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For: Zhang S, Shi Y, Jin H, Liu Z, Zhang L, Zhang L. Covalent complexes of proteasome model with peptide aldehyde inhibitors MG132 and MG101: docking and molecular dynamics study. J Mol Model 2009;15:1481-90. [DOI: 10.1007/s00894-009-0515-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Accepted: 04/01/2009] [Indexed: 01/23/2023]
Number Cited by Other Article(s)
1
Bukhari SNA, Abdelgawad MA, Ahmed N, Amjad MW, Hussain MA, Elsherif MA, Ejaz H, Alotaibi NH, Filipović I, Janković N. Synthesis, Characterization, and Biological Evaluation of Meldrum's Acid Derivatives: Dual Activity and Molecular Docking Study. Pharmaceuticals (Basel) 2023;16:281. [PMID: 37259425 PMCID: PMC9968196 DOI: 10.3390/ph16020281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 09/28/2023]  Open
2
Boike L, Henning NJ, Nomura DK. Advances in covalent drug discovery. Nat Rev Drug Discov 2022;21:881-898. [PMID: 36008483 PMCID: PMC9403961 DOI: 10.1038/s41573-022-00542-z] [Citation(s) in RCA: 375] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 01/04/2023]
3
Hotinger JA, Pendergrass HA, Peterson D, Wright HT, May AE. Phage-Related Ribosomal Protease (Prp) of Staphylococcus aureus: In Vitro Michaelis-Menten Kinetics, Screening for Inhibitors, and Crystal Structure of a Covalent Inhibition Product Complex. Biochemistry 2022;61:1323-1336. [PMID: 35731716 DOI: 10.1021/acs.biochem.2c00010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
4
Yang WL, Li Q, Sun J, Huat Tan S, Tang YH, Zhao MM, Li YY, Cao X, Zhao JC, Yang JK. Potential drug discovery for COVID-19 treatment targeting Cathepsin L using a deep learning-based strategy. Comput Struct Biotechnol J 2022;20:2442-2454. [PMID: 35602976 PMCID: PMC9110316 DOI: 10.1016/j.csbj.2022.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 01/06/2023]  Open
5
Santos Nascimento IJD, Aquino TMD, Silva-Júnior EFD. Repurposing FDA-approved Drugs Targeting SARS-CoV2 3CLpro: a study by applying Virtual Screening, Molecular Dynamics, MM-PBSA Calculations and Covalent Docking. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220106110133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
6
Estrada FGA, Miccoli S, Aniceto N, García-Sosa AT, Guedes RC. Exploring EZH2-Proteasome Dual-Targeting Drug Discovery through a Computational Strategy to Fight Multiple Myeloma. Molecules 2021;26:5574. [PMID: 34577052 PMCID: PMC8468724 DOI: 10.3390/molecules26185574] [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: 07/23/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/29/2022]  Open
7
Yuan XY, Li M, Yu X, Li H. Structural analysis, simulation, and molecular docking of aza-nitrile into cathepsins to explain the high selectivity. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
8
Covalent docking modelling-based discovery of tripeptidyl epoxyketone proteasome inhibitors composed of aliphatic-heterocycles. Eur J Med Chem 2019;164:602-614. [DOI: 10.1016/j.ejmech.2018.12.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 02/08/2023]
9
Omar SI, Lepre MG, Morbiducci U, Deriu MA, Tuszynski JA. Virtual screening using covalent docking to find activators for G245S mutant p53. PLoS One 2018;13:e0200769. [PMID: 30192754 PMCID: PMC6128461 DOI: 10.1371/journal.pone.0200769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/01/2018] [Indexed: 11/19/2022]  Open
10
Sotriffer C. Docking of Covalent Ligands: Challenges and Approaches. Mol Inform 2018;37:e1800062. [PMID: 29927068 DOI: 10.1002/minf.201800062] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
11
Götze S, Saborowski R, Martínez-Cruz O, Muhlia-Almazán A, Sánchez-Paz A. Proteasome properties of hemocytes differ between the whiteleg shrimp Penaeus vannamei and the brown shrimp Crangon crangon (Crustacea, Decapoda). Cell Stress Chaperones 2017;22:879-891. [PMID: 28646424 PMCID: PMC5655376 DOI: 10.1007/s12192-017-0819-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 10/19/2022]  Open
12
Ge Y, Li A, Wu J, Feng H, Wang L, Liu H, Xu Y, Xu Q, Zhao L, Li Y. Design, synthesis and biological evaluation of novel non-peptide boronic acid derivatives as proteasome inhibitors. Eur J Med Chem 2017;128:180-191. [PMID: 28182990 DOI: 10.1016/j.ejmech.2017.01.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/03/2016] [Accepted: 01/21/2017] [Indexed: 10/20/2022]
13
Computational Approaches for the Discovery of Human Proteasome Inhibitors: An Overview. Molecules 2016;21:molecules21070927. [PMID: 27438821 PMCID: PMC6274525 DOI: 10.3390/molecules21070927] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 01/10/2023]  Open
14
Chandra K, Das P, Mamidi S, Hurevich M, Iosub-Amir A, Metanis N, Reches M, Friedler A. Covalent Inhibition of HIV-1 Integrase by N-Succinimidyl Peptides. ChemMedChem 2016;11:1987-94. [PMID: 27331774 DOI: 10.1002/cmdc.201600190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/24/2016] [Indexed: 11/08/2022]
15
Adeniyi AA, Muthusamy R, Soliman MES. New drug design with covalent modifiers. Expert Opin Drug Discov 2016;11:79-90. [DOI: 10.1517/17460441.2016.1115478] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
16
Czerwinski A, Basava C, Dauter M, Dauter Z. Crystal structure of N-{N-[N-acetyl-(S)-leuc-yl]-(S)-leuc-yl}norleucinal (ALLN), an inhibitor of proteasome. ACTA CRYSTALLOGRAPHICA SECTION E-CRYSTALLOGRAPHIC COMMUNICATIONS 2015;71:254-7. [PMID: 25844180 PMCID: PMC4350719 DOI: 10.1107/s2056989015002091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 01/30/2015] [Indexed: 12/04/2022]
17
Theory and applications of covalent docking in drug discovery: merits and pitfalls. Molecules 2015;20:1984-2000. [PMID: 25633330 PMCID: PMC6272664 DOI: 10.3390/molecules20021984] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/19/2014] [Accepted: 01/12/2015] [Indexed: 11/17/2022]  Open
18
Li A, Sun H, Du L, Wu X, Cao J, You Q, Li Y. Discovery of novel covalent proteasome inhibitors through a combination of pharmacophore screening, covalent docking, and molecular dynamics simulations. J Mol Model 2014;20:2515. [PMID: 25394401 DOI: 10.1007/s00894-014-2515-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/27/2014] [Indexed: 12/11/2022]
19
Hovhannisyan A, Pham TH, Bouvier D, Piroyan A, Dufau L, Qin L, Cheng Y, Melikyan G, Reboud-Ravaux M, Bouvier-Durand M. New C(4)- and C(1)-derivatives of furo[3,4-c]pyridine-3-ones and related compounds: evidence for site-specific inhibition of the constitutive proteasome and its immunoisoform. Bioorg Med Chem Lett 2014;24:1571-80. [PMID: 24534487 DOI: 10.1016/j.bmcl.2014.01.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 01/24/2023]
20
Halasi M, Wang M, Chavan TS, Gaponenko V, Hay N, Gartel AL. ROS inhibitor N-acetyl-L-cysteine antagonizes the activity of proteasome inhibitors. Biochem J 2013;454:201-8. [PMID: 23772801 PMCID: PMC4322432 DOI: 10.1042/bj20130282] [Citation(s) in RCA: 287] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
21
Bugliani M, Liechti R, Cheon H, Suleiman M, Marselli L, Kirkpatrick C, Filipponi F, Boggi U, Xenarios I, Syed F, Ladriere L, Wollheim C, Lee MS, Marchetti P. Microarray analysis of isolated human islet transcriptome in type 2 diabetes and the role of the ubiquitin-proteasome system in pancreatic beta cell dysfunction. Mol Cell Endocrinol 2013;367:1-10. [PMID: 23246353 DOI: 10.1016/j.mce.2012.12.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 12/04/2012] [Accepted: 12/04/2012] [Indexed: 12/14/2022]
22
Hovhannisyan A, Pham TH, Bouvier D, Qin L, Melikyan G, Reboud-Ravaux M, Bouvier-Durand M. C1 and N5 derivatives of cerpegin: synthesis of a new series based on structure-activity relationships to optimize their inhibitory effect on 20S proteasome. Bioorg Med Chem Lett 2013;23:2696-703. [PMID: 23541650 DOI: 10.1016/j.bmcl.2013.02.079] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 02/15/2013] [Accepted: 02/18/2013] [Indexed: 11/25/2022]
23
Schröder J, Klinger A, Oellien F, Marhöfer RJ, Duszenko M, Selzer PM. Docking-based virtual screening of covalently binding ligands: an orthogonal lead discovery approach. J Med Chem 2013;56:1478-90. [PMID: 23350811 DOI: 10.1021/jm3013932] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
24
Yuan XY, Fu DY, Ren XF, Fang X, Wang L, Zou S, Wu Y. Highly selective aza-nitrile inhibitors for cathepsin K, structural optimization and molecular modeling. Org Biomol Chem 2013;11:5847-52. [DOI: 10.1039/c3ob41165f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
25
Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recognit 2010;24:149-64. [DOI: 10.1002/jmr.1077] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022]
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