In silico approaches and tools for the prediction of drug metabolism and fate: A review
暂无分享,去创建一个
Ren Jun | Dokyun Na | Myeong-Sang Yu | Sayada Reemsha Kazmi | Chanjin Jung | D. Na | Myeong-Sang Yu | Chanjin Jung | Ren Jun
[1] Carolina Horta Andrade,et al. Advances in methods for predicting phase I metabolism of polyphenols. , 2014, Current drug metabolism.
[2] J. Bajorath,et al. Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.
[3] H Kubinyi,et al. Chance favors the prepared mind--from serendipity to rational drug design. , 1999, Journal of receptor and signal transduction research.
[4] Thierry Langer,et al. Predicting drug metabolism induction in silico. , 2006, Current topics in medicinal chemistry.
[5] David S. Wishart,et al. HMDB: a knowledgebase for the human metabolome , 2008, Nucleic Acids Res..
[6] R. Cramer,et al. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.
[7] J. Gready,et al. Combining docking and molecular dynamic simulations in drug design , 2006, Medicinal research reviews.
[8] Byunghan Lee,et al. Deep learning in bioinformatics , 2016, Briefings Bioinform..
[9] G. Wilkinson,et al. Drug metabolism and variability among patients in drug response. , 2005, The New England journal of medicine.
[10] C. Andrade,et al. In silico prediction of drug metabolism by P450. , 2014, Current drug metabolism.
[11] J. Blake,et al. On the Connection between Chemical Constitution and Physiological Action , 1886, Nature.
[12] Aurélien Grosdidier,et al. Fast docking using the CHARMM force field with EADock DSS , 2011, J. Comput. Chem..
[13] Thomas Fox,et al. Machine learning techniques for in silico modeling of drug metabolism. , 2006, Current topics in medicinal chemistry.
[14] T. Akabane,et al. A practical and direct comparison of intrinsic metabolic clearance of several non-CYP enzyme substrates in freshly isolated and cryopreserved hepatocytes. , 2012, Drug metabolism and pharmacokinetics.
[15] Mitchell A. Lazar,et al. De-Meaning of Metabolism , 2012, Science.
[16] Vladimir B Bajic,et al. In silico toxicology: computational methods for the prediction of chemical toxicity , 2016, Wiley interdisciplinary reviews. Computational molecular science.
[17] Jiunn H. Lin,et al. Role of P-Glycoprotein in Pharmacokinetics , 2003, Clinical pharmacokinetics.
[18] U. Tillmann,et al. A systematic approach for evaluating the quality of experimental toxicological and ecotoxicological data. , 1997, Regulatory toxicology and pharmacology : RTP.
[19] Alex M. Clark,et al. Accessible Machine Learning Approaches for Toxicology , 2018 .
[20] David S. Wishart,et al. DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..
[21] Shufeng Zhou. Drugs behave as substrates, inhibitors and inducers of human cytochrome P450 3A4. , 2008, Current drug metabolism.
[22] Michael J. Keiser,et al. Relating protein pharmacology by ligand chemistry , 2007, Nature Biotechnology.
[23] Lu Zhang,et al. From machine learning to deep learning: progress in machine intelligence for rational drug discovery. , 2017, Drug discovery today.
[24] E. Ovidi,et al. Natural products for human health: an historical overview of the drug discovery approaches , 2018, Natural product research.
[25] B. Ring,et al. In vitro methods for assessing human hepatic drug metabolism: their use in drug development. , 1993, Drug metabolism reviews.
[26] Helmut Segner,et al. Data quality assessment for in silico methods: A survey of approaches and needs , 2010 .
[27] Ying Xue,et al. Quantitative structure–activity relationship study of influenza virus neuraminidase A/PR/8/34 (H1N1) inhibitors by genetic algorithm feature selection and support vector regression , 2013 .
[28] C. Hansch,et al. p-σ-π Analysis. A Method for the Correlation of Biological Activity and Chemical Structure , 1964 .
[29] N. Meanwell,et al. The expanding role of prodrugs in contemporary drug design and development , 2018, Nature Reviews Drug Discovery.
[30] Antonio Lavecchia,et al. Machine-learning approaches in drug discovery: methods and applications. , 2015, Drug discovery today.
[31] Samina Kausar,et al. An automated framework for QSAR model building , 2018, Journal of Cheminformatics.
[32] S. Hochreiter,et al. DeepTox: Toxicity prediction using deep learning , 2017 .
[33] Yong Wang,et al. Site of metabolism prediction for six biotransformations mediated by cytochromes P450 , 2009, Bioinform..
[34] Eric T. Kim,et al. How does a drug molecule find its target binding site? , 2011, Journal of the American Chemical Society.
[35] Hongbin Yang,et al. Multiclassification Prediction of Enzymatic Reactions for Oxidoreductases and Hydrolases Using Reaction Fingerprints and Machine Learning Methods , 2018, J. Chem. Inf. Model..
[36] Emilio Benfenati,et al. In silico methods to predict drug toxicity. , 2013, Current opinion in pharmacology.
[37] Lu Tan,et al. Software for Metabolism Prediction , 2014 .
[38] Lydia E. Kavraki,et al. Molecular docking: a problem with thousands of degrees of freedom , 2001, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164).
[39] Chris Oostenbrink,et al. Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450 , 2008 .
[40] D. Koshland. The Key–Lock Theory and the Induced Fit Theory , 1995 .
[41] Olexandr Isayev,et al. Transforming Computational Drug Discovery with Machine Learning and AI. , 2018, ACS medicinal chemistry letters.
[42] Vinícius Gonçalves Maltarollo,et al. Applying machine learning techniques for ADME-Tox prediction: a review , 2015, Expert opinion on drug metabolism & toxicology.
[43] Simone Brogi,et al. Identification of novel fluorescent probes preventing PrPSc replication in prion diseases. , 2017, European journal of medicinal chemistry.
[44] Guo-Wei Wei,et al. Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks , 2017, J. Chem. Inf. Model..
[45] Russ B Altman,et al. Machine learning in chemoinformatics and drug discovery. , 2018, Drug discovery today.
[46] R. Kream,et al. Endogenous morphine: up-to-date review 2011. , 2012, Folia biologica.
[47] Arthur J. Olson,et al. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..
[48] R L Nation,et al. Characterization of the human cytochrome P450 enzymes involved in the metabolism of dihydrocodeine. , 2003, British journal of clinical pharmacology.
[49] Yoshihiro Yamanishi,et al. Prediction of drug–target interaction networks from the integration of chemical and genomic spaces , 2008, ISMB.
[50] Saeed Alqahtani,et al. In silico ADME-Tox modeling: progress and prospects , 2017, Expert opinion on drug metabolism & toxicology.
[51] G. Mangiatordi,et al. Applicability Domain for QSAR models: where theory meets reality , 2016 .
[52] J C Gertrudes,et al. Machine learning techniques and drug design. , 2012, Current medicinal chemistry.
[53] D. Yin,et al. Using molecular docking-based binding energy to predict toxicity of binary mixture with different binding sites. , 2013, Chemosphere.
[54] Juan M. Luco,et al. QSAR Based on Multiple Linear Regression and PLS Methods for the Anti-HIV Activity of a Large Group of HEPT Derivatives , 1997, J. Chem. Inf. Comput. Sci..
[55] Vladimir Poroikov,et al. SOMP: web server for in silico prediction of sites of metabolism for drug-like compounds , 2015, Bioinform..
[56] M. Schwab,et al. Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation. , 2013, Pharmacology & therapeutics.
[57] Taeho Jo,et al. Improving Protein Fold Recognition by Deep Learning Networks , 2015, Scientific Reports.
[58] Raghuraman Venkatapathy,et al. Developmental toxicity prediction. , 2013, Methods in molecular biology.
[59] Rona R. Ramsay,et al. A perspective on multi-target drug discovery and design for complex diseases , 2018, Clinical and Translational Medicine.
[60] Yi Wang,et al. In silico search of putative adverse drug reaction related proteins as a potential tool for facilitating drug adverse effect prediction. , 2006, Toxicology letters.
[61] Yojiro Sakiyama,et al. Predicting human liver microsomal stability with machine learning techniques. , 2008, Journal of molecular graphics & modelling.
[62] Nic Fleming,et al. How artificial intelligence is changing drug discovery , 2018, Nature.
[63] Zhiwei Cao,et al. Insight into potential toxicity mechanisms of melamine: an in silico study. , 2011, Toxicology.
[64] Z R Li,et al. Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins. , 2007, Journal of pharmaceutical sciences.
[65] Andrew A Somogyi,et al. Advances in drug metabolism and pharmacogenetics research in Australia , 2017, Pharmacological research.
[66] Christopher R. Corbeil,et al. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go , 2008, British journal of pharmacology.
[67] Jian Peng,et al. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields , 2015, Scientific Reports.
[68] A. Nafziger,et al. Pharmacogenetics affects dosing, efficacy, and toxicity of cytochrome P450-metabolized drugs. , 2002, The American journal of medicine.
[69] Nidhi Singh,et al. Integrated machine learning, molecular docking and 3D-QSAR based approach for identification of potential inhibitors of trypanosomal N-myristoyltransferase. , 2016, Molecular bioSystems.
[70] Jianlin Cheng,et al. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[71] Charles C. Persinger,et al. How to improve R&D productivity: the pharmaceutical industry's grand challenge , 2010, Nature Reviews Drug Discovery.
[72] H. Carlson. Protein flexibility and drug design: how to hit a moving target. , 2002, Current opinion in chemical biology.
[73] Michael I. Jordan,et al. Machine learning: Trends, perspectives, and prospects , 2015, Science.
[74] Li Li,et al. In silico prediction of cytochrome P450-mediated drug metabolism. , 2011, Combinatorial chemistry & high throughput screening.
[75] D. M. Ryan,et al. Rational design of potent sialidase-based inhibitors of influenza virus replication , 1993, Nature.
[76] Mingshe Zhu,et al. In vitro and in vivo human metabolism of a new synthetic cannabinoid NM-2201 (CBL-2201) , 2016, Forensic Toxicology.
[77] Petra Schneider,et al. Generative Recurrent Networks for De Novo Drug Design , 2017, Molecular informatics.
[78] William J. Allen,et al. DOCK 6: Impact of new features and current docking performance , 2015, J. Comput. Chem..
[79] Alka Kurup. C-QSAR: a database of 18,000 QSARs and associated biological and physical data , 2003, J. Comput. Aided Mol. Des..
[80] Y. Z. Chen,et al. Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach. , 2001, Journal of molecular graphics & modelling.
[81] Jonathan D. Hirst,et al. New approaches to QSAR: Neural networks and machine learning , 1993 .
[82] Hao Zhu,et al. Experimental Errors in QSAR Modeling Sets: What We Can Do and What We Cannot Do , 2017, ACS omega.
[83] Antje Chang,et al. BRENDA , the enzyme database : updates and major new developments , 2003 .
[84] Hui Zhang,et al. Applications of Machine Learning Methods in Drug Toxicity Prediction. , 2018, Current topics in medicinal chemistry.
[85] Michelle L Coote,et al. Molecular dynamics-driven drug discovery: leaping forward with confidence. , 2017, Drug discovery today.
[86] John B. O. Mitchell. Machine learning methods in chemoinformatics , 2014, Wiley interdisciplinary reviews. Computational molecular science.
[87] O. Drummer,et al. Review: Pharmacogenetic aspects of the effect of cytochrome P450 polymorphisms on serotonergic drug metabolism, response, interactions, and adverse effects , 2011, Forensic science, medicine, and pathology.
[88] Aaron Park,et al. In silico prediction of potential chemical reactions mediated by human enzymes , 2018, BMC Bioinformatics.
[89] R. W. Hansen,et al. Journal of Health Economics , 2016 .
[90] Bing Niu,et al. Prediction of Substrate-Enzyme-Product Interaction Based on Molecular Descriptors and Physicochemical Properties , 2013, BioMed research international.
[91] S. Free,et al. A MATHEMATICAL CONTRIBUTION TO STRUCTURE-ACTIVITY STUDIES. , 1964, Journal of medicinal chemistry.
[92] Supa Hannongbua,et al. In-silico ADME models: a general assessment of their utility in drug discovery applications. , 2011, Current topics in medicinal chemistry.
[93] C. Ong,et al. In vitro and in silico Approaches to Study Cytochrome P450-Mediated Interactions. , 2017, Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques.
[94] T. Mak,et al. Regulation of cancer cell metabolism , 2011, Nature Reviews Cancer.
[95] Tom L Blundell,et al. Advantages of fine-grained side chain conformer libraries. , 2003, Protein engineering.
[96] S. Hannongbua,et al. Quantitative Structure–Activity Relationship (QSAR) Methods for the Prediction of Substrates, Inhibitors, and Inducers of Metabolic Enzymes , 2014 .
[97] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[98] D. Flockhart,et al. In vitro inhibition of the cytochrome P450 (CYP450) system by the antiplatelet drug ticlopidine: potent effect on CYP2C19 and CYP2D6. , 2000, British journal of clinical pharmacology.
[99] W. L. Jorgensen. The Many Roles of Computation in Drug Discovery , 2004, Science.
[100] Z R Li,et al. Quantitative structure-pharmacokinetic relationships for drug clearance by using statistical learning methods. , 2006, Journal of molecular graphics & modelling.
[101] David F. V. Lewis,et al. Structure–activity relationship for human cytochrome P450 substrates and inhibitors , 2002, Drug metabolism reviews.
[102] Yun Pyo Kang,et al. Recent advances in cancer metabolism: a technological perspective , 2018, Experimental & Molecular Medicine.
[103] Scott Boyer,et al. Generation of in-silico cytochrome P450 1A2, 2C9, 2C19, 2D6, and 3A4 inhibition QSAR models , 2007, J. Comput. Aided Mol. Des..
[104] T. Lynch,et al. The effect of cytochrome P450 metabolism on drug response, interactions, and adverse effects. , 2007, American family physician.
[105] C. George Priya Doss,et al. Computational approaches and resources in single amino acid substitutions analysis toward clinical research. , 2014, Advances in protein chemistry and structural biology.
[106] Uko Maran,et al. QSAR DataBank repository: open and linked qualitative and quantitative structure–activity relationship models , 2015, Journal of Cheminformatics.
[107] Sean Ekins. The Next Era: Deep Learning in Pharmaceutical Research , 2016, Pharmaceutical Research.
[108] Yan Xu,et al. Deep learning of feature representation with multiple instance learning for medical image analysis , 2014, 2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).
[109] Ovidiu Ivanciuc. Machine Learning Quantitative Structure-Activity Relationships (QSAR) for Peptides Binding to the Human Amphiphysin-1 SH3 Domain , 2009 .
[110] K. Chou,et al. Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design. , 2008, Current protein & peptide science.
[111] Dan Li,et al. ADMET Evaluation in Drug Discovery. 16. Predicting hERG Blockers by Combining Multiple Pharmacophores and Machine Learning Approaches. , 2016, Molecular pharmaceutics.
[112] David Jou,et al. Drug design targeting protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning: discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 interface. , 2014, Journal of medicinal chemistry.