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Zhang Y, Chen L, Wang Z, Zhu Y, Jiang H, Xu J, Xiong F. Design of novel DABO derivatives as HIV-1 RT inhibitors using molecular docking, molecular dynamics simulations and ADMET properties. J Biomol Struct Dyn 2024; 42:4196-4213. [PMID: 37272892 DOI: 10.1080/07391102.2023.2219331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
HIV-1 reverse transcriptase is an important target for developing effective anti-HIV-1 inhibitors. Different types of small molecules have been designed based on this target, showing different levels of inhibitory activity against various types of HIV-1 strains. The relationship between structure and activity of DABO derivatives was investigated by means of 3D-QSAR molecular model, molecular docking, molecular dynamics and ADMET properties. The statistical results of molecular models show that the CoMFA and CoMSIA models have good internal stability (CoMFA: q2 = 0.623, r2 = 0.946; CoMSIA: q2 = 0.668, r2 = 0.983) and external prediction ability (CoMFA: rpred2 = 0.961; CoMSIA: rpred2 = 0.961). In addition, molecular docking has explored the mechanism of action between small molecules and receptor proteins, and the results show that hydrogen bonding between amino acid Lys101 and small molecules can improve the affinity of ligands to receptor binding. A total of 12 novel molecules were designed and their activities were predicted based on the 3D-QSAR model and molecular docking results. The results showed that the designed molecules had higher predictive activity. Subsequently, 100 ns MD simulation and binding free energy verified the stability of molecular docking results. Finally, the pharmacokinetic properties of the novel designed molecule were verified by using ADMET to predict its properties. These results can provide reference for the design and development of novel and effective HIV-1 RT inhibitors, and provide new ideas for the design of subsequent drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Lu Chen
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Zhonghua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
| | - Yiren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Huifang Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Jie Xu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
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Tang H, Zhao D. Studies of febuxostat analogues as xanthine oxidase inhibitors through 3D-QSAR, Topomer CoMFA and molecular modeling. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-019-01726-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Wang Y, Guo H, Tang G, He Q, Zhang Y, Hu Y, Wang Y, Lin Z. A selectivity study of benzenesulfonamide derivatives on human carbonic anhydrase II/IX by 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation. Comput Biol Chem 2019; 80:234-243. [DOI: 10.1016/j.compbiolchem.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/14/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
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Padariya M, Kalathiya U, Baginski M. Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds. Biotechnol Appl Biochem 2017; 64:810-826. [DOI: 10.1002/bab.1543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/31/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Monikaben Padariya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Umesh Kalathiya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
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Samanta PN, Das KK. Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations. J Mol Graph Model 2017. [DOI: 10.1016/j.jmgm.2017.06.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Santos LH, Ferreira RS, Caffarena ER. Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. Mem Inst Oswaldo Cruz 2016; 110:847-64. [PMID: 26560977 PMCID: PMC4660614 DOI: 10.1590/0074-02760150239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/08/2015] [Indexed: 01/05/2023] Open
Abstract
Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency
virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts
against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors
(NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the
highly active antiretroviral therapy in combination with other anti-HIV drugs.
However, the rapid emergence of drug-resistant viral strains has limited the
successful rate of the anti-HIV agents. Computational methods are a significant part
of the drug design process and indispensable to study drug resistance. In this
review, recent advances in computer-aided drug design for the rational design of new
compounds against HIV-1 RT using methods such as molecular docking, molecular
dynamics, free energy calculations, quantitative structure-activity relationships,
pharmacophore modelling and absorption, distribution, metabolism, excretion and
toxicity prediction are discussed. Successful applications of these methodologies are
also highlighted.
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Affiliation(s)
| | - Rafaela Salgado Ferreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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Duan X, Zhang X, Xu B, Wang F, Lei M. Computational Study and Modified Design of Selective Dopamine D3 Receptor Agonists. Chem Biol Drug Des 2016; 88:142-54. [PMID: 26851125 DOI: 10.1111/cbdd.12743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/27/2015] [Accepted: 01/31/2016] [Indexed: 12/15/2022]
Abstract
Dopamine D3 receptor (D3 R) is considered as a potential target for the treatment of nervous system disorders, such as Parkinson's disease. Current research interests primarily focus on the discovery and design of potent D3 agonists. In this work, we selected 40 D3 R agonists as the research system. Comparative molecular field analysis (CoMFA) of three-dimensional quantitative structure-activity relationship (3D-QSAR), structure-selectivity relationship (3D-QSSR), and molecular docking was performed on D3 receptor agonists to obtain the details at atomic level. The results indicated that both the CoMFA model (r(2) = 0.982, q(2) = 0.503, rpred2 = 0.893, SEE = 0.057, F = 166.308) for structure-activity and (r(2) = 0.876, q(2) = 0.436, rpred2 = 0.828, F = 52.645) for structure-selectivity have good predictive capabilities. Furthermore, docking studies on three compounds binding to D3 receptor were performed to analyze the binding modes and interactions. The results elucidate that agonists formed hydrogen bond and hydrophobic interactions with key residues. Finally, we designed six molecules under the guidance of 3D-QSAR/QSSR models. The activity and selectivity of designed molecules have been improved, and ADMET properties demonstrate they have low probability of hepatotoxicity (<0.5). These results from 3D-QSAR/QSSR and docking studies have great significance for designing novel dopamine D3 selective agonists in the future.
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Affiliation(s)
- Xinli Duan
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Binglin Xu
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Fang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing, 100029, China
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Dong MH, Chen HF, Ren YJ, Shao FM. Molecular modeling studies, synthesis and biological evaluation of dabigatran analogues as thrombin inhibitors. Bioorg Med Chem 2015; 24:73-84. [PMID: 26690913 DOI: 10.1016/j.bmc.2015.11.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/17/2015] [Accepted: 11/20/2015] [Indexed: 11/16/2022]
Abstract
In this work, 48 thrombin inhibitors based on the structural scaffold of dabigatran were analyzed using a combination of molecular modeling techniques. We generated three-dimensional quantitative structure-activity relationship (3D-QSAR) models based on three alignments for both comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) to highlight the structural requirements for thrombin protein inhibition. In addition to the 3D-QSAR study, Topomer CoMFA model also was established with a higher leave-one-out cross-validation q(2) and a non-cross-validation r(2), which suggest that the three models have good predictive ability. The results indicated that the steric, hydrophobic and electrostatic fields play key roles in QSAR model. Furthermore, we employed molecular docking and re-docking simulation explored the binding relationship of the ligand and the receptor protein in detail. Molecular docking simulations identified several key interactions that were also indicated through 3D-QSAR analysis. On the basis of the obtained results, two compounds were designed and predicted by three models, the biological evaluation in vitro (IC50) demonstrated that these molecular models were effective for the development of novel potent thrombin inhibitors.
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Affiliation(s)
- Ming-Hui Dong
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Hai-Feng Chen
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Yu-Jie Ren
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Fang-Ming Shao
- School of Science, East China University of Science and Technology, Shanghai 200237, China
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Xu C, Ren Y. Molecular modeling studies of [6,6,5] Tricyclic Fused Oxazolidinones as FXa inhibitors using 3D-QSAR, Topomer CoMFA, molecular docking and molecular dynamics simulations. Bioorg Med Chem Lett 2015; 25:4522-8. [PMID: 26343829 DOI: 10.1016/j.bmcl.2015.08.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/22/2015] [Accepted: 08/26/2015] [Indexed: 10/23/2022]
Abstract
Coagulation factor Xa (Factor Xa, FXa) is a particularly promising target for novel anticoagulant therapy. The first oral factor Xa inhibitor has been approved in the EU and Canada in 2008. In this work, 38 [6,6,5] Tricyclic Fused Oxazolidinones were studied using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, molecular dynamics and Topomer CoMFA (comparative molecular field analysis) were used to build 3D-QSAR models. The results show that the best CoMFA model has q(2)=0.511 and r(2)=0.984, the best CoMSIA (comparative molecular similarity indices analysis) model has q(2)=0.700 and r(2)=0.993 and the Topomer CoMFA analysis has q(2)=0.377 and r(2)=0.886. The results indicated the steric, hydrophobic, H-acceptor and electrostatic fields play key roles in models. Molecular docking and molecular dynamics explored the binding relationship of the ligand and the receptor protein.
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Affiliation(s)
- Cheng Xu
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China
| | - Yujie Ren
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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Ma S, Tan S, Fang D, Zhang R, Zhou S, Wu W, Zheng K. Probing the binding mechanism of novel dual NF-κB/AP-1 inhibitors by 3D-QSAR, docking and molecular dynamics simulations. RSC Adv 2015. [DOI: 10.1039/c5ra10831d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Potent dual NF-κB/AP-1 inhibitors could effectively treat immunoinflammatory diseases. An integrated computational study was carried out to identify the most favourable binding sites, the structural features and the interaction mechanisms.
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Affiliation(s)
- Shaojie Ma
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Shepei Tan
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Danqing Fang
- Department of Cardiothoracic Surgery
- Affiliated Second Hospital of Guangzhou Medical University
- Guangzhou 510260
- PR China
| | - Rong Zhang
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Shengfu Zhou
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Wenjuan Wu
- Department of Physical Chemistry
- College of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- PR China
| | - Kangcheng Zheng
- School of Chemistry and Chemical Engineering
- SunYat-Sen University
- Guangzhou 510275
- PR China
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