1
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Nuqui X, Casalino L, Zhou L, Shehata M, Wang A, Tse AL, Ojha AA, Kearns FL, Rosenfeld MA, Miller EH, Acreman CM, Ahn SH, Chandran K, McLellan JS, Amaro RE. Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nat Commun 2024; 15:7370. [PMID: 39191724 PMCID: PMC11350062 DOI: 10.1038/s41467-024-50976-9] [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: 11/15/2023] [Accepted: 07/25/2024] [Indexed: 08/29/2024] Open
Abstract
The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 subunit. S2, in contrast, is the most evolutionarily conserved region of the spike and can elicit broadly neutralizing and protective antibodies. Yet, S2's usage as an alternative vaccine strategy is hampered by its general instability. Here, we use a simulation-driven approach to design S2-only immunogens stabilized in a closed prefusion conformation. Molecular simulations provide a mechanistic characterization of the S2 trimer's opening, informing the design of tryptophan substitutions that impart kinetic and thermodynamic stabilization. Structural characterization via cryo-EM shows the molecular basis of S2 stabilization in the closed prefusion conformation. Informed by molecular simulations and corroborated by experiments, we report an engineered S2 immunogen that exhibits increased protein expression, superior thermostability, and preserved immunogenicity against sarbecoviruses.
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Affiliation(s)
- Xandra Nuqui
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Lorenzo Casalino
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Mohamed Shehata
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Albert Wang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexandra L Tse
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anupam A Ojha
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Fiona L Kearns
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Happy Miller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cory M Acreman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California Davis, Davis, CA, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
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2
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Raisinghani N, Alshahrani M, Gupta G, Tian H, Xiao S, Tao P, Verkhivker GM. Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. J Chem Theory Comput 2024; 20:5317-5336. [PMID: 38865109 DOI: 10.1021/acs.jctc.4c00222] [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: 06/13/2024]
Abstract
Despite the success of AlphaFold methods in predicting single protein structures, these methods showed intrinsic limitations in the characterization of multiple functional conformations of allosteric proteins. The recent NMR-based structural determination of the unbound ABL kinase in the active state and discovery of the inactive low-populated functional conformations that are unique for ABL kinase present an ideal challenge for the AlphaFold2 approaches. In the current study, we employ several adaptations of the AlphaFold2 methodology to predict protein conformational ensembles and allosteric states of the ABL kinase including randomized alanine sequence scanning combined with the multiple sequence alignment subsampling proposed in this study. We show that the proposed new AlphaFold2 adaptation combined with local frustration profiling of conformational states enables accurate prediction of the protein kinase structures and conformational ensembles, also offering a robust approach for interpretable characterization of the AlphaFold2 predictions and detection of hidden allosteric states. We found that the large high frustration residue clusters are uniquely characteristic of the low-populated, fully inactive ABL form and can define energetically frustrated cracking sites of conformational transitions, presenting difficult targets for AlphaFold2. The results of this study uncovered previously unappreciated fundamental connections between local frustration profiles of the functional allosteric states and the ability of AlphaFold2 methods to predict protein structural ensembles of the active and inactive states. This study showed that integration of the randomized sequence scanning adaptation of AlphaFold2 with a robust landscape-based analysis allows for interpretable atomistic predictions and characterization of protein conformational ensembles, providing a physical basis for the successes and limitations of current AlphaFold2 methods in detecting functional allosteric states that play a significant role in protein kinase regulation.
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Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Hao Tian
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Gennady M Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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3
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Bernetti M, Bosio S, Bresciani V, Falchi F, Masetti M. Probing allosteric communication with combined molecular dynamics simulations and network analysis. Curr Opin Struct Biol 2024; 86:102820. [PMID: 38688074 DOI: 10.1016/j.sbi.2024.102820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Understanding the allosteric mechanisms within biomolecules involved in diseases is of paramount importance for drug discovery. Indeed, characterizing communication pathways and critical hotspots in signal transduction can guide a rational approach to leverage allosteric modulation for therapeutic purposes. While the atomistic signatures of allosteric processes are difficult to determine experimentally, computational methods can be a remarkable resource. Network analysis built on Molecular Dynamics simulation data is particularly suited in this respect and is gradually becoming of routine use. Herein, we collect the recent literature in the field, discussing different aspects and available options for network construction and analysis. We further highlight interesting refinements and extensions, eventually providing our perspective on this topic.
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Affiliation(s)
- Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy.
| | - Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/Stefano__Bosio
| | - Veronica Bresciani
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy. https://twitter.com/V_Bresciani
| | - Federico Falchi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Computational and Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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4
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Ray A, Minh Tran TT, Santos Natividade RD, Moreira RA, Simpson JD, Mohammed D, Koehler M, L Petitjean SJ, Zhang Q, Bureau F, Gillet L, Poma AB, Alsteens D. Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2. ACS NANOSCIENCE AU 2024; 4:136-145. [PMID: 38644967 PMCID: PMC11027127 DOI: 10.1021/acsnanoscienceau.3c00060] [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] [Received: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/23/2024]
Abstract
The SARS-CoV-2 pandemic spurred numerous research endeavors to comprehend the virus and mitigate its global severity. Understanding the binding interface between the virus and human receptors is pivotal to these efforts and paramount to curbing infection and transmission. Here we employ atomic force microscopy and steered molecular dynamics simulation to explore SARS-CoV-2 receptor binding domain (RBD) variants and angiotensin-converting enzyme 2 (ACE2), examining the impact of mutations at key residues upon binding affinity. Our results show that the Omicron and Delta variants possess strengthened binding affinity in comparison to the Mu variant. Further, using sera from individuals either vaccinated or with acquired immunity following Delta strain infection, we assess the impact of immunity upon variant RBD/ACE2 complex formation. Single-molecule force spectroscopy analysis suggests that vaccination before infection may provide stronger protection across variants. These results underscore the need to monitor antigenic changes in order to continue developing innovative and effective SARS-CoV-2 abrogation strategies.
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Affiliation(s)
- Ankita Ray
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Thu Thi Minh Tran
- Faculty
of Materials Science and Technology, University
of Science—VNU HCM, 227 Nguyen Van Cu Street, District 5, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University, 700000 Ho Chi Minh City, Vietnam
| | - Rita dos Santos Natividade
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rodrigo A. Moreira
- Basque
Center for Applied Mathematics, Mazarredo 14, 48009 Bilbao, Spain
| | - Joshua D. Simpson
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Simon J. L Petitjean
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Qingrong Zhang
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Fabrice Bureau
- Laboratory
of Cellular and Molecular Immunology, GIGA Institute, Liège University, 4000 Liège, Belgium
| | - Laurent Gillet
- Immunology-Vaccinology
Lab of the Faculty of Veterinary Medicine, Liège University, 4000 Liège, Belgium
| | - Adolfo B. Poma
- Institute
of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- WELBIO
department, WEL Research Institute, 1300 Wavre, Belgium
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5
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Desai A, Mahajan V, Ramabhadran RO, Mukherjee R. Binding order of substrate and cofactor in sulfonamide monooxygenase during sulfa drug degradation: in silico studies. J Biomol Struct Dyn 2024:1-15. [PMID: 38263732 DOI: 10.1080/07391102.2024.2306495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024]
Abstract
For decades, sulfonamide antibiotics have been used across industries such as agriculture and animal husbandry. However, the use and inadvertent misuse of these antibiotics have resulted in the advent of sulfonamide-drug-resistant strains due to antibiotic pollution. Enzymatic bioremediation of antibiotics remains a potential emerging solution to combat antibiotic pollution. Here, we propose an enzymatic model for the degradation of sulfonamides by Microbacterium sp. We have employed a multi-pronged computational strategy involving - protein structure modelling, ligand docking and molecular dynamics simulations to decipher a plausible binding order for the enzymatic degradation of sulfonamides by the bacterial sulfonamide monooxygenase, SulX. Our results enable us to predict that this degradation is achieved through the sequential binding of the antibiotic sulfonamide followed by the reduced flavin cofactor FMNH2, thereby laying the computational foundation for further advancements in enzyme-mediated degradation of the antibiotic. We also provide a list of experiments which may be performed to verify and follow-up on our in-silico studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amogh Desai
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Ved Mahajan
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research Tirupati, Tirupati, India
| | - Raju Mukherjee
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, India
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6
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Cox M, Peacock TP, Harvey WT, Hughes J, Wright DW, Willett BJ, Thomson E, Gupta RK, Peacock SJ, Robertson DL, Carabelli AM. SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nat Rev Microbiol 2023; 21:112-124. [PMID: 36307535 PMCID: PMC9616429 DOI: 10.1038/s41579-022-00809-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 01/20/2023]
Abstract
Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.
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Affiliation(s)
- MacGregor Cox
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Derek W Wright
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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7
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Barnes JE, Lund-Andersen PK, Patel JS, Ytreberg FM. The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6. Sci Rep 2022; 12:18819. [PMID: 36335244 PMCID: PMC9637166 DOI: 10.1038/s41598-022-23482-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Abstract
SARS-CoV-2 is the pathogen responsible for COVID-19 that has claimed over six million lives as of July 2022. The severity of COVID-19 motivates a need to understand how it could evolve to escape potential treatments and to find ways to strengthen existing treatments. Here, we used the molecular modeling methods MD + FoldX and PyRosetta to study the SARS-CoV-2 spike receptor binding domain (S-RBD) bound to two neutralizing antibodies, B38 and CB6 and generated lists of antibody escape and antibody strengthening mutations. Our resulting watchlist contains potential antibody escape mutations against B38/CB6 and consists of 211/186 mutations across 35/22 S-RBD sites. Some of these mutations have been identified in previous studies as being significant in human populations (e.g., N501Y). The list of potential antibody strengthening mutations that are predicted to improve binding of B38/CB6 to S-RBD consists of 116/45 mutations across 29/13 sites. These mutations could be used to improve the therapeutic value of these antibodies.
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Affiliation(s)
- Jonathan E Barnes
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA
| | - Peik K Lund-Andersen
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83843, USA
| | - Jagdish Suresh Patel
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA.
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83843, USA.
| | - F Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83843, USA.
- Department of Physics, University of Idaho, Moscow, ID, 83843, USA.
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