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For: Delgado JM, Duro N, Rogers DM, Tkatchenko A, Pandit SA, Varma S. Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor. Proteins 2021;89:1134-1144. [PMID: 33864655 PMCID: PMC8250905 DOI: 10.1002/prot.26086] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 12/19/2022]
Number Cited by Other Article(s)
1
Higbee PS, Dayhoff GW, Anbanandam A, Varma S, Daughdrill G. Structural Adaptation of Secondary p53 Binding Sites on MDM2 and MDMX. J Mol Biol 2024;436:168626. [PMID: 38810774 DOI: 10.1016/j.jmb.2024.168626] [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: 03/12/2024] [Revised: 04/24/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
2
Shim W, Lee A, Lee JH. The Role of Extracellular Vesicles in Pandemic Viral Infections. J Microbiol 2024;62:419-427. [PMID: 38916789 DOI: 10.1007/s12275-024-00144-x] [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: 01/29/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/26/2024]
3
Unke OT, Stöhr M, Ganscha S, Unterthiner T, Maennel H, Kashubin S, Ahlin D, Gastegger M, Medrano Sandonas L, Berryman JT, Tkatchenko A, Müller KR. Biomolecular dynamics with machine-learned quantum-mechanical force fields trained on diverse chemical fragments. SCIENCE ADVANCES 2024;10:eadn4397. [PMID: 38579003 DOI: 10.1126/sciadv.adn4397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024]
4
Maity S, Acharya A. Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding. ACS APPLIED BIO MATERIALS 2024;7:646-656. [PMID: 36947738 PMCID: PMC10880061 DOI: 10.1021/acsabm.2c01064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023]
5
Delgado JM, Nagy PR, Varma S. Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes. J Chem Inf Model 2024;64:378-392. [PMID: 38051630 PMCID: PMC11345861 DOI: 10.1021/acs.jcim.3c01513] [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] [Indexed: 12/07/2023]
6
Abduljalil JM, Elghareib AM, Samir A, Ezat AA, Elfiky AA. How helpful were molecular dynamics simulations in shaping our understanding of SARS-CoV-2 spike protein dynamics? Int J Biol Macromol 2023:125153. [PMID: 37268078 DOI: 10.1016/j.ijbiomac.2023.125153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 05/27/2023] [Indexed: 06/04/2023]
7
Xiao S, Verkhivker GM, Tao P. Machine learning and protein allostery. Trends Biochem Sci 2023;48:375-390. [PMID: 36564251 PMCID: PMC10023316 DOI: 10.1016/j.tibs.2022.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/16/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
8
Ghoula M, Naceri S, Sitruk S, Flatters D, Moroy G, Camproux AC. Identifying promising druggable binding sites and their flexibility to target the receptor-binding domain of SARS-CoV-2 spike protein. Comput Struct Biotechnol J 2023;21:2339-2351. [PMID: 36998674 PMCID: PMC10023212 DOI: 10.1016/j.csbj.2023.03.029] [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: 10/25/2022] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]  Open
9
Vásquez V, Orozco J. Detection of COVID-19-related biomarkers by electrochemical biosensors and potential for diagnosis, prognosis, and prediction of the course of the disease in the context of personalized medicine. Anal Bioanal Chem 2023;415:1003-1031. [PMID: 35970970 PMCID: PMC9378265 DOI: 10.1007/s00216-022-04237-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 02/07/2023]
10
Sharfin Rahman M, De Alwis Watuthanthrige N, Chandrarathne BM, Page RC, Konkolewicz D. Polymer modification of SARS-CoV-2 spike protein impacts its ability to bind key receptor. Eur Polym J 2023;184:111767. [PMID: 36531158 PMCID: PMC9749382 DOI: 10.1016/j.eurpolymj.2022.111767] [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: 10/20/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
11
Nejat R, Torshizi MF, Najafi DJ. S Protein, ACE2 and Host Cell Proteases in SARS-CoV-2 Cell Entry and Infectivity; Is Soluble ACE2 a Two Blade Sword? A Narrative Review. Vaccines (Basel) 2023;11:204. [PMID: 36851081 PMCID: PMC9968219 DOI: 10.3390/vaccines11020204] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]  Open
12
The Development of Pharmacophore Models for the Search of New Natural Inhibitors of SARS-CoV-2 Spike RBD-ACE2 Binding Interface. Molecules 2022;27:molecules27248938. [PMID: 36558067 PMCID: PMC9788546 DOI: 10.3390/molecules27248938] [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: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]  Open
13
Unravelling viral dynamics through molecular dynamics simulations - A brief overview. Biophys Chem 2022;291:106908. [DOI: 10.1016/j.bpc.2022.106908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022]
14
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: 13] [Impact Index Per Article: 6.5] [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
15
Isobe A, Arai Y, Kuroda D, Okumura N, Ono T, Ushiba S, Nakakita SI, Daidoji T, Suzuki Y, Nakaya T, Matsumoto K, Watanabe Y. ACE2 N-glycosylation modulates interactions with SARS-CoV-2 spike protein in a site-specific manner. Commun Biol 2022;5:1188. [PMID: 36335195 PMCID: PMC9637154 DOI: 10.1038/s42003-022-04170-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022]  Open
16
Monroe JM, Haralambieva IH, Warner ND, Grill DE, Quach HQ, Kennedy RB. Longitudinal antibody titer, avidity, and neutralizing responses after SARS-CoV-2 infection. Heliyon 2022;8:e11676. [PMID: 36439767 PMCID: PMC9675084 DOI: 10.1016/j.heliyon.2022.e11676] [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: 06/29/2022] [Revised: 10/05/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]  Open
17
Mattiuzzi C, Henry BM, Lippi G. Regional Association between Mean Air Temperature and Case Numbers of Multiple SARS-CoV-2 Lineages throughout the Pandemic. Viruses 2022;14:v14091913. [PMID: 36146720 PMCID: PMC9501826 DOI: 10.3390/v14091913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 12/31/2022]  Open
18
Dutta S, Panthi B, Chandra A. All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes. J Phys Chem B 2022;126:5375-5389. [PMID: 35833966 PMCID: PMC9328126 DOI: 10.1021/acs.jpcb.2c00833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/25/2022] [Indexed: 12/18/2022]
19
Vásquez V, Navas MC, Jaimes JA, Orozco J. SARS-CoV-2 electrochemical immunosensor based on the spike-ACE2 complex. Anal Chim Acta 2022;1205:339718. [PMID: 35414393 PMCID: PMC8941303 DOI: 10.1016/j.aca.2022.339718] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/22/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023]
20
Mechanistic Origin of Different Binding Affinities of SARS-CoV and SARS-CoV-2 Spike RBDs to Human ACE2. Cells 2022;11:cells11081274. [PMID: 35455955 PMCID: PMC9032924 DOI: 10.3390/cells11081274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 12/04/2022]  Open
21
Capraz T, Kienzl NF, Laurent E, Perthold JW, Föderl-Höbenreich E, Grünwald-Gruber C, Maresch D, Monteil V, Niederhöfer J, Wirnsberger G, Mirazimi A, Zatloukal K, Mach L, Penninger JM, Oostenbrink C, Stadlmann J. Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor. eLife 2021;10:e73641. [PMID: 34927585 PMCID: PMC8730730 DOI: 10.7554/elife.73641] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/17/2021] [Indexed: 11/17/2022]  Open
22
Capponi S, Wang S, Navarro EJ, Bianco S. AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021;44:123. [PMID: 34613523 PMCID: PMC8493367 DOI: 10.1140/epje/s10189-021-00119-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/24/2021] [Indexed: 05/02/2023]
23
Vázquez-Valadez VH, Hernández-Serda A, Jiménez-Cabiedes MF, Aguirre-Vidal P, González-Tapia I, Carreño-Vargas L, Alarcón-López YA, Espejel-Fuentes A, Martínez-Soriano P, Lugo Álvarez M, Velázquez-Sánchez AM, Markarian NM, Angeles E, Abrahamyan L. Evaluation of Inhibitory Activity In Silico of In-House Thiomorpholine Compounds between the ACE2 Receptor and S1 Subunit of SARS-CoV-2 Spike. Pathogens 2021;10:1208. [PMID: 34578240 PMCID: PMC8468748 DOI: 10.3390/pathogens10091208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/22/2022]  Open
24
ALTIOK D, SAVCI EZ, ÖZKARA B, ALKAN K, NAMDAR DS, TUNÇER G, KILINÇ BR, SUİÇMEZ E, ÇETİN G, ÜNAL S, DÖNMÜŞ B, KARAGÜLLEOĞLU ZY, UNCUOĞLU DB, TEKELİ C, MENDİ HA, BENGİ VU, CENGİZ SEVAL G, KILIÇ P, GÜNEŞ ALTUNTAŞ E, DEMİR-DORA D. Host variations in SARS-CoV-2 infection. Turk J Biol 2021;45:404-424. [PMID: 34803443 PMCID: PMC8573834 DOI: 10.3906/biy-2104-67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022]  Open
25
Cong Y, Feng Y, Ni H, Zhi F, Miao Y, Fang B, Zhang L, Zhang JZH. Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis. J Chem Inf Model 2021;61:3529-3542. [PMID: 34156227 PMCID: PMC8265722 DOI: 10.1021/acs.jcim.1c00241] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/11/2022]
26
Crook JM, Murphy I, Carter DP, Pullan ST, Carroll M, Vipond R, Cunningham AA, Bell D. Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe. Sci Rep 2021;11:14723. [PMID: 34282196 PMCID: PMC8289822 DOI: 10.1038/s41598-021-94011-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023]  Open
27
Singh R, Bhardwaj VK, Sharma J, Kumar D, Purohit R. Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. Comput Biol Med 2021;136:104631. [PMID: 34273770 PMCID: PMC8264305 DOI: 10.1016/j.compbiomed.2021.104631] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/14/2023]
28
Acharya A, Lynch DL, Pavlova A, Pang YT, Gumbart JC. ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV. Chem Commun (Camb) 2021;57:5949-5952. [PMID: 34019602 DOI: 10.1039/d1cc02305e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
29
Pavlova A, Zhang Z, Acharya A, Lynch DL, Pang YT, Mou Z, Parks JM, Chipot C, Gumbart JC. Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. J Phys Chem Lett 2021;12:5494-5502. [PMID: 34086459 PMCID: PMC8204752 DOI: 10.1021/acs.jpclett.1c01494] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 05/06/2023]
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