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Rencilin CF, Chatterjee A, Ansari MY, Deshpande S, Mukherjee S, Singh R, Jayatheertha SB, Reddy PM, Hingankar N, Varadarajan R, Bhattacharya J, Dutta S. Cryo-EM reveals conformational variability in the SARS-CoV-2 spike protein RBD induced by two broadly neutralizing monoclonal antibodies. RSC Adv 2025; 15:14385-14399. [PMID: 40330036 PMCID: PMC12053377 DOI: 10.1039/d5ra00373c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 03/21/2025] [Indexed: 05/08/2025] Open
Abstract
SARS-CoV-2 spike proteins play a critical role in infection by interacting with the ACE2 receptors. Their receptor-binding domains and N-terminal domains exhibit remarkable flexibility and can adopt various conformations that facilitate receptor engagement. Previous structural studies have reported the RBD of the spike protein in "up", "down", and various intermediate states, as well as its different conformational changes during ACE2 binding. This flexibility also influences its interactions with the neutralizing antibodies, yet its role in the antibody complexes remains understudied. In this study, we used cryo-electron microscopy to investigate the structural properties of two broadly neutralizing monoclonal antibodies, THSC20.HVTR04 and THSC20.HVTR26. These antibodies were isolated from an unvaccinated individual and demonstrated potent neutralization of multiple SARS-CoV-2 variants. Our analysis revealed distinct binding characteristics and conformational changes in the spike RBD upon binding with the monoclonal antibodies. The structural characterization of the spike protein-monoclonal antibody complexes provided valuable insights into the structural variability of the spike protein and the possible mechanisms for antibody-mediated neutralization.
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Affiliation(s)
| | - Arnab Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bengaluru 560012 India
| | - Mohammad Yousuf Ansari
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Suprit Deshpande
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
- BRIC-Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Sohini Mukherjee
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
- IAVI Gurugram Haryana 122022 India
- IAVI New York NY 10004 USA
| | - Randhir Singh
- Mynvax Private Limited Vani Vilas Road, Basavanagudi Bengaluru 560004 India
| | | | - Poorvi M Reddy
- Mynvax Private Limited Vani Vilas Road, Basavanagudi Bengaluru 560004 India
| | - Nitin Hingankar
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science Bengaluru 560012 India
- Mynvax Private Limited Vani Vilas Road, Basavanagudi Bengaluru 560004 India
| | - Jayanta Bhattacharya
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
- BRIC-Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science Bengaluru 560012 India
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Shi Y, Wang S, Hao Y, Shen X, Zhang J, Wang S, Zhang J, Fu Y, Chen R, Wang D, Shao Y, Li D, Liu Y. Isolation and Characterization of E8 Monoclonal Antibodies from Donors Vaccinated with Recombinant Vaccinia Vaccine with Efficient Neutralization of Authentic Monkeypox Virus. Vaccines (Basel) 2025; 13:471. [PMID: 40432083 PMCID: PMC12116032 DOI: 10.3390/vaccines13050471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2025] [Revised: 04/25/2025] [Accepted: 04/26/2025] [Indexed: 05/29/2025] Open
Abstract
BACKGROUND/OBJECTIVES Monkeypox, twice declared a public health emergency of international concern by the WHO, currently lacks approved targeted therapeutics. This study focused on the development of monkeypox virus (MPXV) E8-specific human monoclonal antibodies (mAbs) derived from recipients of the recombinant vaccinia vaccine (rTV), with subsequent evaluation of their cross-neutralizing activity against orthopoxviruses, including the vaccinia virus (VACV) and MPXV. METHODS Three mAbs (C5, C9, and F8) were isolated from rTV vaccinees. Structural mapping characterized their binding domains on the MPXV E8 and VACV D8 proteins. Neutralization potency was assessed against the VACV TianTan strain and MPXV clade IIb. A combo was further evaluated in a VACV-infected mice model for clinical recovery and viral load reduction. Complement-dependent enhancement mechanisms were also investigated in vitro. RESULTS C9 targets the virion surface region of E8 and both the virion surface region and intravirion region of D8, showing cross-neutralization activity against the MPXV (IC50 = 3.0 μg/mL) and VACV (IC50 = 51.1 ng/mL) in vitro. All three antibodies demonstrated potent neutralization against the VACV in vitro: C5 (IC50 = 3.9 ng/mL), C9 (IC50 = 51.1 ng/mL), and F8 (IC50 = 101.1 ng/mL). Notably, complement enhanced neutralization against the VACV by >50-fold, although no enhancement was observed for the MPXV. In vivo administration accelerated clinical recovery by 24 h and achieved significant viral clearance (0.9-log reduction). CONCLUSIONS E8-targeting mAbs exhibited broad-spectrum neutralization against orthopoxviruses, demonstrating therapeutic potential against both historical (VACV) and emerging (MPXV) pathogens. However, MPXV's resistance to complement-dependent enhancement highlights the necessity for pathogen-adapted optimization. These findings establish E8 as a critical conserved target for pan-poxvirus VACV and MPXV countermeasure development.
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Affiliation(s)
- Yutao Shi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Shuhui Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Yanling Hao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Xiuli Shen
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China; (X.S.); (Y.S.)
| | - Jun Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Shuo Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Junjie Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Yuyu Fu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Ran Chen
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Dong Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Yiming Shao
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China; (X.S.); (Y.S.)
| | - Dan Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
| | - Ying Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.S.); (S.W.); (Y.H.); (J.Z.); (S.W.); (J.Z.); (Y.F.); (R.C.); (D.W.)
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Luo S, Xiong D, Tang B, Liu B, Zhao X, Duan L. Evaluating mAbs binding abilities to Omicron subvariant RBDs: implications for selecting effective mAb therapies. Phys Chem Chem Phys 2024; 26:11414-11428. [PMID: 38591159 DOI: 10.1039/d3cp05893j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The ongoing evolution of the Omicron lineage of SARS-CoV-2 has led to the emergence of subvariants that pose challenges to antibody neutralization. Understanding the binding dynamics between the receptor-binding domains (RBD) of these subvariants spike and monoclonal antibodies (mAbs) is pivotal for elucidating the mechanisms of immune escape and for advancing the development of therapeutic antibodies. This study focused on the RBD regions of Omicron subvariants BA.2, BA.5, BF.7, and XBB.1.5, employing molecular dynamics simulations to unravel their binding mechanisms with a panel of six mAbs, and subsequently analyzing the origins of immune escape from energetic and structural perspectives. Our results indicated that the antibody LY-COV1404 maintained binding affinities across all studied systems, suggesting the resilience of certain antibodies against variant-induced immune escape, as seen with the mAb 1D1-Fab. The newly identified mAb 002-S21F2 showed a similar efficacy profile to LY-COV1404, though with a slightly reduced binding to BF.7. In parallel, mAb REGN-10933 emerged as a potential therapeutic candidate against BF.7 and XBB.1.5, reflecting the importance of identifying variant-specific antibody interactions, akin to the binding optimization observed in BA.4/5 and XBB.1.5. And key residues that facilitate RBD-mAb binding were identified (T345, L441, K444, V445, and T500), alongside residues that hinder protein-protein interactions (D420, L455, K440, and S446). Particularly noteworthy was the inhibited binding of V445 and R509 with mAbs in the presence of mAb 002-S21F2, suggesting a mechanism for immune escape, especially through the reduction of V445 hydrophobicity. These findings enhance our comprehension of the binding interactions between mAbs and RBDs, contributing to the understanding of immune escape mechanisms. They also lay the groundwork for the design and optimization of antiviral drugs and have significant implications for the development of treatments against current and future coronaviruses.
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Affiliation(s)
- Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Danyang Xiong
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Bolin Tang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Bangyu Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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