1
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Buddle JE, Fagan RP. Pathogenicity and virulence of Clostridioides difficile. Virulence 2023; 14:2150452. [PMID: 36419222 DOI: 10.1080/21505594.2022.2150452] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/02/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is the most common cause of nosocomial antibiotic-associated diarrhea, and is responsible for a spectrum of diseases characterized by high levels of recurrence, morbidity, and mortality. Treatment is complex, since antibiotics constitute both the main treatment and the major risk factor for infection. Worryingly, resistance to multiple antibiotics is becoming increasingly widespread, leading to the classification of this pathogen as an urgent threat to global health. As a consummate opportunist, C. difficile is well equipped for promoting disease, owing to its arsenal of virulence factors: transmission of this anaerobe is highly efficient due to the formation of robust endospores, and an array of adhesins promote gut colonization. C. difficile produces multiple toxins acting upon gut epithelia, resulting in manifestations typical of diarrheal disease, and severe inflammation in a subset of patients. This review focuses on such virulence factors, as well as the importance of antimicrobial resistance and genome plasticity in enabling pathogenesis and persistence of this important pathogen.
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Affiliation(s)
- Jessica E Buddle
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Robert P Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
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2
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Vance DJ, Rudolph MJ, Davis SA, Mantis NJ. Structural Basis of Antibody-Mediated Inhibition of Ricin Toxin Attachment to Host Cells. Biochemistry 2023; 62:3181-3187. [PMID: 37903428 DOI: 10.1021/acs.biochem.3c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Monoclonal antibodies, JB4 and SylH3, neutralize ricin toxin (RT) by inhibiting the galactose-specific lectin activity of the B subunit of the toxin (RTB), which is required for cell attachment and entry. It is not immediately apparent how the antibodies accomplish this feat, considering that RTB consists of two globular domains (D1, D2) each divided into three homologous subdomains (α, β, γ) with the two functional galactosyl-specific carbohydrate recognition domains (CRDs) situated on opposite poles (subdomains 1α and 2γ). Here, we report the X-ray crystal structures of JB4 and SylH3 Fab fragments bound to RTB in the context of RT. The structures revealed that neither Fab obstructed nor induced detectable conformational alterations in subdomains 1α or 2γ. Rather, JB4 and SylH3 Fabs recognize nearly identical epitopes within an ancillary carbohydrate recognition pocket located in subdomain 1β. Despite limited amino acid sequence similarity between SylH3 and JB4 Fabs, each paratope inserts a Phe side chain from the heavy (H) chain complementarity determining region (CDR3) into the 1β CRD pocket, resulting in local aromatic stacking interactions that potentially mimic a ligand interaction. Reconciling the fact that stoichiometric amounts of SylH3 and JB4 are sufficient to disarm RTB's lectin activity without evidence of allostery, we propose that subdomain 1β functions as a "coreceptor" required to stabilize glycan interactions principally mediated by subdomains 1α and 2γ. Further investigation into subdomain 1β will yield fundamental insights into the large family of R-type lectins and open novel avenues for countermeasures aimed at preventing toxin uptake into vulnerable tissues and cells.
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Affiliation(s)
- David J Vance
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Michael J Rudolph
- New York Structural Biology Center, New York, New York 10027, United States
| | - Simon A Davis
- New York Structural Biology Center, New York, New York 10027, United States
| | - Nicholas J Mantis
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
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3
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Bharathkar SK, Miller MJ, Stadtmueller BM. Engineered Secretory Immunoglobulin A provides insights on antibody-based effector mechanisms targeting Clostridiodes difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566291. [PMID: 37986930 PMCID: PMC10659285 DOI: 10.1101/2023.11.08.566291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Secretory (S) Immunoglobin (Ig) A is the predominant mucosal antibody, which mediates host interactions with commensal and pathogenic microbes, including Clostridioides difficile. SIgA adopts a polymeric IgA structure that is bound by secretory component (SC). Despite significance, how SIgA supports diverse effector mechanisms is poorly characterized and SIgA-based therapies nonexistent. We engineered chimeric (c) SIgAs, in which we replaced SC domain D2 with a single domain antibody or a monomeric fluorescent protein, allowing us to investigate and enhance SIgA effector mechanisms. cSIgAs exhibited increased neutralization potency against C. difficile toxins, promoted bacterial clumping and cell rupture, and decreased cytotoxicity. cSIgA also allowed us to visualize and/or quantify C. difficile morphological changes and clumping events. Results reveal mechanisms by which SIgA combats C. difficile infection, demonstrate that cSIgA design can modulate these mechanisms, and demonstrate cSIgA's adaptability to modifications that might target a broad range of antigens and effector mechanisms.
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Affiliation(s)
- Sonya Kumar Bharathkar
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Michael J. Miller
- Carle R. Woese Institute of Genomic Biology
- Department of food science and Human Nutrition, University of Illinois Urbana-Champaign, Illinois 61801 USA
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Carle R. Woese Institute of Genomic Biology
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4
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Sarma S, Catella CM, San Pedro ET, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK. Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells. Commun Biol 2023; 6:878. [PMID: 37634026 PMCID: PMC10460389 DOI: 10.1038/s42003-023-05242-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Infections by Clostridioides difficile, a bacterium that targets the large intestine (colon), impact a large number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can be delivered to the gut and inhibit the biocatalytic activity of these toxins represent a promising therapeutic strategy to prevent and treat C. diff. infection. We describe an approach that combines a Peptide Binding Design (PepBD) algorithm, molecular-level simulations, a rapid screening assay to evaluate peptide:toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells. One peptide, SA1, is found to block TcdA toxicity in primary-derived human colon (large intestinal) epithelial cells. SA1 binds TcdA with a KD of 56.1 ± 29.8 nM as measured by surface plasmon resonance (SPR).
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Affiliation(s)
- Sudeep Sarma
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Carly M Catella
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Ellyce T San Pedro
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Xingqing Xiao
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Deniz Durmusoglu
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Stefano Menegatti
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC, 27695, USA
| | - Nathan Crook
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Scott T Magness
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Carol K Hall
- Department of Chemical Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA.
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5
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Hussack G, Rossotti MA, van Faassen H, Murase T, Eugenio L, Schrag JD, Ng KKS, Tanha J. Structure-guided design of a potent Clostridiodes difficile toxin A inhibitor. Front Microbiol 2023; 14:1110541. [PMID: 36778856 PMCID: PMC9909335 DOI: 10.3389/fmicb.2023.1110541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Crystal structures of camelid heavy-chain antibody variable domains (VHHs) bound to fragments of the combined repetitive oligopeptides domain of Clostridiodes difficile toxin A (TcdA) reveal that the C-terminus of VHH A20 was located 30 Å away from the N-terminus of VHH A26. Based on this observation, we generated a biparatopic fusion protein with A20 at the N-terminus, followed by a (GS)6 linker and A26 at the C-terminus. This A20-A26 fusion protein shows an improvement in binding affinity and a dramatic increase in TcdA neutralization potency (>330-fold [IC 50]; ≥2,700-fold [IC 99]) when compared to the unfused A20 and A26 VHHs. A20-A26 also shows much higher binding affinity and neutralization potency when compared to a series of control antibody constructs that include fusions of two A20 VHHs, fusions of two A26 VHHs, a biparatopic fusion with A26 at the N-terminus and A20 at the C-terminus (A26-A20), and actoxumab. In particular, A20-A26 displays a 310-fold (IC 50) to 29,000-fold (IC 99) higher neutralization potency than A26-A20. Size-exclusion chromatography-multiangle light scattering (SEC-MALS) analyses further reveal that A20-A26 binds to TcdA with 1:1 stoichiometry and simultaneous engagement of both A20 and A26 epitopes as expected based on the biparatopic design inspired by the crystal structures of TcdA bound to A20 and A26. In contrast, the control constructs show varied and heterogeneous binding modes. These results highlight the importance of molecular geometric constraints in generating highly potent antibody-based reagents capable of exploiting the simultaneous binding of more than one paratope to an antigen.
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Affiliation(s)
- Greg Hussack
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Martin A. Rossotti
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Henk van Faassen
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Tomohiko Murase
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Luiz Eugenio
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Joseph D. Schrag
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, QC, Canada
| | - Kenneth K.-S. Ng
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada,Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada,*Correspondence: Kenneth K.-S. Ng,
| | - Jamshid Tanha
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, Canada,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada,Jamshid Tanha,
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6
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Sarma S, Catella CM, Pedro ETS, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK. Design of 8-mer Peptides that Block Clostridioides difficile Toxin A in Intestinal Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523493. [PMID: 36711911 PMCID: PMC9882058 DOI: 10.1101/2023.01.10.523493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Clostridioides difficile ( C. diff .) is a bacterium that causes severe diarrhea and inflammation of the colon. The pathogenicity of C. diff . infection is derived from two major toxins, toxins A (TcdA) and B (TcdB). Peptide inhibitors that can be delivered to the gut to inactivate these toxins are an attractive therapeutic strategy. In this work, we present a new approach that combines a pep tide b inding d esign algorithm (PepBD), molecular-level simulations, rapid screening of candidate peptides for toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block the glucosyltransferase activity of TcdA by targeting its glucosyltransferase domain (GTD). Using PepBD and explicit-solvent molecular dynamics simulations, we identified seven candidate peptides, SA1-SA7. These peptides were selected for specific TcdA GTD binding through a custom solid-phase peptide screening system, which eliminated the weaker inhibitors SA5-SA7. The efficacies of SA1-SA4 were then tested using a trans-epithelial electrical resistance (TEER) assay on monolayers of the human gut epithelial culture model. One peptide, SA1, was found to block TcdA toxicity in primary-derived human jejunum (small intestinal) and colon (large intestinal) epithelial cells. SA1 bound TcdA with a K D of 56.1 ± 29.8 nM as measured by surface plasmon resonance (SPR). Significance Statement Infections by Clostridioides difficile , a bacterium that targets the large intestine (colon), impact a significant number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can inhibit the biocatalytic activity of these toxins represent a promising strategy to prevent and treat C. diff . infection. We describe an approach that combines a Peptide B inding D esign (PepBD) algorithm, molecular-level simulations, a rapid screening assay to evaluate peptide:toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in small intestinal and colon epithelial cells. Importantly, our designed peptide, SA1, bound toxin A with nanomolar affinity and blocked toxicity in colon cells.
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Affiliation(s)
- Sudeep Sarma
- Department of Chemical Engineering, North Carolina State University, Raleigh NC 27695-7905, USA
| | - Carly M. Catella
- Department of Chemical Engineering, North Carolina State University, Raleigh NC 27695-7905, USA
| | - Ellyce T. San Pedro
- Department of Medicine, University of North Carolina at Chapel Hill, NC 27514, United States
| | - Xingqing Xiao
- Department of Chemical Engineering, North Carolina State University, Raleigh NC 27695-7905, USA
| | - Deniz Durmusoglu
- Department of Chemical Engineering, North Carolina State University, Raleigh NC 27695-7905, USA
| | - Stefano Menegatti
- Department of Chemical Engineering, North Carolina State University, Raleigh NC 27695-7905, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, United States
| | - Nathan Crook
- Department of Chemical Engineering, North Carolina State University, Raleigh NC 27695-7905, USA
| | - Scott T. Magness
- Department of Medicine, University of North Carolina at Chapel Hill, NC 27514, United States
| | - Carol K. Hall
- Department of Chemical Engineering, North Carolina State University, Raleigh NC 27695-7905, USA
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7
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Chen B, Perry K, Jin R. Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies. Front Immunol 2022; 13:978858. [PMID: 36466927 PMCID: PMC9709291 DOI: 10.3389/fimmu.2022.978858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
Toxin A (TcdA) and toxin B (TcdB) are two key virulence factors secreted by Clostridioides difficile, which is listed as an urgent threat by the CDC. These two large homologous exotoxins are mainly responsible for diseases associated with C. difficile infection (CDI) with symptoms ranging from diarrhea to life threatening pseudomembranous colitis. Single-domain camelid antibodies (VHHs) AH3 and AA6 are two potent antitoxins against TcdA, which when combined with two TcdB-targeting VHHs showed effective protection against both primary and recurrent CDI in animal models. Here, we report the co-crystal structures of AH3 and AA6 when they form complexes with the glucosyltransferase domain (GTD) and a fragment of the delivery and receptor-binding domain (DRBD) of TcdA, respectively. Based on these structures, we find that AH3 binding enhances the overall stability of the GTD and interferes with its unfolding at acidic pH, and AA6 may inhibit the pH-dependent conformational changes in the DRBD that is necessary for pore formation of TcdA. These studies reveal two functionally critical epitopes on TcdA and shed new insights into neutralizing mechanisms and potential development of epitope-focused vaccines against TcdA.
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Affiliation(s)
- Baohua Chen
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, United States
| | - Kay Perry
- NE-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, United States,Department of Chemistry and Chemical Biology, Cornell University, Argonne, IL, United States
| | - Rongsheng Jin
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, United States,*Correspondence: Rongsheng Jin,
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8
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Raeisi H, Azimirad M, Nabavi-Rad A, Asadzadeh Aghdaei H, Yadegar A, Zali MR. Application of recombinant antibodies for treatment of Clostridioides difficile infection: Current status and future perspective. Front Immunol 2022; 13:972930. [PMID: 36081500 PMCID: PMC9445313 DOI: 10.3389/fimmu.2022.972930] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile (C. difficile), known as the major cause of antibiotic-associated diarrhea, is regarded as one of the most common healthcare-associated bacterial infections worldwide. Due to the emergence of hypervirulent strains, development of new therapeutic methods for C. difficile infection (CDI) has become crucially important. In this context, antibodies have been introduced as valuable tools in the research and clinical environments, as far as the effectiveness of antibody therapy for CDI was reported in several clinical investigations. Hence, production of high-performance antibodies for treatment of CDI would be precious. Traditional approaches of antibody generation are based on hybridoma technology. Today, application of in vitro technologies for generating recombinant antibodies, like phage display, is considered as an appropriate alternative to hybridoma technology. These techniques can circumvent the limitations of the immune system and they can be exploited for production of antibodies against different types of biomolecules in particular active toxins. Additionally, DNA encoding antibodies is directly accessible in in vitro technologies, which enables the application of antibody engineering in order to increase their sensitivity and specificity. Here, we review the application of antibodies for CDI treatment with an emphasis on recombinant fragment antibodies. Also, this review highlights the current and future prospects of the aforementioned approaches for antibody-mediated therapy of CDI.
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Affiliation(s)
- Hamideh Raeisi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Abbas Yadegar, ;
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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9
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Kordus SL, Thomas AK, Lacy DB. Clostridioides difficile toxins: mechanisms of action and antitoxin therapeutics. Nat Rev Microbiol 2022; 20:285-298. [PMID: 34837014 PMCID: PMC9018519 DOI: 10.1038/s41579-021-00660-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 01/03/2023]
Abstract
Clostridioides difficile is a Gram-positive anaerobe that can cause a spectrum of disorders that range in severity from mild diarrhoea to fulminant colitis and/or death. The bacterium produces up to three toxins, which are considered the major virulence factors in C. difficile infection. These toxins promote inflammation, tissue damage and diarrhoea. In this Review, we highlight recent biochemical and structural advances in our understanding of the mechanisms that govern host-toxin interactions. Understanding how C. difficile toxins affect the host forms a foundation for developing novel strategies for treatment and prevention of C. difficile infection.
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Affiliation(s)
- Shannon L. Kordus
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Structural Biology, Vanderbilt University, Nashville, TN, USA,These authors contributed equally: Shannon L. Kordus, Audrey K. Thomas
| | - Audrey K. Thomas
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Structural Biology, Vanderbilt University, Nashville, TN, USA,These authors contributed equally: Shannon L. Kordus, Audrey K. Thomas
| | - D. Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Structural Biology, Vanderbilt University, Nashville, TN, USA,The Veterans Affairs, Tennessee Valley Healthcare, System, Nashville, TN, USA,
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10
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Liu J, Kothe M, Zhang J, Oloo E, Stegalkina S, Mundle ST, Li L, Zhang J, Cole LE, Barone L, Biemann HP, Kleanthous H, Anosova NG, Anderson SF. Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B. Curr Res Struct Biol 2022; 4:96-105. [PMID: 35469152 PMCID: PMC9034018 DOI: 10.1016/j.crstbi.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/11/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Abstract
Clostridium difficile toxins are the primary causative agents for hospital-acquired diarrhea and pseudomembranous colitis. Numerous monoclonal antibodies (mAbs) targeting different domains of Clostridium difficile toxin have been reported. Here we report the crystal structures of two mAbs, B1 and B2, in complex with the glycosyltransferase domain (GTD) of the Clostridium difficile toxin B (TcdB). B2 bound to the N-terminal 4 helix bundle of the GTD, a conserved membrane localization domain (MLD) found in the large clostridial glycosylating toxin family implicated in targeting plasma membrane. B1 bound to a distinct epitope at the hinge region between the MLD and the catalytic subdomain of the GTD. Functional studies revealed the potency of these mAbs in vitro and in vivo to be synergistic when given in combination. Identified 2 novel potent mAbs B1 and B2 targeting the TcdB GTD domain and synergistic effects were observed when combined. Novel non-overlapped epitopes were identified for B1 and B2 through X-ray crystallography. B2 epitope belongs to a conserved MLD (membrane localization domain) in the large clostridial glycosylating toxin family. B2 was shown to target the key regions (Loop 1 and Loop 3) of MLD proposed to be essential for membrane localization. B1 epitope was found to be at the hinge region between the GTD catalytic domain and the MLD of GTD.
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11
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Chen B, Basak S, Chen P, Zhang C, Perry K, Tian S, Yu C, Dong M, Huang L, Bowen ME, Jin R. Structure and conformational dynamics of Clostridioides difficile toxin A. Life Sci Alliance 2022; 5:5/6/e202201383. [PMID: 35292538 PMCID: PMC8924006 DOI: 10.26508/lsa.202201383] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 01/05/2023] Open
Abstract
This study presents a complete structural model of TcdA holotoxin and sheds new lights into the conformational dynamics of TcdA and its roles in TcdA intoxication. Clostridioides difficile toxin A and B (TcdA and TcdB) are two major virulence factors responsible for diseases associated with C. difficile infection (CDI). Here, we report the 3.18-Å resolution crystal structure of a TcdA fragment (residues L843–T2481), which advances our understanding of the complete structure of TcdA holotoxin. Our structural analysis, together with complementary single molecule FRET and limited proteolysis studies, reveal that TcdA adopts a dynamic structure and its CROPs domain can sample a spectrum of open and closed conformations in a pH-dependent manner. Furthermore, a small globular subdomain (SGS) and the CROPs protect the pore-forming region of TcdA in the closed state at neutral pH, which could contribute to modulating the pH-dependent pore formation of TcdA. A rationally designed TcdA mutation that trapped the CROPs in the closed conformation showed drastically reduced cytotoxicity. Taken together, these studies shed new lights into the conformational dynamics of TcdA and its roles in TcdA intoxication.
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Affiliation(s)
- Baohua Chen
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Sujit Basak
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Peng Chen
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Changcheng Zhang
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, USA
| | - Songhai Tian
- Department of Urology, Boston Children's Hospital, Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Rongsheng Jin
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA
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12
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Maestro B, Zamora-Carreras H, Jiménez MÁ, Sanz JM. Inter-hairpin linker sequences determine the structure of the ββ-solenoid fold: a "bottom-up" study of pneumococcal LytA choline-binding module. Int J Biol Macromol 2021; 190:679-692. [PMID: 34506863 DOI: 10.1016/j.ijbiomac.2021.08.223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022]
Abstract
The ββ-solenoid structures are part of many proteins involved in the recognition of bacterial cell wall. They are elongated polypeptides consisting of repeated β-hairpins connected by linker sequences and disposed around a superhelical axis stabilised by short-range interactions. Among the most studied ββ-solenoids are those belonging to the family of choline-binding modules (CBMs) from the respiratory pathogen Streptococcus pneumoniae (pneumococcus) and its bacteriophages, and their properties have been employed to develop several biotechnological and biomedical tools. We have carried out a theoretical, spectroscopic and thermodynamic study of the ββ-solenoid structure of the CBM from the pneumococcal LytA autolysin using peptides of increasing length containing 1-3 repeats of this structure. Our results show that hints of native-like tertiary structure are only observed with a minimum of three β-hairpins, corresponding to one turn of the solenoid superhelix, and identify the linker sequences between hairpins as the major directors of the solenoid folding. This study paves the way for the rational structural engineering of ββ-solenoids aimed to find novel applications.
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Affiliation(s)
- Beatriz Maestro
- Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain
| | - Héctor Zamora-Carreras
- Instituto de Química-Física "Rocasolano", Spanish National Research Council (CSIC), Madrid, Spain; Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - M Ángeles Jiménez
- Instituto de Química-Física "Rocasolano", Spanish National Research Council (CSIC), Madrid, Spain.
| | - Jesús M Sanz
- Centro de Investigaciones Biológicas Margarita Salas, Spanish National Research Council (CSIC), Madrid, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Elche, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
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13
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Iqbal S, Li F, Akutsu T, Ascher DB, Webb GI, Song J. Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Brief Bioinform 2021; 22:6289890. [PMID: 34058752 DOI: 10.1093/bib/bbab184] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/07/2021] [Accepted: 04/21/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding how a mutation might affect protein stability is of significant importance to protein engineering and for understanding protein evolution genetic diseases. While a number of computational tools have been developed to predict the effect of missense mutations on protein stability protein stability upon mutations, they are known to exhibit large biases imparted in part by the data used to train and evaluate them. Here, we provide a comprehensive overview of predictive tools, which has provided an evolving insight into the importance and relevance of features that can discern the effects of mutations on protein stability. A diverse selection of these freely available tools was benchmarked using a large mutation-level blind dataset of 1342 experimentally characterised mutations across 130 proteins from ThermoMutDB, a second test dataset encompassing 630 experimentally characterised mutations across 39 proteins from iStable2.0 and a third blind test dataset consisting of 268 mutations in 27 proteins from the newly published ProThermDB. The performance of the methods was further evaluated with respect to the site of mutation, type of mutant residue and by ranging the pH and temperature. Additionally, the classification performance was also evaluated by classifying the mutations as stabilizing (∆∆G ≥ 0) or destabilizing (∆∆G < 0). The results reveal that the performance of the predictors is affected by the site of mutation and the type of mutant residue. Further, the results show very low performance for pH values 6-8 and temperature higher than 65 for all predictors except iStable2.0 on the S630 dataset. To illustrate how stability and structure change upon single point mutation, we considered four stabilizing, two destabilizing and two stabilizing mutations from two proteins, namely the toxin protein and bovine liver cytochrome. Overall, the results on S268, S630 and S1342 datasets show that the performance of the integrated predictors is better than the mechanistic or individual machine learning predictors. We expect that this paper will provide useful guidance for the design and development of next-generation bioinformatic tools for predicting protein stability changes upon mutations.
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Affiliation(s)
- Shahid Iqbal
- Computer System Engineering from Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Pakistan
| | - Fuyi Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, the University of Melbourne, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan
| | | | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Victoria 3800, Australia
| | - Jiangning Song
- Monash Biomedicine Discovery Institute, Monash University, Australia
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14
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Chen W, Li Z, Dong X, Wang X. A tetravalent single-chain variable fragment antibody for the detection of staphylococcal enterotoxin A. J Zhejiang Univ Sci B 2021; 22:305-309. [PMID: 33835764 DOI: 10.1631/jzus.b2000661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Staphylococcal enterotoxin A (SEA) synthesized by Staphylococcus aureus is a foodborne and heat-stable toxin, which is a great threat to human health (Pexaraet al., 2010). Highly sensitive antibodies are a key factor in the immunological detection of SEA, which is one of the most effective ways to detect SEA because of its accuracy, agility, and efficiency (Nouri et al., 2018). In this study, we constructed a tetravalent anti-SEA antibody gene by linking the tetramerization domain of human p53 to the C-terminus of the anti-SEA single-chain variable fragment (scFv), which was then transformed into Escherichia coli BL21 (DE3) for the production of a SEA-specific tetravalent antibody. Successful expression of the tetravalent antibody was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot. An indirect non-competitive enzyme-linked immunosorbent assay (ELISA) revealed that the tetravalent antibody exhibited SEA-specific binding activity. A sandwich ELISA demonstrated that compared to the scFv monomer, the tetravalent antibody was more sensitive in detecting SEA. Molecular docking analysis revealed that the SEA interacted with the scFv mainly on the opposite side of the residue linked to p53. Thus, this study indicated that genetically engineered tetramerization is a potential way to improve the sensitivity of SEA-specific scFv.
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Affiliation(s)
- Weifeng Chen
- School of Food and Bioengineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China.,Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiwei Li
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingxing Dong
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohong Wang
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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15
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van Faassen H, Ryan S, Henry KA, Raphael S, Yang Q, Rossotti MA, Brunette E, Jiang S, Haqqani AS, Sulea T, MacKenzie CR, Tanha J, Hussack G. Serum albumin‐binding V
H
Hs with variable pH sensitivities enable tailored half‐life extension of biologics. FASEB J 2020; 34:8155-8171. [DOI: 10.1096/fj.201903231r] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Henk van Faassen
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Kevin A. Henry
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Qingling Yang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Martin A. Rossotti
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Eric Brunette
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Susan Jiang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Arsalan S. Haqqani
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre National Research Council Canada Montréal QC Canada
| | - C. Roger MacKenzie
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
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16
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Chen P, Lam KH, Liu Z, Mindlin FA, Chen B, Gutierrez CB, Huang L, Zhang Y, Hamza T, Feng H, Matsui T, Bowen ME, Perry K, Jin R. Structure of the full-length Clostridium difficile toxin B. Nat Struct Mol Biol 2019; 26:712-719. [PMID: 31308519 PMCID: PMC6684407 DOI: 10.1038/s41594-019-0268-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/07/2019] [Indexed: 01/07/2023]
Abstract
Clostridium difficile is an opportunistic pathogen that establishes in the colon when the gut microbiota are disrupted by antibiotics or disease. C. difficile infection (CDI) is largely caused by two virulence factors, TcdA and TcdB. Here, we report a 3.87-Å-resolution crystal structure of TcdB holotoxin that captures a unique conformation of TcdB at endosomal pH. Complementary biophysical studies suggest that the C-terminal combined repetitive oligopeptides (CROPs) domain of TcdB is dynamic and can sample open and closed conformations that may facilitate modulation of TcdB activity in response to environmental and cellular cues during intoxication. Furthermore, we report three crystal structures of TcdB-antibody complexes that reveal how antibodies could specifically inhibit the activities of individual TcdB domains. Our studies provide novel insight into the structure and function of TcdB holotoxin and identify intrinsic vulnerabilities that could be exploited to develop new therapeutics and vaccines for the treatment of CDI.
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Affiliation(s)
- Peng Chen
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Kwok-Ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Zheng Liu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Frank A Mindlin
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Baohua Chen
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Craig B Gutierrez
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Yongrong Zhang
- Department of Microbial Pathogenesis, University of Maryland Baltimore, Baltimore, MD, USA
| | - Therwa Hamza
- Department of Microbial Pathogenesis, University of Maryland Baltimore, Baltimore, MD, USA
| | - Hanping Feng
- Department of Microbial Pathogenesis, University of Maryland Baltimore, Baltimore, MD, USA
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, USA
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.
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17
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Hussack G, Ryan S, van Faassen H, Rossotti M, MacKenzie CR, Tanha J. Neutralization of Clostridium difficile toxin B with VHH-Fc fusions targeting the delivery and CROPs domains. PLoS One 2018; 13:e0208978. [PMID: 30540857 PMCID: PMC6291252 DOI: 10.1371/journal.pone.0208978] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 11/28/2018] [Indexed: 02/08/2023] Open
Abstract
An increasing number of antibody-based therapies are being considered for controlling bacterial infections, including Clostridium difficile by targeting toxins A and B. In an effort to develop novel C. difficile immunotherapeutics, we previously isolated several single-domain antibodies (VHHs) capable of toxin A neutralization through recognition of the extreme C-terminal combined repetitive oligopeptides (CROPs) domain, but failed at identifying neutralizing VHHs that bound a similar region on toxin B. Here we report the isolation of a panel of 29 VHHs targeting at least seven unique epitopes on a toxin B immunogen composed of a portion of the central delivery domain and the entire CROPs domain. Despite monovalent affinities as high as KD = 70 pM, none of the VHHs tested were capable of toxin B neutralization; however, modest toxin B inhibition was observed with VHH-VHH dimers and to a much greater extent with VHH-Fc fusions, reaching the neutralizing potency of the recently approved anti-toxin B monoclonal antibody bezlotoxumab in in vitro assays. Epitope binning revealed that several VHH-Fcs bound toxin B at sites distinct from the region recognized by bezlotoxumab, while other VHH-Fcs partially competed with bezlotoxumab for toxin binding. Therefore, the VHHs described here are effective at toxin B neutralization when formatted as bivalent VHH-Fc fusions by targeting toxin B at regions both similar and distinct from the bezlotoxumab binding site.
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Affiliation(s)
- Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- * E-mail:
| | - Shannon Ryan
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Martin Rossotti
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - C. Roger MacKenzie
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
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18
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Sulea T, Hussack G, Ryan S, Tanha J, Purisima EO. Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody. Sci Rep 2018; 8:2260. [PMID: 29396522 PMCID: PMC5797146 DOI: 10.1038/s41598-018-20599-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/17/2018] [Indexed: 02/07/2023] Open
Abstract
Assisted Design of Antibody and Protein Therapeutics (ADAPT) is an affinity maturation platform interleaving predictions and testing that was previously validated on monoclonal antibodies (mAbs). This study expands the applicability of ADAPT to single-domain antibodies (sdAbs), a promising class of recombinant antibody-based biologics. As a test case, we used the camelid sdAb A26.8, a VHH that binds Clostridium difficile toxin A (TcdA) relatively weakly but displays a reasonable level of TcdA neutralization. ADAPT-guided A26.8 affinity maturation resulted in an improvement of one order of magnitude by point mutations only, reaching an equilibrium dissociation constant (KD) of 2 nM, with the best binding mutants having similar or improved stabilities relative to the parent sdAb. This affinity improvement generated a 6-fold enhancement of efficacy at the cellular level; the A26.8 double-mutant T56R,T103R neutralizes TcdA cytotoxicity with an IC50 of 12 nM. The designed mutants with increased affinities are predicted to establish novel electrostatic interactions with the antigen. Almost full additivity of mutation effects is observed, except for positively charged residues introduced at adjacent positions. Furthermore, analysis of false-positive predictions points to general directions for improving the ADAPT platform. ADAPT guided the efficacy enhancement of an anti-toxin sdAb, an alternative therapeutic modality for C. difficile.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada.,Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Enrico O Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, H4P 2R2, Canada. .,Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada.
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19
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Kroh HK, Chandrasekaran R, Rosenthal K, Woods R, Jin X, Ohi MD, Nyborg AC, Rainey GJ, Warrener P, Spiller BW, Lacy DB. Use of a neutralizing antibody helps identify structural features critical for binding of Clostridium difficile toxin TcdA to the host cell surface. J Biol Chem 2017; 292:14401-14412. [PMID: 28705932 DOI: 10.1074/jbc.m117.781112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/05/2017] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile is a clinically significant pathogen that causes mild-to-severe (and often recurrent) colon infections. Disease symptoms stem from the activities of two large, multidomain toxins known as TcdA and TcdB. The toxins can bind, enter, and perturb host cell function through a multistep mechanism of receptor binding, endocytosis, pore formation, autoproteolysis, and glucosyltransferase-mediated modification of host substrates. Monoclonal antibodies that neutralize toxin activity provide a survival benefit in preclinical animal models and prevent recurrent infections in human clinical trials. However, the molecular mechanisms involved in these neutralizing activities are unclear. To this end, we performed structural studies on a neutralizing monoclonal antibody, PA50, a humanized mAb with both potent and broad-spectrum neutralizing activity, in complex with TcdA. Electron microscopy imaging and multiangle light-scattering analysis revealed that PA50 binds multiple sites on the TcdA C-terminal combined repetitive oligopeptides (CROPs) domain. A crystal structure of two PA50 Fabs bound to a segment of the TcdA CROPs helped define a conserved epitope that is distinct from previously identified carbohydrate-binding sites. Binding of TcdA to the host cell surface was directly blocked by either PA50 mAb or Fab and suggested that receptor blockade is the mechanism by which PA50 neutralizes TcdA. These findings highlight the importance of the CROPs C terminus in cell-surface binding and a role for neutralizing antibodies in defining structural features critical to a pathogen's mechanism of action. We conclude that PA50 protects host cells by blocking the binding of TcdA to cell surfaces.
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Affiliation(s)
- Heather K Kroh
- From the Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2363
| | - Ramyavardhanee Chandrasekaran
- From the Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2363
| | | | - Rob Woods
- MedImmune LLC, Gaithersburg, Maryland 20878-2204
| | - Xiaofang Jin
- MedImmune LLC, Gaithersburg, Maryland 20878-2204
| | - Melanie D Ohi
- the Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232-8240
| | | | | | | | - Benjamin W Spiller
- From the Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2363, .,the Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232-6600, and
| | - D Borden Lacy
- From the Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2363, .,the Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37212-2637
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20
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Abstract
Clostridium difficile is the cause of antibiotics-associated diarrhea and pseudomembranous colitis. The pathogen produces three protein toxins: C. difficile toxins A (TcdA) and B (TcdB), and C. difficile transferase toxin (CDT). The single-chain toxins TcdA and TcdB are the main virulence factors. They bind to cell membrane receptors and are internalized. The N-terminal glucosyltransferase and autoprotease domains of the toxins translocate from low-pH endosomes into the cytosol. After activation by inositol hexakisphosphate (InsP6), the autoprotease cleaves and releases the glucosyltransferase domain into the cytosol, where GTP-binding proteins of the Rho/Ras family are mono-O-glucosylated and, thereby, inactivated. Inactivation of Rho proteins disturbs the organization of the cytoskeleton and affects multiple Rho-dependent cellular processes, including loss of epithelial barrier functions, induction of apoptosis, and inflammation. CDT, the third C. difficile toxin, is a binary actin-ADP-ribosylating toxin that causes depolymerization of actin, thereby inducing formation of the microtubule-based protrusions. Recent progress in understanding of the toxins' actions include insights into the toxin structures, their interaction with host cells, and functional consequences of their actions.
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Affiliation(s)
- Klaus Aktories
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79104 Freiburg, Germany; , ,
| | - Carsten Schwan
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79104 Freiburg, Germany; , ,
| | - Thomas Jank
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, 79104 Freiburg, Germany; , ,
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21
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Péchiné S, Janoir C, Collignon A. Emerging monoclonal antibodies against Clostridium difficile infection. Expert Opin Biol Ther 2017; 17:415-427. [PMID: 28274145 DOI: 10.1080/14712598.2017.1300655] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Clostridium difficile infections are characterized by a high recurrence rate despite antibiotic treatments and there is an urgent need to develop new treatments such as fecal transplantation and immonotherapy. Besides active immunotherapy with vaccines, passive immunotherapy has shown promise, especially with monoclonal antibodies. Areas covered: Herein, the authors review the different assays performed with monoclonal antibodies against C. difficile toxins and surface proteins to treat or prevent primary or recurrent episodes of C. difficile infection in animal models and in clinical trials as well. Notably, the authors lay emphasis on the phase III clinical trial (MODIFY II), which allowed bezlotoxumab to be approved by the Food and Drug Administration and the European Medicines Agency. They also review new strategies for producing single domain antibodies and nanobodies against C. difficile and new approaches to deliver them in the digestive tract. Expert opinion: Only two human Mabs against TcdA and TcdB have been tested alone or in combination in clinical trials. However, many animal model studies have provided rationale for the use of Mabs and nanobodies in C. difficile infection and pave the way for further clinical investigation.
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Affiliation(s)
- Séverine Péchiné
- a EA4043 Faculté de Pharmacie , Univ Paris-Sud, Université Paris-Saclay , Chatenay-Malabry , France
| | - Claire Janoir
- a EA4043 Faculté de Pharmacie , Univ Paris-Sud, Université Paris-Saclay , Chatenay-Malabry , France
| | - Anne Collignon
- a EA4043 Faculté de Pharmacie , Univ Paris-Sud, Université Paris-Saclay , Chatenay-Malabry , France
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22
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Epitopes and Mechanism of Action of the Clostridium difficile Toxin A-Neutralizing Antibody Actoxumab. J Mol Biol 2017; 429:1030-1044. [PMID: 28232034 DOI: 10.1016/j.jmb.2017.02.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/14/2017] [Accepted: 02/14/2017] [Indexed: 12/17/2022]
Abstract
The exotoxins toxin A (TcdA) and toxin B (TcdB) are produced by the bacterial pathogen Clostridium difficile and are responsible for the pathology associated with C. difficile infection (CDI). The antitoxin antibodies actoxumab and bezlotoxumab bind to and neutralize TcdA and TcdB, respectively. Bezlotoxumab was recently approved by the FDA for reducing the recurrence of CDI. We have previously shown that a single molecule of bezlotoxumab binds to two distinct epitopes within the TcdB combined repetitive oligopeptide (CROP) domain, preventing toxin binding to host cells. In this study, we characterize the binding of actoxumab to TcdA and examine its mechanism of toxin neutralization. Using a combination of approaches including a number of biophysical techniques, we show that there are two distinct actoxumab binding sites within the CROP domain of TcdA centered on identical amino acid sequences at residues 2162-2189 and 2410-2437. Actoxumab binding caused the aggregation of TcdA especially at higher antibody:toxin concentration ratios. Actoxumab prevented the association of TcdA with target cells demonstrating that actoxumab neutralizes toxin activity by inhibiting the first step of the intoxication cascade. This mechanism of neutralization is similar to that observed with bezlotoxumab and TcdB. Comparisons of the putative TcdA epitope sequences across several C. difficile ribotypes and homologous repeat sequences within TcdA suggest a structural basis for observed differences in actoxumab binding and/or neutralization potency. These data provide a mechanistic basis for the protective effects of the antibody in vitro and in vivo, including in various preclinical models of CDI.
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23
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Henry KA, Sulea T, van Faassen H, Hussack G, Purisima EO, MacKenzie CR, Arbabi-Ghahroudi M. A Rational Engineering Strategy for Designing Protein A-Binding Camelid Single-Domain Antibodies. PLoS One 2016; 11:e0163113. [PMID: 27631624 PMCID: PMC5025174 DOI: 10.1371/journal.pone.0163113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/04/2016] [Indexed: 12/21/2022] Open
Abstract
Staphylococcal protein A (SpA) and streptococcal protein G (SpG) affinity chromatography are the gold standards for purifying monoclonal antibodies (mAbs) in therapeutic applications. However, camelid VHH single-domain Abs (sdAbs or VHHs) are not bound by SpG and only sporadically bound by SpA. Currently, VHHs require affinity tag-based purification, which limits their therapeutic potential and adds considerable complexity and cost to their production. Here we describe a simple and rapid mutagenesis-based approach designed to confer SpA binding upon a priori non-SpA-binding VHHs. We show that SpA binding of VHHs is determined primarily by the same set of residues as in human mAbs, albeit with an unexpected degree of tolerance to substitutions at certain core and non-core positions and some limited dependence on at least one residue outside the SpA interface, and that SpA binding could be successfully introduced into five VHHs against three different targets with no adverse effects on expression yield or antigen binding. Next-generation sequencing of llama, alpaca and dromedary VHH repertoires suggested that species differences in SpA binding may result from frequency variation in specific deleterious polymorphisms, especially Ile57. Thus, the SpA binding phenotype of camelid VHHs can be easily modulated to take advantage of tag-less purification techniques, although the frequency with which this is required may depend on the source species.
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Affiliation(s)
- Kevin A. Henry
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
| | - Traian Sulea
- Human Health Therapeutics Portfolio, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada, H4P 2R2
| | - Henk van Faassen
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
| | - Greg Hussack
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
| | - Enrico O. Purisima
- Human Health Therapeutics Portfolio, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada, H4P 2R2
| | - C. Roger MacKenzie
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Portfolio, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario, Canada, K1A 0R6
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada, N1G 2W1
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6
- * E-mail:
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24
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Abstract
Clostridium difficile continues to be one of the most prevalent hospital-acquired bacterial infections in the developed world, despite the recent introduction of a novel and effective antibiotic agent (fidaxomicin). Alternative approaches under investigation to combat the anaerobic Gram-positive bacteria include fecal transplantation therapy, vaccines, and antibody-based immunotherapies. In this review, we catalog the recent advances in antibody-based approaches under development and in the clinic for the treatment of C. difficile infection. By and large, inhibitory antibodies that recognize the primary C. difficile virulence factors, toxin A and toxin B, are the most popular passive immunotherapies under investigation. We provide a detailed summary of the toxin epitopes recognized by various antitoxin antibodies and discuss general trends on toxin inhibition efficacy. In addition, antibodies to other C. difficile targets, such as surface-layer proteins, binary toxin, motility factors, and adherence and colonization factors, are introduced in this review.
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Affiliation(s)
- Greg Hussack
- Human Health Therapeutics Portfolio, National Research Council Canada, Ottawa
| | - Jamshid Tanha
- Human Health Therapeutics Portfolio, National Research Council Canada, Ottawa; School of Environmental Sciences, University of Guelph, Guelph; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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25
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Herrera C, Klokk TI, Cole R, Sandvig K, Mantis NJ. A Bispecific Antibody Promotes Aggregation of Ricin Toxin on Cell Surfaces and Alters Dynamics of Toxin Internalization and Trafficking. PLoS One 2016; 11:e0156893. [PMID: 27300140 PMCID: PMC4907443 DOI: 10.1371/journal.pone.0156893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 05/21/2016] [Indexed: 11/19/2022] Open
Abstract
JJX12 is an engineered bispecific antibody against ricin, a member of the medically important A-B family of toxins that exploits retrograde transport as means to gain entry into the cytosol of target cells. JJX12 consists of RTA-D10, a camelid single variable domain (VHH) antibody directed against an epitope on ricin's enzymatic subunit (RTA), linked via a 15-mer peptide to RTB-B7, a VHH against ricin's bivalent galactose binding subunit (RTB). We previously reported that JJX12, but not an equimolar mixture of RTA-D10 and RTB-B7 monomers, was able to passively protect mice against a lethal dose ricin challenge, demonstrating that physically linking RTB-B7 and RTA-D10 is critical for toxin-neutralizing activity in vivo. We also reported that JJX12 promotes aggregation of ricin in solution, presumably through the formation of intermolecular crosslinking. In the current study, we now present evidence that JJX12 affects the dynamics of ricin uptake and trafficking in human epithelial cells. Confocal microscopy, as well as live cell imaging coupled with endocytosis pathway-specific inhibitors, revealed that JJX12-toxin complexes are formed on the surfaces of mammalian cells and internalized via a pathway sensitive to amiloride, a known inhibitor of macropinocytosis. Moreover, in the presence of JJX12, retrograde transport of ricin to the trans-Golgi network was significantly reduced, while accumulation of the toxin in late endosomes was significantly enhanced. In summary, we propose that JJX12, by virtue of its ability to crosslink ricin toxin, alters the route of toxin uptake and trafficking within cells.
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Affiliation(s)
- Cristina Herrera
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
| | - Tove Irene Klokk
- Department of Molecular Cell Biology and Centre for Cancer Biomedicine, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Richard Cole
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Kirsten Sandvig
- Department of Molecular Cell Biology and Centre for Cancer Biomedicine, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nicholas J. Mantis
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York, United States of America
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26
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Di Bella S, Ascenzi P, Siarakas S, Petrosillo N, di Masi A. Clostridium difficile Toxins A and B: Insights into Pathogenic Properties and Extraintestinal Effects. Toxins (Basel) 2016; 8:E134. [PMID: 27153087 PMCID: PMC4885049 DOI: 10.3390/toxins8050134] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile infection (CDI) has significant clinical impact especially on the elderly and/or immunocompromised patients. The pathogenicity of Clostridium difficile is mainly mediated by two exotoxins: toxin A (TcdA) and toxin B (TcdB). These toxins primarily disrupt the cytoskeletal structure and the tight junctions of target cells causing cell rounding and ultimately cell death. Detectable C. difficile toxemia is strongly associated with fulminant disease. However, besides the well-known intestinal damage, recent animal and in vitro studies have suggested a more far-reaching role for these toxins activity including cardiac, renal, and neurologic impairment. The creation of C. difficile strains with mutations in the genes encoding toxin A and B indicate that toxin B plays a major role in overall CDI pathogenesis. Novel insights, such as the role of a regulator protein (TcdE) on toxin production and binding interactions between albumin and C. difficile toxins, have recently been discovered and will be described. Our review focuses on the toxin-mediated pathogenic processes of CDI with an emphasis on recent studies.
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Affiliation(s)
- Stefano Di Bella
- 2nd Infectious Diseases Division, National Institute for Infectious Diseases "L. Spallanzani", Rome 00149, Italy.
| | - Paolo Ascenzi
- Department of Science, Roma Tre University, Rome 00154, Italy.
| | - Steven Siarakas
- Department of Microbiology and Infectious Diseases, Concord Repatriation General Hospital, Sydney 2139, Australia.
| | - Nicola Petrosillo
- 2nd Infectious Diseases Division, National Institute for Infectious Diseases "L. Spallanzani", Rome 00149, Italy.
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27
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Abstract
Infection of the colon with the Gram-positive bacterium Clostridium difficile is potentially life threatening, especially in elderly people and in patients who have dysbiosis of the gut microbiota following antimicrobial drug exposure. C. difficile is the leading cause of health-care-associated infective diarrhoea. The life cycle of C. difficile is influenced by antimicrobial agents, the host immune system, and the host microbiota and its associated metabolites. The primary mediators of inflammation in C. difficile infection (CDI) are large clostridial toxins, toxin A (TcdA) and toxin B (TcdB), and, in some bacterial strains, the binary toxin CDT. The toxins trigger a complex cascade of host cellular responses to cause diarrhoea, inflammation and tissue necrosis - the major symptoms of CDI. The factors responsible for the epidemic of some C. difficile strains are poorly understood. Recurrent infections are common and can be debilitating. Toxin detection for diagnosis is important for accurate epidemiological study, and for optimal management and prevention strategies. Infections are commonly treated with specific antimicrobial agents, but faecal microbiota transplants have shown promise for recurrent infections. Future biotherapies for C. difficile infections are likely to involve defined combinations of key gut microbiota.
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Affiliation(s)
- Wiep Klaas Smits
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Victoria, Australia
| | - D. Borden Lacy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, and The Veterans Affairs Tennessee Valley Healthcare System, Nashville Tennessee, USA
| | - Mark H. Wilcox
- Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Ed J. Kuijper
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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28
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Chumbler NM, Rutherford SA, Zhang Z, Farrow MA, Lisher JP, Farquhar E, Giedroc DP, Spiller BW, Melnyk RA, Lacy DB. Crystal structure of Clostridium difficile toxin A. Nat Microbiol 2016; 1:15002. [PMID: 27571750 PMCID: PMC4976693 DOI: 10.1038/nmicrobiol.2015.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/18/2015] [Indexed: 02/04/2023]
Abstract
Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics.
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Affiliation(s)
- Nicole M. Chumbler
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Stacey A. Rutherford
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Zhifen Zhang
- Department of Biochemistry, University of Toronto and the Molecular Structure & Function Research Institute at The Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
| | - Melissa A. Farrow
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - John P. Lisher
- Interdisciplinary Graduate Program in Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Erik Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences, National Synchrotron Light Source, Building 725, Brookhaven National Laboratory, New York 11973, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Benjamin W. Spiller
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA
| | - Roman A. Melnyk
- Department of Biochemistry, University of Toronto and the Molecular Structure & Function Research Institute at The Hospital for Sick Children, Toronto, Ontario M5S 1A8, Canada
| | - D. Borden Lacy
- Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, USA
- The Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee 37212, USA
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29
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Herrera C, Tremblay JM, Shoemaker CB, Mantis NJ. Mechanisms of Ricin Toxin Neutralization Revealed through Engineered Homodimeric and Heterodimeric Camelid Antibodies. J Biol Chem 2015; 290:27880-9. [PMID: 26396190 DOI: 10.1074/jbc.m115.658070] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 11/06/2022] Open
Abstract
Novel antibody constructs consisting of two or more different camelid heavy-chain only antibodies (VHHs) joined via peptide linkers have proven to have potent toxin-neutralizing activity in vivo against Shiga, botulinum, Clostridium difficile, anthrax, and ricin toxins. However, the mechanisms by which these so-called bispecific VHH heterodimers promote toxin neutralization remain poorly understood. In the current study we produced a new collection of ricin-specific VHH heterodimers, as well as VHH homodimers, and characterized them for their ability neutralize ricin in vitro and in vivo. We demonstrate that the VHH heterodimers, but not homodimers were able to completely protect mice against ricin challenge, even though the two classes of antibodies (heterodimers and homodimers) had virtually identical affinities for ricin holotoxin and similar IC50 values in a Vero cell cytotoxicity assay. The VHH heterodimers did differ from the homodimers in their ability to promote toxin aggregation in solution, as revealed through analytical ultracentrifugation. Moreover, the VHH heterodimers that were most effective at promoting ricin aggregation in solution were also the most effective at blocking ricin attachment to cell surfaces. Collectively, these data suggest that heterodimeric VHH-based neutralizing agents may function through the formation of antibody-toxin complexes that are impaired in their ability to access host cell receptors.
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Affiliation(s)
- Cristina Herrera
- From the Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York 12208, the Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York 12201, and
| | - Jacqueline M Tremblay
- the Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachuetts 01536
| | - Charles B Shoemaker
- the Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachuetts 01536
| | - Nicholas J Mantis
- From the Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York 12208, the Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York 12201, and
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30
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Nguyen VS, Spinelli S, Desmyter A, Le TTH, Kellenberger C, Cascales E, Cambillau C, Roussel A. Production, crystallization and X-ray diffraction analysis of a complex between a fragment of the TssM T6SS protein and a camelid nanobody. Acta Crystallogr F Struct Biol Commun 2015; 71:266-71. [PMID: 25760699 PMCID: PMC4356300 DOI: 10.1107/s2053230x15000709] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/13/2015] [Indexed: 11/10/2022] Open
Abstract
The type VI secretion system (T6SS) is a machine evolved by Gram-negative bacteria to deliver toxin effectors into target bacterial or eukaryotic cells. The T6SS is functionally and structurally similar to the contractile tail of the Myoviridae family of bacteriophages and can be viewed as a syringe anchored to the bacterial membrane by a transenvelope complex. The membrane complex is composed of three proteins: the TssM and TssL inner membrane components and the TssJ outer membrane lipoprotein. The TssM protein is central as it interacts with both TssL and TssJ, therefore linking the membranes. Using controlled trypsinolysis, a 32.4 kDa C-terminal fragment of enteroaggregative Escherichia coli TssM (TssM32Ct) was purified. A nanobody obtained from llama immunization, nb25, exhibited subnanomolar affinity for TssM32Ct. Crystals of the TssM32Ct-nb25 complex were obtained and diffracted to 1.9 Å resolution. The crystals belonged to space group P64, with unit-cell parameters a = b = 95.23, c = 172.95 Å. Molecular replacement with a model nanobody indicated the presence of a dimer of TssM32Ct-nb25 in the asymmetric unit.
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Affiliation(s)
- Van Son Nguyen
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Campus de Luminy, Case 932, 13288 Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288 Marseille, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Campus de Luminy, Case 932, 13288 Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288 Marseille, France
| | - Aline Desmyter
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Campus de Luminy, Case 932, 13288 Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288 Marseille, France
| | - Thi Thu Hang Le
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Campus de Luminy, Case 932, 13288 Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288 Marseille, France
| | - Christine Kellenberger
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Campus de Luminy, Case 932, 13288 Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288 Marseille, France
| | - Eric Cascales
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Campus de Luminy, Case 932, 13288 Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288 Marseille, France
| | - Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Campus de Luminy, Case 932, 13288 Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288 Marseille, France
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31
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Desmyter A, Spinelli S, Roussel A, Cambillau C. Camelid nanobodies: killing two birds with one stone. Curr Opin Struct Biol 2015; 32:1-8. [PMID: 25614146 DOI: 10.1016/j.sbi.2015.01.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 12/23/2014] [Accepted: 01/05/2015] [Indexed: 01/09/2023]
Abstract
In recent years, the use of single-domain camelid immunoglobulins, termed vHHs or nanobodies, has seen increasing growth in biotechnology, pharmaceutical applications and structure/function research. The usefulness of nanobodies in structural biology is now firmly established, as they provide access to new epitopes in concave and hinge regions - and stabilize them. These sites are often associated with enzyme inhibition or receptor neutralization, and, at the same time, provide favorable surfaces for crystal packing. Remarkable results have been achieved by using nanobodies with flexible multi-domain proteins, large complexes and, last but not least, membrane proteins. While generating nanobodies is still a rather long and expensive procedure, the advent of naive libraries might be expected to facilitate the whole process.
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Affiliation(s)
- Aline Desmyter
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Silvia Spinelli
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Alain Roussel
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Christian Cambillau
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France.
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32
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Sha H, Zou Z, Xin K, Bian X, Cai X, Lu W, Chen J, Chen G, Huang L, Blair AM, Cao P, Liu B. Tumor-penetrating peptide fused EGFR single-domain antibody enhances cancer drug penetration into 3D multicellular spheroids and facilitates effective gastric cancer therapy. J Control Release 2014; 200:188-200. [PMID: 25553823 DOI: 10.1016/j.jconrel.2014.12.039] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 12/02/2014] [Accepted: 12/25/2014] [Indexed: 12/23/2022]
Abstract
Human tumors, including gastric cancer, frequently express high levels of epidermal growth factor receptors (EGFRs), which are associated with a poor prognosis. Targeted delivery of anticancer drugs to cancerous tissues shows potential in sparing unaffected tissues. However, it has been a major challenge for drug penetration in solid tumor tissues due to the complicated tumor microenvironment. We have constructed a recombinant protein named anti-EGFR-iRGD consisting of an anti-EGFR VHH (the variable domain from the heavy chain of the antibody) fused to iRGD, a tumor-specific binding peptide with high permeability. Anti-EGFR-iRGD, which targets EGFR and αvβ3, spreads extensively throughout both the multicellular spheroids and the tumor mass. The recombinant protein anti-EGFR-iRGD also exhibited antitumor activity in tumor cell lines, multicellular spheroids, and mice. Moreover, anti-EGFR-iRGD could improve anticancer drugs, such as doxorubicin (DOX), bevacizumab, nanoparticle permeability and efficacy in multicellular spheroids. This study draws attention to the importance of iRGD peptide in the therapeutic approach of anti-EGFR-iRGD. As a consequence, anti-EGFR-iRGD could be a drug candidate for cancer treatment and a useful adjunct of other anticancer drugs.
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Affiliation(s)
- Huizi Sha
- The Comprehensive Cancer Center of Drum-Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Zhengyun Zou
- The Comprehensive Cancer Center of Drum-Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Kai Xin
- The Comprehensive Cancer Center of Drum-Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Xinyu Bian
- The Comprehensive Cancer Center of Drum-Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Xueting Cai
- Laboratory of Cellular and Molecular Biology, Jiangsu Province Academy of Chinese Medicine, Nanjing, China; Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wuguang Lu
- Laboratory of Cellular and Molecular Biology, Jiangsu Province Academy of Chinese Medicine, Nanjing, China; Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiao Chen
- Laboratory of Cellular and Molecular Biology, Jiangsu Province Academy of Chinese Medicine, Nanjing, China; Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Gang Chen
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Leaf Huang
- Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Andrew M Blair
- Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Peng Cao
- Laboratory of Cellular and Molecular Biology, Jiangsu Province Academy of Chinese Medicine, Nanjing, China; Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Baorui Liu
- The Comprehensive Cancer Center of Drum-Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China.
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33
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Mizrahi A, Collignon A, Péchiné S. Passive and active immunization strategies against Clostridium difficile infections: State of the art. Anaerobe 2014; 30:210-9. [DOI: 10.1016/j.anaerobe.2014.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/07/2014] [Accepted: 07/18/2014] [Indexed: 02/04/2023]
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34
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Kim DY, Hussack G, Kandalaft H, Tanha J. Mutational approaches to improve the biophysical properties of human single-domain antibodies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1983-2001. [DOI: 10.1016/j.bbapap.2014.07.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/05/2014] [Accepted: 07/11/2014] [Indexed: 01/06/2023]
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35
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Orth P, Xiao L, Hernandez LD, Reichert P, Sheth PR, Beaumont M, Yang X, Murgolo N, Ermakov G, DiNunzio E, Racine F, Karczewski J, Secore S, Ingram RN, Mayhood T, Strickland C, Therien AG. Mechanism of action and epitopes of Clostridium difficile toxin B-neutralizing antibody bezlotoxumab revealed by X-ray crystallography. J Biol Chem 2014; 289:18008-21. [PMID: 24821719 DOI: 10.1074/jbc.m114.560748] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The symptoms of Clostridium difficile infections are caused by two exotoxins, TcdA and TcdB, which target host colonocytes by binding to unknown cell surface receptors, at least in part via their combined repetitive oligopeptide (CROP) domains. A combination of the anti-TcdA antibody actoxumab and the anti-TcdB antibody bezlotoxumab is currently under development for the prevention of recurrent C. difficile infections. We demonstrate here through various biophysical approaches that bezlotoxumab binds to specific regions within the N-terminal half of the TcdB CROP domain. Based on this information, we solved the x-ray structure of the N-terminal half of the TcdB CROP domain bound to Fab fragments of bezlotoxumab. The structure reveals that the TcdB CROP domain adopts a β-solenoid fold consisting of long and short repeats and that bezlotoxumab binds to two homologous sites within the CROP domain, partially occluding two of the four putative carbohydrate binding pockets located in TcdB. We also show that bezlotoxumab neutralizes TcdB by blocking binding of TcdB to mammalian cells. Overall, our data are consistent with a model wherein a single molecule of bezlotoxumab neutralizes TcdB by binding via its two Fab regions to two epitopes within the N-terminal half of the TcdB CROP domain, partially blocking the carbohydrate binding pockets of the toxin and preventing toxin binding to host cells.
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Affiliation(s)
- Peter Orth
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | - Li Xiao
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | - Paul Reichert
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | - Payal R Sheth
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | - Xiaoyu Yang
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | | | | | - Fred Racine
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
| | | | - Susan Secore
- Merck & Co., Inc., West Point, Pennsylvania 19486
| | | | - Todd Mayhood
- From Merck & Co., Inc., Kenilworth, New Jersey 07023
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Antibodies for treatment of Clostridium difficile infection. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2014; 21:913-23. [PMID: 24789799 DOI: 10.1128/cvi.00116-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antibodies for the treatment of Clostridium difficile infection (CDI) have been demonstrated to be effective in the research and clinical environments. Early uncertainties about molecular and treatment modalities now appear to have converged upon the systemic dosing of mixtures of human IgG1. Although multiple examples of high-potency monoclonal antibodies (MAbs) exist, significant difficulties were initially encountered in their discovery. This minireview describes historical and contemporary MAbs and highlights differences between the most potent MAbs, which may offer insight into the pathogenesis and treatment of CDI.
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Translocation domain mutations affecting cellular toxicity identify the Clostridium difficile toxin B pore. Proc Natl Acad Sci U S A 2014; 111:3721-6. [PMID: 24567384 DOI: 10.1073/pnas.1400680111] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Disease associated with Clostridium difficile infection is caused by the actions of the homologous toxins TcdA and TcdB on colonic epithelial cells. Binding to target cells triggers toxin internalization into acidified vesicles, whereupon cryptic segments from within the 1,050-aa translocation domain unfurl and insert into the bounding membrane, creating a transmembrane passageway to the cytosol. Our current understanding of the mechanisms underlying pore formation and the subsequent translocation of the upstream cytotoxic domain to the cytosol is limited by the lack of information available regarding the identity and architecture of the transmembrane pore. Here, through systematic perturbation of conserved sites within predicted membrane-insertion elements of the translocation domain, we uncovered highly sensitive residues--clustered between amino acids 1,035 and 1,107--that when individually mutated, reduced cellular toxicity by as much as >1,000-fold. We demonstrate that defective variants are defined by impaired pore formation in planar lipid bilayers and biological membranes, resulting in an inability to intoxicate cells through either apoptotic or necrotic pathways. These findings along with the unexpected similarities uncovered between the pore-forming "hotspots" of TcdB and the well-characterized α-helical diphtheria toxin translocation domain provide insights into the structure and mechanism of formation of the translocation pore for this important class of pathogenic toxins.
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