Literature DB >> 23521795

Bayesian models leveraging bioactivity and cytotoxicity information for drug discovery.

Sean Ekins1, 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.   

Abstract

Identification of unique leads represents a significant challenge in drug discovery. This hurdle is magnified in neglected diseases such as tuberculosis. We have leveraged public high-throughput screening (HTS) data to experimentally validate a virtual screening approach employing Bayesian models built with bioactivity information (single-event model) as well as bioactivity and cytotoxicity information (dual-event model). We virtually screened a commercial library and experimentally confirmed actives with hit rates exceeding typical HTS results by one to two orders of magnitude. This initial dual-event Bayesian model identified compounds with antitubercular whole-cell activity and low mammalian cell cytotoxicity from a published set of antimalarials. The most potent hit exhibits the in vitro activity and in vitro/in vivo safety profile of a drug lead. These Bayesian models offer significant economies in time and cost to drug discovery.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2013        PMID: 23521795      PMCID: PMC3607962          DOI: 10.1016/j.chembiol.2013.01.011

Source DB:  PubMed          Journal:  Chem Biol        ISSN: 1074-5521


  62 in total

Review 1.  Non-nucleoside inhibitors of HIV reverse transcriptase: screening successes--clinical failures.

Authors:  J Saunders
Journal:  Drug Des Discov       Date:  1992-07

2.  Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure.

Authors:  Andreas Bender; Josef Scheiber; Meir Glick; John W Davies; Kamal Azzaoui; Jacques Hamon; Laszlo Urban; Steven Whitebread; Jeremy L Jenkins
Journal:  ChemMedChem       Date:  2007-06       Impact factor: 3.466

Review 3.  Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery.

Authors:  Sean Ekins; Joel S Freundlich; Inhee Choi; Malabika Sarker; Carolyn Talcott
Journal:  Trends Microbiol       Date:  2010-12-02       Impact factor: 17.079

4.  Novel inhibitors of InhA efficiently kill Mycobacterium tuberculosis under aerobic and anaerobic conditions.

Authors:  Catherine Vilchèze; Anthony D Baughn; JoAnn Tufariello; Lawrence W Leung; Mack Kuo; Christopher F Basler; David Alland; James C Sacchettini; Joel S Freundlich; William R Jacobs
Journal:  Antimicrob Agents Chemother       Date:  2011-05-31       Impact factor: 5.191

5.  A collaborative database and computational models for tuberculosis drug discovery.

Authors:  Sean Ekins; Justin Bradford; Krishna Dole; Anna Spektor; Kellan Gregory; David Blondeau; Moses Hohman; Barry A Bunin
Journal:  Mol Biosyst       Date:  2010-02-09

6.  A predictive ligand-based Bayesian model for human drug-induced liver injury.

Authors:  Sean Ekins; Antony J Williams; Jinghai J Xu
Journal:  Drug Metab Dispos       Date:  2010-09-15       Impact factor: 3.922

7.  Antituberculosis activity of the molecular libraries screening center network library.

Authors:  Joseph A Maddry; Subramaniam Ananthan; Robert C Goldman; Judith V Hobrath; Cecil D Kwong; Clinton Maddox; Lynn Rasmussen; Robert C Reynolds; John A Secrist; Melinda I Sosa; E Lucile White; Wei Zhang
Journal:  Tuberculosis (Edinb)       Date:  2009-09-26       Impact factor: 3.131

8.  Predicting cytotoxicity from heterogeneous data sources with Bayesian learning.

Authors:  Sarah R Langdon; Joanna Mulgrew; Gaia V Paolini; Willem P van Hoorn
Journal:  J Cheminform       Date:  2010-12-09       Impact factor: 5.514

9.  Redefining Cheminformatics with Intuitive Collaborative Mobile Apps.

Authors:  Alex M Clark; Sean Ekins; Antony J Williams
Journal:  Mol Inform       Date:  2012-07-04       Impact factor: 3.353

10.  PA-824 kills nonreplicating Mycobacterium tuberculosis by intracellular NO release.

Authors:  Ramandeep Singh; Ujjini Manjunatha; Helena I M Boshoff; Young Hwan Ha; Pornwaratt Niyomrattanakit; Richard Ledwidge; Cynthia S Dowd; Ill Young Lee; Pilho Kim; Liang Zhang; Sunhee Kang; Thomas H Keller; Jan Jiricek; Clifton E Barry
Journal:  Science       Date:  2008-11-28       Impact factor: 63.714

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  54 in total

1.  Computational models for neglected diseases: gaps and opportunities.

Authors:  Elizabeth L Ponder; Joel S Freundlich; Malabika Sarker; Sean Ekins
Journal:  Pharm Res       Date:  2013-08-30       Impact factor: 4.200

Review 2.  Molecular processes that drive cigarette smoke-induced epithelial cell fate of the lung.

Authors:  Toru Nyunoya; Yohannes Mebratu; Amelia Contreras; Monica Delgado; Hitendra S Chand; Yohannes Tesfaigzi
Journal:  Am J Respir Cell Mol Biol       Date:  2014-03       Impact factor: 6.914

3.  Naïve Bayesian Models for Vero Cell Cytotoxicity.

Authors:  Alexander L Perryman; Jimmy S Patel; Riccardo Russo; Eric Singleton; Nancy Connell; Sean Ekins; Joel S Freundlich
Journal:  Pharm Res       Date:  2018-06-29       Impact factor: 4.200

4.  Machine Learning Platform to Discover Novel Growth Inhibitors of Neisseria gonorrhoeae.

Authors:  Janaina Cruz Pereira; Samer S Daher; Kimberley M Zorn; Matthew Sherwood; Riccardo Russo; Alexander L Perryman; Xin Wang; Madeleine J Freundlich; Sean Ekins; Joel S Freundlich
Journal:  Pharm Res       Date:  2020-07-13       Impact factor: 4.200

5.  High-throughput screening and Bayesian machine learning for copper-dependent inhibitors of Staphylococcus aureus.

Authors:  Alex G Dalecki; Kimberley M Zorn; Alex M Clark; Sean Ekins; Whitney T Narmore; Nichole Tower; Lynn Rasmussen; Robert Bostwick; Olaf Kutsch; Frank Wolschendorf
Journal:  Metallomics       Date:  2019-03-20       Impact factor: 4.526

6.  Bayesian models for screening and TB Mobile for target inference with Mycobacterium tuberculosis.

Authors:  Sean Ekins; Allen C Casey; David Roberts; Tanya Parish; Barry A Bunin
Journal:  Tuberculosis (Edinb)       Date:  2013-12-19       Impact factor: 3.131

7.  An FtsZ-targeting prodrug with oral antistaphylococcal efficacy in vivo.

Authors:  Malvika Kaul; Lilly Mark; Yongzheng Zhang; Ajit K Parhi; Edmond J Lavoie; Daniel S Pilch
Journal:  Antimicrob Agents Chemother       Date:  2013-09-16       Impact factor: 5.191

8.  Structure-activity relationship studies on 2,5,6-trisubstituted benzimidazoles targeting Mtb-FtsZ as antitubercular agents.

Authors:  Krupanandan Haranahalli; Simon Tong; Saerom Kim; Monaf Awwa; Lei Chen; Susan E Knudson; Richard A Slayden; Eric Singleton; Riccardo Russo; Nancy Connell; Iwao Ojima
Journal:  RSC Med Chem       Date:  2020-10-16

9.  Evolution of a thienopyrimidine antitubercular relying on medicinal chemistry and metabolomics insights.

Authors:  Shao-Gang Li; Catherine Vilchèze; Sumit Chakraborty; Xin Wang; Hiyun Kim; Monica Anisetti; Sean Ekins; Kyu Y Rhee; William R Jacobs; Joel S Freundlich
Journal:  Tetrahedron Lett       Date:  2015-06-03       Impact factor: 2.415

10.  Are bigger data sets better for machine learning? Fusing single-point and dual-event dose response data for Mycobacterium tuberculosis.

Authors:  Sean Ekins; Joel S Freundlich; Robert C Reynolds
Journal:  J Chem Inf Model       Date:  2014-07-17       Impact factor: 4.956

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