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For: Caballero J, Morales-Bayuelo A, Navarro-Retamal C. Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. J Comput Aided Mol Des 2018;32:1315-1336. [PMID: 30367309 DOI: 10.1007/s10822-018-0173-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/20/2018] [Indexed: 12/17/2022]
Number Cited by Other Article(s)
1
Valdés-Albuernes JL, Díaz-Pico E, Alfaro S, Caballero J. Advanced modeling of salt-inducible kinase (SIK) inhibitors incorporating protein flexibility through molecular dynamics and cross-docking. Sci Rep 2025;15:18868. [PMID: 40442221 PMCID: PMC12122877 DOI: 10.1038/s41598-025-03699-w] [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: 03/18/2025] [Accepted: 05/21/2025] [Indexed: 06/02/2025]  Open
2
Alruwaili M, Elsaman T, Mohamed MA, Elderdery AY, Mills J, Alruwaili Y, Hamza SMA, Mekki SEI, Alotaibi HA, Alrowily MJ, Althobiti MM. Molecular docking, free energy calculations, ADMETox studies, DFT analysis, and dynamic simulations highlighting a chromene glycoside as a potential inhibitor of PknG in Mycobacterium tuberculosis. Front Chem 2025;13:1531152. [PMID: 40070405 PMCID: PMC11893855 DOI: 10.3389/fchem.2025.1531152] [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: 11/19/2024] [Accepted: 01/30/2025] [Indexed: 03/14/2025]  Open
3
Flores N, Rivillas-Acevedo L, Caballero J, Melo F, Caballero L, Areche C, Fuentealba D, Aguilar F, Cornejo A. Rosmarinic acid turned α-syn oligomers into non-toxic species preserving microtubules in Raw 264.7 cells. Bioorg Chem 2024;151:107669. [PMID: 39067421 DOI: 10.1016/j.bioorg.2024.107669] [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: 04/19/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
4
Thongdee P, Hanwarinroj C, Pakamwong B, Kamsri P, Punkvang A, Leanpolchareanchai J, Ketrat S, Saparpakorn P, Hannongbua S, Ariyachaokun K, Suttisintong K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Mukamolova GV, Blood RA, Takebayashi Y, Spencer J, Mulholland AJ, Pungpo P. Virtual Screening Identifies Novel and Potent Inhibitors of Mycobacterium tuberculosis PknB with Antibacterial Activity. J Chem Inf Model 2022;62:6508-6518. [PMID: 35994014 DOI: 10.1021/acs.jcim.2c00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
5
Swain SP, Gupta S, Das N, Franca TCC, Goncalves ADS, Ramalho TC, Subrahmanya S, Narsaria U, Deb D, Mishra N. Flavanones: A potential natural inhibitor of the ATP binding site of PknG of Mycobacterium tuberculosis. J Biomol Struct Dyn 2022;40:11885-11899. [PMID: 34409917 DOI: 10.1080/07391102.2021.1965913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
6
Arica-Sosa A, Alcántara R, Jiménez-Avalos G, Zimic M, Milón P, Quiliano M. Identifying RO9021 as a Potential Inhibitor of PknG from Mycobacterium tuberculosis: Combinative Computational and In Vitro Studies. ACS OMEGA 2022;7:20204-20218. [PMID: 35721990 PMCID: PMC9201901 DOI: 10.1021/acsomega.2c02093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/12/2022] [Indexed: 06/07/2023]
7
Burastero O, Cabrera M, Lopez ED, Defelipe LA, Arcon JP, Durán R, Marti MA, Turjanski AG. Specificity and Reactivity of Mycobacterium tuberculosis Serine/Threonine Kinases PknG and PknB. J Chem Inf Model 2022;62:1723-1733. [PMID: 35319884 DOI: 10.1021/acs.jcim.1c01358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
8
Chen XZ, Huang Q, Yu XY, Dai C, Shen Y, Lin ZH. Insights into the structural requirements of PKCζ inhibitors as potential anti-arthritis agents based on 3D-QSAR, homology modeling and docking approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
9
Molecular Modeling Studies of N-phenylpyrimidine-4-amine Derivatives for Inhibiting FMS-like Tyrosine Kinase-3. Int J Mol Sci 2021;22:ijms222212511. [PMID: 34830393 PMCID: PMC8622510 DOI: 10.3390/ijms222212511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023]  Open
10
Natural products from Brazilian biodiversity identified as potential inhibitors of PknA and PknB of M. tuberculosis using molecular modeling tools. Comput Biol Med 2021;136:104694. [PMID: 34365277 DOI: 10.1016/j.compbiomed.2021.104694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/07/2021] [Accepted: 07/23/2021] [Indexed: 11/21/2022]
11
Computational Modeling to Explain Why 5,5-Diarylpentadienamides are TRPV1 Antagonists. Molecules 2021;26:molecules26061765. [PMID: 33801115 PMCID: PMC8004144 DOI: 10.3390/molecules26061765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/14/2021] [Accepted: 03/18/2021] [Indexed: 11/29/2022]  Open
12
Esfandi B, Atabati M. Sequential Dihedral Angles (SDAs): A Method for Evaluating the 3D Structure of Proteins. Protein J 2021;40:1-7. [PMID: 33442828 DOI: 10.1007/s10930-020-09961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
13
Caballero J. The latest automated docking technologies for novel drug discovery. Expert Opin Drug Discov 2020;16:625-645. [PMID: 33353444 DOI: 10.1080/17460441.2021.1858793] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
14
Caballero J. Considerations for Docking of Selective Angiotensin-Converting Enzyme Inhibitors. Molecules 2020;25:molecules25020295. [PMID: 31940798 PMCID: PMC7024173 DOI: 10.3390/molecules25020295] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/30/2023]  Open
15
Miranda PHDS, Lourenço EMG, Morais AMS, de Oliveira PIC, Silverio PSDSN, Jordão AK, Barbosa EG. Molecular modeling of a series of dehydroquinate dehydratase type II inhibitors of Mycobacterium tuberculosis and design of new binders. Mol Divers 2019;25:1-12. [PMID: 31820222 DOI: 10.1007/s11030-019-10020-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/22/2019] [Indexed: 11/24/2022]
16
Structural Requirements of N-alpha-Mercaptoacetyl Dipeptide (NAMdP) Inhibitors of Pseudomonas Aeruginosa Virulence Factor LasB: 3D-QSAR, Molecular Docking, and Interaction Fingerprint Studies. Int J Mol Sci 2019;20:ijms20246133. [PMID: 31817391 PMCID: PMC6940830 DOI: 10.3390/ijms20246133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022]  Open
17
Qasaymeh RM, Rotondo D, Oosthuizen CB, Lall N, Seidel V. Predictive Binding Affinity of Plant-Derived Natural Products Towards the Protein Kinase G Enzyme of Mycobacterium tuberculosis (MtPknG). PLANTS 2019;8:plants8110477. [PMID: 31698813 PMCID: PMC6918344 DOI: 10.3390/plants8110477] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022]
18
Velázquez-Libera JL, Rossino G, Navarro-Retamal C, Collina S, Caballero J. Docking, Interaction Fingerprint, and Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) of Sigma1 Receptor Ligands, Analogs of the Neuroprotective Agent RC-33. Front Chem 2019;7:496. [PMID: 31355187 PMCID: PMC6637851 DOI: 10.3389/fchem.2019.00496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/27/2019] [Indexed: 01/25/2023]  Open
19
Li K, Zhu J, Xu L, Jin J. Rational Design of Novel Phosphoinositide 3-Kinase Gamma (PI3Kγ) Selective Inhibitors: A Computational Investigation Integrating 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation. Chem Biodivers 2019;16:e1900105. [PMID: 31111650 DOI: 10.1002/cbdv.201900105] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/20/2019] [Indexed: 11/08/2022]
20
Campos-Fernández L, Barrientos-Salcedo C, Herrera Valencia EE, Ortiz-Muñiz R, Soriano-Correa C. Substituent effects on the stability, physicochemical properties and chemical reactivity of nitroimidazole derivatives with potential antiparasitic effect: a computational study. NEW J CHEM 2019. [DOI: 10.1039/c9nj02207d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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