Recent Advances in Drug Repurposing Using Machine Learning

Overview

Journal Curr Opin Chem Biol

Publisher Elsevier

Specialty Biochemistry

Date 2021 Jul 18

PMID 34274565

Citations 18

Authors

Fabio Urbina

Ana C Puhl

Sean Ekins

Affiliations

Soon will be listed here.

Abstract

Drug repurposing aims to find new uses for already existing and approved drugs. We now provide a brief overview of recent developments in drug repurposing using machine learning alongside other computational approaches for comparison. We also highlight several applications for cancer using kinase inhibitors, Alzheimer's disease as well as COVID-19.

Citing Articles

Identification of critical genes and drug repurposing targets in entorhinal cortex of Alzheimer's disease.

Hosseinpouri A, Sadegh K, Zarei-Behjani Z, Dehghan Z, Karbalaei R Neurogenetics. 2025; 26(1):27.

PMID: 39928227 DOI: 10.1007/s10048-025-00806-x.

Near-Term Quantum Classification Algorithms Applied to Antimalarial Drug Discovery.

Dorsey M, Dsouza K, Ranganath D, Harris J, Lane T, Urbina F J Chem Inf Model. 2024; 64(15):5922-5930.

PMID: 39013438 PMC: 11338495. DOI: 10.1021/acs.jcim.4c00953.

Leveraging Artificial Intelligence for Synergies in Drug Discovery: From Computers to Clinics.

Arora P, Behera M, Saraf S, Shukla R Curr Pharm Des. 2024; 30(28):2187-2205.

PMID: 38874046 DOI: 10.2174/0113816128308066240529121148.

Repurposing of anti-malarial drugs for the treatment of tuberculosis: realistic strategy or fanciful dead end?.

Hanscheid T, Ruiz Del Portal Luyten C, Hermans S, Grobusch M Malar J. 2024; 23(1):132.

PMID: 38702649 PMC: 11067164. DOI: 10.1186/s12936-024-04967-2.

Databases of ligand-binding pockets and protein-ligand interactions.

Carpenter K, Altman R Comput Struct Biotechnol J. 2024; 23:1320-1338.

PMID: 38585646 PMC: 10997877. DOI: 10.1016/j.csbj.2024.03.015.

References

Rothan H, Teoh T . Cell-Based High-Throughput Screening Protocol for Discovering Antiviral Inhibitors Against SARS-COV-2 Main Protease (3CLpro). Mol Biotechnol. 2021; 63(3):240-248. PMC: 7814170. DOI: 10.1007/s12033-021-00299-7. View

Smith E, Davis-Gardner M, Garcia-Ordonez R, Nguyen T, Hull M, Chen E . High-Throughput Screening for Drugs That Inhibit Papain-Like Protease in SARS-CoV-2. SLAS Discov. 2020; 25(10):1152-1161. PMC: 7550789. DOI: 10.1177/2472555220963667. View

Shibata S, Matsushita M, Saito Y, Suzuki T . Anticancer Drug Prescription Patterns in Japan: Future Directions in Cancer Therapy. Ther Innov Regul Sci. 2018; 52(6):718-723. DOI: 10.1177/2168479017751404. View

Roskoski Jr R . Properties of FDA-approved small molecule protein kinase inhibitors: A 2020 update. Pharmacol Res. 2019; 152:104609. DOI: 10.1016/j.phrs.2019.104609. View

Wouters O, Mckee M, Luyten J . Estimated Research and Development Investment Needed to Bring a New Medicine to Market, 2009-2018. JAMA. 2020; 323(9):844-853. PMC: 7054832. DOI: 10.1001/jama.2020.1166. View

Menden M, Iorio F, Garnett M, McDermott U, Benes C, Ballester P . Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS One. 2013; 8(4):e61318. PMC: 3640019. DOI: 10.1371/journal.pone.0061318. View

Ekins S, Kaneko T, Lipinski C, Bradford J, Dole K, Spektor A . Analysis and hit filtering of a very large library of compounds screened against Mycobacterium tuberculosis. Mol Biosyst. 2010; 6(11):2316-2324. DOI: 10.1039/c0mb00104j. View

Dittmar M, Lee J, Whig K, Segrist E, Li M, Kamalia B . Drug repurposing screens reveal cell-type-specific entry pathways and FDA-approved drugs active against SARS-Cov-2. Cell Rep. 2021; 35(1):108959. PMC: 7985926. DOI: 10.1016/j.celrep.2021.108959. View

Nguyen D, Mathias S, Bologa C, Brunak S, Fernandez N, Gaulton A . Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 2016; 45(D1):D995-D1002. PMC: 5210555. DOI: 10.1093/nar/gkw1072. View

10.

Lamb J . The Connectivity Map: a new tool for biomedical research. Nat Rev Cancer. 2006; 7(1):54-60. DOI: 10.1038/nrc2044. View

11.

Zhang Y, Huang N, Yan F, Jin H, Zhou S, Shi J . Diabetes mellitus and Alzheimer's disease: GSK-3β as a potential link. Behav Brain Res. 2017; 339:57-65. DOI: 10.1016/j.bbr.2017.11.015. View

12.

Walz A, Ugolkov A, Chandra S, Kozikowski A, Carneiro B, OHalloran T . Molecular Pathways: Revisiting Glycogen Synthase Kinase-3β as a Target for the Treatment of Cancer. Clin Cancer Res. 2017; 23(8):1891-1897. PMC: 5392367. DOI: 10.1158/1078-0432.CCR-15-2240. View

13.

Virdi R, Bavisotto R, Hopper N, Vuksanovic N, Melkonian T, Silvaggi N . Discovery of Drug-Like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3. SLAS Discov. 2020; 25(10):1162-1170. PMC: 7684785. DOI: 10.1177/2472555220960428. View

14.

Gorshkov K, Chen C, Xu M, de la Torre J, Martinez-Sobrido L, Moran T . Development of a High-Throughput Homogeneous AlphaLISA Drug Screening Assay for the Detection of SARS-CoV-2 Nucleocapsid. ACS Pharmacol Transl Sci. 2020; 3(6):1233-1241. PMC: 7553038. DOI: 10.1021/acsptsci.0c00122. View

15.

Chen C, Shinn P, Itkin Z, Eastman R, Bostwick R, Rasmussen L . Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2. Front Pharmacol. 2021; 11:592737. PMC: 7942396. DOI: 10.3389/fphar.2020.592737. View

16.

Cichonska A, Ravikumar B, Parri E, Timonen S, Pahikkala T, Airola A . Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PLoS Comput Biol. 2017; 13(8):e1005678. PMC: 5560747. DOI: 10.1371/journal.pcbi.1005678. View

17.

Boucherie D, Duarte G, Machado T, Faustino P, Sampaio C, Rascol O . Parkinson's Disease Drug Development Since 1999: A Story of Repurposing and Relative Success. J Parkinsons Dis. 2021; 11(2):421-429. PMC: 8150606. DOI: 10.3233/JPD-202184. View

18.

KalantarMotamedi Y, Eastman R, Guha R, Bender A . A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. Malar J. 2018; 17(1):160. PMC: 5896032. DOI: 10.1186/s12936-018-2294-5. View

19.

Xiao T, Qi X, Chen Y, Jiang Y . Development of Ligand-based Big Data Deep Neural Network Models for Virtual Screening of Large Compound Libraries. Mol Inform. 2018; 37(11):e1800031. DOI: 10.1002/minf.201800031. View

20.

Richardson P, Griffin I, Tucker C, Smith D, Oechsle O, Phelan A . Baricitinib as potential treatment for 2019-nCoV acute respiratory disease. Lancet. 2020; 395(10223):e30-e31. PMC: 7137985. DOI: 10.1016/S0140-6736(20)30304-4. View