowest Tonset for the mutants was 45.0° C., whereas two of the wild-type VHHs (A5.1, A20.1) already had Tonsets of  ̃37° C. at pH 2.0 (physiological stomach conditions).







TABLE 7







Onset temperatures (Tonsets) of wild-type and mutant VHHs. Tonset


is defined as the temperature at which 5% of the VHH is unfolded.












Tonset

Tonset




pH 7.3 (° C.)

pH 2.0 (° C.)














VHH
Wild-type
Mutant
Wild-type
Mutant






A4.2/A4.2m
76.5
80.0
43.7
53.1



A5.1/A5.1m
65.2
76.6
37.8
48.4



A19.2/A19.2m
68.3
71.4
45.3
45.0



A20.1/A20.1m
64.6
72.0
37.8
46.3



A24.1/A24.1m
68.2
71.7
42.2
46.0



A26.8/A26.8m
70.7
77.8
40.3
45.2









EXAMPLE 13
Protease Resistance Profile Analysis of Mutant and Wild-type VHHs
The sensitivity of wild-type and mutant VHHs to the three major gastrointestinal proteases pepsin, trypsin, and chymotrypsin, was explored to determine whether the Cys54-Cys78 disulfide bond improved VHH resistance to proteolytic degradation. The effects of the proteases were analyzed by SDS-PAGE and MS analysis.
All reactions were performed in 20 μl volumes with 4.8 μg of VHH diluted in PBS pH 7.3. For pepsin digestions, reactions contained 17 μl of VHH, 2 μl of porcine stomach pepsin (460 U/mg; Sigma), and 1 μl of 1 M HCl (final pH=2.0). Final pepsin concentrations in each reaction ranged from 0.1 μg/ml to 100 μg/ml. Digestions were incubated at 37° C. for 60 min and neutralized with 1 μl of 1 M NaOH. For trypsin and chymotrypsin digestions, reactions contained 18 μl of VHH (diluted in PBS supplemented with 10 mM CaCl2) and 2 μl of either trypsin or chymotrypsin (sequencing grade, Hoffmann-La Roche). Final trypsin/chymotrypsin concentrations ranged from 0.1 μg/ml to 100 μg/ml. Digestions were incubated at 37° C. for 60 min and neutralized with 1 μl of protease inhibitor cocktail (Sigma). All neutralized VHH-protease reactions and controls (VHHs with no protease) were separated by SDS-PAGE, stained with Coomassie and photographed using an ALPHAIMAGER 3400 (Alpha Innotech Corporation, San Leandro, Calif.). To determine the percent of VHH retained after protease digestions, densitometry analysis was performed using the ALPHAEASE Fc software package (Version 7.0.1, Alpha Innotech Corporation) on control and digested VHHs. A total of three independent digestion reactions were performed on all of the VHHs at each protease concentration and each were run on separate SDS-PAGE gels. Digestions at the highest protease concentration (100 μg/ml) that were not analyzed by SDS-PAGE were buffer exchanged into ddH2O using Millipore BIOMAX 5K MWCO spin columns (Millipore, Billerica, Mass.) and subjected to MS analysis to identify the cleavage products, or analyzed by SPR for TcdA binding activity.
Protease concentrations of 0.1 μg/ml, 1 μg/ml, 10 μg/ml, and 100 μg/ml were explored. When the lowest concentrations of proteases (0.1 μg/ml and 1 μg/ml) were used in digestion reactions, wild-type and mutants appeared similar to undigested controls on SDS-PAGE (data not shown). Similarly, VHHs were only moderately susceptible to protease degradation at 10 μg/ml (data not shown). In order to see clear differences in the proteolytic susceptibility of wild-type and mutant VHHs, all remaining digestions were performed at protease concentrations of 100 μg/ml.
A representative SDS-PAGE gel comparing A5.1 wild-type and mutant VHH digestion with various concentrations of pepsin is shown in FIG. 22A. A reduction in VHH size from  ̃16 kDa (control) to either  ̃14 kDa, or complete digestion to smaller fragments can be observed. The band at  ̃14 kDa routinely appeared in digestions with each of the proteases and was shown by MS mass analysis to correspond to cleavage at various positions within the VHH C-terminal c-Myc epitope tag. Loss of the epitope tag corresponded to reductions of 1641.7 Da, 1754.8 Da, and 1641.7 Da for pepsin, trypsin, and chymotrypsin digested VHHs, respectively (data not shown). Overall, significant increases in pepsin resistance were found for all mutant VHHs compared to their wild-type counterparts (p=0.026, Mann-Whitney U test) (FIG. 22B, E; Table 8). All mutant VHHs were found to possess greater pepsin resistance, a protease that functions at acidic pH, compared to the wild-type VHHs (p=0.026, Mann-Whitney U test) (FIG. 22B, E and Table 8). The increase in mutant VHH pepsin resistance relative to corresponding wild-type ranged from almost 4.5% to 63% (Table 8). For example, A5.1 was completely degraded after incubation with pepsin, while nearly 50% of A5.1m remained intact (FIG. 22A, B). The biggest increase in pepsin resistance was found for A4.2m, where an almost 63% increase in intact VHH structure was found relative to A4.2. Interestingly, A4.2m also had the highest Tm and Tonset at pH 2.0 (Table 7), the same pH at which the pepsin digestions were performed.
In general, VHHs with a higher Tm at pH 2 correlated with a greater resistance to pepsin degradation (FIG. 23A) (R2=0.735). Thus, while wild type VHHs with lower Tms occupied the low protease resistance region of the graph, the mutants with higher Tms occupied the high protease resistance region of the graph. There was also a moderate correlation between VHH pepsin resistance and Tms at pH 7.3 (r2=0.500, data not shown). In addition, a strong correlation between wild-type VHH pepsin resistance and wild-type VHH Tonset at pH 2.0 was noted (r2=0.975, FIG. 23B). No correlation was evident between mutant VHH pepsin resistance and mutant VHH Tonset at pH 2.0 (r2=0.191, data not shown); without wishing to be bound by theory, this was likely because mutant VHH Tonset temperatures were much higher than the temperature at which pepsin digestions were performed (37° C.).







TABLE 8







Comparison of wild-type (WT) and mutant (Mut) VHH resistance profiles to the major


gastrointestinal proteases. All VHH digestions were performed at 37° C. for 1 hour in the


presence of 100 μg/ml of protease; resistance profiles were obtained by comparing the


intensity of protease-digested VHHs relative to untreated controls using SDS-PAGE and


imaging software; values represent the mean ± SEM of three independent experiments.











Pepsin 
Trypsin
Chymotrypsin



Resistance (%)
Resistance (%)
Resistance (%)













VHH
WT
Mut
WT
Mut
WT
Mut
















A4.2
11.08 ± 1.88 
73.87 ± 7.23
35.72 ± 7.08
4.80 ± 0.61
13.60 ± 6.50
 3.18 ± 1.10


A5.1
0.53 ± 0.15
46.63 ± 1.99
96.23 ± 7.09
83.30 ± 4.96 
14.03 ± 3.15
27.00 ± 4.05


A19.2
30.37 ± 3.16 
52.27 ± 0.32
 0.73 ± 0.73
0.27 ± 0.27
 8.30 ± 1.14
 0.18 ± 0.10


A20.1
0.68 ± 0.68
 5.04 ± 0.76
72.77 ± 4.85
82.80 ± 1.97 
10.17 ± 1.85
16.17 ± 5.26


A24.1
10.45 ± 2.39 
36.02 ± 1.11
75.03 ± 9.63
66.50 ± 3.58 
22.03 ± 5.01
43.80 ± 2.08


A26.8
3.17 ± 1.24
24.56 ± 1.45
 2.03 ± 2.03
4.10 ± 1.27
 8.40 ± 1.23
40.83 ± 8.81









The resistance profiles of wild-type and mutant VHHs to trypsin and chymotrypsin, proteases that function at neutral pH, were more varied without a clearly defined trend (FIG. 22C-E and Table 8). 4 of 6 mutant VHHs showed increased resistance to chymotrypsin, with significant increases found in clones A5.1m, A24.1m, and A26.8m (p<0.05) compared to their wild-type counterparts. No statistical differences were found between trypsin digested wild-type and mutant VHHs (FIG. 22C-E; Table 8), except for A4.2m, where trypsin resistance was actually reduced from almost 36% in the wild-type VHH to almost 5% in the mutant. Both the wild-type and mutant versions of A19.2 and A26.8 were very susceptible to trypsin degradation. No correlation was evident between VHH trypsin resistance and Tms at pH 7.3 or pH 2.0 (r2=0.138 and r2=0.138, respectively) or between VHH chymotrypsin resistance and Tms at pH 7.3 or pH 2.0 (r2=0.012 and r2=0.004, respectively).
The ability of pepsin-treated mutants (A4.2m, A5.1m, A20.1m, and A26.8m) to bind TcdA was evaluated by SPR. SPR analyses confirmed the pepsin-treated mutants (“VHH-tag”) retained TcdA binding as their koff values (FIG. 23C) were essentially the same as those of untreated controls (Table 4; FIG. 23C). SPR analysis on pepsin-digested wild-type VHHs could not be performed since these VHHs were significantly degraded by pepsin. Without wishing to be bound by theory, this highlights the impact a second disulfide bond in the hydrophobic core has on VHH conformational stability at low pH and resistance to proteolytic degradation by pepsin.
EXAMPLE 14
TcdA Toxin Neutralization Assay
In vitro TcdA neutralization assays were performed essentially as described [20]. Human lung fibroblast cell rounding was reported 24 h post addition of TcdA (100 ng/ml), TcdA+wild-type VHH (1000 nM) or TcdA+mutant VHH (1000 nM). Specifically, VHHs were added as pooled mixtures of A4.2, A5.1, A20.1, and A26.8 (250 nM each, 1000 nM total) or A4.2m, A5.1m, A20.1m, and A26.8m (250 nM each, 1000 nM total). The percentage of cell rounding was scored visually using light microscopy and the reported values are the average of two independent experiments in which each VHH mixture was tested in triplicate.
Mutant VHHs retained their ability to neutralize to cytotoxic effects of TcdA on monolayers of fibroblast cells. Comparison of the neutralization capacity of pooled mixtures (1000 nM total) of wild-type and mutant VHHs revealed mutants performed nearly as well as wild-types at reducing TcdA-mediated cell rounding (FIG. 24). Given that 3 of 4 mutants showed weaker affinity for TcdA the reduction in neutralizing capacity relative to wild-type VHHs was not unexpected.
As indicated above, the mutant antibodies were compared to their wild-type counterparts with respect to expression, yield, solubility, affinity for TcdA, thermal unfolding at neutral and acidic pH, and protease resistance. Mutant VHHs were found to be soluble, non-aggregating monomers, possessing similar affinity constants to that of WT VHHs. A significant increase in the midpoint temperature of unfolding (4-12° C.) was observed for all mutants, at both neutral and acidic pH (p<0.05; unpaired two-tailed t test). Digestion of the VHHs with major gastrointestinal proteases at biologically relevant concentrations revealed a significant increase in pepsin resistance for all mutants (p<0.05; unpaired two-tailed Mann-Whitney U test), However, increases in resistance profiles to chymotrypsin and trypsin were not as universal. Overall, the introduction of an additional disulfide bond in the hydrophobic core of the anti-TcdA VHHs not only increased thermal stability at neutral pH, but also represents a generic strategy to increase antibody stability at low pH and impart pepsin resistance which is desirable for protein-based oral therapeutics.
EXAMPLE 15
Sequence Identities Between VHHs
The sequences of VHH pairs were aligned using ClustalW (Thompson et al, 1994), and the percentage identity between the VHH pairs was calculated using the BIOEDIT Sequence Alignment Editor. Results are shown in Tables 9 and 10, below.







TABLE 9







Percentage amino acid sequence identities between


TcdA-binding VHHs.











VHH 1
VHH 2
Identity (%)














A4.2
A5.1
82



A4.2
A19.2
76



A4.2
A20.1
82



A4.2
A24.1
78



A4.2
A26.8
75



A5.1
A19.2
77



A5.1
A20.1
78



A5.1
A24.1
77



A5.1
A26.8
78



A19.2
A20.1
77



A19.2
A24.1
75



A19.2
A26.8
75



A20.1
A24.1
80



A20.1
A26.8
77



A24.1
A26.8
74



A4.2
A4.2m
98.4



A5.1
A5.1m
98.4



A19.2
A19.2m
98.4



A20.1
A20.1m
98.4



A24.1
A24.1m
98.4



A26.8
A26.8m
98.4
















TABLE 10







Percentage amino acid sequence identities between


TcdB-binding VHHs.











VHH 1
VHH 2
Identity (%)














B5.2
B7.3
69



B5.2
B13.6
81



B5.2
B15.3
66



B5.2
B15.5
73



B7.3
B13.6
74



B7.3
B15.3
72



B7.3
B15.5
69



B13.6
B15.3
68



B13.6
B15.5
71



B15.3
B15.5
69



B5.2
B5.2m
98.3



B7.3
B7.3m
98.4



B13.6
B13.6m
98.3



B15.3
B15.3m
98.4



B15.5
B15.5m
98.3









The embodiments and examples described herein are illustrative and are not meant to limit the scope of the invention as claimed. Variations of the foregoing embodiments, including alternatives, modifications and equivalents, are intended by the inventors to be encompassed by the claims. Furthermore, the discussed combination of features might not be necessary for the inventive solution.
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## Claims

1. An isolated or purified single domain antibody, comprising a sequence of CDR 1 of GRTFSMYR (SEQ ID NO:2); CDR2 of ITRNGSST (SEQ ID NO:8); and CDR3 of AATSGSSYLDAAHVYDY (SEQ ID NO:14).

2. The isolated or purified single domain antibody of claim 1, comprising a sequence selected from the group consisting of:







(SEQ ID NO: 35)


QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVGV


 


ITRNGSSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTALYYCAATS


 


GSSYLDAAHVYDYWGQGTQVTVSS;


and


 


(SEQ ID NO: 46)


QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVCV


 


ITRNGSSTYYADSVKGRFTCSRDNAKNTVYLQMNSLKPEDTALYYCAATS


 


GSSYLDAAHVYDYWGQGTQVTVSS,






or a sequence at least 90% identical thereto, wherein any differences in sequence are limited to framework regions of the single domain antibody.

3. A multivalent polypeptide comprising at least one of the isolated or purified single domain antibody of claim 1.

4. The isolated or purified single domain antibody of claim 1, wherein the antibody is immobilized onto a surface.

5. The isolated or purified single domain antibody of claim 1, wherein the antibody is linked to a cargo molecule.

6. The isolated or purified single domain antibody of claim 5, wherein the cargo molecule is a detectable agent, a therapeutic, a drug, a peptide, a carbohydrate moiety, an enzyme, or a cytotoxic agent; one or more liposomes loaded with a detectable agent, a therapeutic, a drug, a peptide, an enzyme, or a cytotoxic agent; or one or more nanoparticle, nanowire, nanotube, or quantum dots.

7. A composition comprising one or more than one of the isolated or purified single domain antibody of claim 1 and a pharmaceutically-acceptable carrier, diluent, or excipient.

8. A method of treating a Clostridium difficile infection, comprising administering isolated or purified single domain antibody, comprising a sequence selected from the group consisting of:







(SEQ ID NO: 35)


QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVGV


 


ITRNGSSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTALYYCAATS


 


GSSYLDAAHVYDYWGQGTQVTVSS;


and


 


(SEQ ID NO: 46)


QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVCV


 


ITRNGSSTYYADSVKGRFTCSRDNAKNTVYLQMNSLKPEDTALYYCAATS


 


GSSYLDAAHVYDYWGQGTQVTVSS






to a subject in need thereof.

9. A method of detecting Clostridium difficile toxins comprising contacting a sample with an isolated or purified single domain antibody comprising a sequence selected from the group consisting of







(SEQ ID NO: 35)


QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVGV


 


ITRNGSSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTALYYCAATS


 


GSSYLDAAHVYDYWGQGTQVTVSS


and


 


(SEQ ID NO: 46)


QVKLEESGGGLVQAGGSLRLSCAASGRTFSMYRMGWFRQAPGKEREFVCV


 


ITRNGSSTYYADSVKGRFTCSRDNAKNTVYLQMNSLKPEDTALYYCAATS


 


GSSYLDAAHVYDYWGQGTQVTVSS;






allowing the Clostridium difficile toxin to bind the isolated or purified single domain antibody; and detecting the bound single domain antibody or fragment thereof using a suitable detection and/or imaging technology.