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Alanko I, Sandberg R, Brockmann E, de Haas CJC, van Strijp JAG, Lamminmäki U, Salo‐Ahen OMH. Isolation and functional analysis of phage-displayed antibody fragments targeting the staphylococcal superantigen-like proteins. Microbiologyopen 2023; 12:e1371. [PMID: 37642487 PMCID: PMC10350561 DOI: 10.1002/mbo3.1371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 08/31/2023] Open
Abstract
Staphylococcus aureus produces numerous virulence factors that manipulate the immune system, helping the bacteria avoid phagocytosis. In this study, we are investigating three immune evasion molecules called the staphylococcal superantigen-like proteins 1, 5, and 10 (SSL1, SSL5, and SSL10). All three SSLs inhibit vital host immune processes and contribute to S. aureus immune evasion. This study aimed to identify single-chain variable fragment (scFvs) antibodies from synthetic antibody phage libraries, which can recognize either of the three SSLs and could block the interaction between the SSLs and their respective human targets. The antibodies were isolated after three rounds of panning against SSL1, SSL5, and SSL10, and their ability to bind to the SSLs was studied using a time-resolved fluorescence-based immunoassay. We successfully obtained altogether 44 unique clones displaying binding activity to either SSL1, SSL5, or SSL10. The capability of the SSL-recognizing scFvs to inhibit the SSLs' function was tested in an MMP9 enzymatic activity assay, a P-selectin glycoprotein ligand 1 competitive binding assay, and an IgG1-mediated phagocytosis assay. We could show that one scFv was able to inhibit SSL1 and maintain MMP9 activity in a concentration-dependent manner. Finally, the structure of this inhibiting scFv was modeled and used to create putative scFv-SSL1-complex models by protein-protein docking. The complex models were subjected to a 100-ns molecular dynamics simulation to assess the possible binding mode of the antibody.
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Affiliation(s)
- Ida Alanko
- Faculty of Sciences and Engineering, Pharmaceutical Sciences Laboratory (Pharmacy) & Structural Bioinformatics Laboratory (Biochemistry) TurkuÅbo Akademi UniversityTurkuFinland
| | - Rebecca Sandberg
- Faculty of Sciences and Engineering, Pharmaceutical Sciences Laboratory (Pharmacy) & Structural Bioinformatics Laboratory (Biochemistry) TurkuÅbo Akademi UniversityTurkuFinland
| | | | - Carla J. C. de Haas
- Department of Medical Microbiology, University Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Jos A. G. van Strijp
- Department of Medical Microbiology, University Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Urpo Lamminmäki
- Department of Life TechnologiesUniversity of TurkuTurkuFinland
| | - Outi M. H. Salo‐Ahen
- Faculty of Sciences and Engineering, Pharmaceutical Sciences Laboratory (Pharmacy) & Structural Bioinformatics Laboratory (Biochemistry) TurkuÅbo Akademi UniversityTurkuFinland
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Mahajan SP, Ruffolo JA, Frick R, Gray JJ. Hallucinating structure-conditioned antibody libraries for target-specific binders. Front Immunol 2022; 13:999034. [PMID: 36341416 PMCID: PMC9635398 DOI: 10.3389/fimmu.2022.999034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Antibodies are widely developed and used as therapeutics to treat cancer, infectious disease, and inflammation. During development, initial leads routinely undergo additional engineering to increase their target affinity. Experimental methods for affinity maturation are expensive, laborious, and time-consuming and rarely allow the efficient exploration of the relevant design space. Deep learning (DL) models are transforming the field of protein engineering and design. While several DL-based protein design methods have shown promise, the antibody design problem is distinct, and specialized models for antibody design are desirable. Inspired by hallucination frameworks that leverage accurate structure prediction DL models, we propose the FvHallucinator for designing antibody sequences, especially the CDR loops, conditioned on an antibody structure. Such a strategy generates targeted CDR libraries that retain the conformation of the binder and thereby the mode of binding to the epitope on the antigen. On a benchmark set of 60 antibodies, FvHallucinator generates sequences resembling natural CDRs and recapitulates perplexity of canonical CDR clusters. Furthermore, the FvHallucinator designs amino acid substitutions at the VH-VL interface that are enriched in human antibody repertoires and therapeutic antibodies. We propose a pipeline that screens FvHallucinator designs to obtain a library enriched in binders for an antigen of interest. We apply this pipeline to the CDR H3 of the Trastuzumab-HER2 complex to generate in silico designs predicted to improve upon the binding affinity and interfacial properties of the original antibody. Thus, the FvHallucinator pipeline enables generation of inexpensive, diverse, and targeted antibody libraries enriched in binders for antibody affinity maturation.
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Affiliation(s)
- Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Jeffrey A. Ruffolo
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Rahel Frick
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
- *Correspondence: Jeffrey J. Gray,
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Pennington LF, Gasser P, Kleinboelting S, Zhang C, Skiniotis G, Eggel A, Jardetzky TS. Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex. Nat Commun 2021; 12:7069. [PMID: 34862384 PMCID: PMC8642555 DOI: 10.1038/s41467-021-27397-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/11/2021] [Indexed: 11/15/2022] Open
Abstract
Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional mechanism where antibody-mediated “disruption” of stable high-affinity macromolecular complexes can potentially enhance therapeutic efficacy. However, this mechanism is not well understood or utilized therapeutically. Here, we investigate and engineer the weak disruptive activity of an existing therapeutic antibody, omalizumab, which targets IgE antibodies to block the allergic response. We develop a yeast display approach to select for and engineer antibody disruptive efficiency and generate potent omalizumab variants that dissociate receptor-bound IgE. We determine a low resolution cryo-EM structure of a transient disruption intermediate containing the IgE-Fc, its partially dissociated receptor and an antibody inhibitor. Our results provide a conceptual framework for engineering disruptive inhibitors for other targets, insights into the failure in clinical trials of the previous high affinity omalizumab HAE variant and anti-IgE antibodies that safely and rapidly disarm allergic effector cells. Facilitated dissociation is a mechanism where antibody-mediated disruption of high-affinity complexes can enhance the therapeutic effects of a drug. Here the authors present a yeast display approach to select and engineer omalizumab variants that dissociate receptor-bound IgE to accelerate its inhibition of the allergic response.
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Affiliation(s)
- Luke F Pennington
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Progam in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Sean N. Parker Center for Allergy Research at Stanford University, Stanford, CA, 94305, USA
| | - Pascal Gasser
- Department of Rheumatology and Immunology, University Hospital Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Silke Kleinboelting
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chensong Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander Eggel
- Department of Rheumatology and Immunology, University Hospital Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Theodore S Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Progam in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Sean N. Parker Center for Allergy Research at Stanford University, Stanford, CA, 94305, USA.
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