Literature DB >> 20438859

Evolving molecules using multi-objective optimization: applying to ADME/Tox.

Sean Ekins1, J Dana Honeycutt, James T Metz.   

Abstract

Modern drug discovery involves the simultaneous optimization of many physicochemical and biological properties that transcends the historical focus on bioactivity alone. The process of resolving many requirements is termed 'multi-objective optimization', and here we discuss how this can be used for drug discovery, focusing on evolutionary molecule design to incorporate optimal predicted absorption, distribution, metabolism, excretion and toxicity properties. We provide several examples of how Pareto optimization implemented in Pareto Ligand Designer can be used to make trade-offs between these different predicted or real molecular properties to result in better predicted compounds. (c) 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID: 20438859     DOI: 10.1016/j.drudis.2010.04.003

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  22 in total

1.  Chemical space: missing pieces in cheminformatics.

Authors:  Sean Ekins; Rishi R Gupta; Eric Gifford; Barry A Bunin; Chris L Waller
Journal:  Pharm Res       Date:  2010-08-04       Impact factor: 4.200

2.  Thermodynamic Proxies to Compensate for Biases in Drug Discovery Methods.

Authors:  Sean Ekins; Nadia K Litterman; Christopher A Lipinski; Barry A Bunin
Journal:  Pharm Res       Date:  2015-08-27       Impact factor: 4.200

3.  Genome-scale stoichiometry analysis to elucidate the innate capability of the cyanobacterium Synechocystis for electricity generation.

Authors:  Longfei Mao; Wynand S Verwoerd
Journal:  J Ind Microbiol Biotechnol       Date:  2013-07-14       Impact factor: 3.346

4.  Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting.

Authors:  Feng Zhu; Chu Qin; Lin Tao; Xin Liu; Zhe Shi; Xiaohua Ma; Jia Jia; Ying Tan; Cheng Cui; Jinshun Lin; Chunyan Tan; Yuyang Jiang; Yuzong Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2011-07-18       Impact factor: 11.205

5.  In vivo-in vitro-in silico pharmacokinetic modelling in drug development: current status and future directions.

Authors:  Olavi Pelkonen; Miia Turpeinen; Hannu Raunio
Journal:  Clin Pharmacokinet       Date:  2011-08       Impact factor: 6.447

6.  Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets.

Authors:  Alexandru Korotcov; Valery Tkachenko; Daniel P Russo; Sean Ekins
Journal:  Mol Pharm       Date:  2017-11-13       Impact factor: 4.939

7.  Opportunities and challenges using artificial intelligence in ADME/Tox.

Authors:  Barun Bhhatarai; W Patrick Walters; Cornelis E C A Hop; Guido Lanza; Sean Ekins
Journal:  Nat Mater       Date:  2019-05       Impact factor: 43.841

8.  Discovery of novel antimalarial compounds enabled by QSAR-based virtual screening.

Authors:  Liying Zhang; Denis Fourches; Alexander Sedykh; Hao Zhu; Alexander Golbraikh; Sean Ekins; Julie Clark; Michele C Connelly; Martina Sigal; Dena Hodges; Armand Guiguemde; R Kiplin Guy; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2013-01-23       Impact factor: 4.956

9.  Bayesian models leveraging bioactivity and cytotoxicity information for drug discovery.

Authors:  Sean Ekins; Robert C Reynolds; Hiyun Kim; Mi-Sun Koo; Marilyn Ekonomidis; Meliza Talaue; Steve D Paget; Lisa K Woolhiser; Anne J Lenaerts; Barry A Bunin; Nancy Connell; Joel S Freundlich
Journal:  Chem Biol       Date:  2013-03-21

Review 10.  Rethinking drug design in the artificial intelligence era.

Authors:  Petra Schneider; W Patrick Walters; Alleyn T Plowright; Norman Sieroka; Jennifer Listgarten; Robert A Goodnow; Jasmin Fisher; Johanna M Jansen; José S Duca; Thomas S Rush; Matthias Zentgraf; John Edward Hill; Elizabeth Krutoholow; Matthias Kohler; Jeff Blaney; Kimito Funatsu; Chris Luebkemann; Gisbert Schneider
Journal:  Nat Rev Drug Discov       Date:  2019-12-04       Impact factor: 84.694

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