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Applications of the Novel Quantitative Pharmacophore Activity Relationship Method QPhAR in Virtual Screening and Lead-Optimisation. Pharmaceuticals (Basel) 2022; 15:ph15091122. [PMID: 36145343 PMCID: PMC9504690 DOI: 10.3390/ph15091122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022] Open
Abstract
Pharmacophores are an established concept for the modelling of ligand–receptor interactions based on the abstract representations of stereoelectronic molecular features. They became widely popular as filters for the fast virtual screening of large compound libraries. A lot of effort has been put into the development of sophisticated algorithms and strategies to increase the computational efficiency of the screening process. However, hardly any focus has been put on the development of automated procedures that optimise pharmacophores towards higher discriminatory power, which still has to be done manually by a human expert. In the age of machine learning, the researcher has become the decision-maker at the top level, outsourcing analysis tasks and recurrent work to advanced algorithms and automation workflows. Here, we propose an algorithm for the automated selection of features driving pharmacophore model quality using SAR information extracted from validated QPhAR models. By integrating the developed method into an end-to-end workflow, we present a fully automated method that is able to derive best-quality pharmacophores from a given input dataset. Finally, we show how the QPhAR-generated models can be used to guide the researcher with insights regarding (un-)favourable interactions for compounds of interest.
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Search for Potent and Selective Aurora A Inhibitors Based on General Ser/Thr Kinase Pharmacophore Model. Pharmaceuticals (Basel) 2016; 9:ph9020019. [PMID: 27089349 PMCID: PMC4932537 DOI: 10.3390/ph9020019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 11/17/2022] Open
Abstract
Based on the data for compounds known from the literature to be active against various types of Ser/Thr kinases, a general pharmachophore model for these types of kinases was developed. The search for the molecules fitting to this pharmacophore among the ASINEX proprietary library revealed a number of compounds, which were tested and appeared to possess some activity against Ser/Thr kinases such as Aurora A, Aurora B and Haspin. Our work on the optimization of these molecules against Aurora A kinase allowed us to achieve several hits in a 3–5 nM range of activity with rather good selectivity and Absorption, Distribution, Metabolism, and Excretion (ADME) properties, and cytotoxicity against 16 cancer cell lines. Thus, we showed the possibility to fine-tune the general Ser/Thr pharmacophore to design active and selective compounds against desired types of kinases.
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Vasilevich NI, Aksenova EA, Kazyulkin DN, Afanasyev II. General Ser/Thr Kinases Pharmacophore Approach for Selective Kinase Inhibitors Search as Exemplified by Design of Potent and Selective Aurora A Inhibitors. Chem Biol Drug Des 2016; 88:54-65. [PMID: 26825399 DOI: 10.1111/cbdd.12733] [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: 10/08/2015] [Revised: 12/29/2015] [Accepted: 01/07/2016] [Indexed: 11/30/2022]
Abstract
A general pharmachophore model for various types of Ser/Thr kinases was developed. Search for the molecules fitting to this pharmacophore among ASINEX proprietary library revealed a number of compounds, which were tested and appeared to possess some activity against several Ser/Thr kinases such as Aurora A, Aurora B and Haspin. The possibility of performing the fine-tuning of the general Ser/Thr pharmacophore to desired types of kinase to get active and selective inhibitors was exemplified by Aurora A kinase. As a result, several hits in 3-5 nm range of activity against Aurora A kinase with rather good selectivity and ADME properties were obtained.
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Affiliation(s)
- Natalya I Vasilevich
- Novie Nauchnie Tekhnologii Ltd. (ASINEX Company Group), 20 Geroev Panfilovtsev Str., Moscow, 125480, Russia
| | - Elena A Aksenova
- Novie Nauchnie Tekhnologii Ltd. (ASINEX Company Group), 20 Geroev Panfilovtsev Str., Moscow, 125480, Russia
| | - Denis N Kazyulkin
- Novie Nauchnie Tekhnologii Ltd. (ASINEX Company Group), 20 Geroev Panfilovtsev Str., Moscow, 125480, Russia
| | - Ilya I Afanasyev
- Novie Nauchnie Tekhnologii Ltd. (ASINEX Company Group), 20 Geroev Panfilovtsev Str., Moscow, 125480, Russia
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4
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Nonpeptidic angiotensin II AT1 receptor antagonists derived from 6-substituted aminocarbonyl and acylamino benzimidazoles. Eur J Med Chem 2013; 69:44-54. [DOI: 10.1016/j.ejmech.2013.08.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 12/17/2022]
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5
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Yang Y, Zhang W, Cheng J, Tang Y, Peng Y, Li Z. Pharmacophore, 3D-QSAR, and Bayesian Model Analysis for Ligands Binding at the Benzodiazepine Site of GABAAReceptors: the Key Roles of Amino Group and Hydrophobic Sites. Chem Biol Drug Des 2013; 81:583-90. [DOI: 10.1111/cbdd.12100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 01/19/2023]
Affiliation(s)
- Ying Yang
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
| | - Wei Zhang
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
| | | | - Yun Tang
- Shanghai Key Laboratory of New Drug Design; School of Pharmacy; East China University of Science and Technology; PO Box 544, 130 Meilong Road; Shanghai; 200237; China
| | - Yanqing Peng
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology; School of Pharmacy; East China University of Science and Technology; Shanghai; China
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Lu S, Sun SL, Liu HC, Chen YD, Yuan HL, Gao YP, Yang P, Lu T. Identification of novel polo-like kinase 1 inhibitors by a hybrid virtual screening. Chem Biol Drug Des 2012; 80:328-39. [PMID: 22583481 DOI: 10.1111/j.1747-0285.2012.01412.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Polo-like kinase 1 is an important and attractive oncological target that plays a key role in mitosis and cytokinesis. A combined pharmacophore- and docking-based virtual screening was performed to identify novel polo-like kinase 1 inhibitors. A total of 34 hit compounds were selected and tested in vitro, and some compounds showed inhibition of polo-like kinase 1 and human tumor cell growth. The most potent compound (66) inhibited polo-like kinase 1 with an IC(50) value of 6.99 μm. The docked binding models of two hit compounds were discussed in detail. These compounds contained novel chemical scaffolds and may be used as foundations for the development of novel classes of polo-like kinase 1 inhibitors.
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Affiliation(s)
- Shuai Lu
- Laboratory of Molecular Design and Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
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Design, synthesis and biological activity of 6-substituted carbamoyl benzimidazoles as new nonpeptidic angiotensin II AT1 receptor antagonists. Bioorg Med Chem 2012; 20:4208-16. [DOI: 10.1016/j.bmc.2012.05.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 01/23/2023]
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8
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Wang JL, Zhang J, Zhou ZM, Li ZH, Xue WZ, Xu D, Hao LP, Han XF, Fei F, Liu T, Liang AH. Design, synthesis and biological evaluation of 6-substituted aminocarbonyl benzimidazole derivatives as nonpeptidic angiotensin II AT1 receptor antagonists. Eur J Med Chem 2012; 49:183-90. [DOI: 10.1016/j.ejmech.2012.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 12/29/2011] [Accepted: 01/05/2012] [Indexed: 01/26/2023]
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Sun H, Zhu J, Chen Y, Sun Y, Zhi H, Li H, You Y, Xiao Q. Docking Study and Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) Analyses and Novel Molecular Design of a Series of 4-Aminoquinazolines as Inhibitors of Aurora B Kinase. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180315] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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Identification of critical chemical features for Aurora kinase-B inhibitors using Hip-Hop, virtual screening and molecular docking. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.08.050] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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He G, Qiu M, Li R, Song X, Zheng X, Shi J, Xu G, Han J, Yu L, Yang S, Chen L, Wei Y. Molecular docking-based 3D-QSAR studies of pyrrolo[3,4-c]pyrazole derivatives as Aurora-A inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.517529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- G. He
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - M.H. Qiu
- b Institute of Botany, The Chinese Academy of Sciences , Kunming, 650204, P.R. China
| | - R. Li
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - X.R. Song
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - X. Zheng
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - J.Y. Shi
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - G.B. Xu
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - J. Han
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - L.T. Yu
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - S.Y. Yang
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - L.J. Chen
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
| | - Y.Q. Wei
- a State Key Laboratory of Biotherapy , West China Hospital, Sichuan University , Chengdu, 610041, P.R. China
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Chen JJ, Liu TL, Yang LJ, Li LL, Wei YQ, Yang SY. Pharmacophore modeling and virtual screening studies of checkpoint kinase 1 inhibitors. Chem Pharm Bull (Tokyo) 2009; 57:704-9. [PMID: 19571415 DOI: 10.1248/cpb.57.704] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this study, chemical feature-based 3-dimensional (3D) pharmacophore models of Checkpoint kinase 1 (Chk1) inhibitors were developed based on the known inhibitors of Chk1. The best pharmacophore model Hypo1 was characterized by the best correlation coefficient (0.9577), and the lowest root mean square deviation (0.8871). Hypo1 consists of one hydrogen-bond acceptor, one hydrogen-bond donor, and two hydrophobic features, as well as one excluded volume. This pharmacophore model was further validated by both test set and cross validation methods. A comparison analysis of Hypo1 with chemical features in the active site of Chk1 indicates that the pharmacophore model Hypo1 can correctly reflect the interactions between Chk1 and its ligands. Then Hypo1 was used to screen chemical databases, including Specs and Chinese Nature Product Database (CNPD) for potential lead compounds. The hit compounds were subsequently subjected to filtering by Lipinski's rule of five and docking study to refine the retrieved hits. Finally some of the most potent (estimated) compounds were selected from the final refined hits and suggested for further experimental investigation.
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Affiliation(s)
- Jin-Juan Chen
- State Key Laboratory of Biotherapy, West China Hospital, West China School of Pharmacy, Sichuan University
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