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For: Kneller DW, Phillips G, O'Neill HM, Jedrzejczak R, Stols L, Langan P, Joachimiak A, Coates L, Kovalevsky A. Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography. Nat Commun 2020;11:3202. [PMID: 32581217 PMCID: PMC7314768 DOI: 10.1038/s41467-020-16954-7] [Citation(s) in RCA: 327] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/04/2020] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Atatreh N, Mahgoub RE, Ghattas MA. Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds. J Enzyme Inhib Med Chem 2025;40:2460045. [PMID: 39912405 PMCID: PMC11803818 DOI: 10.1080/14756366.2025.2460045] [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: 07/30/2024] [Revised: 01/16/2025] [Accepted: 01/24/2025] [Indexed: 02/07/2025]  Open
2
Zhang ZQ, Zhu GH, Zhu R, Lei JX, Liu SY, Tu DZ, Zhang YN, Song YQ, Hou XD, Zhuang XY, Wang P, Cao YB, Ge GB. Discovery of baicalein derivatives as novel covalent inhibitors of SARS CoV-2 Mpro: Structure-activity relationships and inhibitory mechanisms. Bioorg Chem 2025;161:108560. [PMID: 40367796 DOI: 10.1016/j.bioorg.2025.108560] [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: 02/26/2025] [Revised: 05/02/2025] [Accepted: 05/05/2025] [Indexed: 05/16/2025]
3
Hu S, Zhang Y, Wang C, Li J, Su H, Xie X, Wang J, Wang J, Cao J, He X, Xu Y, Zhang L, Dai W, Liu H. Development of Orally Bioavailable Octahydroindole-Based Peptidomimetic Derivative as a Broad-Spectrum Inhibitor against HCoV-OC43 and SARS-CoV-2. J Med Chem 2025. [PMID: 40400488 DOI: 10.1021/acs.jmedchem.4c03024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2025]
4
Wang J, Yu Y, Dong H, Ji Y, Ning W, Li Y. The interface hydrophilic-hydrophobic integration of fluorinated defective graphene towards biomedical applications. Phys Chem Chem Phys 2025;27:7538-7555. [PMID: 40167997 DOI: 10.1039/d5cp00075k] [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: 04/02/2025]
5
Wang W, Zhou X, Li W, Zeng P, Guo L, Wang Q, Li J. Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 Mpro mutants and MERS-CoV Mpro. Commun Biol 2025;8:493. [PMID: 40133408 PMCID: PMC11937426 DOI: 10.1038/s42003-025-07929-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Accepted: 03/11/2025] [Indexed: 03/27/2025]  Open
6
Hu Q, Zhang YW, Zhang YN, Zhu GH, Chen PC, Liu W, Hu XP, Song FF, Pan ZF, Zheng SL, Shen NE, Ge GB, Huang P. Uncovering the naturally occurring covalent inhibitors of SARS-CoV-2 Mpro from the Chinese medicine sappanwood and deciphering their synergistic anti-Mpro effects. JOURNAL OF ETHNOPHARMACOLOGY 2025;342:119397. [PMID: 39870336 DOI: 10.1016/j.jep.2025.119397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/21/2025] [Accepted: 01/22/2025] [Indexed: 01/29/2025]
7
Jing L, Zhao F, Zheng L, Meng B, Gao S, Laporte M, Jochmans D, De Jonghe S, Neyts J, Zhan P, Kang D, Liu X. Optimization of SARS-CoV-2 Mpro Inhibitors by a Structure-Based Multilevel Virtual Screening Method. Int J Mol Sci 2025;26:670. [PMID: 39859382 PMCID: PMC11765572 DOI: 10.3390/ijms26020670] [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: 12/04/2024] [Revised: 01/04/2025] [Accepted: 01/12/2025] [Indexed: 01/30/2025]  Open
8
Lee E, Rauscher S. The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery. Biochemistry 2025;64:32-46. [PMID: 39513739 DOI: 10.1021/acs.biochem.4c00575] [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: 11/15/2024]
9
Gu X, Zhang X, Zhang X, Wang X, Sun W, Zhang Y, Hu Z. Unveiling the mechanism of action of a novel natural dual inhibitor of SARS-CoV-2 Mpro and PLpro with molecular dynamics simulations. NATURAL PRODUCTS AND BIOPROSPECTING 2025;15:3. [PMID: 39753911 PMCID: PMC11699025 DOI: 10.1007/s13659-024-00486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 11/27/2024] [Indexed: 01/06/2025]
10
Garcia-Segura P, Llop-Peiró A, Novau-Ferré N, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. SARS-CoV-2 main protease (M-pro) mutational profiling: An insight into mutation coldspots. Comput Biol Med 2025;184:109344. [PMID: 39531923 DOI: 10.1016/j.compbiomed.2024.109344] [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: 07/09/2024] [Revised: 09/20/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024]
11
Lu J, He Y, Li Y, Chen X, Li H, Chen X, Xu J, Chen H, Wang Y, He X, Liu S, Chen L. Exploring bifunctional molecules for anti-SARS-CoV-2 and anti-inflammatory activity through structure-based virtual screening, SAR investigation, and biological evaluation. Int J Biol Macromol 2025;287:138529. [PMID: 39653224 DOI: 10.1016/j.ijbiomac.2024.138529] [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: 09/04/2024] [Revised: 11/26/2024] [Accepted: 12/06/2024] [Indexed: 12/16/2024]
12
Xiong M, Nie T, Li Z, Hu M, Su H, Hu H, Xu Y, Shao Q. Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale Simulations. J Chem Inf Model 2024;64:9501-9516. [PMID: 39605253 DOI: 10.1021/acs.jcim.4c01594] [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: 11/29/2024]
13
Benício LFMA, Nascimento ÉCM, Martins JBL. Docking heparan sulfate-based ligands as a promising inhibitor for SARS-CoV-2. J Mol Model 2024;31:19. [PMID: 39666205 DOI: 10.1007/s00894-024-06236-0] [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: 06/20/2024] [Accepted: 11/26/2024] [Indexed: 12/13/2024]
14
Biernacki K, Ciupak O, Daśko M, Rachon J, Flis D, Budka J, Inkielewicz-Stępniak I, Czaja A, Rak J, Demkowicz S. Development of potent and effective SARS-CoV-2 main protease inhibitors based on maleimide analogs for the potential treatment of COVID-19. J Enzyme Inhib Med Chem 2024;39:2290910. [PMID: 38093611 PMCID: PMC10732195 DOI: 10.1080/14756366.2023.2290910] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]  Open
15
Ganapathy A A, Hari Priya VM, Baby K, Bindhu S, Jayan R, Krishnamoorthi R, Somappa SB, Nayak Y, Kumaran A. Flavone-C-glycosides from Cassia auriculata L. as possible inhibitors of phosphodiesterase-5 (PDE5): in vitro, molecular docking and molecular dynamics studies. J Biomol Struct Dyn 2024:1-23. [PMID: 39589221 DOI: 10.1080/07391102.2024.2431659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/03/2024] [Indexed: 11/27/2024]
16
Grabiński W, Karachitos A, Kicińska A. Backstage Heroes-Yeast in COVID-19 Research. Int J Mol Sci 2024;25:12661. [PMID: 39684373 PMCID: PMC11640846 DOI: 10.3390/ijms252312661] [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: 10/01/2024] [Revised: 11/14/2024] [Accepted: 11/22/2024] [Indexed: 12/18/2024]  Open
17
Wang J, Dong H, Ji Y, Li Y, Lee ST. Patterned graphene: An effective platform for adsorption, immobilization, and destruction of SARS-CoV-2 Mpro. J Colloid Interface Sci 2024;673:202-215. [PMID: 38875787 DOI: 10.1016/j.jcis.2024.06.072] [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: 02/07/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024]
18
Wlodawer A, Dauter Z, Rubach P, Minor W, Loch JI, Brzezinski D, Gilski M, Jaskolski M. Waterless structures in the Protein Data Bank. IUCRJ 2024;11:966-976. [PMID: 39465564 PMCID: PMC11533996 DOI: 10.1107/s2052252524009928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 10/10/2024] [Indexed: 10/29/2024]
19
Yang M, Lee MK, Gao S, Song L, Jang H, Jo I, Yang C, Sylvester K, Ko C, Wang S, Ye B, Tang K, Li J, Gu M, Müller CE, Sträter N, Liu X, Kim M, Zhan P. Miniaturized Modular Click Chemistry-enabled Rapid Discovery of Unique SARS-CoV-2 Mpro Inhibitors With Robust Potency and Drug-like Profile. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2404884. [PMID: 39319611 PMCID: PMC11578313 DOI: 10.1002/advs.202404884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/30/2024] [Indexed: 09/26/2024]
20
Butalewicz JP, Sipe SN, Juetten KJ, James VK, Kim K, Zhang YJ, Meek TD, Brodbelt JS. Insights into the Main Protease of SARS-CoV-2: Thermodynamic Analysis, Structural Characterization, and the Impact of Inhibitors. Anal Chem 2024;96:15898-15906. [PMID: 39319663 PMCID: PMC11499983 DOI: 10.1021/acs.analchem.4c02311] [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: 09/26/2024]
21
Bazzi-Allahri F, Shiri F, Ahmadi S, Toropova AP, Toropov AA. SMILES-based QSAR virtual screening to identify potential therapeutics for COVID-19 by targeting 3CLpro and RdRp viral proteins. BMC Chem 2024;18:191. [PMID: 39363220 PMCID: PMC11451266 DOI: 10.1186/s13065-024-01302-3] [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: 04/15/2024] [Accepted: 09/18/2024] [Indexed: 10/05/2024]  Open
22
Purohit P, Panda M, Muya JT, Bandyopadhyay P, Meher BR. Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance. J Biomol Struct Dyn 2024;42:8865-8884. [PMID: 37599474 DOI: 10.1080/07391102.2023.2248519] [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: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
23
Duvvuri V, Shire F, Isabel S, Braukmann T, Clark S, Marchand-Austin A, Eshaghi A, Bandukwala H, Varghese N, Li Y, Sivaraman K, Hussain H, Cronin K, Sullivan A, Li A, Zygmunt A, Ramotar K, Kus J, Hasso M, Corbeil A, Gubbay J, Patel S. Large scale analysis of the SARS-CoV-2 main protease reveals marginal presence of nirmatrelvir-resistant SARS-CoV-2 Omicron mutants in Ontario, Canada, December 2021-September 2023. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2024;50:365-374. [PMID: 39386278 PMCID: PMC11464099 DOI: 10.14745/ccdr.v50i10a05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
24
Zhao C, Rong Y, Shi S, Gao WC, Zhang C. A novel method for synthesizing authentic SARS-CoV-2 main protease. Protein Expr Purif 2024;222:106531. [PMID: 38852715 DOI: 10.1016/j.pep.2024.106531] [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: 05/01/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 06/11/2024]
25
Jhanwar A, Sharma D, Das U. Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics. Int J Biol Macromol 2024;278:134850. [PMID: 39168210 DOI: 10.1016/j.ijbiomac.2024.134850] [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: 01/12/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
26
Aniana A, Nashed NT, Ghirlando R, Drago VN, Kovalevsky A, Louis JM. Characterization of alternate encounter assemblies of SARS-CoV-2 main protease. J Biol Chem 2024;300:107675. [PMID: 39128719 PMCID: PMC11416275 DOI: 10.1016/j.jbc.2024.107675] [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: 07/03/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/13/2024]  Open
27
Al Adem K, Ferreira J, Villanueva A, Fadl S, El-Sadaany F, Masmoudi I, Gidiya Y, Gurudza T, Cardoso T, Saksena N, Rabeh W. 3-chymotrypsin-like protease in SARS-CoV-2. Biosci Rep 2024;44:BSR20231395. [PMID: 39036877 PMCID: PMC11300678 DOI: 10.1042/bsr20231395] [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: 01/31/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024]  Open
28
Lohachova KO, Kyrychenko A, Kalugin ON. Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2. Biophys Chem 2024;311:107258. [PMID: 38776839 DOI: 10.1016/j.bpc.2024.107258] [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: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
29
Huang L, Gish M, Boehlke J, Jeep RH, Chen C. Assay Development and Validation for Innovative Antiviral Development Targeting the N-Terminal Autoprocessing of SARS-CoV-2 Main Protease Precursors. Viruses 2024;16:1218. [PMID: 39205192 PMCID: PMC11359197 DOI: 10.3390/v16081218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/14/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]  Open
30
Dampalla CS, Kim Y, Zabiegala A, Howard DJ, Nguyen HN, Madden TK, Thurman HA, Cooper A, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. J Med Chem 2024;67:11937-11956. [PMID: 38953866 DOI: 10.1021/acs.jmedchem.4c00551] [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: 07/04/2024]
31
Anton DB, de Lima JC, Dahmer BR, Camini AM, Goettert MI, Timmers LFSM. Taming the storm: potential anti-inflammatory compounds targeting SARS-CoV-2 MPro. Inflammopharmacology 2024:10.1007/s10787-024-01525-9. [PMID: 39048773 DOI: 10.1007/s10787-024-01525-9] [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: 12/01/2023] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
32
Kovalevsky A, Aniana A, Coates L, Ghirlando R, Nashed NT, Louis JM. Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease. J Mol Biol 2024;436:168616. [PMID: 38762033 PMCID: PMC11182712 DOI: 10.1016/j.jmb.2024.168616] [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: 04/02/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
33
Nepravishta R, Ramírez-Cárdenas J, Rocha G, Walpole S, Hicks T, Monaco S, Muñoz-García JC, Angulo J. Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy. J Med Chem 2024;67:10025-10034. [PMID: 38848103 PMCID: PMC11215723 DOI: 10.1021/acs.jmedchem.4c00204] [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: 01/24/2024] [Revised: 04/26/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
34
Shayo MJ, Samwel B, Shadrack DM, Cassel J, Salvino JM, Montaner LJ, Deogratias G, Tietjen I, Kiruri L, Hilonga S, Innocent E. Drug repositioning identifies salvinorin A and deacetylgedunin (DCG) enriched plant extracts as novel inhibitors of Mpro, RBD-ACE2 and TMPRRS2 proteins. RSC Adv 2024;14:21203-21212. [PMID: 38966817 PMCID: PMC11223729 DOI: 10.1039/d4ra02593h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/21/2024] [Indexed: 07/06/2024]  Open
35
Yang M, Lin L, Flaumenhaft R. Protocol to identify flavonoid antagonists of the SARS-CoV-2 main protease. STAR Protoc 2024;5:102990. [PMID: 38583157 PMCID: PMC11002865 DOI: 10.1016/j.xpro.2024.102990] [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: 12/28/2023] [Revised: 02/12/2024] [Accepted: 03/14/2024] [Indexed: 04/09/2024]  Open
36
Khachatryan H, Matevosyan M, Harutyunyan V, Gevorgyan S, Shavina A, Tirosyan I, Gabrielyan Y, Ayvazyan M, Bozdaganyan M, Fakhar Z, Gharaghani S, Zakaryan H. Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme. Sci Rep 2024;14:14255. [PMID: 38902397 PMCID: PMC11189913 DOI: 10.1038/s41598-024-65228-5] [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: 03/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]  Open
37
Hazemann J, Kimmerlin T, Lange R, Mac Sweeney A, Bourquin G, Ritz D, Czodrowski P. Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches. RSC Med Chem 2024;15:2146-2159. [PMID: 38911172 PMCID: PMC11187573 DOI: 10.1039/d4md00106k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/20/2024] [Indexed: 06/25/2024]  Open
38
Blankenship L, Yang KS, Vulupala VR, Alugubelli YR, Khatua K, Coleman D, Ma XR, Sankaran B, Cho CCD, Ma Y, Neuman BW, Xu S, Liu WR. SARS-CoV-2 Main Protease Inhibitors That Leverage Unique Interactions with the Solvent Exposed S3 Site of the Enzyme. ACS Med Chem Lett 2024;15:950-957. [PMID: 38894905 PMCID: PMC11181478 DOI: 10.1021/acsmedchemlett.4c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024]  Open
39
Altomare A, Baron G, Cambiaghi G, Ferrario G, Zoanni B, Della Vedova L, Fumagalli GM, D’Alessandro S, Parapini S, Vittorio S, Vistoli G, Riso P, Carini M, Delbue S, Aldini G. Screening of Mpro Protease (SARS-CoV-2) Covalent Inhibitors from an Anthocyanin-Rich Blueberry Extract Using an HRMS-Based Analytical Platform. Molecules 2024;29:2702. [PMID: 38893578 PMCID: PMC11173886 DOI: 10.3390/molecules29112702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]  Open
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Tripathi A, Dubey KD. The mechanistic insights into different aspects of promiscuity in metalloenzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024;141:23-66. [PMID: 38960476 DOI: 10.1016/bs.apcsb.2023.12.022] [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: 07/05/2024]
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Lin S, Wang X, Tang RWL, Duan R, Leung KW, Dong TTX, Webb SE, Miller AL, Tsim KWK. Computational Docking as a Tool in Guiding the Drug Design of Rutaecarpine Derivatives as Potential SARS-CoV-2 Inhibitors. Molecules 2024;29:2636. [PMID: 38893512 PMCID: PMC11173897 DOI: 10.3390/molecules29112636] [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: 05/17/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]  Open
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Deshmukh N, Talkal R, Lakshmi B. In silico screening of potential inhibitors from Cordyceps species against SARS-CoV-2 main protease. J Biomol Struct Dyn 2024;42:4395-4411. [PMID: 37325819 DOI: 10.1080/07391102.2023.2225110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
43
Kenward C, Vuckovic M, Paetzel M, Strynadka NCJ. Kinetic comparison of all eleven viral polyprotein cleavage site processing events by SARS-CoV-2 main protease using a linked protein FRET platform. J Biol Chem 2024;300:107367. [PMID: 38750796 PMCID: PMC11209022 DOI: 10.1016/j.jbc.2024.107367] [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: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]  Open
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Matúška J, Bucinsky L, Gall M, Pitoňák M, Štekláč M. SchNetPack Hyperparameter Optimization for a More Reliable Top Docking Scores Prediction. J Phys Chem B 2024;128:4943-4951. [PMID: 38733335 DOI: 10.1021/acs.jpcb.4c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
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Zhang J, Zhao L, Bai Y, Li S, Zhang M, Wei B, Wang X, Xue Y, Li L, Ma G, Tang Y, Wang X. An ascidian Polycarpa aurata-derived pan-inhibitor against coronaviruses targeting Mpro. Bioorg Med Chem Lett 2024;103:129706. [PMID: 38508325 DOI: 10.1016/j.bmcl.2024.129706] [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: 12/06/2023] [Revised: 03/09/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
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Mohammed Hashim KK, Manoj E. Aminoguanidine-based bioactive proligand as AIEE probe for anticancer and anticovid studies. RSC Adv 2024;14:13654-13668. [PMID: 38665490 PMCID: PMC11044126 DOI: 10.1039/d4ra00554f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]  Open
47
Azevedo PHRDA, Camargo PG, Constant LEC, Costa SDS, Silva CS, Rosa AS, Souza DDC, Tucci AR, Ferreira VNS, Oliveira TKF, Borba NRR, Rodrigues CR, Albuquerque MG, Dias LRS, Garrett R, Miranda MD, Allonso D, Lima CHDS, Muri EMF. Statine-based peptidomimetic compounds as inhibitors for SARS-CoV-2 main protease (SARS-CoV‑2 Mpro). Sci Rep 2024;14:8991. [PMID: 38637583 PMCID: PMC11026380 DOI: 10.1038/s41598-024-59442-4] [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: 10/26/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024]  Open
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Mohebbi A, Eskandarzadeh M, Zangi H, Fatehi M. In silico study of alkaloids with quercetin nucleus for inhibition of SARS-CoV-2 protease and receptor cell protease. PLoS One 2024;19:e0298201. [PMID: 38626042 PMCID: PMC11020608 DOI: 10.1371/journal.pone.0298201] [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: 09/26/2023] [Accepted: 01/21/2024] [Indexed: 04/18/2024]  Open
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de Santiago-Silva KM, Camargo PG, Carvalho Constant LE, Costa SDS, Frensel GB, Allonso D, Nakazato G, Lima CHDS, Bispo MDLF. Molecular modelling studies and in vitro enzymatic assays identified A 4-(nitrobenzyl)guanidine derivative as inhibitor of SARS-CoV-2 Mpro. Sci Rep 2024;14:8620. [PMID: 38616188 PMCID: PMC11016540 DOI: 10.1038/s41598-024-59292-0] [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: 12/28/2023] [Accepted: 04/09/2024] [Indexed: 04/16/2024]  Open
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Wang F, Liu D, Gao D, Yuan J, Zhao J, Yuan S, Cen Y, Lin GQ, Zhao J, Tian P. Discovery of natural catechol derivatives as covalent SARS-CoV-2 3CLpro inhibitors. Int J Biol Macromol 2024;264:130377. [PMID: 38395279 DOI: 10.1016/j.ijbiomac.2024.130377] [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: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
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