1
|
Mind the Gap—Deciphering GPCR Pharmacology Using 3D Pharmacophores and Artificial Intelligence. Pharmaceuticals (Basel) 2022; 15:ph15111304. [DOI: 10.3390/ph15111304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. Three-dimensional pharmacophore models are powerful computational tools in in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, the discovery of biased and allosteric ligands, scaffold hopping, QSAR analysis, hit-to-lead optimization, GPCR de-orphanization, mechanistic understanding of GPCR pharmacology and the elucidation of ligand–receptor interactions. Furthermore, advances in the incorporation of dynamics and machine learning are highlighted. The review will analyze challenges in the field of GPCR drug discovery, detailing how 3D pharmacophore modeling can be used to address them. Finally, we will present opportunities afforded by 3D pharmacophore modeling in the advancement of our understanding and targeting of GPCRs.
Collapse
|
2
|
Zhao S, Zhang H, Jin H, Cai X, Zhang R, Jin Z, Yang W, Yu P, Zhang L, Liu Z. Design, synthesis and biological activities of benzo[d]imidazo[1,2-a]imidazole derivatives as TRPM2-specfic inhibitors. Eur J Med Chem 2021; 225:113750. [PMID: 34416664 DOI: 10.1016/j.ejmech.2021.113750] [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] [Received: 04/20/2021] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Transient receptor potential melastatin 2 (TRPM2) channel is associated with ischemia/reperfusion injury, inflammation, cancer and neurodegenerative diseases. However, the lack of specific inhibitors impedes the development of TRPM2 targeted therapeutic agents. To develop a selective TRPM2 inhibitor, three-dimensional similarity-based screening strategy was employed using the energy-minimized conformation of non-selective TRPM2 inhibitor 2-APB as the query structure, which resulted in the discovery of a novel tricyclic TRPM2 inhibitor Z-4 with benzo[d]imidazo[1,2-a]imidazole skeleton. A series of Z-4 derivatives were subsequently synthesized and evaluated using calcium imaging and electrophysiology approaches. Among them, preferred compounds ZA10 and ZA18 inhibited the TRPM2 channel with micromolar half-maximal inhibitory concentration values and exhibited TRPM2 selectivity over the TRPM8 channel, TRPV1 channel, InsP3 receptor and Orai channel. The analysis of structure-activity relationship provides valuable insights for further development of selective TRPM2 inhibitors. Neuroprotection assay showed that ZA10 and ZA18 could effectively reduce the mortality of SH-SY5Y cells induced by H2O2. These findings enrich the structure types of existing TRPM2 inhibitors and might provide a new tool for the study of TRPM2 function in Reactive oxygen species (ROS) -related diseases.
Collapse
Affiliation(s)
- Siqi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Han Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Xiaobo Cai
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, PR China
| | - Rongxue Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Zefang Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Wei Yang
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, PR China
| | - Peilin Yu
- Department of Toxicology, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, 310058, PR China.
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China.
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China.
| |
Collapse
|
3
|
Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. Property-Unmatched Decoys in Docking Benchmarks. J Chem Inf Model 2021; 61:699-714. [PMID: 33494610 DOI: 10.1021/acs.jcim.0c00598] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enrichment of ligands versus property-matched decoys is widely used to test and optimize docking library screens. However, the unconstrained optimization of enrichment alone can mislead, leading to false confidence in prospective performance. This can arise by over-optimizing for enrichment against property-matched decoys, without considering the full spectrum of molecules to be found in a true large library screen. Adding decoys representing charge extrema helps mitigate over-optimizing for electrostatic interactions. Adding decoys that represent the overall characteristics of the library to be docked allows one to sample molecules not represented by ligands and property-matched decoys but that one will encounter in a prospective screen. An optimized version of the DUD-E set (DUDE-Z), as well as Extrema and sets representing broad features of the library (Goldilocks), is developed here. We also explore the variability that one can encounter in enrichment calculations and how that can temper one's confidence in small enrichment differences. The new tools and new decoy sets are freely available at http://tldr.docking.org and http://dudez.docking.org.
Collapse
Affiliation(s)
- Reed M Stein
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Ying Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Trent E Balius
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, Maryland 21702, United States
| | - Matt J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Palmer Commons, 100 Washtenaw Ave. #2017, Ann Arbor, Michigan 48109, United States
| | - Jiankun Lyu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Jennifer Young
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Khanh Tang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
4
|
Antelo-Collado A, Carrasco-Velar R, García-Pedrajas N, Cerruela-García G. Maximum common property: a new approach for molecular similarity. J Cheminform 2020; 12:61. [PMID: 33372638 PMCID: PMC7547443 DOI: 10.1186/s13321-020-00462-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/14/2020] [Indexed: 12/02/2022] Open
Abstract
The maximum common property similarity (MCPhd) method is presented using descriptors as a new approach to determine the similarity between two chemical compounds or molecular graphs. This method uses the concept of maximum common property arising from the concept of maximum common substructure and is based on the electrotopographic state index for atoms. A new algorithm to quantify the similarity values of chemical structures based on the presented maximum common property concept is also developed in this paper. To verify the validity of this approach, the similarity of a sample of compounds with antimalarial activity is calculated and compared with the results obtained by four different similarity methods: the small molecule subgraph detector (SMSD), molecular fingerprint based (OBabel_FP2), ISIDA descriptors and shape-feature similarity (SHAFTS). The results obtained by the MCPhd method differ significantly from those obtained by the compared methods, improving the quantification of the similarity. A major advantage of the proposed method is that it helps to understand the analogy or proximity between physicochemical properties of the molecular fragments or subgraphs compared with the biological response or biological activity. In this new approach, more than one property can be potentially used. The method can be considered a hybrid procedure because it combines descriptor and the fragment approaches. ![]()
Collapse
Affiliation(s)
- Aurelio Antelo-Collado
- University of Informatics Science, Carretera San Antonio de los Baños Km. 2 1/2 , Boyeros, La Habana, Cuba, Havana, Cuba
| | - Ramón Carrasco-Velar
- University of Informatics Science, Carretera San Antonio de los Baños Km. 2 1/2 , Boyeros, La Habana, Cuba, Havana, Cuba.
| | - Nicolás García-Pedrajas
- Department of Computing and Numerical Analysis, University of Cordoba, Campus de Rabanales, Albert Einstein Building, E-14071, Córdoba, Spain
| | - Gonzalo Cerruela-García
- Department of Computing and Numerical Analysis, University of Cordoba, Campus de Rabanales, Albert Einstein Building, E-14071, Córdoba, Spain
| |
Collapse
|
5
|
Pérez-Sianes J, Pérez-Sánchez H, Díaz F. Virtual Screening Meets Deep Learning. Curr Comput Aided Drug Des 2019; 15:6-28. [PMID: 30338743 DOI: 10.2174/1573409914666181018141602] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 10/08/2018] [Accepted: 10/11/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Automated compound testing is currently the de facto standard method for drug screening, but it has not brought the great increase in the number of new drugs that was expected. Computer- aided compounds search, known as Virtual Screening, has shown the benefits to this field as a complement or even alternative to the robotic drug discovery. There are different methods and approaches to address this problem and most of them are often included in one of the main screening strategies. Machine learning, however, has established itself as a virtual screening methodology in its own right and it may grow in popularity with the new trends on artificial intelligence. OBJECTIVE This paper will attempt to provide a comprehensive and structured review that collects the most important proposals made so far in this area of research. Particular attention is given to some recent developments carried out in the machine learning field: the deep learning approach, which is pointed out as a future key player in the virtual screening landscape.
Collapse
Affiliation(s)
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Fernando Díaz
- Departamento de Informática, Escuela de Ingeniería Informática, University of Valladolid, Segovia, Spain
| |
Collapse
|
6
|
He LJ, Zhu YB, Fan QZ, Miao DD, Zhang SP, Liu XP, Zhang C. Shape-based virtual screen for the discovery of novel CDK8 inhibitor chemotypes. Bioorg Med Chem Lett 2019; 29:549-555. [PMID: 30630717 DOI: 10.1016/j.bmcl.2018.12.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/29/2018] [Accepted: 12/31/2018] [Indexed: 11/15/2022]
Abstract
With the aim of discovering novel cyclin-dependent kinase 8 (CDK8) inhibitors, a combined similarity search and molecular docking approach was employed, which led to 32 hits. Biological tests led to the discovery of several novel submicromolar inhibitors. In particular, compound C768-0769 (ZC0201) showed good CDK8 inhibitory activity, and compound ZC0201 effectively suppressed HCT-116 colorectal cancer cell proliferation by inducing G1/S transition arrest. Furthermore, modulation of phosphorylated signal transducer and activator of transcription 1 (Ser 727) (STAT1SER727), a pharmacodynamic biomarker of CDK8 activity, demonstrated that ZC0201 may cause G1/S transition arrest through CDK8 activity inhibition. Due to its good cellular activity, ZC0201 may be an ideal lead compound for further modification as a potential cancer therapeutic agent.
Collapse
Affiliation(s)
- Lian-Jun He
- Center of Drug Screening and Evaluation, Wannan Medical College, Wuhu, Anhui 241000, PR China
| | - Yi-Bao Zhu
- Center of Drug Screening and Evaluation, Wannan Medical College, Wuhu, Anhui 241000, PR China
| | - Qing-Zhu Fan
- Center of Drug Screening and Evaluation, Wannan Medical College, Wuhu, Anhui 241000, PR China
| | - Dong-Dong Miao
- Center of Drug Screening and Evaluation, Wannan Medical College, Wuhu, Anhui 241000, PR China
| | - Sheng-Peng Zhang
- Center of Drug Screening and Evaluation, Wannan Medical College, Wuhu, Anhui 241000, PR China; School of Pharmacy, Wannan Medical College, Wuhu, Anhui 241000, PR China
| | - Xiao-Ping Liu
- Center of Drug Screening and Evaluation, Wannan Medical College, Wuhu, Anhui 241000, PR China.
| | - Chao Zhang
- Center of Drug Screening and Evaluation, Wannan Medical College, Wuhu, Anhui 241000, PR China; Anhui Provincial Engineering Research Center for Polysaccharide Drugs, Wannan Medical College, Wuhu, Anhui 241000, PR China; School of Pharmacy, Wannan Medical College, Wuhu, Anhui 241000, PR China.
| |
Collapse
|
7
|
Chen WL, Wang ZH, Feng TT, Li DD, Wang CH, Xu XL, Zhang XJ, You QD, Guo XK. Discovery, design and synthesis of 6H-anthra[1,9-cd]isoxazol-6-one scaffold as G9a inhibitor through a combination of shape-based virtual screening and structure-based molecular modification. Bioorg Med Chem 2016; 24:6102-6108. [PMID: 27720557 DOI: 10.1016/j.bmc.2016.09.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 01/29/2023]
Abstract
Protein lysine methyltransferase G9a is widely considered as an appealing antineoplastic target. Herein we present an integrated workflow combining shape-based virtual screening and structure-based molecular modification for the identification of novel G9a inhibitors. The shape-based similarity screening through ROCS overlay on the basis of the structure of UNC0638 was performed to identify CPUY074001 contained a 6H-anthra[1,9-cd]isoxazol-6-one scaffold as a hit. Analysis of the binding mode of CPUY074001 with G9a and 3D-QSAR results, two series compounds were designed and synthesized. The derivatives were confirmed to be active by in vitro assay and the SAR was explored by docking stimulations. Besides, several analogues showed acceptable anti-proliferative effects against several cancer cell lines. Among them, CPUY074020 displayed potent dual G9a inhibitory activity and anti-proliferative activity. Furthermore, CPUY074020 induced cell apoptosis in a dose-dependent manner and displayed a significant decrease in dimethylation of H3K9. Simultaneously, CPUY074020 showed reasonable in vivo PK properties. Altogether, our workflow supplied a high efficient strategy in the identification of novel G9a inhibitors. Compounds reported here can serve as promising leads for further study.
Collapse
Affiliation(s)
- Wei-Lin Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Zhi-Hui Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Tao-Tao Feng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Dong-Dong Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Chu-Hui Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Li Xu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Jin Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiao-Ke Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
8
|
Wang J, Shu M, Wang Y, Hu Y, Wang Y, Luo Y, Lin Z. Identification of potential CCR5 inhibitors through pharmacophore-based virtual screening, molecular dynamics simulation and binding free energy analysis. MOLECULAR BIOSYSTEMS 2016; 12:3396-3406. [DOI: 10.1039/c6mb00577b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Employing the combined strategy to identify novel CCR5 inhibitors and provide a basis for rational drug design.
Collapse
Affiliation(s)
- Juan Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Mao Shu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yong Hu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanliang Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Yanfeng Luo
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Zhihua Lin
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- College of Chemistry and Chemical Engineering
| |
Collapse
|
9
|
Ibrahim TM, Bauer MR, Dörr A, Veyisoglu E, Boeckler FM. pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening. J Chem Inf Model 2015; 55:2297-307. [DOI: 10.1021/acs.jcim.5b00475] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamer M. Ibrahim
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias R. Bauer
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
| | - Alexander Dörr
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls University Tübingen, Sand 1, 72076 Tübingen, Germany
| | - Erdem Veyisoglu
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany
- Center
for Bioinformatics Tübingen (ZBIT), Eberhard Karls University Tübingen, Sand 1, 72076 Tübingen, Germany
| |
Collapse
|
10
|
Hou X, Du J, Liu R, Zhou Y, Li M, Xu W, Fang H. Enhancing the Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Customized ZBG Features: A Case Study Using Histone Deacetylase 8. J Chem Inf Model 2015; 55:861-71. [DOI: 10.1021/ci500762z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuben Hou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Jintong Du
- Shandong Cancer Hospital and Institute, Jinan, Shandong 250117, China
| | - Renshuai Liu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Yi Zhou
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Minyong Li
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Wenfang Xu
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Hao Fang
- Department
of Medicinal Chemistry, Key Laboratory of Chemical Biology of Natural
Products (MOE), School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| |
Collapse
|
11
|
Bian J, Qian X, Deng B, Xu X, Guo X, Wang Y, Li X, Sun H, You Q, Zhang X. Discovery of NAD(P)H:quinone oxidoreductase 1 (NQO1) inhibitors with novel chemical scaffolds by shape-based virtual screening combined with cascade docking. RSC Adv 2015. [DOI: 10.1039/c5ra05919d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A number of novel NAD(P)H:quinone oxidoreductase 1 (NQO1) inhibitors were discovered from the ChemDiv database via a simple protocol.
Collapse
|
12
|
Xu XL, Sun HP, Liu F, Jia JM, Guo XK, Pan Y, Huang HZ, Zhang XJ, You QD. Discovery and Bioevaluation of Novel Pyrazolopyrimidine Analogs as Competitive Hsp90 Inhibitors Through Shape-Based Similarity Screening. Mol Inform 2014; 33:293-306. [PMID: 27485776 DOI: 10.1002/minf.201300150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 02/13/2014] [Indexed: 12/14/2022]
Abstract
Hsp90 as a promising therapeutic target for the treatment of cancer has received great attention. Many Hsp90 inhibitors such as BIIB021 and CUDC-305 have been in clinical. In this paper shape-based similarity screening through ROCS overlays on the basis of CUDC-305, BIIB021, PU-H71 and PU-3 were performed to discover HSP90 inhibitors. A set of 19 novel pyrazolopyrimidine analogues was identified and evaluated on enzyme level and cell-based level as Hsp90 inhibitors. The compound HDI4-04 with IC50 0.35 µM in the Hsp90 ATP hydrolysis assay exhibited potent cytotoxicity against five human cancer cell lines. Western blot analysis and Hsp70 luciferase reporter assay further confirmed that HDI4-04 targeted the Hsp90 protein folding machinery. And according to the biological assay, the SAR was discussed and summarized, which will guide us for further optimization of these compounds.
Collapse
Affiliation(s)
- Xiao-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hao-Peng Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271216
| | - Fang Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jian-Min Jia
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiao-Ke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yang Pan
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hao-Ze Huang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiao-Jin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Qi-Dong You
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351. , .,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China. , .,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271216. ,
| |
Collapse
|
13
|
Kalászi A, Szisz D, Imre G, Polgár T. Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method. J Chem Inf Model 2014; 54:1036-49. [DOI: 10.1021/ci400620f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Adrián Kalászi
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| | - Dániel Szisz
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| | - Gábor Imre
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| | - Tímea Polgár
- ChemAxon Ltd., Graphisoft park, Zahony
u. 7, Budapest, Hungary, 1037
| |
Collapse
|
14
|
Maggiora G, Vogt M, Stumpfe D, Bajorath J. Molecular similarity in medicinal chemistry. J Med Chem 2013; 57:3186-204. [PMID: 24151987 DOI: 10.1021/jm401411z] [Citation(s) in RCA: 350] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Similarity is a subjective and multifaceted concept, regardless of whether compounds or any other objects are considered. Despite its intrinsically subjective nature, attempts to quantify the similarity of compounds have a long history in chemical informatics and drug discovery. Many computational methods employ similarity measures to identify new compounds for pharmaceutical research. However, chemoinformaticians and medicinal chemists typically perceive similarity in different ways. Similarity methods and numerical readouts of similarity calculations are probably among the most misunderstood computational approaches in medicinal chemistry. Herein, we evaluate different similarity concepts, highlight key aspects of molecular similarity analysis, and address some potential misunderstandings. In addition, a number of practical aspects concerning similarity calculations are discussed.
Collapse
Affiliation(s)
- Gerald Maggiora
- College of Pharmacy and BIO5 Institute, University of Arizona , 1295 North Martin, P.O. Box 210202, Tucson, Arizona 85721, United States
| | | | | | | |
Collapse
|
15
|
'Fuzziness' in pharmacophore-based virtual screening and de novo design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 7:e203-70. [PMID: 24103799 DOI: 10.1016/j.ddtec.2010.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
16
|
Sun H, Xu X, Wu X, Zhang X, Liu F, Jia J, Guo X, Huang J, Jiang Z, Feng T, Chu H, Zhou Y, Zhang S, Liu Z, You Q. Discovery and design of tricyclic scaffolds as protein kinase CK2 (CK2) inhibitors through a combination of shape-based virtual screening and structure-based molecular modification. J Chem Inf Model 2013; 53:2093-102. [PMID: 23937544 DOI: 10.1021/ci400114f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein kinase CK2 (CK2), a ubiquitous serine/threonine protein kinase for hundreds of endogenous substrates, serves as an attractive anticancer target. One of its most potent inhibitors, CX-4945, has entered a phase I clinical trial. Herein we present an integrated workflow combining shape-based virtual screening for the identification of novel CK2 inhibitors. A shape-based model derived from CX-4945 was built, and the subsequent virtual screening led to the identification of several novel scaffolds with high shape similarity to that of CX-4945. Among them two tricyclic scaffolds named [1,2,4]triazolo[4,3-c]quinazolin and [1,2,4]triazolo[4,3-a]quinoxalin attracted us the most. Combining strictly chemical similarity analysis, a second-round shape-based screening was performed based on the two tricyclic scaffolds, leading to 28 derivatives. These compounds not only targeted CK2 with potent and dose-dependent activities but also showed acceptable antiproliferative effects against a series of cancer cell lines. Our workflow supplies a high efficient strategy in the identification of novel CK2 inhibitors. Compounds reported here can serve as ideal leads for further modifications.
Collapse
Affiliation(s)
- Haopeng Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
BACKGROUND Although virtual screening is now widely applied as a hit-finding methodology within drug discovery programmes, there are relatively few reports of its contributing to compounds on the market or in the clinic. OBJECTIVE To assess the impact of virtual screening on drug discovery. METHOD Such cases as can be found in the public domain at the current time are reviewed. Additionally, some of the current challenges in structure- and ligand-based virtual screening are discussed. CONCLUSION It is concluded that virtual screening has contributed to the discovery of several compounds that have either reached the market or entered clinical trials. In terms of praxis, there is 'no free lunch' in virtual screening and as many methods as possible should be applied to maximise the likelihood of success.
Collapse
Affiliation(s)
- David E Clark
- Argenta Discovery Ltd, 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex, CM19 5TR, United Kingdom +44 (0)1279 645611 ; +44 (0)1279 645646 ;
| |
Collapse
|
18
|
Al-Nadaf A, Taha MO. Ligand-based pharmacophore exploration and QSAR analysis of transition state analogues followed by in silico screening guide the discovery of new sub-micromolar β-secreatase inhibitors. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0204-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
19
|
Schuffenhauer A. Computational methods for scaffold hopping. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
20
|
Scior T, Bender A, Tresadern G, Medina-Franco JL, Martínez-Mayorga K, Langer T, Cuanalo-Contreras K, Agrafiotis DK. Recognizing Pitfalls in Virtual Screening: A Critical Review. J Chem Inf Model 2012; 52:867-81. [DOI: 10.1021/ci200528d] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Scior
- Pharmacy Department, Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Pue, México
| | - Andreas Bender
- Unilever Centre for Molecular
Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Gary Tresadern
- Research Informatics & Integrative Genomics, Janssen Research & Development, Calle Jarama 75, Poligono Industrial, Toledo 45007, Spain
| | - José L. Medina-Franco
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port
St. Lucie, Florida 34987, United States
| | - Karina Martínez-Mayorga
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port
St. Lucie, Florida 34987, United States
| | - Thierry Langer
- Prestwick Chemical, Blvd Gonthier dʼAndernach, F-67400 Illkirch, France
| | - Karina Cuanalo-Contreras
- Pharmacy Department, Facultad de Ciencias Químicas, Universidad Autónoma de Puebla, Puebla, Pue, México
| | - Dimitris K. Agrafiotis
- Johnson & Johnson Pharmaceutical Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| |
Collapse
|
21
|
Sato T, Yuki H, Takaya D, Sasaki S, Tanaka A, Honma T. Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors. J Chem Inf Model 2012; 52:1015-26. [DOI: 10.1021/ci200562p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tomohiro Sato
- RIKEN Systems and Structural Biology Center, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Systems and Structural Biology Center, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Daisuke Takaya
- RIKEN Systems and Structural Biology Center, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shunta Sasaki
- RIKEN Systems and Structural Biology Center, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Akiko Tanaka
- RIKEN Systems and Structural Biology Center, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Teruki Honma
- RIKEN Systems and Structural Biology Center, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| |
Collapse
|
22
|
Distinto S, Esposito F, Kirchmair J, Cardia MC, Gaspari M, Maccioni E, Alcaro S, Markt P, Wolber G, Zinzula L, Tramontano E. Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint- and pharmacophore-based virtual screening approach. Eur J Med Chem 2012; 50:216-29. [PMID: 22361685 DOI: 10.1016/j.ejmech.2012.01.056] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 12/26/2011] [Accepted: 01/27/2012] [Indexed: 01/23/2023]
Abstract
We report the first application of ligand-based virtual screening (VS) methods for discovering new compounds able to inhibit both human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT)-associated functions, DNA polymerase and ribonuclease H (RNase H) activities. The overall VS campaign consisted of two consecutive screening processes. In the first, the VS platform Rapid Overlay of Chemical Structures (ROCS) was used to perform in silico shape-based similarity screening on the NCI compounds database in which a hydrazone derivative, previously shown to inhibit the HIV-1 RT, was chosen. As a result, 34 hit molecules were selected and assayed on both RT-associated functions. In the second, the 4 most potent RT inhibitors identified were selected as queries for parallel VS performed by combining shape-based, 2D-fingerprint and 3D-pharmacophore VS methods. Overall, a set of molecules characterized by new different scaffolds were identified as novel inhibitors of both HIV-1 RT-associated activities in the low micromolar range.
Collapse
Affiliation(s)
- Simona Distinto
- Dipartimento di Scienze della Salute, Università degli Studi Magna Grecia di Catanzaro, Campus Salvatore Venuta, 88100, Catanzaro, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Applying similarity for finding new promising compounds is a key issue in drug design. Conversely, quantifying similarity between molecules has remained a difficult task despite the numerous approaches. Here, some general aspects along with recent developments regarding similarity criteria are collected. For the purpose of virtual screening, the compounds have to be encoded into a computer-readable format that permits a comparison, according to given similarity criteria, comprising the use of the 3D structure, fingerprints, graph-based and alignment-based approaches. Whereas finding the most common substructures is the most obvious method, more recent approaches take into account chemical modifications that appear throughout existing drugs, from various therapeutic categories and targets.
Collapse
|
24
|
Ebalunode JO, Zheng W, Tropsha A. Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design. Methods Mol Biol 2011; 685:111-33. [PMID: 20981521 DOI: 10.1007/978-1-60761-931-4_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Optimization of chemical library composition affords more efficient identification of hits from biological screening experiments. The optimization could be achieved through rational selection of reagents used in combinatorial library synthesis. However, with a rapid advent of parallel synthesis methods and availability of millions of compounds synthesized by many vendors, it may be more efficient to design targeted libraries by means of virtual screening of commercial compound collections. This chapter reviews the application of advanced cheminformatics approaches such as quantitative structure-activity relationships (QSAR) and pharmacophore modeling (both ligand and structure based) for virtual screening. Both approaches rely on empirical SAR data to build models; thus, the emphasis is placed on achieving models of the highest rigor and external predictive power. We present several examples of successful applications of both approaches for virtual screening to illustrate their utility. We suggest that the expert use of both QSAR and pharmacophore models, either independently or in combination, enables users to achieve targeted libraries enriched with experimentally confirmed hit compounds.
Collapse
Affiliation(s)
- Jerry O Ebalunode
- Department of Pharmaceutical Sciences, BRITE Institute, North Carolina Center University, Durham, NC, USA.
| | | | | |
Collapse
|
25
|
Giganti D, Guillemain H, Spadoni JL, Nilges M, Zagury JF, Montes M. Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment. J Chem Inf Model 2010; 50:992-1004. [PMID: 20527883 DOI: 10.1021/ci900507g] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the early stage of drug discovery programs, when the structure of a complex involving a target and a small molecule is available, structure-based virtual ligand screening methods are generally preferred. However, ligand-based strategies like shape-similarity search methods can also be applied. Shape-similarity search methods consist in exploring a pseudo-binding-site derived from the known small molecule used as a reference. Several of these methods use conformational sampling algorithms which are also shared by corresponding docking methods: for example Surflex-dock/Surflex-sim, FlexX/FlexS, ICM, and OMEGA-FRED/OMEGA-ROCS. Using 11 systems issued from the challenging "own" subsets of the Directory of Useful Decoys (DUD-own), we evaluated and compared the performance of the above-cited programs in terms of molecular alignment accuracy, enrichment in active compounds, and enrichment in different chemotypes (scaffold-hopping). Since molecular alignment is a crucial aspect of performance for the different methods, we have assessed its impact on enrichment. We have also illustrated the paradox of retrieving active compounds with good scores even if they are inaccurately positioned. Finally, we have highlighted possible positive aspects of using shape-based approaches in drug-discovery protocols when the structure of the target in complex with a small molecule is known.
Collapse
Affiliation(s)
- David Giganti
- Unite de Bioinformatique Structurale, Institut Pasteur, 26 rue du Dr Roux, 75015 Paris, France
| | | | | | | | | | | |
Collapse
|
26
|
López-Ramos M, Perruccio F. HPPD: ligand- and target-based virtual screening on a herbicide target. J Chem Inf Model 2010; 50:801-14. [PMID: 20359237 DOI: 10.1021/ci900498n] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxyphenylpyruvate dioxygenase (HPPD) has proven to be a very successful target for the development of herbicides with bleaching properties, and today HPPD inhibitors are well established in the agrochemical market. Syngenta has a long history of HPPD-inhibitor research, and HPPD was chosen as a case study for the validation of diverse ligand- and target-based virtual screening approaches to identify compounds with inhibitory properties. Two-dimensional extended connectivity fingerprints, three-dimensional shape-based tools (ROCS, EON, and Phase-shape) and a pharmacophore approach (Phase) were used as ligand-based methods; Glide and Gold were used as target-based. Both the virtual screening utility and the scaffold-hopping ability of the screening tools were assessed. Particular emphasis was put on the specific pitfalls to take into account for the design of a virtual screening campaign in an agrochemical context, as compared to a pharmaceutical environment.
Collapse
Affiliation(s)
- Miriam López-Ramos
- Syngenta Crop Protection, Muenchwilen AG, WST-820.1.15, Schaffhauserstrasse, CH-4332 Stein, Switzerland.
| | | |
Collapse
|
27
|
Abdula AM, Khalaf RA, Mubarak MS, Taha MO. Discovery of new β-D-galactosidase inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening. J Comput Chem 2010; 32:463-82. [PMID: 20730780 DOI: 10.1002/jcc.21635] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 05/14/2010] [Accepted: 06/23/2010] [Indexed: 11/11/2022]
|
28
|
Discovery of new β-d-glucosidase inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening. J Mol Model 2010; 17:443-64. [PMID: 20490878 DOI: 10.1007/s00894-010-0737-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 04/28/2010] [Indexed: 10/19/2022]
|
29
|
Krüger DM, Evers A. Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. ChemMedChem 2010; 5:148-58. [PMID: 19908272 DOI: 10.1002/cmdc.200900314] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Structure- and ligand-based virtual-screening methods (docking, 2D- and 3D-similarity searching) were analysed for their effectiveness in virtual screening against four different targets: angiotensin-converting enzyme (ACE), cyclooxygenase 2 (COX-2), thrombin and human immunodeficiency virus 1 (HIV-1) protease. The relative performance of the tools was compared by examining their ability to recognise known active compounds from a set of actives and nonactives. Furthermore, we investigated whether the application of different virtual-screening methods in parallel provides complementary or redundant hit lists. Docking was performed with GOLD, Glide, FlexX and Surflex. The obtained docking poses were rescored by using nine different scoring functions in addition to the scoring functions implemented as objective functions in the docking algorithms. Ligand-based virtual screening was done with ROCS (3D-similarity searching), Feature Trees and Scitegic Functional Fingerprints (2D-similarity searching). The results show that structure- and ligand-based virtual-screening methods provide comparable enrichments in detecting active compounds. Interestingly, the hit lists that are obtained from different virtual-screening methods are generally highly complementary. These results suggest that a parallel application of different structure- and ligand-based virtual-screening methods increases the chance of identifying more (and more diverse) active compounds from a virtual-screening campaign.
Collapse
Affiliation(s)
- Dennis M Krüger
- Institut für pharmazeutische und medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | | |
Collapse
|
30
|
Lee HS, Lee CS, Kim JS, Kim DH, Choe H. Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket. J Chem Inf Model 2010; 49:2419-28. [PMID: 19852439 DOI: 10.1021/ci9002365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report, we present a novel virtual high-throughput screening methodology to assist in computer-aided drug discovery. Our method, designated as SLIM, involves ligand-free shape and chemical feature matching. The procedure takes advantage of a negative image of a binding pocket in a target receptor. The negative image is a set of virtual atoms representing the inner shape and chemical features of the binding pocket. Using this image, SLIM implements a shape-based similarity search based on molecular volume superposition for the ensemble of conformers of each molecule. The superposed structures, prioritized by shape similarity, are subjected to comparison of chemical feature similarities. To validate the merits of the SLIM method, we compared its performance with those of three distinct widely used tools ROCS, GLIDE, and GOLD. ROCS was selected as a representative of the ligand-centric methods, and docking programs GLIDE and GOLD as representatives of the receptor-centric methods. Our data suggest that SLIM has overall hit ranking ability that is comparable to that of the docking method, retaining the high computational speed of the ligand-centric method. It is notable that the SLIM method offers consistently reliable screening quality against conformational variations of receptors, whereas the docking methods have limited screening performance.
Collapse
Affiliation(s)
- Hui Sun Lee
- Department of Physiology, University of Ulsan College of Medicine, Seoul 138-736, South Korea
| | | | | | | | | |
Collapse
|
31
|
Freitas RF, Bauab RL, Montanari CA. Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4. J Chem Inf Model 2010; 50:97-109. [DOI: 10.1021/ci900074t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. F. Freitas
- Grupo de Estudos em Química Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Química de São Carlos - Universidade de São Paulo, 13560-970 - São Carlos - SP, Brazil
| | - R. L. Bauab
- Grupo de Estudos em Química Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Química de São Carlos - Universidade de São Paulo, 13560-970 - São Carlos - SP, Brazil
| | - C. A. Montanari
- Grupo de Estudos em Química Medicinal de Produtos Naturais - NEQUIMED-PN, Instituto de Química de São Carlos - Universidade de São Paulo, 13560-970 - São Carlos - SP, Brazil
| |
Collapse
|
32
|
Neale DS, Thompson PE, White PJ, Chalmers DK, Yuriev E, Manallack DT. Binding Mode Prediction of PDE4 Inhibitors: A Comparison of Modelling Methods. Aust J Chem 2010. [DOI: 10.1071/ch09463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Molecular modelling is widely used in support of medicinal chemistry programs, with several theoretical approaches used in attempts to expedite drug discovery. In this study, three methods – molecular docking (Glide), shape similarity (ROCS), and pharmacophore modelling (Phase) – were evaluated for their ability to reproduce experimentally determined binding modes of 25 PDE4 inhibitors, identified by X-ray crystallography. Molecular docking was able to provide a good approximation (RMSD less than 2 Å) in 59% of cases, when considering the top binding pose. The pairwise comparisons, using molecular shape similarity, gave good matches in 42% of cases. Pharmacophore models were unable to predict good binding modes for a series of PDE4 inhibitors.
Collapse
|
33
|
Mackey MD, Melville JL. Better than Random? The Chemotype Enrichment Problem. J Chem Inf Model 2009; 49:1154-62. [DOI: 10.1021/ci8003978] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark D. Mackey
- Cresset BioMolecular Discovery Ltd., BioPark Hertfordshire, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - James L. Melville
- Cresset BioMolecular Discovery Ltd., BioPark Hertfordshire, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| |
Collapse
|
34
|
Abu Hammad AM, Taha MO. Pharmacophore Modeling, Quantitative Structure−Activity Relationship Analysis, and Shape-Complemented in Silico Screening Allow Access to Novel Influenza Neuraminidase Inhibitors. J Chem Inf Model 2009; 49:978-96. [PMID: 19341295 DOI: 10.1021/ci8003682] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Areej M. Abu Hammad
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Mutasem O. Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
| |
Collapse
|
35
|
Kortagere S, Krasowski MD, Ekins S. The importance of discerning shape in molecular pharmacology. Trends Pharmacol Sci 2009; 30:138-47. [PMID: 19187977 PMCID: PMC2854656 DOI: 10.1016/j.tips.2008.12.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 11/27/2008] [Accepted: 12/02/2008] [Indexed: 11/24/2022]
Abstract
Shape is a fundamentally important molecular feature that often determines the fate of a compound in terms of molecular interactions with preferred and non-preferred biological targets. Complementarity of binding in small-molecule-protein, peptide-receptor, antigen-antibody and protein-protein interactions is the key to life and survival and also to targeting molecules with bioactivity. We review the application of shape in various biological systems such as substrate recognition, ligand specificity or selectivity and antibody recognition in the context of computational methods such as docking, quantitative structure-activity relationships, classification models and similarity-search algorithms. These in silico pharmacology methods have recently demonstrated the importance and applicability of determining molecular shape in drug discovery, virtual screening and predictive toxicology. The results from recently published studies show that shape and shape-based descriptors are at least as useful as other traditional molecular descriptors.
Collapse
Affiliation(s)
- Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | | | | |
Collapse
|
36
|
Kirchmair J, Distinto S, Markt P, Schuster D, Spitzer GM, Liedl KR, Wolber G. How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. J Chem Inf Model 2009; 49:678-92. [DOI: 10.1021/ci8004226] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johannes Kirchmair
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Simona Distinto
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Patrick Markt
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Daniela Schuster
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Gudrun M. Spitzer
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Gerhard Wolber
- Department of Pharmaceutical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, Inte:Ligand Software-Entwicklungs- and Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria, and Institute of Theoretical Chemistry, Faculty of Chemistry and Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| |
Collapse
|
37
|
Vainio MJ, Puranen JS, Johnson MS. ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. J Chem Inf Model 2009; 49:492-502. [DOI: 10.1021/ci800315d] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mikko J. Vainio
- Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6A (BioCity), FI-20520 Turku, Finland
| | - J. Santeri Puranen
- Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6A (BioCity), FI-20520 Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Department of Biochemistry and Pharmacy, Åbo Akademi University, Tykistökatu 6A (BioCity), FI-20520 Turku, Finland
| |
Collapse
|
38
|
Proschak E, Zettl H, Tanrikulu Y, Weisel M, Kriegl J, Rau O, Schubert‐Zsilavecz M, Schneider G. From Molecular Shape to Potent Bioactive Agents I: Bioisosteric Replacement of Molecular Fragments. ChemMedChem 2009; 4:41-4. [DOI: 10.1002/cmdc.200800313] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ewgenij Proschak
- Goethe‐University, Institute of Organic Chemistry and Chemical Biology, LiFF/ZAFES, Siesmayerstr. 70, 60323 Frankfurt am Main (Germany), Fax: (+49) 69‐798‐24880
| | - Heiko Zettl
- Goethe‐University, Institute of Pharmaceutical Chemistry, Liff/ZAFES, Max‐von‐Laue‐Str. 9, 60438 Frankfurt am Main (Germany)
| | - Yusuf Tanrikulu
- Goethe‐University, Institute of Organic Chemistry and Chemical Biology, LiFF/ZAFES, Siesmayerstr. 70, 60323 Frankfurt am Main (Germany), Fax: (+49) 69‐798‐24880
| | - Martin Weisel
- Goethe‐University, Institute of Organic Chemistry and Chemical Biology, LiFF/ZAFES, Siesmayerstr. 70, 60323 Frankfurt am Main (Germany), Fax: (+49) 69‐798‐24880
| | - Jan M. Kriegl
- Boehringer‐Ingelheim Pharma GmbH & Co. KG, Department of Lead Discovery ‐ Computational Chemistry, Birkendorfer Str. 65, 88397 Biberach an der Riss (Germany)
| | - Oliver Rau
- Goethe‐University, Institute of Pharmaceutical Chemistry, Liff/ZAFES, Max‐von‐Laue‐Str. 9, 60438 Frankfurt am Main (Germany)
| | - Manfred Schubert‐Zsilavecz
- Goethe‐University, Institute of Pharmaceutical Chemistry, Liff/ZAFES, Max‐von‐Laue‐Str. 9, 60438 Frankfurt am Main (Germany)
| | - Gisbert Schneider
- Goethe‐University, Institute of Organic Chemistry and Chemical Biology, LiFF/ZAFES, Siesmayerstr. 70, 60323 Frankfurt am Main (Germany), Fax: (+49) 69‐798‐24880
| |
Collapse
|
39
|
|