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For: Bissaro M, Sturlese M, Moro S. The rise of molecular simulations in fragment-based drug design (FBDD): an overview. Drug Discov Today 2020;25:1693-1701. [PMID: 32592867 PMCID: PMC7314695 DOI: 10.1016/j.drudis.2020.06.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/24/2020] [Accepted: 06/19/2020] [Indexed: 12/31/2022]
Number Cited by Other Article(s)
1
Ibrahim PEGF, Zuccotto F, Zachariae U, Gilbert I, Bodkin M. Accurate prediction of dynamic protein-ligand binding using P-score ranking. J Comput Chem 2024;45:1762-1778. [PMID: 38647338 DOI: 10.1002/jcc.27370] [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: 10/20/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
2
Bütikofer M, Stadler GR, Kadavath H, Cadalbert R, Torres F, Riek R. Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR. J Am Chem Soc 2024;146:17974-17985. [PMID: 38957136 PMCID: PMC11228983 DOI: 10.1021/jacs.4c04000] [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: 07/04/2024]
3
Wang X, Chen X, Chen Z, Xu W, Lai R, Qiu X, Zeng Z, Wang C, Wang Z, Wang J. Integrated Anchored Stapling and Hierarchical Dynamics: MSICDA-Driven CREBBP Bromodomain Inhibition. J Chem Inf Model 2024;64:4739-4758. [PMID: 38863138 DOI: 10.1021/acs.jcim.4c00381] [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: 06/13/2024]
4
Mishra VK, Khanna A, Tiwari G, Tyagi R, Sagar R. Recent developments on the synthesis of biologically active glycohybrids. Bioorg Chem 2024;145:107172. [PMID: 38340475 DOI: 10.1016/j.bioorg.2024.107172] [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: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
5
Nandi S, Bhaduri S, Das D, Ghosh P, Mandal M, Mitra P. Deciphering the Lexicon of Protein Targets: A Review on Multifaceted Drug Discovery in the Era of Artificial Intelligence. Mol Pharm 2024;21:1563-1590. [PMID: 38466810 DOI: 10.1021/acs.molpharmaceut.3c01161] [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] [Indexed: 03/13/2024]
6
Favaro A, Sturlese M. A Novel NMR-Based Protocol to Screen Ultralow Molecular Weight Fragments. J Med Chem 2024;67:3874-3884. [PMID: 38426508 DOI: 10.1021/acs.jmedchem.3c02222] [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: 03/02/2024]
7
Xu X, Han W, Ning X, Zang C, Xu C, Zeng C, Pu C, Zhang Y, Chen Y, Liu H. Constructing Innovative Covalent and Noncovalent Compound Libraries: Insights from 3D Protein-Ligand Interactions. J Chem Inf Model 2024;64:1543-1559. [PMID: 38381562 DOI: 10.1021/acs.jcim.3c01689] [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: 02/23/2024]
8
Zhang L, Rao V, Cornell W. r-BRICS - A Revised BRICS Module That Breaks Ring Structures and Carbon Chains. ChemMedChem 2024;19:e202300202. [PMID: 37574458 DOI: 10.1002/cmdc.202300202] [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: 04/13/2023] [Revised: 07/24/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023]
9
Liu C, Hu L, Dong G, Zhang Y, Ferreira da Silva-Júnior E, Liu X, Menéndez-Arias L, Zhan P. Emerging drug design strategies in anti-influenza drug discovery. Acta Pharm Sin B 2023;13:4715-4732. [PMID: 38045039 PMCID: PMC10692392 DOI: 10.1016/j.apsb.2023.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/12/2023] [Accepted: 08/03/2023] [Indexed: 12/05/2023]  Open
10
Wang L, Zhang Z, Yu D, Yang L, Li L, He Y, Shi J. Recent research of BTK inhibitors: Methods of structural design, pharmacological activities, manmade derivatives and structure-activity relationship. Bioorg Chem 2023;138:106577. [PMID: 37178649 DOI: 10.1016/j.bioorg.2023.106577] [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: 03/06/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
11
Hsieh YC, Delarue M, Orland H, Koehl P. Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories. Viruses 2023;15:1366. [PMID: 37376665 DOI: 10.3390/v15061366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]  Open
12
Zhan F, Zhu J, Xie S, Xu J, Xu S. Advances of bioorthogonal coupling reactions in drug development. Eur J Med Chem 2023;253:115338. [PMID: 37037138 DOI: 10.1016/j.ejmech.2023.115338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
13
Zhu KF, Yuan C, Du YM, Sun KL, Zhang XK, Vogel H, Jia XD, Gao YZ, Zhang QF, Wang DP, Zhang HW. Applications and prospects of cryo-EM in drug discovery. Mil Med Res 2023;10:10. [PMID: 36872349 PMCID: PMC9986049 DOI: 10.1186/s40779-023-00446-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/14/2023] [Indexed: 03/07/2023]  Open
14
Wang ZZ, Shi XX, Huang GY, Hao GF, Yang GF. Fragment-based drug discovery supports drugging 'undruggable' protein-protein interactions. Trends Biochem Sci 2023;48:539-552. [PMID: 36841635 DOI: 10.1016/j.tibs.2023.01.008] [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: 06/29/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
15
Multicomponent coupling and macrocyclization enabled by Rh(III)-catalyzed dual C–H activation: Macrocyclic oxime inhibitor of influenza H1N1. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
16
Alibay I, Magarkar A, Seeliger D, Biggin PC. Evaluating the use of absolute binding free energy in the fragment optimisation process. Commun Chem 2022;5:105. [PMID: 36697714 PMCID: PMC9814858 DOI: 10.1038/s42004-022-00721-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/10/2022] [Indexed: 02/01/2023]  Open
17
Pavan M, Menin S, Bassani D, Sturlese M, Moro S. Implementing a Scoring Function Based on Interaction Fingerprint for Autogrow4: Protein Kinase CK1δ as a Case Study. Front Mol Biosci 2022;9:909499. [PMID: 35874609 PMCID: PMC9301033 DOI: 10.3389/fmolb.2022.909499] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/25/2022] [Indexed: 01/23/2023]  Open
18
Goel H, Hazel A, Yu W, Jo S, MacKerell AD. Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design. NEW J CHEM 2022;46:919-932. [PMID: 35210743 PMCID: PMC8863107 DOI: 10.1039/d1nj04028f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
19
Zhang C, Wu J, Chen Q, Tan H, Huang F, Guo J, Zhang X, Yu H, Shi W. Allosteric binding on nuclear receptors: Insights on screening of non-competitive endocrine-disrupting chemicals. ENVIRONMENT INTERNATIONAL 2022;159:107009. [PMID: 34883459 DOI: 10.1016/j.envint.2021.107009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
20
Zara L, Efrém NL, van Muijlwijk-Koezen JE, de Esch IJP, Zarzycka B. Progress in Free Energy Perturbation: Options for Evolving Fragments. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021;40:36-42. [PMID: 34916020 DOI: 10.1016/j.ddtec.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 01/18/2023]
21
Kaitoh K, Yamanishi Y. TRIOMPHE: Transcriptome-Based Inference and Generation of Molecules with Desired Phenotypes by Machine Learning. J Chem Inf Model 2021;61:4303-4320. [PMID: 34528432 DOI: 10.1021/acs.jcim.1c00967] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
22
Maleki R, Rezvantalab S, Shahbazi MA. Role of molecular simulation in the future of nanomedicine. Nanomedicine (Lond) 2021;16:2133-2136. [PMID: 34519542 DOI: 10.2217/nnm-2021-0120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
23
Alzahrani FA, Hawsawi YM, Altayeb HN, Alsiwiehri NO, Alzahrani OR, Alatwi HE, Al‐Amer OM, Alomar S, Mansour L. In silico modeling of the interaction between TEX19 and LIRE1, and analysis of TEX19 gene missense SNPs. Mol Genet Genomic Med 2021;9:e1707. [PMID: 34036740 PMCID: PMC8372073 DOI: 10.1002/mgg3.1707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 12/24/2022]  Open
24
Wang S, Miao E, Wang H, Song B, Huang W, Yang W. Rh-Catalyzed cascade C-H activation/C-C cleavage/cyclization of carboxylic acids with cyclopropanols. Chem Commun (Camb) 2021;57:5929-5932. [PMID: 34013935 DOI: 10.1039/d1cc01778k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
25
Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021;12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]  Open
26
Koehl P, Delarue M, Orland H. Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach. J Phys Chem B 2021;125:5052-5067. [PMID: 33973782 DOI: 10.1021/acs.jpcb.1c02658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
27
Lawson ADG, MacCoss M, Baeten DL, Macpherson A, Shi J, Henry AJ. Modulating Target Protein Biology Through the Re-mapping of Conformational Distributions Using Small Molecules. Front Chem 2021;9:668186. [PMID: 34017820 PMCID: PMC8129178 DOI: 10.3389/fchem.2021.668186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022]  Open
28
Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020;16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
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