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Tamang JSD, Banerjee S, Baidya SK, Ghosh B, Adhikari N, Jha T. Employing comparative QSAR techniques for the recognition of dibenzofuran and dibenzothiophene derivatives toward MMP-12 inhibition. J Biomol Struct Dyn 2024; 42:7304-7320. [PMID: 37498149 DOI: 10.1080/07391102.2023.2239923] [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: 04/26/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Among various matrix metalloproteinases (MMPs), MMP-12 is one of the potential targets for cancer and other diseases. However, none of the MMP-12 inhibitors has passed the clinical trials to date. Therefore, designing potential MMP-12 inhibitors as new drug molecules can provide effective therapeutic strategies for several diseases. In this study, a series of dibenzofuran and dibenzothiophene derivatives were subjected to different 2D and 3D-QSAR techniques to point out the crucial structural contributions highly influential toward the MMP-12 inhibitory activity. These techniques identified some structural attributes of these compounds that are responsible for influencing their MMP-12 inhibition. The carboxylic group may enhance proper binding with catalytic Zn2+ ion at the MMP-12 active site. Again, the i-propyl sulfonamido carboxylic acid function contributed positively toward MMP-12 inhibition. Moreover, the dibenzofuran moiety conferred stable binding at the S1' pocket for higher MMP-12 inhibition. The steric and hydrophobic groups were found favourable near the furan ring substituted at the dibenzofuran moiety. Besides these ligand-based approaches, molecular docking and molecular dynamic (MD) simulation studies not only elucidated the importance of several aspects of these MMP-12 inhibitors while disclosing the significance of the finding of these QSAR studies and their influences toward MMP-12 inhibition. The MD simulation study also revealed stable and compact binding between such compounds at the MMP-12 active site. Therefore, the findings of these validated ligand-based and structure-based molecular modeling studies can aid the development of selective and potent lead molecules that can be used for the treatment of MMP-12-associated diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jigme Sangay Dorjay Tamang
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Tian YY, Tong JB, Liu Y, Tian Y. QSAR Study, Molecular Docking and Molecular Dynamic Simulation of Aurora Kinase Inhibitors Derived from Imidazo[4,5- b]pyridine Derivatives. Molecules 2024; 29:1772. [PMID: 38675594 PMCID: PMC11052498 DOI: 10.3390/molecules29081772] [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: 03/09/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer is a serious threat to human life and social development and the use of scientific methods for cancer prevention and control is necessary. In this study, HQSAR, CoMFA, CoMSIA and TopomerCoMFA methods are used to establish models of 65 imidazo[4,5-b]pyridine derivatives to explore the quantitative structure-activity relationship between their anticancer activities and molecular conformations. The results show that the cross-validation coefficients q2 of HQSAR, CoMFA, CoMSIA and TopomerCoMFA are 0.892, 0.866, 0.877 and 0.905, respectively. The non-cross-validation coefficients r2 are 0.948, 0.983, 0.995 and 0.971, respectively. The externally validated complex correlation coefficients r2pred of external validation are 0.814, 0.829, 0.758 and 0.855, respectively. The PLS analysis verifies that the QSAR models have the highest prediction ability and stability. Based on these statistics, virtual screening based on R group is performed using the ZINC database by the Topomer search technology. Finally, 10 new compounds with higher activity are designed with the screened new fragments. In order to explore the binding modes and targets between ligands and protein receptors, these newly designed compounds are conjugated with macromolecular protein (PDB ID: 1MQ4) by molecular docking technology. Furthermore, to study the nature of the newly designed compound in dynamic states and the stability of the protein-ligand complex, molecular dynamics simulation is carried out for N3, N4, N5 and N7 docked with 1MQ4 protease structure for 50 ns. A free energy landscape is computed to search for the most stable conformation. These results prove the efficient and stability of the newly designed compounds. Finally, ADMET is used to predict the pharmacology and toxicity of the 10 designed drug molecules.
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Affiliation(s)
- Yang-Yang Tian
- College of Petroleum Engineering, Xi’an Shiyou University, Xi’an 710065, China;
- Shaanxi Key Laboratory of Advanced Stimulation Technology for Oil & Gas Reservoirs, Xi’an 710065, China
| | - Jian-Bo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (Y.L.); (Y.T.)
| | - Yuan Liu
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (Y.L.); (Y.T.)
| | - Yu Tian
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (Y.L.); (Y.T.)
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3
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QSAR study, molecular docking, and ADMET prediction of vinyl sulfone-containing Nrf2 activator derivatives for treating Parkinson disease. Struct Chem 2022. [DOI: 10.1007/s11224-022-01909-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Li X, Guo T, Feng Q, Bai T, Wu L, Liu Y, Zheng X, Jia J, Pei J, Wu S, Song Y, Zhang Y. Progress of thrombus formation and research on the structure-activity relationship for antithrombotic drugs. Eur J Med Chem 2022; 228:114035. [PMID: 34902735 DOI: 10.1016/j.ejmech.2021.114035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/11/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
Many populations suffer from thrombotic disorders such as stroke, myocardial infarction, unstable angina and thromboembolic disease. Thrombus is one of the major threatening factors to human health and the prevalence of cardio-cerebrovascular diseases induced by thrombus is growing worldwide, even some persons got rare and severe blood clots after receiving the AstraZeneca COVID vaccine unexpectedly. In terms of mechanism of thrombosis, antithrombotic drugs have been divided into three categories including anticoagulants, platelet inhibitors and fibrinolytics. Nowadays, a large number of new compounds possessing antithrombotic activities are emerging in an effort to remove the inevitable drawbacks of previously approved drugs such as the high risk of bleeding, a slow onset of action and a narrow therapeutic window. In this review, we describe the causes and mechanisms of thrombus formation firstly, and then summarize these reported active compounds as potential antithrombotic candidates based on their respective mechanism, hoping to promote the development of more effective bioactive molecules for treating thrombotic disorders.
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Affiliation(s)
- Xiaoan Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China; Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tiantian Guo
- College of Food Science and Technology, Northwest University, Xi'an, 710069, China
| | - Qian Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Tiantian Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Lei Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Yubo Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Xu Zheng
- Shaanxi Institute for Food and Drug, Xi'an, 710000, China
| | - Jianzhong Jia
- Shaanxi Institute for Food and Drug, Xi'an, 710000, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shaoping Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China.
| | - Yiming Song
- School of Chemical Engineering, Northwest University, 229 Taibai Road, Xi'an, Shaanxi, 710069, China.
| | - Yongmin Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi'an, 710069, China; Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232, 4 Place Jussieu, 75005, Paris, France
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5
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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Tong JB, Bian S, Zhang X, Luo D. QSAR analysis of 3-pyrimidin-4-yl-oxazolidin-2-one derivatives isocitrate dehydrogenase inhibitors using Topomer CoMFA and HQSAR methods. Mol Divers 2021; 26:1017-1037. [PMID: 33974175 DOI: 10.1007/s11030-021-10222-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/02/2021] [Indexed: 01/03/2023]
Abstract
A series of mIDH1 inhibitors derived from 3-pyrimidine-4-oxazolidin-2-ketone derivatives were studied by QSAR model to explore the key factors that inhibit mIDH1 activity. The generated model was cross-verified and non-cross-verified by Topomer CoMFA and HQSAR methods; the independent test set was verified by PLS method; the Topomer search technology was used for virtual screening and molecular design; and the Surflex-Dock method and ADMET technology were used for molecular docking, pharmacology and toxicity prediction of the designed drug molecules. The Topomer CoMFA and HQSAR cross-validation coefficients q2 are 0.783 and 0.784, respectively, and the non-cross-validation coefficients r2 are 0.978 and 0.934, respectively. Ten new drug molecules have been designed using Topomer search technology. The results of molecular docking and ADMET show that the newly designed drug molecules are effective. The docking situation, pharmacology and toxicity prediction results are good. The model can be used to predict the bioactivity of the same type of new compounds and their derivatives. The prediction results of molecular design, molecular docking and ADMET can provide some ideas for the design and development of novel mIDH1 inhibitor anticancer drugs, and provide certain theoretical basis of the experimental verification of new compounds in the future. Newly designed molecules after docking with corresponding proteins in the PDB library, it can explore the targets of drug molecules acting with large proteins and the related force, which is very helpful for the design of new drugs and the mechanism of drug action.
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Affiliation(s)
- Jian-Bo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China. .,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China.
| | - Shuai Bian
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
| | - Xing Zhang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
| | - Ding Luo
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
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7
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Abdizadeh R, Heidarian E, Hadizadeh F, Abdizadeh T. Investigation of pyrimidine analogues as xanthine oxidase inhibitors to treat of hyperuricemia and gout through combined QSAR techniques, molecular docking and molecular dynamics simulations. J Taiwan Inst Chem Eng 2020. [DOI: 10.1016/j.jtice.2020.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Molecular docking, linear and nonlinear QSAR studies on factor Xa inhibitors. Struct Chem 2020. [DOI: 10.1007/s11224-020-01535-7] [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]
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9
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Zhao H, Zhao W, Cheng S, Lu H, Zhang D, Huang H. Efficient and stereoselective one-pot synthesis of benzo[b]oxazolo[3,4-d][1,4]oxazin-1-ones. RSC Adv 2020; 10:24037-24044. [PMID: 35517369 PMCID: PMC9055095 DOI: 10.1039/d0ra04104a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/05/2020] [Indexed: 11/21/2022] Open
Abstract
An efficient and mild one-pot convergent synthesis protocol has been developed for benzo[b]oxazolo[3,4-d][1,4]oxazin-1-one derivatives through the Mitsunobu reaction and sequential cyclization. Various tricyclic fused benzoxazinyl-oxazolidinones (20 examples) were obtained in good to excellent yields and high enantioselectivities with facile operation. Furthermore, four stereoisomers were afforded respectively in high ee values (>97.8%) via using different chiral 2,3-epoxy-4-trityloxybutanol. This methodology has been applied to the synthesis of key intermediates of drug candidates. An efficient and mild one-pot convergent synthesis protocol has been developed for benzo[b]oxazolo[3,4-d][1,4]oxazin-1-one derivatives through the Mitsunobu reaction and sequential cyclization.![]()
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Affiliation(s)
- Hongyi Zhao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100050
| | - Wenting Zhao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100050
| | - Shihao Cheng
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100050
| | - Haijia Lu
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100050
| | - Dongfeng Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100050
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation
- Institute of Materia Medica
- Peking Union Medical College
- Chinese Academy of Medical Sciences
- Beijing 100050
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10
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Tong J, Wang T, Feng Y. Drug design and molecular docking simulations of Polo-like kinase 1 inhibitors based on QSAR study. NEW J CHEM 2020. [DOI: 10.1039/d0nj04367b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Computationally exploring novel potential Polo-like kinase 1 inhibitors using a systematic modeling study.
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Affiliation(s)
- Jianbo Tong
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Key Laboratory of Chemical Additives for China National Light Industry
| | - Tianhao Wang
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Key Laboratory of Chemical Additives for China National Light Industry
| | - Yi Feng
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Key Laboratory of Chemical Additives for China National Light Industry
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Zhu J, Ke K, Xu L, Jin J. Theoretical studies on the selectivity mechanisms of PI3Kδ inhibition with marketed idelalisib and its derivatives by 3D-QSAR, molecular docking, and molecular dynamics simulation. J Mol Model 2019; 25:242. [DOI: 10.1007/s00894-019-4129-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/09/2019] [Indexed: 01/01/2023]
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12
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Kabankin AS, Sinauridze EI, Lipets EN, Ataullakhanov FI. Computer Design of Low-Molecular-Weight Inhibitors of Coagulation Factors. BIOCHEMISTRY (MOSCOW) 2019; 84:119-136. [PMID: 31216971 DOI: 10.1134/s0006297919020032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses main approaches to searching for new low-molecular-weight inhibitors of coagulation factors IIa, Xa, IXa, and XIa and the results of such studies conducted from 2015 to 2018. For each of these factors, several inhibitors with IC50 < 10 nM have been found, some of which are now tested in clinical trials. However, none of the identified inhibitors meets the requirements for an "ideal" anticoagulant, so further studies are required.
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Affiliation(s)
- A S Kabankin
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - E I Sinauridze
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, 119991, Russia.,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - E N Lipets
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, 119991, Russia.,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - F I Ataullakhanov
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, Moscow, 119991, Russia. .,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Physics, Moscow, 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
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Li X, Zhou H, Mo X, Zhang L, Li J. In silico study of febuxostat analogs as inhibitors of xanthine oxidoreductase: A combined 3D-QSAR and molecular docking study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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14
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Tong J, Jiang G, Li L, Li Y. Molecular Virtual Screening Studies of Herbicidal Sulfonylurea Analogues Using Molecular Docking and Topomer CoMFA Research. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619020057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Tong J, Jiang G, Li L, Li Y. Molecular Docking and 3D QSAR Research of Indolocarbazole Series as Cyclin-Dependent Kinase Inhibitors. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618070065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Shang R, Yi Y, Zhang C, Fu Y, Liang J, Pu W. Antibacterial activity and pharmacokinetic profile of a promising antibacterial agent: 14-O-[(4-Amino-6-hydroxy-pyrimidine-2-yl)thioacetyl] mutilin. Pharmacol Res 2017; 129:424-431. [PMID: 29133214 DOI: 10.1016/j.phrs.2017.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/09/2017] [Accepted: 11/09/2017] [Indexed: 01/21/2023]
Abstract
A new pleuromutilin derivative, 14-O-[(4-Amino-6-hydroxy-pyrimidine-2-yl)thioacetyl] mutilin (APTM), has been synthesized and proved most potent antibacterial agent in in vitro assays, suggesting that further development of this compound may lead to a promising antibacterial drug. In this study, we further evaluated the cytotoxicity, antibacterial efficacy and the pharmacokinetic profile of APTM. In BRL 3A cells, 50% of viability was obtained when 363μg/mL of APTM was used, while retapamulin and tiamulin fumarate needed 49 and 28μg/mL, respectively, to reach this viability. Compared to tiamulin fumarate, APTM showed higher inhibition efficacy and faster bactericidal activity against S. aureus and lower 50% effective dose (ED50) in mice after a lethal challenge with methicillin-resistant Staphylococcus aureus (MRSA). Docking experiment for APTM showed a similar binding pattern with tiamulin. Furthermore, a simple, accurate and sensitive HPLC method for the determination of APTM in rabbit plasma was developed and successfully applied to pharmacokinetic study, in which the half life (t1/2), clearance rate (Cl) and the area under the plasma concentration-time curve (AUC0→∞) were 3.37h, 0.35L/h/kg and 70.68μg·h/m, respectively.
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Affiliation(s)
- Ruofeng Shang
- Key Laboratory of New Animal Drug Project of Gansu Province; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, P. R. China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, 730050 Lanzhou, China.
| | - Yunpeng Yi
- Key Laboratory of New Animal Drug Project of Gansu Province; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, P. R. China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, 730050 Lanzhou, China
| | - Chao Zhang
- Lianyungang Animal Health Inspection Institute, Lianyungang, 222000, Lianyungang, China
| | - Yunxing Fu
- Key Laboratory of New Animal Drug Project of Gansu Province; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, P. R. China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, 730050 Lanzhou, China
| | - Jianping Liang
- Key Laboratory of New Animal Drug Project of Gansu Province; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, P. R. China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, 730050 Lanzhou, China
| | - Wanxia Pu
- Key Laboratory of New Animal Drug Project of Gansu Province; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, P. R. China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, 730050 Lanzhou, China.
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Li DD, Wu FL, Wang ZH, Huang LL, Yin Y, Wu FH. Identification of 2,4-diarylaminopyrimidine analogues as ALK inhibitors by using 3D-QSAR, molecular docking, and molecular dynamics simulations. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-017-1999-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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First report on the structural exploration and prediction of new BPTES analogs as glutaminase inhibitors. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.04.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Halder AK, Amin SA, Jha T, Gayen S. Insight into the structural requirements of pyrimidine-based phosphodiesterase 10A (PDE10A) inhibitors by multiple validated 3D QSAR approaches. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:253-273. [PMID: 28322591 DOI: 10.1080/1062936x.2017.1302991] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
Schizophrenia is a complex disorder of thinking and behaviour (0.3-0.7% of the population is affected). The over-expression of phosphodiesterase 10A (PDE10A) enzyme may be a potential target for schizophrenia and Huntington's disease. Because 3D QSAR analysis is one of the most frequently used modelling techniques, in the present study, five different 3D QSAR tools, namely CoMFA, CoMSIA, kNN-MFA, Open3DQSAR and topomer CoMFA methods, were used on a dataset of pyrimidine-based PDE10A inhibitors. All developed models were validated internally and externally. The non-commercial Open3DQSAR produced the best statistical results amongst 3D QSAR tools. The structural interpretations obtained from different methods were thoroughly analysed and were justified on the basis of information obtained from the crystal structure. Information from one method was mostly validated by the results of other methods and vice versa. In the current work, the use of multiple tools in the same analysis revealed more complete information about the structural requirements of these compounds. On the basis of the observations of the 3D QSAR studies, 12 new compounds were designed for better PDE10A inhibitory activity. The current investigation may help in further designing new PDE10A inhibitors with promising activity.
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Affiliation(s)
- A K Halder
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
| | - S A Amin
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
- b Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University (A Central University) , Sagar , India
| | - T Jha
- a Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , India
| | - S Gayen
- b Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr. Harisingh Gour University (A Central University) , Sagar , India
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Gao X, Han L, Ren Y. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations. Molecules 2016; 21:molecules21050591. [PMID: 27164065 PMCID: PMC6273173 DOI: 10.3390/molecules21050591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 04/11/2016] [Accepted: 04/28/2016] [Indexed: 12/11/2022] Open
Abstract
Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q2 values (0.531, 0.726), fitted correlation r2 coefficients (higher than 0.90), and standard error of prediction (less than 0.250). These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.
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Affiliation(s)
- Xiaodong Gao
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Liping Han
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
| | - Yujie Ren
- School of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, China.
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3D-QSAR, molecular dynamics simulations and molecular docking studies of benzoxazepine moiety as mTOR inhibitor for the treatment of lung cancer. Bioorg Med Chem Lett 2016; 26:864-874. [DOI: 10.1016/j.bmcl.2015.12.075] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/07/2015] [Accepted: 12/22/2015] [Indexed: 01/18/2023]
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