1
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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,
| |
Collapse
|
2
|
Hussack G, Rossotti MA, van Faassen H, Murase T, Eugenio L, Schrag JD, Ng KKS, Tanha J. Corrigendum: Structure-guided design of a potent Clostridioides difficile toxin A inhibitor. Front Microbiol 2023; 14:1167817. [PMID: 37065148 PMCID: PMC10100925 DOI: 10.3389/fmicb.2023.1167817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/20/2023] [Indexed: 04/18/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1110541.].
Collapse
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
| |
Collapse
|
3
|
Kerk D, Valdés-Tresanco ME, Toth R, Noskov SY, Ng KKS, Moorhead GB. Origin of the Phosphoprotein Phosphatase (PPP) sequence family in Bacteria: Critical ancestral sequence changes, radiation patterns and substrate binding features. BBA Advances 2021; 1:100005. [PMID: 37082010 PMCID: PMC10074919 DOI: 10.1016/j.bbadva.2021.100005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Phosphoprotein phosphatases (PPP) belong to the PPP Sequence family, which in turn belongs to the broader metallophosphoesterase (MPE) superfamily. The relationship between the PPP Sequence family and other members of the MPE superfamily remains unresolved, in particular what transitions took place in an ancestral MPE to ultimately produce the phosphoprotein specific phosphatases (PPPs). Methods We use structural and sequence alignment data, phylogenetic tree analysis, sequence signature (Weblogo) analysis, in silico protein-peptide modeling data, and in silico mutagenesis to trace a likely route of evolution from MPEs to the PPP Sequence family. Hidden Markov Model (HMM) based iterative database search strategies were utilized to identify PPP Sequence Family members from numerous bacterial groups. Results Using Mre11 as proxy for an ancestral nuclease-like MPE we trace a possible evolutionary route that alters a single active site substrate binding His-residue to yield a new substrate binding accessory, the "2-Arg-Clamp". The 2-Arg-Clamp is not found in MPEs, but is present in all PPP Sequence family members, where the phosphomonesterase reaction predominates. Variation in position of the clamp arginines and a supplemental sequence loop likely provide substrate specificity for each PPP Sequence family group. Conclusions Loss of a key substrate binding His-in MPEs opened the path to bind novel substrates and evolution of the 2-Arg-Clamp, a sequence change seen in both bacterial and eukaryotic phosphoprotein phosphatases.General significance: We establish a likely evolutionary route from nuclease-like MPE to PPP Sequence family enzymes, that includes the phosphoprotein phosphatases.
Collapse
|
4
|
Sanhueza CA, Cartmell J, El-Hawiet A, Szpacenko A, Kitova EN, Daneshfar R, Klassen JS, Lang DE, Eugenio L, Ng KKS, Kitov PI, Bundle DR. Evaluation of a focused virtual library of heterobifunctional ligands for Clostridium difficile toxins. Org Biomol Chem 2015; 13:283-98. [DOI: 10.1039/c4ob01838a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Higher activity glycopeptoid ligands for two largeClostridium difficiletoxins TcdA and TcdB were discoveredviamodular fragment-based design and virtual screening.
Collapse
Affiliation(s)
| | | | - Amr El-Hawiet
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | - Adam Szpacenko
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | | | | | | | - Dean E. Lang
- Department of Biological Sciences
- University of Calgary
- Calgary
- Canada
| | - Luiz Eugenio
- Department of Biological Sciences
- University of Calgary
- Calgary
- Canada
| | - Kenneth K.-S. Ng
- Department of Biological Sciences
- University of Calgary
- Calgary
- Canada
| | - Pavel I. Kitov
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | | |
Collapse
|
5
|
Zhang P, Razi N, Eugenio L, Fentabil M, Kitova EN, Klassen JS, Bundle DR, Ng KKS, Ling CC. Unexpected structure of a C. difficile toxin A ligand necessitates an annotation correction in a popular screening library. Chem Commun (Camb) 2011; 47:12397-9. [DOI: 10.1039/c1cc15344g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|