Literature DB >> 34013350

Utilizing graph machine learning within drug discovery and development.

Thomas Gaudelet1, Ben Day1,2, Arian R Jamasb1,2,3, Jyothish Soman1, Cristian Regep1, Gertrude Liu1, Jeremy B R Hayter1, Richard Vickers1, Charles Roberts1,4, Jian Tang5,6, David Roblin1,4,7, Tom L Blundell3, Michael M Bronstein1,8,9, Jake P Taylor-King1,4.   

Abstract

Graph machine learning (GML) is receiving growing interest within the pharmaceutical and biotechnology industries for its ability to model biomolecular structures, the functional relationships between them, and integrate multi-omic datasets - amongst other data types. Herein, we present a multidisciplinary academic-industrial review of the topic within the context of drug discovery and development. After introducing key terms and modelling approaches, we move chronologically through the drug development pipeline to identify and summarize work incorporating: target identification, design of small molecules and biologics, and drug repurposing. Whilst the field is still emerging, key milestones including repurposed drugs entering in vivo studies, suggest GML will become a modelling framework of choice within biomedical machine learning.
© The Author(s) 2021. Published by Oxford University Press.

Entities:  

Keywords:  drug development; drug discovery; graph machine learning

Mesh:

Year:  2021        PMID: 34013350      PMCID: PMC8574649          DOI: 10.1093/bib/bbab159

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  143 in total

1.  Circular fingerprints: flexible molecular descriptors with applications from physical chemistry to ADME.

Authors:  Robert C Glem; Andreas Bender; Catrin H Arnby; Lars Carlsson; Scott Boyer; James Smith
Journal:  IDrugs       Date:  2006-03

2.  Modeling interactome: scale-free or geometric?

Authors:  N Przulj; D G Corneil; I Jurisica
Journal:  Bioinformatics       Date:  2004-07-29       Impact factor: 6.937

3.  Fixed-dose combination pharmacologic therapy to improve hypertension control worldwide: Clinical perspective and policy implications.

Authors:  Donald J DiPette; Jamario Skeete; Emily Ridley; Norm R C Campbell; Patricio Lopez-Jaramillo; Sandeep P Kishore; Marc G Jaffe; Antonio Coca; Raymond R Townsend; Pedro Ordunez
Journal:  J Clin Hypertens (Greenwich)       Date:  2018-11-27       Impact factor: 3.738

4.  Hyperbolic Graph Convolutional Neural Networks.

Authors:  Ines Chami; Rex Ying; Christopher Ré; Jure Leskovec
Journal:  Adv Neural Inf Process Syst       Date:  2019-12

5.  Estimated Research and Development Investment Needed to Bring a New Medicine to Market, 2009-2018.

Authors:  Olivier J Wouters; Martin McKee; Jeroen Luyten
Journal:  JAMA       Date:  2020-03-03       Impact factor: 157.335

6.  HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods.

Authors:  Kirill Veselkov; Guadalupe Gonzalez; Shahad Aljifri; Dieter Galea; Reza Mirnezami; Jozef Youssef; Michael Bronstein; Ivan Laponogov
Journal:  Sci Rep       Date:  2019-07-03       Impact factor: 4.379

7.  Generating functional protein variants with variational autoencoders.

Authors:  Alex Hawkins-Hooker; Florence Depardieu; Sebastien Baur; Guillaume Couairon; Arthur Chen; David Bikard
Journal:  PLoS Comput Biol       Date:  2021-02-26       Impact factor: 4.475

Review 8.  Mass Cytometry Imaging for the Study of Human Diseases-Applications and Data Analysis Strategies.

Authors:  Heeva Baharlou; Nicolas P Canete; Anthony L Cunningham; Andrew N Harman; Ellis Patrick
Journal:  Front Immunol       Date:  2019-11-14       Impact factor: 7.561

9.  Are drug targets with genetic support twice as likely to be approved? Revised estimates of the impact of genetic support for drug mechanisms on the probability of drug approval.

Authors:  Emily A King; J Wade Davis; Jacob F Degner
Journal:  PLoS Genet       Date:  2019-12-12       Impact factor: 5.917

10.  PubChem in 2021: new data content and improved web interfaces.

Authors:  Sunghwan Kim; Jie Chen; Tiejun Cheng; Asta Gindulyte; Jia He; Siqian He; Qingliang Li; Benjamin A Shoemaker; Paul A Thiessen; Bo Yu; Leonid Zaslavsky; Jian Zhang; Evan E Bolton
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

View more
  8 in total

1.  Scoring Functions for Protein-Ligand Binding Affinity Prediction using Structure-Based Deep Learning: A Review.

Authors:  Rocco Meli; Garrett M Morris; Philip C Biggin
Journal:  Front Bioinform       Date:  2022-06-17

Review 2.  Deep Learning Concepts and Applications for Synthetic Biology.

Authors:  William A V Beardall; Guy-Bart Stan; Mary J Dunlop
Journal:  GEN Biotechnol       Date:  2022-08-18

3.  Construction of Knowledge Graph of 3D Clothing Design Resources Based on Multimodal Clustering Network.

Authors:  Jia Zheng; Wei Hong
Journal:  Comput Intell Neurosci       Date:  2022-06-02

Review 4.  Applied machine learning in Alzheimer's disease research: omics, imaging, and clinical data.

Authors:  Ziyi Li; Xiaoqian Jiang; Yizhuo Wang; Yejin Kim
Journal:  Emerg Top Life Sci       Date:  2021-12-21

5.  A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease.

Authors:  James A Timmons; Andrew Anighoro; Robert J Brogan; Jack Stahl; Claes Wahlestedt; David Gordon Farquhar; Jake Taylor-King; Claude-Henry Volmar; William E Kraus; Stuart M Phillips
Journal:  Elife       Date:  2022-01-17       Impact factor: 8.713

Review 6.  Machine learning applications for therapeutic tasks with genomics data.

Authors:  Kexin Huang; Cao Xiao; Lucas M Glass; Cathy W Critchlow; Greg Gibson; Jimeng Sun
Journal:  Patterns (N Y)       Date:  2021-08-09

Review 7.  Graph Neural Networks as a Potential Tool in Improving Virtual Screening Programs.

Authors:  Luiz Anastacio Alves; Natiele Carla da Silva Ferreira; Victor Maricato; Anael Viana Pinto Alberto; Evellyn Araujo Dias; Nt Jose Aguiar Coelho
Journal:  Front Chem       Date:  2022-01-20       Impact factor: 5.221

8.  Drug Properties Prediction Based on Deep Learning.

Authors:  Soyoung Yoo; Junghyun Kim; Guang J Choi
Journal:  Pharmaceutics       Date:  2022-02-21       Impact factor: 6.321

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.