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Zhang X, Wu R, Liu Q, Zhou L. Interfacial water molecules contribute to antibody binding to the receptor-binding domain of SARS-CoV-2 spike protein. J Biomol Struct Dyn 2023; 41:14929-14938. [PMID: 37042961 DOI: 10.1080/07391102.2023.2199336] [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: 11/23/2022] [Accepted: 02/18/2023] [Indexed: 04/13/2023]
Abstract
Antibodies that recognize the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially the neutralizing antibodies, carry great hope in the treatment and final elimination of COVID-19. Driven by a synchronized global effort, thousands of antibodies against the spike protein have been identified during the past two years, with the structural information available at atomistic detail for hundreds of these antibodies. We developed an improved molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method including explicitly treated interfacial water to calculate the binding free energy between representative antibodies and the receptor binding domain (RBD) domain of SARS-COV-2 spike proteins. We discovered that explicit treatment of water molecules located at the interface between RBD and antibody effectively improves the results for the WT and variants of concern (VOC) systems. Interfacial water molecules, together with surface and internal water molecules, behave drastically from bulk water and exert peculiar impacts on protein dynamics and energy, and thus warrant explicit treatment to complement implicit solvent models. Our results illustrate the importance of including interfacial water molecules to approach efficient and reliable prediction of binding free energy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xin Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, P.R. China
| | - Ruiping Wu
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, P.R. China
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong, P. R. China
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Lei Zhou
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, P.R. China
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Fernández-Quintero ML, Ljungars A, Waibl F, Greiff V, Andersen JT, Gjølberg TT, Jenkins TP, Voldborg BG, Grav LM, Kumar S, Georges G, Kettenberger H, Liedl KR, Tessier PM, McCafferty J, Laustsen AH. Assessing developability early in the discovery process for novel biologics. MAbs 2023; 15:2171248. [PMID: 36823021 PMCID: PMC9980699 DOI: 10.1080/19420862.2023.2171248] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/18/2023] [Indexed: 02/25/2023] Open
Abstract
Beyond potency, a good developability profile is a key attribute of a biological drug. Selecting and screening for such attributes early in the drug development process can save resources and avoid costly late-stage failures. Here, we review some of the most important developability properties that can be assessed early on for biologics. These include the influence of the source of the biologic, its biophysical and pharmacokinetic properties, and how well it can be expressed recombinantly. We furthermore present in silico, in vitro, and in vivo methods and techniques that can be exploited at different stages of the discovery process to identify molecules with liabilities and thereby facilitate the selection of the most optimal drug leads. Finally, we reflect on the most relevant developability parameters for injectable versus orally delivered biologics and provide an outlook toward what general trends are expected to rise in the development of biologics.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, University of Oslo, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine and Department of Pharmacology, University of Oslo, Oslo, Norway
| | | | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjørn Gunnar Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lise Marie Grav
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc, Ridgefield, CT, USA
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Peter M. Tessier
- Department of Chemical Engineering, Pharmaceutical Sciences and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - John McCafferty
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Maxion Therapeutics, Babraham Research Campus, Cambridge, UK
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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Yamaguchi Y, Wakaizumi N, Irisa M, Maruno T, Shimada M, Shintani K, Nishiumi H, Yogo R, Yanaka S, Higo D, Torisu T, Kato K, Uchiyama S. The Fab portion of immunoglobulin G has sites in the CL domain that interact with Fc gamma receptor IIIa. MAbs 2022; 14:2038531. [PMID: 35291930 PMCID: PMC8932917 DOI: 10.1080/19420862.2022.2038531] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/16/2022] [Accepted: 02/02/2022] [Indexed: 02/02/2023] Open
Abstract
The interaction between IgG and Fc gamma receptor IIIa (FcγRIIIa) is essential for mediating immune responses. Recent studies have shown that the antigen binding fragment (Fab) and Fc are involved in IgG-FcγRIII interactions. Here, we conducted bio-layer interferometry (BLI) and isothermal titration calorimetry to measure the kinetic and thermodynamic parameters that define the role of Fab in forming the IgG-FcγRIII complex using several marketed therapeutic antibodies. Moreover, hydrogen/deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS) were used to clarify the interaction sites and structural changes upon formation of these IgG-FcγRIII complexes. The results showed that Fab in IgG facilitates the interaction via slower dissociation and a larger enthalpy gain. However, a larger entropy loss led to only a marginal change in the equilibrium dissociation constant. Combined HDX-MS and XL-MS analysis revealed that the CL domain of Fab in IgG was in close proximity to FcγRIIIa, indicating that this domain specifically interacts with the extracellular membrane-distal domain (D1) and membrane-proximal domain (D2) of FcγRIIIa. Together with previous studies, these results demonstrate that IgG-FcγRIII interactions are predominantly mediated by the binding of Fc to D2, and the Fab-FcγRIII interaction stabilizes complex formation. These interaction schemes were essentially fucosylation-independent, with Fc-D2 interactions enhanced by afucosylation and the contribution of Fab slightly reduced. Furthermore, the influence of antigen binding on IgG-FcγRIII interactions was also investigated. Combined BLI and HDX-MS results indicate that structural alterations in Fab caused by antigen binding facilitate stabilization of IgG-FcγRIII interactions. This report provides a comprehensive understanding of the interaction between IgG and FcγRIII.
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Affiliation(s)
- Yuki Yamaguchi
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | | | - Mine Irisa
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Takahiro Maruno
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Mari Shimada
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Koya Shintani
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Haruka Nishiumi
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Aichi, Japan
| | | | - Tetsuo Torisu
- Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Aichi, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
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