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For: Nguyen H, Thai NQ, Nguyen PH, Li MS. SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation. J Phys Chem B 2022;126:4669-4678. [PMID: 35723978 PMCID: PMC9235043 DOI: 10.1021/acs.jpcb.2c01048] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/06/2022] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
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
2
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]
3
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
4
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]
5
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]
6
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]
7
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]
8
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]
9
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]
10
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
11
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
12
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
13
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]
14
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]
15
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]
16
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]
17
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]
18
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
19
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
20
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]
21
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]
22
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]
23
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]
24
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
25
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]
26
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
27
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]
28
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
29
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]
30
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]
31
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]
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