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For: Joshi RP, Schultz KJ, Wilson JW, Kruel A, Varikoti RA, Kombala CJ, Kneller DW, Galanie S, Phillips G, Zhang Q, Coates L, Parvathareddy J, Surendranathan S, Kong Y, Clyde A, Ramanathan A, Jonsson CB, Brandvold KR, Zhou M, Head MS, Kovalevsky A, Kumar N. AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. J Chem Inf Model 2023;63:1438-1453. [PMID: 36808989 PMCID: PMC9969887 DOI: 10.1021/acs.jcim.2c01377] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/23/2023]
Number Cited by Other Article(s)
1
Leung JG, Frazee NC, Brace A, Bogetti AT, Ramanathan A, Chong LT. Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding. J Chem Theory Comput 2025;21:3691-3699. [PMID: 40105797 PMCID: PMC11983707 DOI: 10.1021/acs.jctc.4c01136] [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: 10/29/2024] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/20/2025]
2
Tamura T, Kawano M, Hamachi I. Targeted Covalent Modification Strategies for Drugging the Undruggable Targets. Chem Rev 2025;125:1191-1253. [PMID: 39772527 DOI: 10.1021/acs.chemrev.4c00745] [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: 01/11/2025]
3
McNaughton A, Sankar Ramalaxmi GK, Kruel A, Knutson CR, Varikoti RA, Kumar N. CACTUS: Chemistry Agent Connecting Tool Usage to Science. ACS OMEGA 2024;9:46563-46573. [PMID: 39583666 PMCID: PMC11579734 DOI: 10.1021/acsomega.4c08408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/08/2024] [Accepted: 10/14/2024] [Indexed: 11/26/2024]
4
Kalasin S, Surareungchai W. Artificial intelligence-aiding lab-on-a-chip workforce designed oral [3.1.0] bi and [4.2.0] tricyclic catalytic interceptors inhibiting multiple SARS-CoV-2 protomers assisted by double-shell deep learning. RSC Adv 2024;14:26897-26910. [PMID: 39193274 PMCID: PMC11347926 DOI: 10.1039/d4ra03965c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]  Open
5
Grigoreva TA, Vorona SV, Novikova DS, Tribulovich VG. Rational Design Problematics of Peptide Nucleic Acids as SARS-CoV-2 Inhibitors. ACS OMEGA 2024;9:33000-33010. [PMID: 39100288 PMCID: PMC11292644 DOI: 10.1021/acsomega.4c04023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/24/2024] [Accepted: 07/05/2024] [Indexed: 08/06/2024]
6
Zagórska A, Czopek A, Fryc M, Jończyk J. Inhibitors of SARS-CoV-2 Main Protease (Mpro) as Anti-Coronavirus Agents. Biomolecules 2024;14:797. [PMID: 39062511 PMCID: PMC11275247 DOI: 10.3390/biom14070797] [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: 05/31/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024]  Open
7
Thibert S, Reid DJ, Wilson JW, Varikoti R, Maltseva N, Schultz KJ, Kruel A, Babnigg G, Joachimiak A, Kumar N, Zhou M. Native Mass Spectrometry Dissects the Structural Dynamics of an Allosteric Heterodimer of SARS-CoV-2 Nonstructural Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024;35:912-921. [PMID: 38535992 PMCID: PMC11066969 DOI: 10.1021/jasms.3c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 05/02/2024]
8
Huang Q, Quan B, Chen Y, Zhao X, Zhou Y, Huang C, Qiao J, Wang Y, Li Y, Yang S, Lei J, Li L. Discovery of α-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups. Bioorg Chem 2024;143:107001. [PMID: 38101266 DOI: 10.1016/j.bioorg.2023.107001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
9
Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023;24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023]  Open
10
Varikoti RA, Schultz KJ, Kombala CJ, Kruel A, Brandvold KR, Zhou M, Kumar N. Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease. J Comput Aided Mol Des 2023:10.1007/s10822-023-00509-1. [PMID: 37314632 DOI: 10.1007/s10822-023-00509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
11
Avelar M, Pedraza-González L, Sinicropi A, Flores-Morales V. Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach. Molecules 2023;28:molecules28052333. [PMID: 36903578 PMCID: PMC10005606 DOI: 10.3390/molecules28052333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]  Open
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