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For: Wang Y, Liu C, Zhang C, Wang Y, Hong Q, Xu S, Li Z, Yang Y, Huang Z, Cong Y. Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Nat Commun 2022;13:871. [PMID: 35169135 PMCID: PMC8847413 DOI: 10.1038/s41467-022-28528-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/28/2022] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
51
de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023;37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [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: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
52
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.18.567697. [PMID: 38045395 PMCID: PMC10690158 DOI: 10.1101/2023.11.18.567697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
53
Pezzotti G, Ohgitani E, Fujita Y, Imamura H, Pappone F, Grillo A, Nakashio M, Shin-Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Inaba T, Tanino Y, Nukui Y, Higasa K, Yasukochi Y, Okuma K, Mazda O. Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions. ACS Infect Dis 2023;9:2226-2251. [PMID: 37850869 PMCID: PMC10644350 DOI: 10.1021/acsinfecdis.3c00312] [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: 07/03/2023] [Indexed: 10/19/2023]
54
Yang L, Guo S, Hou C, Jiang S, Shi L, Ma X, Zheng B, Fang Y, Ye L, He X. Low-Entropy Hydration Shells at the Spike RBD's Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants. Biomolecules 2023;13:1628. [PMID: 38002310 PMCID: PMC10669249 DOI: 10.3390/biom13111628] [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: 08/23/2023] [Revised: 10/29/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023]  Open
55
Le K, Kannappan S, Kim T, Lee JH, Lee HR, Kim KK. Structural understanding of SARS-CoV-2 virus entry to host cells. Front Mol Biosci 2023;10:1288686. [PMID: 38033388 PMCID: PMC10683510 DOI: 10.3389/fmolb.2023.1288686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023]  Open
56
Pitsillou E, Yu Y, Beh RC, Liang JJ, Hung A, Karagiannis TC. Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity. Clin Exp Med 2023;23:3277-3298. [PMID: 37615803 DOI: 10.1007/s10238-023-01168-0] [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: 04/24/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
57
Tulsian NK, Palur RV, Qian X, Gu Y, D/O Shunmuganathan B, Samsudin F, Wong YH, Lin J, Purushotorman K, Kozma MM, Wang B, Lescar J, Wang CI, Gupta RK, Bond PJ, MacAry PA. Defining neutralization and allostery by antibodies against COVID-19 variants. Nat Commun 2023;14:6967. [PMID: 37907459 PMCID: PMC10618280 DOI: 10.1038/s41467-023-42408-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023]  Open
58
Chakraborty S, Saha C. A multi-tier computational screening framework to effectively search the mutational space of SARS-CoV-2 receptor binding motif to identify mutants with enhanced ACE2 binding abilities. Mol Inform 2023;42:e2300055. [PMID: 37590498 DOI: 10.1002/minf.202300055] [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: 03/06/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 08/19/2023]
59
Xu C, Han W, Cong Y. Cryo-EM and cryo-ET of the spike, virion, and antibody neutralization of SARS-CoV-2 and VOCs. Curr Opin Struct Biol 2023;82:102664. [PMID: 37544111 DOI: 10.1016/j.sbi.2023.102664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/14/2023] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
60
Verkhivker G, Alshahrani M, Gupta G. Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites. Viruses 2023;15:2009. [PMID: 37896786 PMCID: PMC10610873 DOI: 10.3390/v15102009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]  Open
61
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]
62
Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. J Chem Inf Model 2023;63:5272-5296. [PMID: 37549201 PMCID: PMC11162552 DOI: 10.1021/acs.jcim.3c00778] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
63
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Phys Chem Chem Phys 2023;25:21245-21266. [PMID: 37548589 PMCID: PMC10536792 DOI: 10.1039/d3cp02042h] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
64
Akter S, Oliveira JIN, Barton C, Sarkar MH, Shahab M, Banu TA, Goswami B, Osman E, Uzzaman MS, Nafisa T, Molla MA, Yeasmin M, Farzana M, Habib A, Shaikh AA, Khan S. Spike protein mutations and structural insights of pangolin lineage B.1.1.25 with implications for viral pathogenicity and ACE2 binding affinity. Sci Rep 2023;13:13146. [PMID: 37573409 PMCID: PMC10423208 DOI: 10.1038/s41598-023-40005-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023]  Open
65
Mani S, Kaur A, Jakhar K, Kumari G, Sonar S, Kumar A, Das S, Kumar S, Kumar V, Kundu R, Pandey AK, Singh UP, Majumdar T. Targeting DPP4-RBD interactions by sitagliptin and linagliptin delivers a potential host-directed therapy against pan-SARS-CoV-2 infections. Int J Biol Macromol 2023;245:125444. [PMID: 37385308 PMCID: PMC10293653 DOI: 10.1016/j.ijbiomac.2023.125444] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
66
Maurya AK, Sharma P, Samanta P, Shami AA, Misra SK, Zhang F, Thara R, Kumar D, Shi D, Linhardt RJ, Sharp JS, Doerksen RJ, Tandon R, Pomin VH. Structure, anti-SARS-CoV-2, and anticoagulant effects of two sulfated galactans from the red alga Botryocladia occidentalis. Int J Biol Macromol 2023;238:124168. [PMID: 36963552 PMCID: PMC10175164 DOI: 10.1016/j.ijbiomac.2023.124168] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023]
67
Wuo M, Dugan AE, Halim M, Hauser BM, Feldman J, Caradonna TM, Zhang S, Pepi LE, Atyeo C, Fischinger S, Alter G, Garcia-Beltran WF, Azadi P, Hung D, Schmidt AG, Kiessling LL. Lectin Fingerprinting Distinguishes Antibody Neutralization in SARS-CoV-2. ACS CENTRAL SCIENCE 2023;9:947-956. [PMID: 37252360 PMCID: PMC10214521 DOI: 10.1021/acscentsci.2c01471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Indexed: 05/31/2023]
68
Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541592. [PMID: 37292827 PMCID: PMC10245745 DOI: 10.1101/2023.05.20.541592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
69
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
70
Verkhivker G, Alshahrani M, Gupta G. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Viruses 2023;15:1143. [PMID: 37243229 PMCID: PMC10221141 DOI: 10.3390/v15051143] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]  Open
71
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539337. [PMID: 37205479 PMCID: PMC10187228 DOI: 10.1101/2023.05.03.539337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
72
Corominas J, Garriga C, Prenafeta A, Moros A, Cañete M, Barreiro A, González-González L, Madrenas L, Güell I, Clotet B, Izquierdo-Useros N, Raïch-Regué D, Gallemí M, Blanco J, Pradenas E, Trinité B, Prado JG, Blanch-Lombarte O, Pérez-Caballero R, Plana M, Esteban I, Pastor-Quiñones C, Núñez-Costa X, Taleb RA, McSkimming P, Soriano A, Nava J, Anagua JO, Ramos R, Lluch RM, Comes AC, Romero SO, Gomez XM, Sans-Pola C, Moltó J, Benet S, Bailón L, Arribas JR, Borobia AM, Parada JQ, Navarro-Pérez J, Forner Giner MJ, Lucas RO, Jiménez MDMV, Compán SO, Alvarez-Mon M, Troncoso D, Arana-Arri E, Meijide S, Imaz-Ayo N, García PM, de la Villa Martínez S, Fernández SR, Prat T, Torroella È, Ferrer L. Safety and immunogenicity of the protein-based PHH-1V compared to BNT162b2 as a heterologous SARS-CoV-2 booster vaccine in adults vaccinated against COVID-19: a multicentre, randomised, double-blind, non-inferiority phase IIb trial. THE LANCET REGIONAL HEALTH. EUROPE 2023;28:100613. [PMID: 37131861 PMCID: PMC10102678 DOI: 10.1016/j.lanepe.2023.100613] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 05/04/2023]
73
Li Y, Yu Q, Huang R, Chen H, Ren H, Ma L, He Y, Li W. SARS-CoV-2 SUD2 and Nsp5 Conspire to Boost Apoptosis of Respiratory Epithelial Cells via an Augmented Interaction with the G-Quadruplex of BclII. mBio 2023;14:e0335922. [PMID: 36853058 PMCID: PMC10127692 DOI: 10.1128/mbio.03359-22] [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: 12/07/2022] [Accepted: 02/09/2023] [Indexed: 03/01/2023]  Open
74
Okada S, Muto Y, Zhu B, Ueda H, Nakamura H. Development of a Peptide Sensor Derived from Human ACE2 for Fluorescence Polarization Assays of the SARS-CoV-2 Receptor Binding Domain. Anal Chem 2023;95:6198-6202. [PMID: 37028948 PMCID: PMC10107661 DOI: 10.1021/acs.analchem.2c05818] [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: 12/31/2022] [Accepted: 04/05/2023] [Indexed: 04/09/2023]
75
Li B, Zhao Y, Wu X, Wu H, Tang W, Yu X, Mou J, Tan W, Jin M, Li W, Zhang Q, Liu M. Abiotic Synthetic Antibody Inhibitor with Broad-Spectrum Neutralization and Antiviral Efficacy against Escaping SARS-CoV-2 Variants. ACS NANO 2023;17:7017-7034. [PMID: 36971310 PMCID: PMC10074723 DOI: 10.1021/acsnano.3c02050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
76
Dual mechanism: Epigenetic inhibitor apabetalone reduces SARS-CoV-2 Delta and Omicron variant spike binding and attenuates SARS-CoV-2 RNA induced inflammation. Int Immunopharmacol 2023;117:109929. [PMID: 36857935 PMCID: PMC9946890 DOI: 10.1016/j.intimp.2023.109929] [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: 12/14/2022] [Revised: 02/03/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
77
Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nat Commun 2023;14:1421. [PMID: 36918534 PMCID: PMC10013288 DOI: 10.1038/s41467-023-36745-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/15/2023] [Indexed: 03/15/2023]  Open
78
Kim JW, Heo K, Kim HJ, Yoo Y, Cho HS, Jang HJ, Lee HY, Ko IY, Woo JR, Cho YB, Lee JH, Yang HR, Shin HG, Choi HL, Hwang K, Kim S, Kim H, Chun K, Lee S. Novel bispecific human antibody platform specifically targeting a fully open spike conformation potently neutralizes multiple SARS-CoV-2 variants. Antiviral Res 2023;212:105576. [PMID: 36870394 PMCID: PMC9979629 DOI: 10.1016/j.antiviral.2023.105576] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
79
Jugler C, Sun H, Nguyen K, Palt R, Felder M, Steinkellner H, Chen Q. A novel plant-made monoclonal antibody enhances the synergetic potency of an antibody cocktail against the SARS-CoV-2 Omicron variant. PLANT BIOTECHNOLOGY JOURNAL 2023;21:549-559. [PMID: 36403203 PMCID: PMC9946148 DOI: 10.1111/pbi.13970] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/06/2022] [Accepted: 11/12/2022] [Indexed: 06/01/2023]
80
Wang Q, Ye S, Zhou Z, Song A, Zhu X, Peng J, Liang R, Yang C, Yu X, Huang X, Yu J, Qiu Y, Ge X. Key mutations in the spike protein of SARS-CoV-2 affecting neutralization resistance and viral internalization. J Med Virol 2023;95:e28407. [PMID: 36519597 PMCID: PMC9877909 DOI: 10.1002/jmv.28407] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
81
Zhang Y, Ndzouboukou JB, Lin X, Hou H, Wang F, Yuan L, Gan M, Yao Z, Fu H, Cao J, Fan X. SARS-CoV-2 evolves to reduce but not abolish neutralizing action. J Med Virol 2023;95:e28207. [PMID: 36217880 PMCID: PMC9874811 DOI: 10.1002/jmv.28207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/25/2022] [Accepted: 10/02/2022] [Indexed: 01/27/2023]
82
Guest PC, Kesharwani P, Butler AE, Sahebkar A. The COVID-19 Pandemic: SARS-CoV-2 Structure, Infection, Transmission, Symptomology, and Variants of Concern. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023;1412:3-26. [PMID: 37378759 DOI: 10.1007/978-3-031-28012-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
83
Gupta D, Kumar M, Sharma P, Mohan T, Prakash A, Kumari R, Kaur P. Effect of Double Mutation (L452R and E484Q) on the Binding Affinity of Monoclonal Antibodies (mAbs) against the RBD-A Target for Vaccine Development. Vaccines (Basel) 2022;11:23. [PMID: 36679867 PMCID: PMC9860914 DOI: 10.3390/vaccines11010023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]  Open
84
Zhang X, Hong B, Wei P, Pei P, Xu H, Chen L, Tong Y, Chen J, Luo SZ, Fan H, He C. Pathogen-host adhesion between SARS-CoV-2 spike proteins from different variants and human ACE2 studied at single-molecule and single-cell levels. Emerg Microbes Infect 2022;11:2658-2669. [PMID: 36153659 PMCID: PMC9639500 DOI: 10.1080/22221751.2022.2128887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022]
85
Pavan M, Bassani D, Sturlese M, Moro S. From the Wuhan-Hu-1 strain to the XD and XE variants: is targeting the SARS-CoV-2 spike protein still a pharmaceutically relevant option against COVID-19? J Enzyme Inhib Med Chem 2022;37:1704-1714. [PMID: 35695095 PMCID: PMC9196651 DOI: 10.1080/14756366.2022.2081847] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/20/2022] [Indexed: 11/08/2022]  Open
86
Valenzuela-Fernández A, Cabrera-Rodriguez R, Ciuffreda L, Perez-Yanes S, Estevez-Herrera J, González-Montelongo R, Alcoba-Florez J, Trujillo-González R, García-Martínez de Artola D, Gil-Campesino H, Díez-Gil O, Lorenzo-Salazar JM, Flores C, Garcia-Luis J. Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19. Front Bioeng Biotechnol 2022;10:1052436. [PMID: 36507266 PMCID: PMC9732709 DOI: 10.3389/fbioe.2022.1052436] [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: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022]  Open
87
Chan KC, Song Y, Xu Z, Shang C, Zhou R. SARS-CoV-2 Delta Variant: Interplay between Individual Mutations and Their Allosteric Synergy. Biomolecules 2022;12:biom12121742. [PMID: 36551170 PMCID: PMC9775976 DOI: 10.3390/biom12121742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022]  Open
88
Wang Z, An J, Liu K, Yu P, Fang X, Li J, Zhu H, Zhu Q, Huang C, Zhang C, Zhao B, Bao L, Song Y, Cao X, Hu D, Jiang Y, Shi L, Zhou L, Fan J, Guan W, Zhou C, Hu Z, Yuan Z, Liu J, Shan C, Liu G. A potent, broadly protective vaccine against SARS-CoV-2 variants of concern. NPJ Vaccines 2022;7:144. [PMID: 36371432 PMCID: PMC9653380 DOI: 10.1038/s41541-022-00571-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]  Open
89
Liu Y, Zhao D, Wang Y, Chen Z, Yang L, Li W, Gong Y, Gan C, Tang J, Zhang T, Tang D, Dong X, Yang Q, Valencia CA, Dai L, Qi S, Dong B, Chow HY, Li Y. A vaccine based on the yeast-expressed receptor-binding domain (RBD) elicits broad immune responses against SARS-CoV-2 variants. Front Immunol 2022;13:1011484. [PMID: 36439096 PMCID: PMC9682237 DOI: 10.3389/fimmu.2022.1011484] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/24/2022] [Indexed: 06/23/2024]  Open
90
Planchais C, Reyes‐Ruiz A, Lacombe R, Zarantonello A, Lecerf M, Revel M, Roumenina LT, Atanasov BP, Mouquet H, Dimitrov JD. Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2. Protein Sci 2022;31:e4447. [PMID: 36305765 PMCID: PMC9597384 DOI: 10.1002/pro.4447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 01/27/2023]
91
Dissecting Naturally Arising Amino Acid Substitutions at Position L452 of SARS-CoV-2 Spike. J Virol 2022;96:e0116222. [PMID: 36214577 PMCID: PMC9599599 DOI: 10.1128/jvi.01162-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
92
Jain M, Patil N, Gor D, Sharma MK, Goel N, Kaushik P. Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages. Proteomes 2022;10:34. [PMID: 36278694 PMCID: PMC9624331 DOI: 10.3390/proteomes10040034] [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: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/24/2022]  Open
93
Valdovino-Navarro BJ, Dueñas S, Flores-Acosta GI, Gasperin-Bulbarela J, Bernaldez-Sarabia J, Cabanillas-Bernal O, Cervantes-Luevano KE, Licea-Navarro AF. Neutralizing Ability of a Single Domain VNAR Antibody: In Vitro Neutralization of SARS-CoV-2 Variants of Concern. Int J Mol Sci 2022;23:ijms232012267. [PMID: 36293124 PMCID: PMC9603574 DOI: 10.3390/ijms232012267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]  Open
94
Al-Hindawi A, AlDallal U, Waly YM, Hussain MH, Shelig M, Saleh ElMitwalli OSMM, Deen GR, Henari FZ. An Exploration of Nanoparticle-Based Diagnostic Approaches for Coronaviruses: SARS-CoV-2, SARS-CoV and MERS-CoV. NANOMATERIALS (BASEL, SWITZERLAND) 2022;12:3550. [PMID: 36296739 PMCID: PMC9608708 DOI: 10.3390/nano12203550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
95
Li H, Lu H, Tang Y, Wang H, Xiao Y, Li B. A Rebuilding‐Free Nucleic Acid Detection Strategy Enables Ultrasensitive Genotyping, N‐in‐1 Logic Screening and Accurate Multiplex Assay of Dangerous Pathogens. Angew Chem Int Ed Engl 2022;61:e202209496. [DOI: 10.1002/anie.202209496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Indexed: 11/11/2022]
96
Verma S, Patil VM, Gupta MK. Mutation informatics: SARS-CoV-2 receptor-binding domain of the spike protein. Drug Discov Today 2022;27:103312. [PMID: 35787481 PMCID: PMC9250815 DOI: 10.1016/j.drudis.2022.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/06/2022] [Accepted: 06/29/2022] [Indexed: 01/31/2023]
97
Lv N, Cao Z. RBD spatial orientation of the spike protein and its binding to ACE2: insight into the high infectivity of the SARS-CoV-2 Delta variant from MD simulations. Phys Chem Chem Phys 2022;24:24155-24165. [PMID: 36168828 DOI: 10.1039/d2cp03425e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
98
The Receptor Binding Domain of SARS-CoV-2 Lambda Variant Has a Better Chance Than the Delta Variant in Evading BNT162b2 COVID-19 mRNA Vaccine-Induced Humoral Immunity. Int J Mol Sci 2022;23:ijms231911325. [PMID: 36232627 PMCID: PMC9569855 DOI: 10.3390/ijms231911325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022]  Open
99
Muik A, Lui BG, Bacher M, Wallisch AK, Toker A, Finlayson A, Krüger K, Ozhelvaci O, Grikscheit K, Hoehl S, Ciesek S, Türeci Ö, Sahin U. Omicron BA.2 breakthrough infection enhances cross-neutralization of BA.2.12.1 and BA.4/BA.5. Sci Immunol 2022;7:eade2283. [PMID: 36125366 PMCID: PMC9529054 DOI: 10.1126/sciimmunol.ade2283] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
100
Quandt J, Muik A, Salisch N, Lui BG, Lutz S, Krüger K, Wallisch AK, Adams-Quack P, Bacher M, Finlayson A, Ozhelvaci O, Vogler I, Grikscheit K, Hoehl S, Goetsch U, Ciesek S, Türeci Ö, Sahin U. Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes. Sci Immunol 2022;7:eabq2427. [PMID: 35653438 PMCID: PMC9162083 DOI: 10.1126/sciimmunol.abq2427] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/28/2022] [Indexed: 12/28/2022]
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