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Mao J, Luo QQ, Zhang HR, Zheng XH, Shen C, Qi HZ, Hu ML, Zhang H. Discovery of microtubule stabilizers with novel scaffold structures based on virtual screening, biological evaluation, and molecular dynamics simulation. Chem Biol Interact 2021; 352:109784. [PMID: 34932952 DOI: 10.1016/j.cbi.2021.109784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/20/2021] [Accepted: 12/16/2021] [Indexed: 02/08/2023]
Abstract
Disrupting the dynamics and structures of microtubules can perturb mitotic spindle formation, cause cell cycle arrest in G2/M phase, and subsequently lead to cellular death via apoptosis. In this investigation, the structure-based virtual screening methods, including molecular docking and rescoring, and similarity analysis of interaction molecular fingerprints, were developed to discover novel tubulin inhibitors from ChemDiv database with 1,601,806 compounds. The screened compounds were further filtered by PAINS, ADME/T, Toxscore, SAscore, and Drug-likeness analysis. Finally, 17 hit compounds were selected, and then submitted to the biologic evaluation. Among these hits, the P2 exhibited the strongest antiproliferative activity against four tumor cells including HeLa, HepG2, MCF-7, and A549. The in vitro tubulin polymerization assay revealed P2 could promote tubulin polymerization in a dose dependent manner. Finally, in order to analyze the interaction modes of complexes, the molecular dynamics simulation was performed to investigate the interactions between P2 and tubulin. The molecular dynamics simulation analysis showed that P2 could stably bind to taxane site, induced H6-H7, B9-B10, and M-loop regions changes. The ΔGbind energies of tubulin-P2 and tubulin-paclitaxel were -68.25 ± 12.98 and -146.05 ± 16.17 kJ mol-1, respectively, which were in line with the results of the experimental test. Therefore, P2 has been well characterized as lead compounds for developing new tubulin inhibitors with potential anticancer activity.
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Affiliation(s)
- Jun Mao
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Qing-Qing Luo
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hong-Rui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Xiu-He Zheng
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Chen Shen
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hua-Zhao Qi
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Mei-Ling Hu
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China
| | - Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, Gansu, 730070, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, PR China.
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2
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Federico LB, Silva GM, de Fraga Dias A, Figueiró F, Battastini AMO, Dos Santos CBR, Costa LT, Rosa JMC, de Paula da Silva CHT. Identification of novel αβ-tubulin modulators with antiproliferative activity directed to cancer therapy using ligand and structure-based virtual screening. Int J Biol Macromol 2020; 165:3040-3050. [PMID: 33736292 DOI: 10.1016/j.ijbiomac.2020.10.136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/10/2020] [Accepted: 10/15/2020] [Indexed: 11/19/2022]
Abstract
Among several strategies related to cancer therapy targeting the modulation of αβ-tubulin has shown encouraging findings, more specifically when this is achieved by inhibitors located at the colchicine binding site. In this work, we aim to fish new αβ-tubulin modulators through a diverse and rational VS study, and thus, exhibiting the development of two VS pipelines. This allowed us to identify two compounds 5 and 9 that showed IC50 values of 19.69 and 21.97 μM, respectively, towards possible modulation of αβ-tubulin, such as assessed by in vitro assays in C6 glioma and HEPG2 cell lines. We also evaluated possible mechanisms of action of obtained hits towards the colchicine binding site of αβ-tubulin by using docking approaches. In addition, assessment of the stability of the active (5 and 9) and inactive compounds (3 and 13) within the colchicine binding site was carried out by molecular dynamics (MD) simulations, highlighting the solvent effect and revealing the compound 5 as the most stable in the complex. At last, deep analysis of these results provided some valuable insights on the importance of using mixed ligand- and structure-based strategies in VS campaigns, in order to achieve higher chemical diversity and biological effect as well.
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Affiliation(s)
- Leonardo Bruno Federico
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, s/n, Ribeirão Preto, SP 14040-903, Brazil.
| | - Guilherme Martins Silva
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
| | - Amanda de Fraga Dias
- Graduate Program in Biological Sciences: Biochemistry, Institute of Health Sciences, Federal University of Rio Grande do Sul, Av. Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS 90035-003, Brazil
| | - Fabrício Figueiró
- Graduate Program in Biological Sciences: Biochemistry, Institute of Health Sciences, Federal University of Rio Grande do Sul, Av. Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS 90035-003, Brazil; Department of Biochemistry, Institute of Health Sciences, Federal University of Rio Grande do Sul, Av. Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS 90035-003, Brazil
| | - Ana Maria Oliveira Battastini
- Graduate Program in Biological Sciences: Biochemistry, Institute of Health Sciences, Federal University of Rio Grande do Sul, Av. Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS 90035-003, Brazil
| | - Cleydson Breno Rodrigues Dos Santos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, AP 68902-280, Brazil
| | - Luciano T Costa
- MolMod-CS, Institute of Chemistry, Federal Fluminense University, Outeiro de São João Batista, Niterói, Rio de Janeiro, Brazil
| | - Joaquín Maria Carmpos Rosa
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Institute of Biosanitary Research ibs. GRANADA, University of Granada, 18071, Spain
| | - Carlos Henrique Tomich de Paula da Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, s/n, Ribeirão Preto, SP 14040-903, Brazil; Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
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3
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Navarrete KR, Jiménez VA. Interdimeric Curvature in Tubulin-Tubulin Complexes Delineates the Microtubule-Destabilizing Properties of Plocabulin. J Chem Inf Model 2020; 60:4076-4084. [PMID: 32687349 DOI: 10.1021/acs.jcim.0c00626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plocabulin is a novel microtubule (MT) destabilizer agent with potent antineoplastic activity. This compound binds to the maytansine site at the longitudinal interface between tubulin dimers and exerts a hinge-like effect that disrupts normal microtubule assembly. Plocabulin has emerged as a valuable model for the rational design of novel MT destabilizers because of its unique structural and mechanistic features. To make progress on this matter, detailed molecular-level understanding of the ligand-protein interactions responsible for plocabulin association and the conformation and energetic effects arising from plocabulin binding on the longitudinal interaction between tubulin dimers must be provided. In this work, fully atomistic MD simulations and MM/GBSA binding free-energy calculations were used to examine the association of plocabulin to one or two tubulin dimers in longitudinal arrangement. Our results revealed that plocabulin binding is favored by the addition of a second tubulin dimer and that this ligand promotes the assembly of curved tetrameric arrangements with strengthened longitudinal interdimeric interactions compared to ligand-free systems. The applicability of these findings to the rational discovery of novel MT destabilizers was tested using MD and MM/GBSA calculations as filtering tools to narrow the results of virtual screening among an FDA-approved drug database. Our results confirmed that tight-binding ligands do not necessarily exert the expected conformational and energetic effects on longitudinal tubulin-tubulin interactions, which is a matter to consider in future design strategies.
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Affiliation(s)
- Karen R Navarrete
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
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Exploring the size adaptability of the B ring binding zone of the colchicine site of tubulin with para-nitrogen substituted isocombretastatins. Eur J Med Chem 2015; 100:210-22. [DOI: 10.1016/j.ejmech.2015.05.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/19/2015] [Accepted: 05/31/2015] [Indexed: 01/05/2023]
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5
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Karaman B, Sippl W. Docking and binding free energy calculations of sirtuin inhibitors. Eur J Med Chem 2015; 93:584-98. [PMID: 25748123 DOI: 10.1016/j.ejmech.2015.02.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/25/2015] [Accepted: 02/22/2015] [Indexed: 01/24/2023]
Abstract
Sirtuins form a unique and highly conserved class of NAD(+)-dependent lysine deacylases. Among these the human subtypes Sirt1-3 has been implicated in the pathogenesis of numerous diseases such as cancer, metabolic syndromes, viral diseases and neurological disorders. Most of the sirtuin inhibitors that have been identified so far show limited potency and/or isoform selectivity. Here, we introduce a promising method to generate protein-inhibitor complexes of human Sirt1, Sirt2 and Sirt3 by means of ligand docking and molecular dynamics simulations. This method highly reduces the complexity of such applications and can be applied to other protein targets beside sirtuins. To the best of our knowledge, we present the first binding free energy method developed by using a validated data set of sirtuin inhibitors, where both a fair number of compounds (33 thieno[3,2-d]pyrimidine-6-carboxamide derivatives) was developed and tested in the same laboratory and also crystal structures in complex with the enzyme have been reported. A significant correlation between binding free energies derived from MM-GBSA calculations and in vitro data was found for all three sirtuin subtypes. The developed MM-GBSA protocol is computationally inexpensive and can be applied as a post-docking filter in virtual screening to find novel Sirt1-3 inhibitors as well as to prioritize compounds with similar chemical structures for further biological characterization.
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Affiliation(s)
- Berin Karaman
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle, Saale, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, 06120 Halle, Saale, Germany.
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Flynn BL, Gill GS, Grobelny DW, Chaplin JH, Paul D, Leske AF, Lavranos TC, Chalmers DK, Charman SA, Kostewicz E, Shackleford DM, Morizzi J, Hamel E, Jung MK, Kremmidiotis G. Discovery of 7-hydroxy-6-methoxy-2-methyl-3-(3,4,5-trimethoxybenzoyl)benzo[b]furan (BNC105), a tubulin polymerization inhibitor with potent antiproliferative and tumor vascular disrupting properties. J Med Chem 2011; 54:6014-27. [PMID: 21774499 PMCID: PMC3172808 DOI: 10.1021/jm200454y] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A structure-activity relationship (SAR) guided design of novel tubulin polymerization inhibitors has resulted in a series of benzo[b]furans with exceptional potency toward cancer cells and activated endothelial cells. The potency of early lead compounds has been substantially improved through the synergistic effect of introducing a conformational bias and additional hydrogen bond donor to the pharmacophore. Screening of a focused library of potent tubulin polymerization inhibitors for selectivity against cancer cells and activated endothelial cells over quiescent endothelial cells has afforded 7-hydroxy-6-methoxy-2-methyl-3-(3,4,5-trimethoxybenzoyl)benzo[b]furan (BNC105, 8) as a potent and selective antiproliferative. Because of poor solubility, 8 is administered as its disodium phosphate ester prodrug 9 (BNC105P), which is rapidly cleaved in vivo to return the active 8. 9 exhibits both superior vascular disrupting and tumor growth inhibitory properties compared with the benchmark agent combretastatin A-4 disodium phosphate 5 (CA4P).
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Affiliation(s)
- Bernard L Flynn
- Bionomics Ltd., 31 Dalgleish Street, Thebarton, South Australia, 5031, Australia.
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