1
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Li M, Hu J, Wang Y, Li Y, Zhang L, Liu Z. Challenging Reverse Screening: A Benchmark Study for Comprehensive Evaluation. Mol Inform 2021; 41:e2100063. [PMID: 34787366 DOI: 10.1002/minf.202100063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022]
Abstract
As an efficient way of computational target prediction, reverse docking can find not only potential targets but also binding modes for a query ligand. Though the number of available docking tools keeps expanding, there is still not a comprehensive evaluation study which can uncover the advantages and limitations of these strategies in the research field of computational target-fishing. In this study, we propose a brand-new evaluation dataset tailor-made for reverse docking, which is composed of a true positive set (the core set) and two negative sets (the similar decoy set and the dissimilar decoy set). The proposed evaluation dataset can assess the prediction performance of docking tools as various values affected by varying degrees of inter-target ranking bias. The performance of four classical docking programs (AutoDock, AutoDock Vina, Glide and GOLD) was evaluated utilizing our dataset, and a biased prediction performance was observed regarding binding site properties. The results demonstrated that Glide (SP) and Glide(XP) had the best capacity to find true targets whether there was inter-target ranking bias or not.
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Affiliation(s)
- Mingna Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, 100191, Beijing, P.R. China
| | - Jianxing Hu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, 100191, Beijing, P.R. China
| | - Yanxing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, 100191, Beijing, P.R. China
| | - Yibo Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Yiheyuan Road 5, Haidian District, Beijing, P.R. China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, 100191, Beijing, P.R. China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xueyuan Road 38, Haidian District, 100191, Beijing, P.R. China
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2
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Bhardwaj RM, Reutzel-Edens SM, Johnston BF, Florence AJ. A random forest model for predicting crystal packing of olanzapine solvates. CrystEngComm 2018. [DOI: 10.1039/c8ce00261d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A random forest (RF) classification model obtained from physicochemical properties of solvents and crystal structures of olanzapine has for the first time enabled the prediction of 3-D crystal packings of solvates. A novel solvate was obtained by targeted crystallization from the solvent identified by RF model.
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Affiliation(s)
- Rajni M. Bhardwaj
- Strathclyde Institute of Pharmacy and Biomedical Sciences
- University of Strathclyde
- Glasgow G4 0RE
- UK
- Eli Lilly and Company
| | | | - Blair F. Johnston
- Strathclyde Institute of Pharmacy and Biomedical Sciences
- University of Strathclyde
- Glasgow G4 0RE
- UK
- EPSRC Centre for Continuous Manufacturing and Crystallisation (CMAC)
| | - Alastair J. Florence
- Strathclyde Institute of Pharmacy and Biomedical Sciences
- University of Strathclyde
- Glasgow G4 0RE
- UK
- EPSRC Centre for Continuous Manufacturing and Crystallisation (CMAC)
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3
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Montanari F, Zdrazil B. How Open Data Shapes In Silico Transporter Modeling. Molecules 2017; 22:molecules22030422. [PMID: 28272367 PMCID: PMC5553104 DOI: 10.3390/molecules22030422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/05/2022] Open
Abstract
Chemical compound bioactivity and related data are nowadays easily available from open data sources and the open medicinal chemistry literature for many transmembrane proteins. Computational ligand-based modeling of transporters has therefore experienced a shift from local (quantitative) models to more global, qualitative, predictive models. As the size and heterogeneity of the data set rises, careful data curation becomes even more important. This includes, for example, not only a tailored cutoff setting for the generation of binary classes, but also the proper assessment of the applicability domain. Powerful machine learning algorithms (such as multi-label classification) now allow the simultaneous prediction of multiple related targets. However, the more complex, the less interpretable these models will get. We emphasize that transmembrane transporters are very peculiar, some of which act as off-targets rather than as real drug targets. Thus, careful selection of the right modeling technique is important, as well as cautious interpretation of results. We hope that, as more and more data will become available, we will be able to ameliorate and specify our models, coming closer towards function elucidation and the development of safer medicine.
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Affiliation(s)
- Floriane Montanari
- Pharmacoinformatics Research Group, Department of Pharmaceutical Chemistry, University of Vienna, A-1090 Vienna, Austria.
| | - Barbara Zdrazil
- Pharmacoinformatics Research Group, Department of Pharmaceutical Chemistry, University of Vienna, A-1090 Vienna, Austria.
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First protein drug target’s appraisal of lead-likeness descriptors to unfold the intervening chemical space. J Mol Graph Model 2017; 72:272-282. [DOI: 10.1016/j.jmgm.2016.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/24/2016] [Accepted: 12/29/2016] [Indexed: 11/22/2022]
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Wang J, Yang Y, Li Y, Wang Y. Computational Study Exploring the Interaction Mechanism of Benzimidazole Derivatives as Potent Cattle Bovine Viral Diarrhea Virus Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:5941-5950. [PMID: 27355875 DOI: 10.1021/acs.jafc.6b01067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bovine viral diarrhea virus (BVDV) infections are prevailing in cattle populations on a worldwide scale. The BVDV RNA-dependent RNA polymerase (RdRp), as a promising target for new anti-BVDV drug development, has attracted increasing attention. To explore the interaction mechanism of 65 benzimidazole scaffold-based derivatives as BVDV inhibitors, presently, a computational study was performed based on a combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations. The resultant optimum CoMFA and CoMSIA models present proper reliabilities and strong predictive abilities (with Q(2) = 0. 64, R(2)ncv = 0.93, R(2)pred = 0.80 and Q(2) = 0. 65, R(2)ncv = 0.98, R(2)pred = 0.86, respectively). In addition, there was good concordance between these models, molecular docking, and MD results. Moreover, the MM-PBSA energy analysis reveals that the major driving force for ligand binding is the polar solvation contribution term. Hopefully, these models and the obtained findings could offer better understanding of the interaction mechanism of BVDV inhibitors as well as benefit the new discovery of more potent BVDV inhibitors.
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Affiliation(s)
- Jinghui Wang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yinfeng Yang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yan Li
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology , Dalian, Liaoning 116024, P. R. China
| | - Yonghua Wang
- Key Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Ministry of Education, Shihezi University , Shihezi 832002, China
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Tian S, Wang J, Li Y, Li D, Xu L, Hou T. The application of in silico drug-likeness predictions in pharmaceutical research. Adv Drug Deliv Rev 2015; 86:2-10. [PMID: 25666163 DOI: 10.1016/j.addr.2015.01.009] [Citation(s) in RCA: 258] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 01/14/2015] [Accepted: 01/29/2015] [Indexed: 02/08/2023]
Abstract
The concept of drug-likeness, established from the analyses of the physiochemical properties or/and structural features of existing small organic drugs or/and drug candidates, has been widely used to filter out compounds with undesirable properties, especially poor ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiles. Here, we summarize various approaches for drug-likeness evaluations, including simple rules/filters based on molecular properties/structures and quantitative prediction models based on sophisticated machine learning methods, and provide a comprehensive review of recent advances in this field. Moreover, the strengths and weaknesses of these approaches are briefly outlined. Finally, the drug-likeness analyses of natural products and traditional Chinese medicines (TCM) are discussed.
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Affiliation(s)
- Sheng Tian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Junmei Wang
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, United States
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
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7
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Bhardwaj RM, Johnston A, Johnston BF, Florence AJ. A random forest model for predicting the crystallisability of organic molecules. CrystEngComm 2015. [DOI: 10.1039/c4ce02403f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Wang J, Li Y, Yang Y, Zhang J, Du J, Zhang S, Yang L. Profiling the interaction mechanism of indole-based derivatives targeting the HIV-1 gp120 receptor. RSC Adv 2015. [DOI: 10.1039/c5ra04299b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A glycoprotein exposed on a viral surface, human immunodeficiency virus type 1 (HIV-1) gp120 is essential for virus entry into cells as it plays a vital role in seeking out specific cell surface receptors for entry.
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Affiliation(s)
- Jinghui Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Yinfeng Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Jingxiao Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Jian Du
- Institute of Chemical Process Systems Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Shuwei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Ling Yang
- Laboratory of Pharmaceutical Resource Discovery
- Dalian Institute of Chemical Physics
- Graduate School of the Chinese Academy of Sciences
- Dalian
- China
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Vogel SM, Bauer MR, Boeckler FM. DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions. J Chem Inf Model 2011; 51:2650-65. [DOI: 10.1021/ci2001549] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon M. Vogel
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Matthias R. Bauer
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Frank M. Boeckler
- Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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Han C, Zhang J, Zheng M, Xiao Y, Li Y, Liu G. An integrated drug-likeness study for bicyclic privileged structures: from physicochemical properties to in vitro ADME properties. Mol Divers 2011; 15:857-76. [DOI: 10.1007/s11030-011-9317-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 04/15/2011] [Indexed: 11/24/2022]
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11
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Yu MJ. Natural Product-Like Virtual Libraries: Recursive Atom-Based Enumeration. J Chem Inf Model 2011; 51:541-57. [DOI: 10.1021/ci1002087] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Melvin J. Yu
- Eisai, Inc. 4 Corporate Drive, Andover, Massachusetts 01810, United States
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12
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Abstract
Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization. Historically, topological fingerprints were developed for substructure and similarity searching. ECFPs were developed specifically for structure-activity modeling. ECFPs are circular fingerprints with a number of useful qualities: they can be very rapidly calculated; they are not predefined and can represent an essentially infinite number of different molecular features (including stereochemical information); their features represent the presence of particular substructures, allowing easier interpretation of analysis results; and the ECFP algorithm can be tailored to generate different types of circular fingerprints, optimized for different uses. While the use of ECFPs has been widely adopted and validated, a description of their implementation has not previously been presented in the literature.
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13
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Affiliation(s)
- Oleg Ursu
- Division of Biocomputing, Department of Biochemistry and Molecular Biology and University of New Mexico (UNM) Center for Molecular Discovery, UNM School of Medicine, MSC11 6145, Albuquerque, New Mexico 87131
| | - Tudor I. Oprea
- Division of Biocomputing, Department of Biochemistry and Molecular Biology and University of New Mexico (UNM) Center for Molecular Discovery, UNM School of Medicine, MSC11 6145, Albuquerque, New Mexico 87131
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14
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Geppert H, Vogt M, Bajorath J. Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation. J Chem Inf Model 2010; 50:205-16. [PMID: 20088575 DOI: 10.1021/ci900419k] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hanna Geppert
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universitat, Dahlmannstrasse 2, D-53113 Bonn, Germany
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15
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Mensch J, Oyarzabal J, Mackie C, Augustijns P. In vivo, in vitro and in silico methods for small molecule transfer across the BBB. J Pharm Sci 2009; 98:4429-68. [DOI: 10.1002/jps.21745] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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16
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Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. Quantifying biogenic bias in screening libraries. Nat Chem Biol 2009; 5:479-83. [PMID: 19483698 PMCID: PMC2783405 DOI: 10.1038/nchembio.180] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 04/10/2009] [Indexed: 01/07/2023]
Abstract
In lead discovery, libraries of 106 molecules are screened for biological activity. Given the over 1060 drug-like molecules thought possible, such screens might never succeed. That they do, even occasionally, implies a biased selection of library molecules. Here a method is developed to quantify the bias in screening libraries towards biogenic molecules. With this approach, we consider what is missing from screening libraries and how they can be optimized.
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Affiliation(s)
- Jérôme Hert
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
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17
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Rohrer SG, Baumann K. Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data. J Chem Inf Model 2009; 49:169-84. [PMID: 19434821 DOI: 10.1021/ci8002649] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Refined nearest neighbor analysis was recently introduced for the analysis of virtual screening benchmark data sets. It constitutes a technique from the field of spatial statistics and provides a mathematical framework for the nonparametric analysis of mapped point patterns. Here, refined nearest neighbor analysis is used to design benchmark data sets for virtual screening based on PubChem bioactivity data. A workflow is devised that purges data sets of compounds active against pharmaceutically relevant targets from unselective hits. Topological optimization using experimental design strategies monitored by refined nearest neighbor analysis functions is applied to generate corresponding data sets of actives and decoys that are unbiased with regard to analogue bias and artificial enrichment. These data sets provide a tool for Maximum Unbiased Validation (MUV) of virtual screening methods. The data sets and a software package implementing the MUV design workflow are freely available at http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html.
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Affiliation(s)
- Sebastian G Rohrer
- Institute of Pharmaceutical Chemistry, Beethovenstrasse 55, Braunschweig University of Technology, 38106 Braunschweig, Germany
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Wong WW, Burkowski FJ. A constructive approach for discovering new drug leads: Using a kernel methodology for the inverse-QSAR problem. J Cheminform 2009; 1:4. [PMID: 20142987 PMCID: PMC2816860 DOI: 10.1186/1758-2946-1-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Accepted: 04/28/2009] [Indexed: 12/04/2022] Open
Abstract
Background
The inverse-QSAR problem seeks to find a new molecular descriptor from which one can recover the structure of a molecule that possess a desired activity or property. Surprisingly, there are very few papers providing solutions to this problem. It is a difficult problem because the molecular descriptors involved with the inverse-QSAR algorithm must adequately address the forward QSAR problem for a given biological activity if the subsequent recovery phase is to be meaningful. In addition, one should be able to construct a feasible molecule from such a descriptor. The difficulty of recovering the molecule from its descriptor is the major limitation of most inverse-QSAR methods. Results
In this paper, we describe the reversibility of our previously reported descriptor, the vector space model molecular descriptor (VSMMD) based on a vector space model that is suitable for kernel studies in QSAR modeling. Our inverse-QSAR approach can be described using five steps: (1) generate the VSMMD for the compounds in the training set; (2) map the VSMMD in the input space to the kernel feature space using an appropriate kernel function; (3) design or generate a new point in the kernel feature space using a kernel feature space algorithm; (4) map the feature space point back to the input space of descriptors using a pre-image approximation algorithm; (5) build the molecular structure template using our VSMMD molecule recovery algorithm. Conclusion
The empirical results reported in this paper show that our strategy of using kernel methodology for an inverse-Quantitative Structure-Activity Relationship is sufficiently powerful to find a meaningful solution for practical problems. Electronic supplementary material The online version of this article (doi:10.1186/1758-2946-1-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William Wl Wong
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Rohrer SG, Baumann K. Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics. J Chem Inf Model 2008; 48:704-18. [DOI: 10.1021/ci700099u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian G. Rohrer
- Institute of Pharmaceutical Chemistry, Beethovenstrasse 55, Braunschweig University of Technology, 38106 Braunschweig, Germany
| | - Knut Baumann
- Institute of Pharmaceutical Chemistry, Beethovenstrasse 55, Braunschweig University of Technology, 38106 Braunschweig, Germany
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Brown RD, Rogers D. Is learning drugs the same as learning non-drugs? Chem Cent J 2008. [PMCID: PMC4236220 DOI: 10.1186/1752-153x-2-s1-s5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Vistoli G, Pedretti A, Testa B. Assessing drug-likeness--what are we missing? Drug Discov Today 2008; 13:285-94. [PMID: 18405840 DOI: 10.1016/j.drudis.2007.11.007] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 11/19/2007] [Accepted: 11/22/2007] [Indexed: 11/17/2022]
Abstract
The concept of drug-likeness helps to optimise pharmacokinetic and pharmaceutical properties, for example, solubility, chemical stability, bioavailability and distribution profile. A number of molecular descriptors have emerged as reasonably informative and predictive, for example, the Rule-of-Five. Here, we review some current approaches, then discuss their major shortcoming, namely the static nature of the structural features and physicochemical properties they encode. As we demonstrate, molecules are not 'frozen statues' but 'dancing ballerinas', and several of their computable physicochemical properties are conformation-dependent and lead to the concept of property spaces. Molecular sensitivity (namely, how much a given computable physicochemical property varies as a function of flexibility) appears as a promising descriptor to encode some of the information contained in molecular property spaces.
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Affiliation(s)
- Giulio Vistoli
- Istituto di Chimica Farmaceutica Pietro Pratesi, Facoltà di Farmacia, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
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