1
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Barroso da Silva FL, Paco K, Laaksonen A, Ray A. Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights. Biophys Rev 2025; 17:309-333. [PMID: 40376405 PMCID: PMC12075047 DOI: 10.1007/s12551-025-01276-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Accepted: 01/24/2025] [Indexed: 05/18/2025] Open
Abstract
The spike protein encoded by the SARS-CoV-2 has become one of the most studied macromolecules in recent years due to its central role in COVID-19 pathogenesis. The spike protein's receptor-binding domain (RBD) directly interacts with the host-encoded receptor protein, ACE2. This review critically examines computational insights into RBD's interaction with ACE2 and with therapeutic antibodies designed to interfere with this interaction. We begin by summarizing insights from early computational studies on pre-pandemic SARS-CoV-1 RBD interactions and how these early studies shaped the understanding of SARS-CoV-2. Next, we highlight key theoretical contributions that revealed the molecular mechanisms behind the binding affinity of SARS-CoV-2 RBD against ACE2, and the structural changes that have enhanced the infectivity of emerging variants. Special attention is given to the "RBD charge rule", a predictive framework for determining variant infectivity based on the electrostatic properties of the RBD. Towards applying the computational insights to therapy, we discuss a multiscale computational protocol for optimizing monoclonal antibodies to improve binding affinity across multiple spike protein variants, including representatives from the Omicron family. Finally, we explore how these insights can inform the development of future vaccines and therapeutic interventions for combating future coronavirus diseases.
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Affiliation(s)
- Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av Prof Zeferino Vaz, S/no, Ribeirão Preto, São Paulo BR-14040-903 Brazil
- Department of Chemical and Biomolecular Engineering, NC State University, 911 Partners Way, Engineering Building I (EB1), Raleigh, NC 27695-7905 USA
| | - Karen Paco
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Dr., Claremont, CA 91711 USA
| | - Aatto Laaksonen
- Department of Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius Väg 8, 106 91 Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, NO.30 Puzhu Road(S), Nanjing, 210009 People’s Republic of China
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Laboratorievägen 14, 97187 Luleå, Sweden
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania
| | - Animesh Ray
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Dr., Claremont, CA 91711 USA
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125 USA
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2
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Santos JAA, Duay SS. Molecular dynamics of SARS-CoV-2 omicron variants from Philippine isolates against hesperidin as spike protein inhibitor. Biophys Chem 2025; 318:107387. [PMID: 39742696 DOI: 10.1016/j.bpc.2024.107387] [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: 09/22/2024] [Revised: 12/10/2024] [Accepted: 12/27/2024] [Indexed: 01/04/2025]
Abstract
SARS-CoV-2 remains a global threat with new sublineages posing challenges, particularly in the Philippines. Hesperidin (HD) is being studied as a potential prophylactic for COVID-19. However, the virus's rapid evolution could alter how HD binds to it, affecting its effectiveness. Here, we study the mutation-induced variabilities of HD dynamics and their effects on molecular energetics in SARS-CoV-2 spike receptor complex systems. We considered eight different point mutations present in the Omicron variant. Root-mean-square deviation and binding energy analysis showed that S477N and Omicron did not eject HD throughout the simulation. Hydrogen bond distribution analysis highlighted the involvement of hydrogen bonding in mutant-HD stabilization, especially for S477N and Omicron. Root-mean-square fluctuation analysis revealed evidence of Y505H destabilization on complex systems, while distal-end loop mutations increased loop flexibility for all models bearing the three mutations. Per-residue energy decomposition demonstrated that Q493R substitution increased HD interaction. Free energy landscape and essential dynamics through principal component analysis provided insights into the conformational subspace distribution of mutant model molecular dynamics trajectories. In conclusion, significant mutations contributed to the HD interaction in different ways. S477N has shown significant binding contributions through favorable ligand interaction, while other mutations contribute via conformational modifications, increased affinity due to sidechain mutations, and increased loop flexibility.
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Affiliation(s)
| | - Searle S Duay
- Department of Chemistry, De La Salle University, Manila 0922, Philippines.
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3
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Kalyoncu S, Sayili D, Kuyucu AZ, Soyturk H, Gullu S, Ersayan B, Tarman IO, Avci ME, Mert O, Haskok U, Tekin E, Akinturk H, Orkut R, Demirtas A, Tilmensagir I, Ulker C, Gungor B, Inan M. Development of a Recombinant Omicron BA.1 Subunit Vaccine Candidate in Pichia pastoris. Microb Biotechnol 2025; 18:e70077. [PMID: 39815667 PMCID: PMC11735458 DOI: 10.1111/1751-7915.70077] [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: 05/15/2024] [Revised: 12/05/2024] [Accepted: 12/23/2024] [Indexed: 01/18/2025] Open
Abstract
Low-cost and safe vaccines are needed to fill the vaccine inequity gap for future pandemics. Pichia pastoris is an ideal expression system for recombinant protein production due to its cost-effective and easy-to-scale-up process. Here, we developed a next-generation SARS-CoV2 Omicron BA.1-based recombinant vaccine candidate expressed in P. pastoris. The receptor binding domain of Omicron BA.1 spike protein (RBD-Omicron) was produced at 0.35 g/L in supernatant. With a 60% recovery after two-step purification, RBD-Omicron showed 99% purity. After in vitro characterisation of purified RBD-Omicron via chromatography, mass spectrometry, calorimetry and surface plasmon resonance-based methods, it was injected into mice for immunization studies. Three different doses of Alum and CpG adjuvanted RBD-Omicron were investigated and 10 μg RBD-Omicron gave the highest antigenicity. After two doses of vaccination, IgG titers in mice serum reached to more than 106. These serum antibodies also recognized earlier (Delta Plus: B.1.617.2) and later (Eris: EG.5, Pirola: BA.2.86) SARS-CoV2 variants. The long-term immunological response in mice was measured by analyzing serum antibody titers and T-cell response of splenocytes after 60 weeks. Interestingly, IgG titers and Th1 response were significantly high even after a year. Omicron subvariants are dominantly circulating in the world, so Omicron sub-lineage-based vaccines can be used for future pandemics. The RBD-Omicron-based vaccine candidate developed in this study is suitable for technology transfer and transition into the clinic.
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Affiliation(s)
| | - Dogu Sayili
- Izmir Biomedicine and Genome CenterIzmirTurkey
| | | | - Hakan Soyturk
- Izmir Biomedicine and Genome CenterIzmirTurkey
- Faculty of Biology and CeBiTecBielefeld UniversityBielefeldGermany
| | - Seyda Gullu
- Izmir Biomedicine and Genome CenterIzmirTurkey
| | | | | | - Mehmet Ender Avci
- Izmir Biomedicine and Genome CenterIzmirTurkey
- Dokuz Eylul UniversityIzmirTurkey
| | - Olcay Mert
- Izmir Biomedicine and Genome CenterIzmirTurkey
| | - Umut Haskok
- Izmir Biomedicine and Genome CenterIzmirTurkey
- Dokuz Eylul University, Izmir International Biomedicine and Genome InstituteIzmirTurkey
| | - Ege Tekin
- Izmir Biomedicine and Genome CenterIzmirTurkey
- Dokuz Eylul University, Izmir International Biomedicine and Genome InstituteIzmirTurkey
| | | | | | | | | | - Ceren Ulker
- Izmir Biomedicine and Genome CenterIzmirTurkey
| | | | - Mehmet Inan
- Izmir Biomedicine and Genome CenterIzmirTurkey
- Akdeniz UniversityAntalyaTurkey
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4
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Roy RK, Sharma M, Patra N. SARS-CoV-2 variants and bebtelovimab: immune escape mechanisms revealed by computational studies. Phys Chem Chem Phys 2024; 26:29929-29939. [PMID: 39618233 DOI: 10.1039/d4cp03031a] [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: 12/12/2024]
Abstract
The receptor binding domain (RBD) of SARS-CoV-2 (coronavirus) targets and facilitates the binding with the human ACE2 receptor and is also a target for most monoclonal antibodies for the inhibition process. The emerging mutations in the RBD of SARS-CoV-2 are problematic, as their local and non-local effects can disrupt the binding mechanism of the antibody with the coronavirus's viral protein, thus compromising the antibody's inhibitory function. In this study, we have employed molecular dynamics to elucidate the binding mechanism between human-derived monoclonal antibody, bebtelovimab, and the RBD of the viral spike protein and the effects of mutations on this binding. We have analyzed the unbinding process using molecular dynamics with enhanced sampling methods, such as umbrella sampling. Our findings revealed that certain residues, including 440(N/K), Lys444, 452(L/R), 484(E/A), 498(Q/R), and THR500, are directly or indirectly responsible for altering the binding position and efficacy of bebtelovimab antibody with the RBD when mutations are introduced. The binding energy studies on three different variants, wild-type, delta, and omicron, revealed that the binding efficacy of bebtelovimab with the RBD diminished over time as additional mutations were introduced.
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MESH Headings
- SARS-CoV-2/immunology
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- Humans
- Molecular Dynamics Simulation
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Antibodies, Monoclonal, Humanized/chemistry
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/pharmacology
- Mutation
- Protein Binding
- Immune Evasion
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Binding Sites
- Angiotensin-Converting Enzyme 2/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- COVID-19/virology
- COVID-19/immunology
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Affiliation(s)
- Rakesh Kumar Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad - 826004, India.
| | - Madhur Sharma
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad - 826004, India.
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad - 826004, India.
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5
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Rajput V, Pramanik R, Nannaware K, Malik V, Matra S, Kumar S, Joshi S, Kadam P, Bhalerao U, Tupekar M, Deshpande D, Shah P, Sangewar P, Gogate N, Boargaonkar R, Patil D, Kale S, Bhalerao A, Jain N, Shashidhara LS, Kamble S, Dastager S, Karmodiya K, Dharne M. Wastewater surveillance in post-omicron silent phase uncovers silent waves and cryptic transmission of SARS-CoV-2 variants; a yearlong study in Western India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:176833. [PMID: 39396788 DOI: 10.1016/j.scitotenv.2024.176833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 09/22/2024] [Accepted: 10/07/2024] [Indexed: 10/15/2024]
Abstract
Due to reduced clinical testing and evolving monitoring challenges, tracking the emergence and evolution of SARS-CoV-2 variants has become increasingly complex. To address this gap, we investigated the utility of wastewater-based epidemiology (WBE) as a complementary tool for SARS-CoV-2 variant surveillance in sewage treatment plants (STPs) across Pune, India. We analyzed 1128 wastewater samples collected between May 2022 and May 2023, using Illumina and nanopore sequencing techniques for robust detection and variant characterization. The study revealed critical findings, including "silent waves" with elevated viral load despite minimal clinical cases, suggesting potential cryptic transmission. These silent waves aligned with the dominance of Omicron BA.2 in June-July 2022 and emergence of the recombinant XBB clade in December 2022. Importantly, sequencing detected XBB lineages 130-253 days before their initial clinical identification, demonstrating its significant advantage in early variant detection. Furthermore, wastewater analysis revealed a higher degree of lineage diversity compared to clinical data, indicating its ability to capture a broader spectrum of circulating variants. The BA.2.86.X was identified 103 days prior to its clinical detection in Pune, highlighting WBE's remarkable lead time. Surprisingly, BF.7.X and BQ.X fragments were also detected in wastewater but not yet reported clinically. These findings demonstrate the remarkable value of WBE as an early warning tool for SARS-CoV-2 variants ahead of time. By revealing silent waves, enabling early variant detection, and capturing a broader viral spectrum, WBE effort could empower public health officials to make informed decisions and implement effective strategies to mitigate future waves, especially in contexts with declining clinical testing.
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Affiliation(s)
- Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Rinka Pramanik
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Kiran Nannaware
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India
| | - Vinita Malik
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India
| | - Sejal Matra
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India
| | - Shubham Kumar
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India
| | - Sai Joshi
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India
| | - Pradnya Kadam
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India
| | - Unnati Bhalerao
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India
| | - Manisha Tupekar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India
| | - Dipti Deshpande
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India
| | - Priyanki Shah
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | - Poornima Sangewar
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | - Niharika Gogate
- The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | | | - Dhawal Patil
- Ecosan Services Foundation (ESF), Pune 411030, Maharashtra, India
| | - Saurabh Kale
- Ecosan Services Foundation (ESF), Pune 411030, Maharashtra, India
| | - Asim Bhalerao
- Fluid Robotics Private Limited (FRPL), Pune 411052, Maharashtra, India
| | - Nidhi Jain
- Fluid Robotics Private Limited (FRPL), Pune 411052, Maharashtra, India
| | - L S Shashidhara
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India; The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India; National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research Bellary Road, Bangalore 560065, Karnataka, India
| | - Sanjay Kamble
- Chemical Engineering and Process Development (CEPD) Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India
| | - Syed Dastager
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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6
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Polavarapu N, Doty M, Dobrovolny HM. Exploring the treatment of SARS-CoV-2 with modified vesicular stomatitis virus. J Theor Biol 2024; 595:111959. [PMID: 39366462 DOI: 10.1016/j.jtbi.2024.111959] [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: 07/15/2024] [Revised: 09/13/2024] [Accepted: 09/28/2024] [Indexed: 10/06/2024]
Abstract
SARS-CoV-2 caused a global pandemic and is now an endemic virus that will require continued antiviral and vaccine development. A possible new treatment modality was recently suggested that would use vesicular stomatitis virus (VSV) modified to express the ACE2 receptor. Since the modified VSV expresses the cell surface receptor that is used by the SARS-CoV-2 spike protein, the thought is that SARS-CoV-2 virions would bind to the modified VSV and thus be neutralized. Additionally, since SARS-CoV-2 infected cells also express the spike protein, the modified VSV could potentially infect these cells, allowing for its own replication, but also potentially interfering with replication of SARS-CoV-2. This idea has not yet been tested experimentally, but we can investigate the feasibility of this possible treatment theoretically. In this manuscript, we develop a mathematical model of this suggested treatment and explore conditions under which it might be effective. We find that treatment with modified VSV does little to change the SARS-CoV-2 time course except when the treatment is applied at the onset of the SARS-CoV-2 infection at very high doses. In this case, VSV reduces the peak SARS-CoV-2 viral load, but lengthens the duration of the SARS-CoV-2 infection. Thus, we find that modified VSV treatment is unlikely to be effective largely because it does not prevent infection of cells by SARS-CoV-2.
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Affiliation(s)
- Nishnath Polavarapu
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, United States
| | - Madison Doty
- Burnett School of Medicine at TCU, Fort Worth, TX, USA
| | - Hana M Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, United States.
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7
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Li S, Yang H, Tian F, Li W, Wang H, Shi X, Cui Z, Shan Y. Unveiling the Dynamic Mechanism of SARS-CoV-2 Entry Host Cells at the Single-Particle Level. ACS NANO 2024; 18:27891-27904. [PMID: 39353173 DOI: 10.1021/acsnano.4c04212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Understanding the dynamic features of severe acute respiratory coronavirus 2 (SARS-CoV-2) binding to the cell membrane and entry cells is crucial for comprehending viral pathogenesis and transmission and facilitating the development of effective drugs against COVID-19. Herein, we employed atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) to study the binding dynamics between the virus and cell membrane. Our findings revealed that the Omicron variant of SARS-CoV-2 virus-like particles (VLPs) exhibited a slightly stronger affinity for the angiotensin-converting enzyme-2 (ACE2) receptor compared with the Delta variant and was significantly higher than the wild-type (WT). Using a real-time force-tracing technique, we quantified the dynamic parameters for a single SARS-CoV-2 VLP entry into cells, showing that approximately 200 ms and 60 pN are required. The parameters aligned with the analysis obtained from coarse-grained molecular dynamics (CGMD) simulations. Additionally, the Omicron variant invades cells at a higher entry cell speed, smaller force, and higher probability. Furthermore, single-particle fluorescence tracking visually demonstrated clathrin-dependent endocytosis for SARS-CoV-2 entry into A549 cells. The dynamic features of endocytosis provide valuable insights into the SARS-CoV-2 entry mechanism and possible intervention strategies targeting the viral infection process.
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Affiliation(s)
- Siying Li
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Hui Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Falin Tian
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Wei Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xinghua Shi
- University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
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8
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Stocks BB, Thibeault MP, L'Abbé D, Umer M, Liu Y, Stuible M, Durocher Y, Melanson JE. Characterization of biotinylated human ACE2 and SARS-CoV-2 Omicron BA.4/5 spike protein reference materials. Anal Bioanal Chem 2024; 416:4861-4872. [PMID: 38942955 PMCID: PMC11330416 DOI: 10.1007/s00216-024-05413-7] [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: 02/29/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Accurate diagnostic and serology assays are required for the continued management of the COVID-19 pandemic yet spike protein mutations and intellectual property concerns with antigens and antibodies used in various test kits render comparability assessments difficult. As the use of common, well-characterized reagents can help address this lack of standardization, the National Research Council Canada has produced two protein reference materials (RMs) for use in SARS-CoV-2 serology assays: biotinylated human angiotensin-converting enzyme 2 RM, ACE2-1, and SARS-CoV-2 Omicron BA.4/5 spike protein RM, OMIC-1. Reference values were assigned through a combination of amino acid analysis via isotope dilution liquid chromatography tandem mass spectrometry following acid hydrolysis, and ultraviolet-visible (UV-Vis) spectrophotometry at 280 nm. Vial-to-vial homogeneity was established using UV-Vis measurements, and protein oligomeric status, monitored by size exclusion liquid chromatography (LC-SEC), was used to evaluate transportation, storage, and freeze-thaw stabilities. The molar protein concentration in ACE2-1 was 25.3 ± 1.7 µmol L-1 (k = 2, 95% CI) and consisted almost exclusively (98%) of monomeric ACE2, while OMIC-1 contained 5.4 ± 0.5 µmol L-1 (k = 2) spike protein in a mostly (82%) trimeric form. Glycoprotein molar mass determination by LC-SEC with multi-angle light scattering detection facilitated calculation of corresponding mass concentrations. To confirm protein functionality, the binding of OMIC-1 to immobilized ACE2-1 was investigated with surface plasmon resonance and the resulting dissociation constant, KD ~ 4.4 nM, was consistent with literature values.
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Affiliation(s)
- Bradley B Stocks
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada.
| | - Marie-Pier Thibeault
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Denis L'Abbé
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Muhammad Umer
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Yali Liu
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Matthew Stuible
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Yves Durocher
- Human Health Therapeutics, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Jeremy E Melanson
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
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9
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Nguyen HL, Nguyen TQ, Li MS. SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study. J Phys Chem B 2024; 128:3340-3349. [PMID: 38564480 PMCID: PMC11017248 DOI: 10.1021/acs.jpcb.3c06270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high contagious ability. Studies have shown that the Omicron binds human ACE2 more strongly than the wild type. The prevalence of Omicron in new cases of COVID-19 promotes novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1, and CH.1.1 to human ACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding affinity compared to the BA.1 lineage, and BA.2.75 and BA.2.75.2 subvariants bind ACE2 more strongly than others. However, in general, the binding affinities of the Omicron lineages do not differ significantly from each other. The electrostatic force dominates over the van der Waals force in the interaction between Omicron lineages and human cells. Based on our results, we argue that viral evolution does not further improve the affinity of SARS-CoV-2 for ACE2 but may increase immune evasion.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute
of Fundamental and Applied Sciences, Duy
Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty
of Environmental and Natural Sciences, Duy
Tan University, Da Nang 550000, Vietnam
| | - Thai Quoc Nguyen
- Faculty
of Physics, VNU University of Science, Vietnam
National University, 334 Nguyen Trai, Hanoi 100000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 81000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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10
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Ju SP, Yang YC, Chen HY. Unraveling the binding mechanisms of SARS-CoV-2 variants through molecular simulations. Heliyon 2024; 10:e27193. [PMID: 38495173 PMCID: PMC10940921 DOI: 10.1016/j.heliyon.2024.e27193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024] Open
Abstract
The emergence of SARS-CoV-2 variants like Delta (AY.29) and Omicron (EG.5) poses continued challenges for vaccines and therapeutics. Mutations in the viral spike protein are key in altering infectivity and immune evasion. This study uses computational modeling to investigate the molecular binding mechanisms between spike protein variants and the ACE2 host receptor. Using the MARTNI force field, coarse-grained molecular dynamics (CGMD) simulations and nudged elastic band (NEB) calculations explore spike-ACE2 interactions for the wild type, Delta variant, and Omicron variant. The simulations reveal Omicron has the strongest binding affinity at -128.35 ± 10.91 kcal/mol, followed by Delta and wild type. Key mutations in Delta and Omicron, like Q493R and Q498R, optimize electrostatic contacts, enhancing ACE2 interactions. The wild-type spike has the highest transition state energy barrier at 17.87 kcal/mol, while Delta has the lowest barrier at 9.21 kcal/mol. Despite slightly higher dual barriers, Omicron's increased binding energy lowers its overall barrier to rapidly bind ACE2. These findings provide residue-level insights into mutation effects on SARS-CoV-2 infectivity. The computational modeling elucidates mechanisms underlying spike-ACE2 binding kinetics, aiding the development of vaccines and therapies targeting emerging viral strains.
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Affiliation(s)
- Shin-Pon Ju
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yung-Cheng Yang
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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11
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Lan PD, Nissley DA, O’Brien EP, Nguyen TT, Li MS. Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2. J Chem Phys 2024; 160:055101. [PMID: 38310477 PMCID: PMC11223169 DOI: 10.1063/5.0188053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
The binding of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein to the host cell receptor angiotensin-converting enzyme 2 (ACE2) is the first step in human viral infection. Therefore, understanding the mechanism of interaction between RBD and ACE2 at the molecular level is critical for the prevention of COVID-19, as more variants of concern, such as Omicron, appear. Recently, atomic force microscopy has been applied to characterize the free energy landscape of the RBD-ACE2 complex, including estimation of the distance between the transition state and the bound state, xu. Here, using a coarse-grained model and replica-exchange umbrella sampling, we studied the free energy landscape of both the wild type and Omicron subvariants BA.1 and XBB.1.5 interacting with ACE2. In agreement with experiment, we find that the wild type and Omicron subvariants have similar xu values, but Omicron binds ACE2 more strongly than the wild type, having a lower dissociation constant KD.
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Affiliation(s)
| | - Daniel A. Nissley
- Department of Statistics, University of Oxford, Oxford Protein Bioinformatics Group, Oxford OX1 2JD, United Kingdom
| | | | - Toan T. Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems and Department of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University - Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 11400, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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12
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Balupuri A, Kim JM, Choi KE, No JS, Kim IH, Rhee JE, Kim EJ, Kang NS. Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants. Int J Mol Sci 2023; 24:16069. [PMID: 38003257 PMCID: PMC10671153 DOI: 10.3390/ijms242216069] [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: 10/04/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike (S) protein mutations pose serious threats to current coronavirus disease 2019 (COVID-19) therapies. A comprehensive understanding of the structural stability of SARS-CoV-2 variants is vital for the development of effective therapeutic strategies as it can offer valuable insights into their potential impact on viral infectivity. S protein mediates a virus' attachment to host cells by binding to angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain (RBD), and mutations in this protein can affect its stability and binding affinity. We analyzed S protein structural stability in various Omicron subvariants computationally. Notably, the S protein sequences analyzed in this work were obtained directly from our own sample collection. We evaluated the binding free energy between S protein and ACE2 in several complex forms. Additionally, we measured distances between the RBD of each chain in S protein to analyze conformational changes. Unlike most of the prior studies, we analyzed full-length S protein-ACE2 complexes instead of only RBD-ACE2 complexes. Omicron subvariants including BA.1, BA.2, BA.2.12.1, BA.4/BA.5, BA.2.75, BA.2.75_K147E, BA.4.6 and BA.4.6_N658S showed enhanced stability compared to wild type, potentially due to distinct S protein mutations. Among them, BA.2.75 and BA.4.6_N658S exhibited the highest and lowest level of stability, respectively.
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Affiliation(s)
- Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
| | - Jeong-Min Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Kwang-Eun Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
| | - Jin Sun No
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Jee Eun Rhee
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease, Control and Prevention Agency, 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Republic of Korea; (J.-M.K.); (J.S.N.); (I.-H.K.); (J.E.R.)
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (A.B.); (K.-E.C.)
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13
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Wang WB, Ma YB, Lei ZH, Zhang XF, Li J, Li SS, Dong ZY, Liang Y, Li QM, Su JG. Identification of key mutations responsible for the enhancement of receptor-binding affinity and immune escape of SARS-CoV-2 Omicron variant. J Mol Graph Model 2023; 124:108540. [PMID: 37352723 PMCID: PMC10254043 DOI: 10.1016/j.jmgm.2023.108540] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023]
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised concerns worldwide due to its enhanced transmissibility and immune escapability. The first dominant Omicron BA.1 subvariant harbors more than 30 mutations in the spike protein from the prototype virus, of which 15 mutations are located at the receptor binding domain (RBD). These mutations in the RBD region attracted significant attention, which potentially enhance the binding of the receptor human angiotensin-converting enzyme 2 (hACE2) and decrease the potency of neutralizing antibodies/nanobodies. This study applied the molecular dynamics simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method, to investigate the molecular mechanism behind the impact of the mutations acquired by Omicron on the binding affinity between RBD and hACE2. Our results indicate that five key mutations, i.e., N440K, T478K, E484A, Q493R, and G496S, contributed significantly to the enhancement of the binding affinity by increasing the electrostatic interactions of the RBD-hACE2 complex. Moreover, fourteen neutralizing antibodies/nanobodies complexed with RBD were used to explore the effects of the mutations in Omicron RBD on their binding affinities. The calculation results indicate that the key mutations E484A and Y505H reduce the binding affinities to RBD for most of the studied neutralizing antibodies/nanobodies, mainly attributed to the elimination of the original favorable gas-phase electrostatic and hydrophobic interactions between them, respectively. Our results provide valuable information for developing effective vaccines and antibody/nanobody drugs.
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Affiliation(s)
- Wei Bu Wang
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yi Bo Ma
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Hua Lei
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Xue Feng Zhang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Jiao Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Shan Shan Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Yuan Dong
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yu Liang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Qi Ming Li
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China.
| | - Ji Guo Su
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China.
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14
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Singh JK, Singh J, Srivastava SK. Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations. J Comput Aided Mol Des 2023; 37:551-563. [PMID: 37542610 DOI: 10.1007/s10822-023-00526-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
Omicron derived lineages viz. BA.2, BA.3, BA.4 BA.5, BF.7 and XBBs show prominence with improved immune escape, transmissibility, infectivity, and pathogenicity in general. Sub-variants, XBB.1.5 and XBB.1.16 have shown rapid spread, with mutations embedded throughout the viral genome, including the spike protein. Changing atomic landscapes in spike contributes significantly to modulate host pathogen interactions and infections thereof. In the present work, we computationally analyzed the binding affinities of spike receptor binding domains (RBDs) of XBB.1.5 and XBB.1.16 towards human angiotensin-converting enzyme 2 (hACE2) compared to Omicron. We have employed simulations and binding energy estimation of molecular complexes of spike-hACE2 to assess the interplay of interaction pattern and effect of mutations if any in the binding mode of the RBDs of these novel mutants. We calculated the binding free energy (BFE) of the RBD of the Omicron, XBB.1.5 and XBB.1.16 spike protein to hACE2. We showed that XBB.1.5 and XBB.1.16 can bind to human cells more strongly than Omicron due to the increased charge of the RBD, which enhances the electrostatic interactions with negatively charged hACE2. The per-residue decompositions further show that the Asp339His, Asp405Asn and Asn460Lys mutations in the XBBs RBD play a crucial role in enhancing the electrostatic interactions, by acquiring positively charged residues, thereby influencing the formation/loss of interfacial bonds and thus strongly affecting the spike RBD-hACE2 binding affinity. Simulation results also indicate less interference of heterogeneous glycans of XBB.1.5 spike RBD towards binding to hACE2. Moreover, despite having less interaction at the three interfacial contacts between XBB S RBD and hACE2 compared to Omicron, variants XBB.1.5 and XBB.1.16 had higher total binding free energies (ΔGbind) than Omicron due to the contribution of non-interfacial residues to the free energy, providing insight into the increased binding affinity of XBB1.5 and XBB.1.16. Furthermore, the presence of large positively charged surface patches in the XBBs act as drivers of electrostatic interactions, thus support the possibility of a higher binding affinity to hACE2.
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Affiliation(s)
- Jaikee Kumar Singh
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India
| | - Jai Singh
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India
| | - Sandeep Kumar Srivastava
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan, 303007, India.
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15
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Sun J, Liu X, Zhang S, Li M, Zhang Q, Chen J. Molecular insights and optimization strategies for the competitive binding of engineered ACE2 proteins: a multiple replica molecular dynamics study. Phys Chem Chem Phys 2023; 25:28479-28496. [PMID: 37846774 DOI: 10.1039/d3cp03392a] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.
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Affiliation(s)
- Jiahao Sun
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Meng Li
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
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16
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Pondé RADA. Physicochemical effects of emerging exchanges on the spike protein's RBM of the SARS-CoV-2 Omicron subvariants BA.1-BA.5 and its influence on the biological properties and attributes developed by these subvariants. Virology 2023; 587:109850. [PMID: 37562286 DOI: 10.1016/j.virol.2023.109850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Emerging in South Africa, SARS-CoV-2 Omicron variant was marked by the expression of an exaggerated number of mutations throughout its genome and by the emergence of subvariants, whose attributes developed by them have been associated with amino acid exchanges that occur mainly in the RBM region of the spike protein. The RBM comprises a region within the RBD and is directly involved in the SARS-CoV-2 spike protein interaction with the host cell ACE2 receptor, during the infection mechanism and viral transmission. Defined as the region from aa 437 to aa 508, there are several residues in certain positions that interact directly with the human ACE-2 receptor during these processes. The occurrence of amino acid exchanges in these positions causes physicochemical alterations in the SARS-CoV-2 spike protein, which confer additional advantages and attributes to the agent. In addition, these exchanges serve as a basis for the characterization of new variants and subvariants of SARS-CoV-2. In this review, the amino acid exchanges that have occurred in the RBM of the subvariants BA.1 to BA.5 of SARS-CoV-2 that emerged from the Omicron are described. The physicochemical effects caused by them on spike protein are also described, as well as their influence on the biological properties and attributes developed by the subvariants BA.1, BA.2, BA.3, BA.4 and BA.5.
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Affiliation(s)
- Robério Amorim de Almeida Pondé
- Secretaria de Estado da Saúde -SES/Superintendência de Vigilância em Saúde-SUVISA/GO, Gerência de Vigilância Epidemiológica de Doenças Transmissíveis-GVEDT/Coordenação de Análises e Pesquisas-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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17
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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18
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Jafary F, Joozdani FA, Shahzamani K, Jafari S, Mirhendi H, Ganjalikhany MR. Different aspects in explaining how mutations could affect the binding mechanism of receptor binding domain of SARS-CoV-2 spike protein in interaction with ACE2. PLoS One 2023; 18:e0291210. [PMID: 37682927 PMCID: PMC10490914 DOI: 10.1371/journal.pone.0291210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
During replication, some mutations occur in SARS-CoV-2, the causal agent of COVID-19, leading to the emergence of different variants of the virus. The mutations that accrue in different variants of the virus, influence the virus' ability to bind to human cell receptors and ability to evade the human immune system, the rate of viral transmission, and effectiveness of vaccines. Some of these mutations occur in the receptor binding domain (RBD) of the spike protein that may change the affinity of the virus for the ACE2 receptor. In this study, several in silico techniques, such as MD and SMD simulations, were used to perform comparative studies to deeply understand the effect of mutation on structural and functional details of the interaction of the spike glycoprotein of SARS-CoV-2, with the ACE2 receptor. According to our results, the mutation in the RBD associated with the Omicron variant increase binding affinity of the virus to ACE2 when compared to wild type and Delta variants. We also observed that the flexibility of the spike protein of the Omicron variant was lower than in comparison to other variants. In summary, different mutations in variants of the virus can have an effect on the binding mechanism of the receptor binding domain of the virus with ACE2.
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Affiliation(s)
- Farzaneh Jafary
- Core Research Facilities (CRF), Isfahan University of Medical Science, Isfahan, Iran
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzane Abasi Joozdani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Kiana Shahzamani
- Hepatitis Research Center, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Sepideh Jafari
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Łódź, Poland
| | - Hossein Mirhendi
- Core Research Facilities (CRF), Isfahan University of Medical Science, Isfahan, Iran
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohamad Reza Ganjalikhany
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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19
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Havranek B, Lindsey GW, Higuchi Y, Itoh Y, Suzuki T, Okamoto T, Hoshino A, Procko E, Islam SM. A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo. Commun Biol 2023; 6:513. [PMID: 37173421 PMCID: PMC10177734 DOI: 10.1038/s42003-023-04860-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
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Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, USA
- ComputePharma, LLC., Chicago, IL, USA
| | | | - Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA
- Cyrus Biotechnology, Inc., Seattle, WA, USA
| | - Shahidul M Islam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- ComputePharma, LLC., Chicago, IL, USA.
- Department of Chemistry, Delaware State University, Dover, DE, 19901, USA.
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20
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Peka M, Balatsky V. The impact of mutation sets in receptor-binding domain of SARS-CoV-2 variants on the stability of RBD–ACE2 complex. Future Virol 2023. [PMID: 37064325 PMCID: PMC10089296 DOI: 10.2217/fvl-2022-0152] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/01/2023] [Indexed: 04/08/2023]
Abstract
Aim: Bioinformatic analysis of mutation sets in receptor-binding domain (RBD) of currently and previously circulating SARS-CoV-2 variants of concern (VOCs) and interest (VOIs) to assess their ability to bind the ACE2 receptor. Methods: In silico sequence and structure-oriented approaches were used to evaluate the impact of single and multiple mutations. Results: Mutations detected in VOCs and VOIs led to the reduction of binding free energy of the RBD–ACE2 complex, forming additional chemical bonds with ACE2, and to an increase of RBD–ACE2 complex stability. Conclusion: Mutation sets characteristic of SARS-CoV-2 variants have complex effects on the ACE2 receptor-binding affinity associated with amino acid interactions at mutation sites, as well as on the acquisition of other viral adaptive advantages.
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Affiliation(s)
- Mykyta Peka
- V. N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding & Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, Poltava, 36013, Ukraine
| | - Viktor Balatsky
- V. N. Karazin Kharkiv National University, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding & Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, Poltava, 36013, Ukraine
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21
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Singh JK, Anand S, Srivastava SK. Is BF.7 more infectious than other Omicron subtypes: Insights from structural and simulation studies of BF.7 spike RBD variant. Int J Biol Macromol 2023; 238:124154. [PMID: 36965551 PMCID: PMC10036297 DOI: 10.1016/j.ijbiomac.2023.124154] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023]
Abstract
Fear of a fresh infection wave and a global health issue in the ongoing COVID-19 pandemic have been rekindled by the appearance of two new novel variants BF.7 and BA.4/5 of Omicron lineages. Predictions of increased antibody evasion capabilities and transmissibility have been recognised in addition to the existing lineages (BA.1.1, BA.2, BA.2.12.1 and BA.3) as cause for worry. In comparison to Omicron, BA.4 and BF.7 share nine mutations in the spike protein, Leu371Phe, Thr376Ala, Asp405Asn, Arg408Ser, Ser446Gly, Leu452Arg, Phe486Val, Arg493Gln, Ser496Gly, whereas BF.7 contains an additional mutation, Arg346Thr, in the receptor binding domain (RBD) region. Due to the critical need for analysis and data on the BA.4 and BF.7 variants, we have computationally analyzed the interaction pattern between the Omicron, BA.4 and BF.7 RBD and angiotensin-converting enzyme 2 (ACE2) to determine the influence of these unique mutations on the structures, functions, and binding affinity of RBD towards ACE2. These analyses also allow to compare molecular models to previously reported data to evaluate the robustness of our methods for quick prediction of emerging future variants. The docking results reveal that BA.4 and BF.7 have particularly strong interactions with ACE2 when compared to Omicron, as shown by several parameters such as salt bridge, hydrogen bond, and non-bonded interactions. In addition, the estimations of binding free energy corroborated the findings further. BA.4 and BF.7 were found to bind to ACE2 with similar affinities (-72.14 and - 71.54 kcal/mol, respectively) and slightly stronger than Omicron (-70.04 kcal/mol). The differences in the binding pattern between the Omicron, BA.4 and BF.7 variant complexes indicated that the BA.4 and BF.7 RBD substitutions Asp405Asn, Ser446Gly, Leu452Arg, Phe486Val and Arg493Gln caused additional interactions with ACE2. In addition, normal mode analyses also indicate more stable conformations of BA.4 and BF.7 RBDs against human ACE2. Based on these structural and simulation analyses, we hypothesized that these changes may affect the binding affinity of BA.4 and BF.7 with ACE2.
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Affiliation(s)
- Jaikee Kumar Singh
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Shashi Anand
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India
| | - Sandeep Kumar Srivastava
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, Rajasthan 303007, India.
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22
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Triveri A, Casali E, Frasnetti E, Doria F, Frigerio F, Cinquini F, Pavoni S, Moroni E, Marchetti F, Serapian SA, Colombo G. Conformational Behavior of SARS-Cov-2 Spike Protein Variants: Evolutionary Jumps in Sequence Reverberate in Structural Dynamic Differences. J Chem Theory Comput 2023; 19:2120-2134. [PMID: 36926878 PMCID: PMC10029694 DOI: 10.1021/acs.jctc.3c00077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 has evolved rapidly in the first 3 years of pandemic diffusion. The initial evolution of the virus appeared to proceed through big jumps in sequence changes rather than through the stepwise accumulation of point mutations on already established variants. Here, we examine whether this nonlinear mutational process reverberates in variations of the conformational dynamics of the SARS-CoV-2 Spike protein (S-protein), the first point of contact between the virus and the human host. We run extensive microsecond-scale molecular dynamics simulations of seven distinct variants of the protein in their fully glycosylated state and set out to elucidate possible links between the mutational spectrum of the S-protein and the structural dynamics of the respective variant, at global and local levels. The results reveal that mutation-dependent structural and dynamic modulations mostly consist of increased coordinated motions in variants that acquire stability and in an increased internal flexibility in variants that are less stable. Importantly, a limited number of functionally important substructures (the receptor binding domain, in particular) share the same time of movements in all variants, indicating efficient preorganization for functional regions dedicated to host interactions. Our results support a model in which the internal dynamics of the S-proteins from different strains varies in a way that reflects the observed random and non-stepwise jumps in sequence evolution, while conserving the functionally oriented traits of conformational dynamics necessary to support productive interactions with host receptors.
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Affiliation(s)
- Alice Triveri
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Emanuele Casali
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Elena Frasnetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Filippo Doria
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | - Fabrizio Cinquini
- Upstream & Technical
Services—TECS/STES—Eni Spa, via Emilia 1, 20097 San Donato
Milanese (Mi), Italy
| | - Silvia Pavoni
- Department of Physical Chemistry, R&D
Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi),
Italy
| | | | - Filippo Marchetti
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Stefano A. Serapian
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
| | - Giorgio Colombo
- Dipartimento di Chimica,
Università di Pavia, via Taramelli 12, 27100 Pavia,
Italy
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23
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Thakur S, Verma RK, Kepp KP, Mehra R. Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding. J Mol Graph Model 2023; 119:108379. [PMID: 36481587 PMCID: PMC9690204 DOI: 10.1016/j.jmgm.2022.108379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/04/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
The binding affinity of the SARS-CoV-2 spike (S)-protein to the human membrane protein ACE2 is critical for virus function. Computational structure-based screening of new S-protein mutations for ACE2 binding lends promise to rationalize virus function directly from protein structure and ideally aid early detection of potentially concerning variants. We used a computational protocol based on cryo-electron microscopy structures of the S-protein to estimate the change in ACE2-affinity due to S-protein mutation (ΔΔGbind) in good trend agreement with experimental ACE2 affinities. We then expanded predictions to all possible S-protein mutations in 21 different S-protein-ACE2 complexes (400,000 ΔΔGbind data points in total), using mutation group comparisons to reduce systematic errors. The results suggest that mutations that have arisen in major variants as a group maintain ACE2 affinity significantly more than random mutations in the total protein, at the interface, and at evolvable sites. Omicron mutations as a group had a modest change in binding affinity compared to mutations in other major variants. The single-mutation effects seem consistent with ACE2 binding being optimized and maintained in omicron, despite increased importance of other selection pressures (antigenic drift), however, epistasis, glycosylation and in vivo conditions will modulate these effects. Computational prediction of SARS-CoV-2 evolution remains far from achieved, but the feasibility of large-scale computation is substantially aided by using many structures and mutation groups rather than single mutation effects, which are very uncertain. Our results demonstrate substantial challenges but indicate ways forward to improve the quality of computer models for assessing SARS-CoV-2 mutation effects.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, 492015, Chhattisgarh, India
| | - Rajaneesh Kumar Verma
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, 492015, Chhattisgarh, India
| | - Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800, Kongens Lyngby, Denmark.
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, 492015, Chhattisgarh, India.
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24
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Szpulak A, Garlak U, Ćwirko H, Witkowska B, Rombel-Bryzek A, Witkowska D. SARS-CoV-2 and its impact on the cardiovascular and digestive systems - The interplay between new virus variants and human cells. Comput Struct Biotechnol J 2023; 21:1022-1029. [PMID: 36694807 PMCID: PMC9850860 DOI: 10.1016/j.csbj.2023.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
Since infection with the novel coronavirus SARS-CoV-2 first emerged in Wuhan, China, in December 2019, the world has been battling the pandemic COVID-19. Patients of all ages and genders are now becoming infected with the new coronavirus variant (Omicron) worldwide, and its subvariants continue to pose a threat to health and life. This article provides a literature review of cardiovascular and gastrointestinal complications resulting from SARS-CoV-2 infection. COVID-19 primarily caused respiratory symptoms, but complications can affect many vital organs. SARS-CoV-2 binds to a human cell receptor (angiotensin-converting enzyme 2 - ACE2) that is predominantly expressed primarily in the heart and gastrointestinal tract, which is why we focused on complications in these organs. Since the high transmissibility of Omicron and its ability to evade the immune system have raised worldwide concern, we have tried to summarise the current knowledge about its development from a structural point of view and to highlight the differences in its binding to human receptors and proteases compared to previous VOC.
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Affiliation(s)
- Angelika Szpulak
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Urszula Garlak
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Hanna Ćwirko
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Bogusława Witkowska
- Institute of Health Sciences, University of Opole, Katowicka 68, 45-060 Opole, Poland
| | | | - Danuta Witkowska
- Institute of Health Sciences, University of Opole, Katowicka 68, 45-060 Opole, Poland
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25
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Carter C, Airas J, Parish CA. Atomistic insights into the binding of SARS-CoV-2 spike receptor binding domain with the human ACE2 receptor: The importance of residue 493. J Mol Graph Model 2023; 118:108360. [PMID: 36401897 PMCID: PMC9595494 DOI: 10.1016/j.jmgm.2022.108360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
SARS-CoV-2 is a coronavirus that has created a global pandemic. The virus contains a spike protein which has been shown to bind to the ACE2 receptor on the surface of human cells. Vaccines have been developed that recognize elements of the SARS-CoV-2 spike protein and they have been successful in preventing infection. Recently, the Omicron variant of the SARS-CoV-2 virus was reported and quickly became a variant of concern due to its transmissibility. This variant contained an unusually large number (32) of point mutations, of which 15 of those mutations are in the receptor binding domain of the spike protein. While several computational and experimental investigations comparing the binding of the Omicron and wild type RBD to the human ACE2 receptor have been conducted, many of these report contradictory findings. In order to assess the differential binding ability, we conducted 2 μs of classical molecular dynamics (cMD) simulation to estimate the binding affinities and behaviors. Based upon MM-GBSA binding affinity, per-residue energy decomposition analysis, center of mass distance measurements, ensemble clustering, pairwise residue decomposition and hydrogen bonding analysis, our results suggest that a single point mutation is responsible for the enhanced binding of the Omicron mutant relative to the WT. While the 15-point mutations in the receptor binding domain contribute positively and negatively to the affinity of the spike protein for the human ACE2 receptor, it is the point mutation Q493R that confers enhanced binding while the Q493K mutation results in similar binding. The MM-GBSA binding estimations over a 2 μs trajectory, suggest that the wild type binds to ACE2 with a value of -29.69 kcal/mol while the Q493K and Q493R Omicron mutants bind with energy values of -26.67 and -34.56 kcal/mol, respectively. These values are significantly different, given the error estimates associated with the MM-GBSA method. In general, while some mutations increase binding, more mutations diminish binding, leading to an overall similar picture of binding for Q493K and enhanced binding for Q493R.
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Affiliation(s)
- Camryn Carter
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, 23173, USA
| | - Justin Airas
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, 23173, USA,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Carol A. Parish
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, 23173, USA,Corresponding author
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26
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Conformational Dynamics of the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Biomedicines 2022; 10:biomedicines10123233. [PMID: 36551988 PMCID: PMC9775641 DOI: 10.3390/biomedicines10123233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Variants of SARS-CoV-2 keep emerging and causing new waves of COVID-19 around the world. Effective new approaches in drug development are based on the binding of agents, such as neutralizing monoclonal antibodies to a receptor-binding domain (RBD) of SARS-CoV-2 spike protein. However, mutations in RBD may lower the affinity of previously developed antibodies. Therefore, rapid analysis of new variants and selection of a binding partner with high affinity is of great therapeutic importance. Here, we explore a computational approach based on molecular dynamics simulations and conformational clusterization techniques for the wild-type and omicron variants of RBD. Biochemical experiments support the hypothesis of the presence of several conformational states within the RBD assembly. The development of such an approach will facilitate the selection of neutralization drugs with higher affinity based on the primary structure of the target antigen.
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27
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Bolivar-Muñoz J, Vits S, Bermudez-Santana CI, Galindo JF. Structural Analysis of the Spike Protein of SARS-CoV-2 Variants and Other Betacoronaviruses Using Molecular Dynamics. Chemphyschem 2022; 23:e202200382. [PMID: 35927218 DOI: 10.1002/cphc.202200382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/03/2022] [Indexed: 01/04/2023]
Abstract
A structural analysis over various spike proteins from three highly pathogenic Betacoronavirus was done to understand their structural differences. The proteins were modeled using crystal structures from SARS-CoV, MERS-CoV, and other Betacoronavirus that infect bats and pangolins. The group was split in two sets; the first set corresponds to the non-mutated spike proteins, while the second set corresponds to mutated spike variants alpha, beta, gamma, delta, omicron and mu; five of them classified as variants of concern and the last one as variant of interest. A conformational space exploration was carried out for every protein by using molecular dynamic simulations. Root mean square fluctuations, principal component and cross-correlation analysis were carried out over the dynamics to analyze the flexibility and rigidity of every protein in comparison to the wild type Spike protein from the SARS-CoV-2. The obtained results indicate that the proteins, which are not spread among humans, have smooth movements compared to those of SARS-CoV-2 and its variants. In addition, a relationship between the speed of the virulence and the movement of the protein can explain the behavior of delta and omicron variants.
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Affiliation(s)
- Jonathan Bolivar-Muñoz
- Department of Chemistry, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Sofia Vits
- Department of Biology, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Clara Isabel Bermudez-Santana
- Department of Biology, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Johan Fabian Galindo
- Department of Chemistry, Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
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28
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Sang P, Chen YQ, Liu MT, Wang YT, Yue T, Li Y, Yin YR, Yang LQ. Electrostatic Interactions Are the Primary Determinant of the Binding Affinity of SARS-CoV-2 Spike RBD to ACE2: A Computational Case Study of Omicron Variants. Int J Mol Sci 2022; 23:ijms232314796. [PMID: 36499120 PMCID: PMC9740405 DOI: 10.3390/ijms232314796] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022] Open
Abstract
To explore the mechanistic origin that determines the binding affinity of SARS-CoV-2 spike receptor binding domain (RBD) to human angiotensin converting enzyme 2 (ACE2), we constructed the homology models of RBD-ACE2 complexes of four Omicron subvariants (BA.1, BA.2, BA.3 and BA.4/5), and compared them with wild type complex (RBDWT-ACE2) in terms of various structural dynamic properties by molecular dynamics (MD) simulations and binding free energy (BFE) calculations. The results of MD simulations suggest that the RBDs of all the Omicron subvariants (RBDOMIs) feature increased global structural fluctuations when compared with RBDWT. Detailed comparison of BFE components reveals that the enhanced electrostatic attractive interactions are the main determinant of the higher ACE2-binding affinity of RBDOMIs than RBDWT, while the weakened electrostatic attractive interactions determine RBD of BA.4/5 subvariant (RBDBA.4/5) lowest ACE2-binding affinity among all Omicron subvariants. The per-residue BFE decompositions and the hydrogen bond (HB) networks analyses indicate that the enhanced electrostatic attractive interactions are mainly through gain/loss of the positively/negatively charged residues, and the formation or destruction of the interfacial HBs and salt bridges can also largely affect the ACE2-binding affinity of RBD. It is worth pointing out that since Q493R plays the most important positive contribution in enhancing binding affinity, the absence of this mutation in RBDBA.4/5 results in a significantly weaker binding affinity to ACE2 than other Omicron subvariants. Our results provide insight into the role of electrostatic interactions in determining of the binding affinity of SARS-CoV-2 RBD to human ACE2.
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Affiliation(s)
- Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671000, China
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from West Yunnan, Dali University, Dali 671000, China
| | - Yong-Qin Chen
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Meng-Ting Liu
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Yu-Ting Wang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Ting Yue
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Yi Li
- College of Mathematics and Computer Science, Dali University, Dali 671000, China
| | - Yi-Rui Yin
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali 671000, China
- Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali 671000, China
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from West Yunnan, Dali University, Dali 671000, China
- Correspondence:
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29
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Sarkar P, Banerjee S, Chakrabarti S, Chakrabarti P, Bandyopadhyay A, Mitra AG, Saha S, Roy A, Sarkar S. Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India. Indian J Med Microbiol 2022; 43:66-72. [PMID: 36400646 PMCID: PMC9664238 DOI: 10.1016/j.ijmmb.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022]
Abstract
Purpose The emergence of highly mutated and transmissible BA variants has caused an unprecedented surge in COVID-19 infections worldwide. Thorough analysis of its genome structure and phylogenomic evolutionary details will serve as scientific reference for future research. Method Here, we have analyzed the BA variants from India using whole-genome sequencing, spike protein mutation study, spatio-temporal surveillance, phylogenomic assessment and epitope mapping. Results The predominance of BA.2/BA.2-like was observed in India during COVID-19 third wave. Genome analysis and mutation study highlighted the existence of 2128 amino acid changes within BA as compared to NC_045512.2. Presence of 23 unknown mutation sites (spanning region 61–831) were observed among the Indian BA variants as compared to the global BA strains. Unassigned probable Omicron showed the highest number of mutations (370) followed by BA.1 (104), BA.2.3 (56), and BA.2 (27). Presence of mutations ‘Q493R + Q498R + N501Y’, and ‘K417 N + E484A + N501Y’ remained exclusive to BA.2 as well as unassigned probable Omicron. The time-tree and phylogenomic network assessed the evolutionary relationship of the BA variants. Existence of 424 segregating sites and 113 parsimony informative sites within BA genomes were observed through haplotype network analysis. Epitope mapping depicted the presence of unique antigenic sites within the receptor binding domain of the BA variants that could be exploited for robust vaccine development. Conclusion These findings provide important scientific insights about the nature, diversity, and evolution of Indian BA variants. The study further divulges in the avenues of therapeutic upgradation for better management and eventual eradication of COVID-19.
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Affiliation(s)
- Poulomi Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Sarthak Banerjee
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Saikat Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Partha Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India
| | - Arun Bandyopadhyay
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | | | - Soumen Saha
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Aviral Roy
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Siddik Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India,Corresponding author. CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB-700032, India
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30
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Coderc de Lacam EG, Blazhynska M, Chen H, Gumbart JC, Chipot C. When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy. J Chem Theory Comput 2022; 18:5890-5900. [PMID: 36108303 PMCID: PMC9518821 DOI: 10.1021/acs.jctc.2c00604] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Accurate determination of binding free energy is pivotal for the study of many biological processes and has been applied in a number of theoretical investigations to compare the affinity of severe acute respiratory syndrome coronavirus 2 variants toward the host cell. Diversity of these variants challenges the development of effective general therapies, their transmissibility relying either on an increased affinity toward their dedicated human receptor, the angiotensin-converting enzyme 2 (ACE2), or on escaping the immune response. Now that robust structural data are available, we have determined with utmost accuracy the standard binding free energy of the receptor-binding domain to the most widespread variants, namely, Alpha, Beta, Delta, and Omicron BA.2, as well as the wild type (WT) in complex either with ACE2 or with antibodies, namely, S2E12 and H11-D4, using a rigorous theoretical framework that combines molecular dynamics and potential-of-mean-force calculations. Our results show that an appropriate starting structure is crucial to ensure appropriate reproduction of the binding affinity, allowing the variants to be compared. They also emphasize the necessity to apply the relevant methodology, bereft of any shortcut, to account for all the contributions to the standard binding free energy. Our estimates of the binding affinities support the view that while the Alpha and Beta variants lean on an increased affinity toward the host cell, the Delta and Omicron BA.2 variants choose immune escape. Moreover, the S2E12 antibody, already known to be active against the WT (Starr et al., 2021; Mlcochova et al., 2021), proved to be equally effective against the Delta variant. In stark contrast, H11-D4 retains a low affinity toward the WT compared to that of ACE2 for the latter. Assuming robust structural information, the methodology employed herein successfully addresses the challenging protein-protein binding problem in the context of coronavirus disease 2019 while offering promising perspectives for predictive studies of ever-emerging variants.
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Affiliation(s)
- Emma Goulard Coderc de Lacam
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - Marharyta Blazhynska
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - Haochuan Chen
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
| | - James C. Gumbart
- School of Physics, Georgia Institute of
Technology, Atlanta, Georgia30332, United States
| | - Christophe Chipot
- Laboratoire International Associé Centre
National de la Recherche Scientifique et University of Illinois at Urbana-Champaign,
Unité Mixte de Recherche No 7019, Université de
Lorraine, B.P. 70239, Vandœuvre-lès-Nancy Cedex54506,
France
- Theoretical and Computational Biophysics Group, Beckman
Institute, and Department of Physics, University of Illinois at
Urbana-Champaign, UrbanaIllinois61802, United
States
- Department of Biochemistry and Molecular Biology,
The University of Chicago, 929 E. 57th Street W225, Chicago,
Illinois60637, United States
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Yamacli S, Avci M. Computation of the Binding Energies between Human ACE2 and Spike RBDs of the Original Strain, Delta and Omicron Variants of the SARS-CoV-2: A DFT Simulation Approach. ADVANCED THEORY AND SIMULATIONS 2022; 5:2200337. [PMID: 36248211 PMCID: PMC9538088 DOI: 10.1002/adts.202200337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/31/2022] [Indexed: 11/09/2022]
Abstract
The receptor binding domain (RBD) of SARS-CoV-2 binds to human ACE2 leading to infection. In this study, the complexes that are formed by the attachment of the SARS-CoV-2 spike RBDs of the original strain, delta and omicron variants to the human ACE2 are investigated via density functional theory (DFT) simulations to obtain binding energies. The DFT computations are performed without fragmenting the interfaces to involve longer-range interactions for improved accuracy, which is one of the primary features of the approach used in this study. Basis set superposition error corrections and van der Waals dispersions are also included in the DFT simulations. The binding energies of the SARS-CoV-2 spike RBDs of the original strain, delta and omicron variants to the human ACE2 are computed as -4.76, -6.68, and -11.77 eV, respectively. These binding energy values indicate that the binding of the omicron variant to the ACE2 is much more favorable than the binding of the original strain and the delta variant, which constitute a molecular reason for the takeover of the omicron variant. The binding energies and the decomposition of these energies found in this study are expected to aid in the development of neutralizing agents.
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Affiliation(s)
- Serhan Yamacli
- Department of Electrical‐Electronics EngineeringNuh Naci Yazgan UniversityKayseri38090Turkey
| | - Mutlu Avci
- Department of Biomedical EngineeringCukurova UniversityAdana01330Turkey
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