Literature DB >> 31000803

Exploiting machine learning for end-to-end drug discovery and development.

Sean Ekins1, Ana C Puhl2, Kimberley M Zorn2, Thomas R Lane2, Daniel P Russo2,3, Jennifer J Klein2, Anthony J Hickey4,5, Alex M Clark6.   

Abstract

A variety of machine learning methods such as naive Bayesian, support vector machines and more recently deep neural networks are demonstrating their utility for drug discovery and development. These leverage the generally bigger datasets created from high-throughput screening data and allow prediction of bioactivities for targets and molecular properties with increased levels of accuracy. We have only just begun to exploit the potential of these techniques but they may already be fundamentally changing the research process for identifying new molecules and/or repurposing old drugs. The integrated application of such machine learning models for end-to-end (E2E) application is broadly relevant and has considerable implications for developing future therapies and their targeting.

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Year:  2019        PMID: 31000803      PMCID: PMC6594828          DOI: 10.1038/s41563-019-0338-z

Source DB:  PubMed          Journal:  Nat Mater        ISSN: 1476-1122            Impact factor:   43.841


  91 in total

1.  Development and validation of k-nearest-neighbor QSPR models of metabolic stability of drug candidates.

Authors:  Min Shen; Yunde Xiao; Alexander Golbraikh; Vijay K Gombar; Alexander Tropsha
Journal:  J Med Chem       Date:  2003-07-03       Impact factor: 7.446

2.  Modeling and Prediction of Solvent Effect on Human Skin Permeability using Support Vector Regression and Random Forest.

Authors:  Hiromi Baba; Jun-ichi Takahara; Fumiyoshi Yamashita; Mitsuru Hashida
Journal:  Pharm Res       Date:  2015-06-02       Impact factor: 4.200

3.  How artificial intelligence is changing drug discovery.

Authors:  Nic Fleming
Journal:  Nature       Date:  2018-05       Impact factor: 49.962

4.  Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus.

Authors:  Daniel Reker; Tiago Rodrigues; Petra Schneider; Gisbert Schneider
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-03       Impact factor: 11.205

5.  TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility.

Authors:  Kedi Wu; Zhixiong Zhao; Renxiao Wang; Guo-Wei Wei
Journal:  J Comput Chem       Date:  2018-04-06       Impact factor: 3.376

6.  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

7.  MoleculeNet: a benchmark for molecular machine learning.

Authors:  Zhenqin Wu; Bharath Ramsundar; Evan N Feinberg; Joseph Gomes; Caleb Geniesse; Aneesh S Pappu; Karl Leswing; Vijay Pande
Journal:  Chem Sci       Date:  2017-10-31       Impact factor: 9.825

Review 8.  High Throughput and Computational Repurposing for Neglected Diseases.

Authors:  Helen W Hernandez; Melinda Soeung; Kimberley M Zorn; Norah Ashoura; Melina Mottin; Carolina Horta Andrade; Conor R Caffrey; Jair Lage de Siqueira-Neto; Sean Ekins
Journal:  Pharm Res       Date:  2018-12-17       Impact factor: 4.200

9.  Machine learning methods in chemoinformatics.

Authors:  John B O Mitchell
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2014-09-01

10.  PubChem Substance and Compound databases.

Authors:  Sunghwan Kim; Paul A Thiessen; Evan E Bolton; Jie Chen; Gang Fu; Asta Gindulyte; Lianyi Han; Jane He; Siqian He; Benjamin A Shoemaker; Jiyao Wang; Bo Yu; Jian Zhang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2015-09-22       Impact factor: 16.971

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  66 in total

Review 1.  Déjà vu: Stimulating open drug discovery for SARS-CoV-2.

Authors:  Sean Ekins; Melina Mottin; Paulo R P S Ramos; Bruna K P Sousa; Bruno Junior Neves; Daniel H Foil; Kimberley M Zorn; Rodolpho C Braga; Megan Coffee; Christopher Southan; Ana C Puhl; Carolina Horta Andrade
Journal:  Drug Discov Today       Date:  2020-04-19       Impact factor: 7.851

2.  Comparing Machine Learning Models for Aromatase (P450 19A1).

Authors:  Kimberley M Zorn; Daniel H Foil; Thomas R Lane; Wendy Hillwalker; David J Feifarek; Frank Jones; William D Klaren; Ashley M Brinkman; Sean Ekins
Journal:  Environ Sci Technol       Date:  2020-11-19       Impact factor: 9.028

3.  Comparison of Machine Learning Models for the Androgen Receptor.

Authors:  Kimberley M Zorn; Daniel H Foil; Thomas R Lane; Wendy Hillwalker; David J Feifarek; Frank Jones; William D Klaren; Ashley M Brinkman; Sean Ekins
Journal:  Environ Sci Technol       Date:  2020-10-21       Impact factor: 9.028

4.  Machine Learning Models for Estrogen Receptor Bioactivity and Endocrine Disruption Prediction.

Authors:  Kimberley M Zorn; Daniel H Foil; Thomas R Lane; Daniel P Russo; Wendy Hillwalker; David J Feifarek; Frank Jones; William D Klaren; Ashley M Brinkman; Sean Ekins
Journal:  Environ Sci Technol       Date:  2020-09-15       Impact factor: 9.028

5.  Semi-supervised Hierarchical Drug Embedding in Hyperbolic Space.

Authors:  Ke Yu; Shyam Visweswaran; Kayhan Batmanghelich
Journal:  J Chem Inf Model       Date:  2020-11-03       Impact factor: 4.956

6.  A Nomogram Based on a Collagen Feature Support Vector Machine for Predicting the Treatment Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer Patients.

Authors:  Wei Jiang; Min Li; Jie Tan; Mingyuan Feng; Jixiang Zheng; Dexin Chen; Zhangyuanzhu Liu; Botao Yan; Guangxing Wang; Shuoyu Xu; Weiwei Xiao; Yuanhong Gao; Shuangmu Zhuo; Jun Yan
Journal:  Ann Surg Oncol       Date:  2021-06-19       Impact factor: 5.344

7.  The Antiviral Drug Tilorone Is a Potent and Selective Inhibitor of Acetylcholinesterase.

Authors:  Patricia A Vignaux; Eni Minerali; Thomas R Lane; Daniel H Foil; Peter B Madrid; Ana C Puhl; Sean Ekins
Journal:  Chem Res Toxicol       Date:  2021-01-05       Impact factor: 3.739

8.  Bioactivity Comparison across Multiple Machine Learning Algorithms Using over 5000 Datasets for Drug Discovery.

Authors:  Thomas R Lane; Daniel H Foil; Eni Minerali; Fabio Urbina; Kimberley M Zorn; Sean Ekins
Journal:  Mol Pharm       Date:  2020-12-16       Impact factor: 4.939

Review 9.  An introduction to machine learning and analysis of its use in rheumatic diseases.

Authors:  Kathryn M Kingsmore; Christopher E Puglisi; Amrie C Grammer; Peter E Lipsky
Journal:  Nat Rev Rheumatol       Date:  2021-11-02       Impact factor: 20.543

Review 10.  Machine and deep learning approaches for cancer drug repurposing.

Authors:  Naiem T Issa; Vasileios Stathias; Stephan Schürer; Sivanesan Dakshanamurthy
Journal:  Semin Cancer Biol       Date:  2020-01-03       Impact factor: 15.707

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