1
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Abstract
Background: PRMT5 is an epigenetics-related enzyme, which plays a critical role in cancer development. Hence PRMT5 inhibition has been validated as a promising therapeutic strategy. Methods & Results: We synthesized a series of methylpiperazinyl derivatives as novel PRMT5 inhibitors that were achieved by scaffold-hopping from EPZ015666 by virtual screening followed by rational drug design. Among all compounds 43g, bearing a thiourea linker, showed antitumor activity across multiple cancer cell lines and reduced the level of symmetric arginine dimethylation of SmD3 dose-dependently. Moreover, 43g selectively inhibited PRMT5 among protein arginine methyltransferase isoforms. Further proteomics analysis revealed that 43g remarkably reduced the global arginine dimethylation level in a cellular context. Conclusion: This work provides new chemical templates for future structural optimization of PRMT5-related cancer treatments.
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2
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Yang S, Ye Q, Ding J, Yin, Lu A, Chen X, Hou T, Cao D. Current advances in ligand‐based target prediction. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Su‐Qing Yang
- Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan China
| | - Qing Ye
- College of Pharmaceutical Sciences Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University Hangzhou, Zhejiang China
| | - Jun‐Jie Ding
- Beijing Institute of Pharmaceutical Chemistry Beijing China
| | - Yin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital Central South University Changsha Hunan China
| | - Ai‐Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine Hong Kong Baptist University Hong Kong China
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital Central South University Changsha Hunan China
| | - Ting‐Jun Hou
- College of Pharmaceutical Sciences Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University Hangzhou, Zhejiang China
| | - Dong‐Sheng Cao
- Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan China
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine Hong Kong Baptist University Hong Kong China
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3
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Brown BP, Mendenhall J, Meiler J. BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping. J Chem Inf Model 2019; 59:689-701. [PMID: 30707580 DOI: 10.1021/acs.jcim.9b00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular alignment program. BCL::MolAlign accommodates ligand flexibility through a combination of pregenerated conformers and on-the-fly bond rotation. BCL::MolAlign converges on alignment poses by sampling the relative orientations of mutually matching atom pairs between molecules through Monte Carlo Metropolis sampling. Across six diverse ligand data sets, BCL::MolAlign flexible alignment outperforms MOE, ROCS, and FLEXS in recovering native ligand binding poses. Moreover, the BCL::MolAlign alignment score is more predictive of ligand activity than maximum common substructure similarity across 10 data sets. Finally, on a recently published benchmark set of 20 high quality congeneric ligand-protein complexes, BCL::MolAlign is able to recover a larger fraction of native binding poses than maximum common substructure-based alignment and RosettaLigand. BCL::MolAlign can be obtained as part of the Biology and Chemistry Library (BCL) software package freely with an academic license or can be accessed via Web server at http://meilerlab.org/index.php/servers/molalign .
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Affiliation(s)
- Benjamin P Brown
- Chemical and Physical Biology Program, Medical Scientist Training Program, Center for Structural Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States
| | - Jeffrey Mendenhall
- Department of Chemistry, Center for Structural Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States.,Departments of Pharmacology and Biomedical Informatics , Vanderbilt University , Nashville , Tennessee 37212 , United States
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4
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Cross JB. Methods for Virtual Screening of GPCR Targets: Approaches and Challenges. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1705:233-264. [PMID: 29188566 DOI: 10.1007/978-1-4939-7465-8_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Virtual screening (VS) has become an integral part of the drug discovery process and is a valuable tool for finding novel chemical starting points for GPCR targets. Ligand-based VS makes use of biochemical data for known, active compounds and has been applied successfully to many diverse GPCRs. Recent progress in GPCR X-ray crystallography has made it possible to incorporate detailed structural information into the VS process. This chapter outlines the latest VS techniques along with examples that highlight successful applications of these methods. Best practices for increasing the likelihood of VS success, as well as ongoing challenges, are also discussed.
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Affiliation(s)
- Jason B Cross
- University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.
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5
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Fradera X, Babaoglu K. Overview of Methods and Strategies for Conducting Virtual Small Molecule Screening. ACTA ACUST UNITED AC 2017; 9:196-212. [DOI: 10.1002/cpch.27] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xavier Fradera
- Modeling and Informatics, MRL, Merck & Co., Inc; Boston Massachusetts
| | - Kerim Babaoglu
- Modeling and Informatics, MRL, Merck & Co., Inc; West Point Pennsylvania
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6
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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.
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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.
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7
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Feng T, Chen W, Li D, Lin H, Liu F, Bao Q, Lei Y, Zhang X, Xu X, Guo X, You Q, Sun H. Identification of novel JMJD2A inhibitor scaffold using shape and electrostatic similarity search combined with docking method and MM-GBSA approach. RSC Adv 2015. [DOI: 10.1039/c5ra11896d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We present a hierarchical workflow combining shape- and electrostatic-based virtual screening for the identification of novel Jumonji domain-containing protein 2A (JMJD2A) inhibitors.
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8
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García-Sosa AT, Maran U. Improving the use of ranking in virtual screening against HIV-1 integrase with triangular numbers and including ligand profiling with antitargets. J Chem Inf Model 2014; 54:3172-85. [PMID: 25303089 DOI: 10.1021/ci500300u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A delicate balance exists between a drug molecule's toxicity and its activity. Indeed, efficacy, toxicity, and side effect problems are a common cause for the termination of drug candidate compounds and development projects. To address this, an antitarget interaction profile is built and combined with virtual screening and cross docking for new inhibitors of HIV-1 integrase, in order to consider possible off-target interactions as early as possible in a drug or hit discovery program. New ranking techniques using triangular numbers improve ranking information on the compounds and recovery of known inhibitors into the top compounds using different docking programs. This improved ranking arises from using consensus of ranks between docking programs and ligand efficiencies to derive a new rank, instead of using absolute score values, or average of ranks. The triangular number rerank also allowed the objective combination of results from several protein targets or screen conditions and several programs. Triangular number reranking conserves more information than other reranking methods such as average of scores or averages of ranks. In addition, the use of triangular numbers for reranking makes possible the use of thresholds with a justified leeway based on the number of available known inhibitors, so that the majority of the compounds above the threshold in ranks compare to the compounds that have known experimentally determined biological activity. The battery of anti- or off-targets can be tailored to specific molecular or drug design challenges. In silico filters can thus be deployed in successive stages, for prefiltering, activity profiling, and for further analysis and triaging of libraries of compounds.
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9
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Focused chemical libraries--design and enrichment: an example of protein-protein interaction chemical space. Future Med Chem 2014; 6:1291-307. [PMID: 24773599 DOI: 10.4155/fmc.14.57] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
One of the many obstacles in the development of new drugs lies in the limited number of therapeutic targets and in the quality of screening collections of compounds. In this review, we present general strategies for building target-focused chemical libraries with a particular emphasis on protein-protein interactions (PPIs). We describe the chemical spaces spanned by nine commercially available PPI-focused libraries and compare them to our 2P2I3D academic library, dedicated to orthosteric PPI modulators. We show that although PPI-focused libraries have been designed using different strategies, they share common subspaces. PPI inhibitors are larger and more hydrophobic than standard drugs; however, an effort has been made to improve the drug-likeness of focused chemical libraries dedicated to this challenging class of targets.
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10
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Kumar A, Ito A, Takemoto M, Yoshida M, Zhang KYJ. Identification of 1,2,5-oxadiazoles as a new class of SENP2 inhibitors using structure based virtual screening. J Chem Inf Model 2014; 54:870-80. [PMID: 24512059 DOI: 10.1021/ci4007134] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small ubiquitin like modifier (SUMO) specific proteases (SENPs) are cysteine proteases that carry out the proteolytic processing of SUMO from its pro form as well as the deconjugation of SUMO from substrate proteins. SENPs are attractive targets for drug discovery due to their crucial role in the development of various diseases. However, the SENPs inhibitor discovery efforts were limited, and only a few inhibitors or activity based probes have been identified until now. Here, we report a new class of SENP2 inhibitors identified by a combination of structure based virtual screening and quantitative FRET based assay. Our virtual screening protocol initially involves the identification of small molecules that have similar shape and electrostatic properties with the conjugate of SUMO1 C-terminal residues and substrate lysine. Molecular docking was then used to prioritize these small molecules for a FRET based assay that quantifies their SENP2 endopeptidase activity. The initial round of virtual screening followed by FRET based assay has enabled the identification of eight compounds with >40% SENP2 inhibition at 30 μM compound concentration. Five of these compounds belong to two scaffolds containing a 1,2,5-oxadiazole core that represent a novel class of SENP2 inhibitors. To improve the inhibitory potency and explore the structure-activity relationship of these two 1,2,5-oxadiazole scaffolds, structurally related compounds were identified in another round of virtual screening. The biological assay results confirmed SENP2 inhibitory activity of these two scaffolds. The most potent compound of each scaffold showed an IC50 of 5.9 and 3.7 μM. Most of the compounds also inhibited closely related isoform SENP1, while no detectable inhibition on other proteases, such as papain and trypsin, was observed. Our study suggests that 1,2,5-oxadiazoles could be used as a starting point for the development of novel therapeutic agents against various diseases targeting SENPs.
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Affiliation(s)
- Ashutosh Kumar
- Zhang Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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11
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12
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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.
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Affiliation(s)
- Haopeng Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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13
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Sirci F, Istyastono EP, Vischer HF, Kooistra AJ, Nijmeijer S, Kuijer M, Wijtmans M, Mannhold R, Leurs R, de Esch IJP, de Graaf C. Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints. J Chem Inf Model 2012; 52:3308-24. [DOI: 10.1021/ci3004094] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Francesco Sirci
- Laboratory for Chemometrics
and Chemoinformatics, Chemistry Department, University of Perugia, Via Elce di Sotto, 10, I-06123 Perugia Italy
| | - Enade P. Istyastono
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Molecular Modeling Division, Pharmaceutical
Technology Laboratory, Universitas Sanata Dharma, Yogyakarta, Indonesia
| | - Henry F. Vischer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Albert J. Kooistra
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Saskia Nijmeijer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Martien Kuijer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Maikel Wijtmans
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Raimund Mannhold
- Department of Laser Medicine,
Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Rob Leurs
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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14
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Finn PW, Morris GM. Shape-based similarity searching in chemical databases. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1128] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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15
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Dixit A, Verkhivker GM. Integrating ligand-based and protein-centric virtual screening of kinase inhibitors using ensembles of multiple protein kinase genes and conformations. J Chem Inf Model 2012; 52:2501-15. [PMID: 22992037 DOI: 10.1021/ci3002638] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The rapidly growing wealth of structural and functional information about kinase genes and kinase inhibitors that is fueled by a significant therapeutic role of this protein family provides a significant impetus for development of targeted computational screening approaches. In this work, we explore an ensemble-based, protein-centric approach that allows for simultaneous virtual ligand screening against multiple kinase genes and multiple kinase receptor conformations. We systematically analyze and compare the results of ligand-based and protein-centric screening approaches using both single-receptor and ensemble-based docking protocols. A panel of protein kinase targets that includes ABL, EGFR, P38, CDK2, TK, and VEGFR2 kinases is used in this comparative analysis. By applying various performance metrics we have shown that ligand-centric shape matching can provide an effective enrichment of active compounds outperforming single-receptor docking screening. However, ligand-based approaches can be highly sensitive to the choice of inhibitor queries. Employment of multiple inhibitor queries combined with parallel selection ranking criteria can improve the performance and efficiency of ligand-based virtual screening. We also demonstrated that replica-exchange Monte Carlo docking with kinome-based ensembles of multiple crystal structures can provide a superior early enrichment on the kinase targets. The central finding of this study is that incorporation of the template-based structural information about kinase inhibitors and protein kinase structures in diverse functional states can significantly enhance the overall performance and robustness of both ligand and protein-centric screening strategies. The results of this study may be useful in virtual screening of kinase inhibitors potentially offering a beneficial spectrum of therapeutic activities across multiple disease states.
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Affiliation(s)
- Anshuman Dixit
- Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, 2095 Constant Avenue, Lawrence, Kansas 66047, USA
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16
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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
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17
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AbdulHameed MDM, Chaudhury S, Singh N, Sun H, Wallqvist A, Tawa GJ. Exploring polypharmacology using a ROCS-based target fishing approach. J Chem Inf Model 2012; 52:492-505. [PMID: 22196353 DOI: 10.1021/ci2003544] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Polypharmacology has emerged as a new theme in drug discovery. In this paper, we studied polypharmacology using a ligand-based target fishing (LBTF) protocol. To implement the protocol, we first generated a chemogenomic database that links individual protein targets with a specified set of drugs or target representatives. Target profiles were then generated for a given query molecule by computing maximal shape/chemistry overlap between the query molecule and the drug sets assigned to each protein target. The overlap was computed using the program ROCS (Rapid Overlay of Chemical Structures). We validated this approach using the Directory of Useful Decoys (DUD). DUD contains 2950 active compounds, each with 36 property-matched decoys, against 40 protein targets. We chose a set of known drugs to represent each DUD target, and we carried out ligand-based virtual screens using data sets of DUD actives seeded into DUD decoys for each target. We computed Receiver Operator Characteristic (ROC) curves and associated area under the curve (AUC) values. For the majority of targets studied, the AUC values were significantly better than for the case of a random selection of compounds. In a second test, the method successfully identified off-targets for drugs such as rimantadine, propranolol, and domperidone that were consistent with those identified by recent experiments. The results from our ROCS-based target fishing approach are promising and have potential application in drug repurposing for single and multiple targets, identifying targets for orphan compounds, and adverse effect prediction.
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Affiliation(s)
- Mohamed Diwan M AbdulHameed
- Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, USA.
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18
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Sastry GM, Dixon SL, Sherman W. Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring. J Chem Inf Model 2011; 51:2455-66. [DOI: 10.1021/ci2002704] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Madhavi Sastry
- Schrödinger, Sanali Infopark, 8-2-120/113, Banjara Hills, Hyderabad 500034, Andhra Pradesh, India
| | - Steven L. Dixon
- Schrödinger, 120 West 45th Street, New York, New York 10036, United States
| | - Woody Sherman
- Schrödinger, 120 West 45th Street, New York, New York 10036, United States
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19
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Pérez-Nueno VI, Ritchie DW. Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening. J Chem Inf Model 2011; 51:1233-48. [DOI: 10.1021/ci100492r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - David W. Ritchie
- INRIA Nancy, LORIA, 615 rue du Jardin Botanique, 54600 Villers-lès-Nancy, France
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20
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Planesas JM, Claramunt RM, Teixidó J, Borrell JI, Pérez-Nueno VI. Improving VEGFR-2 Docking-Based Screening by Pharmacophore Postfiltering and Similarity Search Postprocessing. J Chem Inf Model 2011; 51:777-87. [DOI: 10.1021/ci1002763] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jesús M. Planesas
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Senda del Rey 9, E-28040 Madrid, Spain
| | - Rosa M. Claramunt
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias, UNED, Senda del Rey 9, E-28040 Madrid, Spain
| | - Jordi Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - José I. Borrell
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Violeta I. Pérez-Nueno
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain
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21
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Brylinski M, Skolnick J. Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J Chem Inf Model 2011; 50:1839-54. [PMID: 20853887 DOI: 10.1021/ci100235n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The growing interest in the identification of kinase inhibitors, promising therapeutics in the treatment of many diseases, has created a demand for the structural characterization of the entire human kinome. At the outset of the drug development process, the lead-finding stage, approaches that enrich the screening library with bioactive compounds are needed. Here, protein structure based methods can play an important role, but despite structural genomics efforts, it is unlikely that the three-dimensional structures of the entire kinome will be available soon. Therefore, at the proteome level, structure-based approaches must rely on predicted models, with a key issue being their utility in virtual ligand screening. In this study, we employ the recently developed FINDSITE/Q-Dock ligand homology modeling approach, which is well-suited for proteome-scale applications using predicted structures, to provide extensive structural and functional characterization of the human kinome. Specifically, we construct structure models for the human kinome; these are subsequently subject to virtual screening against a library of more than 2 million compounds. To rank the compounds, we employ a hierarchical approach that combines ligand- and structure-based filters. Modeling accuracy is carefully validated using available experimental data with particularly encouraging results found for the ability to identify, without prior knowledge, specific kinase inhibitors. More generally, the modeling procedure results in a large number of predicted molecular interactions between kinases and small ligands that should be of practical use in the development of novel inhibitors. The data set is freely available to the academic community via a user-friendly Web interface at http://cssb.biology.gatech.edu/kinomelhm/ as well as at the ZINC Web site ( http://zinc.docking.org/applications/2010Apr/Brylinski-2010.tar.gz ).
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Affiliation(s)
- Michal Brylinski
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
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22
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Majeed Y, Agarwal AK, Naylor J, Seymour VAL, Jiang S, Muraki K, Fishwick CWG, Beech DJ. Cis-isomerism and other chemical requirements of steroidal agonists and partial agonists acting at TRPM3 channels. Br J Pharmacol 2011; 161:430-41. [PMID: 20735426 DOI: 10.1111/j.1476-5381.2010.00892.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND AND PURPOSE The transient receptor potential melastatin-3 (TRPM3) channel forms calcium-permeable, non-selective, cationic channels that are stimulated by pregnenolone sulphate (PregS). Here, we aimed to define chemical requirements of this acute steroid action and potentially reveal novel stimulators with physiological relevance. EXPERIMENTAL APPROACH We used TRPM3 channels over-expressed in HEK 293 cells, with intracellular calcium measurement and whole-cell patch-clamp recording techniques. KEY RESULTS The stimulation of TRPM3 channels was confined to PregS and closely related steroids and not mimicked by other major classes of steroids, including progesterone. Relatively potent stimulation of TRPM3-dependent calcium entry was observed. A sulphate group positioned at ring A was important for strong stimulation but more striking was the requirement for a cis (beta) configuration of the side group, revealing previously unrecognized stereo-selectivity and supporting existence of a specific binding site. A cis-oriented side group on ring A was not the only feature necessary for high activity because loss of the double bond in ring B reduced potency and loss of the acetyl group at ring D reduced efficacy and potency. Weak steroid stimulators of TRPM3 channels inhibited effects of PregS, suggesting partial agonism. In silico screening of chemical libraries for non-steroid modulators of TRPM3 channels revealed the importance of the steroid backbone for stimulatory effects. CONCLUSIONS AND IMPLICATIONS Our data defined some of the chemical requirements for acute stimulation of TRPM3 channels by steroids, supporting the existence of a specific and unique steroid binding site. Epipregnanolone sulphate was identified as a novel TRPM3 channel stimulator.
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Affiliation(s)
- Y Majeed
- Multidisciplinary Cardiovascular Research Centre and Institute of Membrane & Systems Biology, Faculties of Biological Sciences, University of Leeds, Leeds, UK
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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.
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Affiliation(s)
- Jerry O Ebalunode
- Department of Pharmaceutical Sciences, BRITE Institute, North Carolina Center University, Durham, NC, USA.
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