Generic placeholder image

Mini-Reviews in Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 1389-5575
ISSN (Online): 1875-5607

Review Article

Artificial Intelligence in Drug Discovery: A Bibliometric Analysis and Literature Review

Author(s): Baoyu He, Jingjing Guo, Henry H.Y. Tong and Wai Ming To*

Volume 24, Issue 14, 2024

Published on: 12 January, 2024

Page: [1353 - 1367] Pages: 15

DOI: 10.2174/0113895575271267231123160503

Price: $65

Open Access Journals Promotions 2
conference banner
Abstract

Drug discovery is a complex and iterative process, making it ideal for using artificial intelligence (AI). This paper uses a bibliometric approach to reveal AI's trend and underlying structure in drug discovery (AIDD). A total of 4310 journal articles and reviews indexed in Scopus were analyzed, revealing that AIDD has been rapidly growing over the past two decades, with a significant increase after 2017. The United States, China, and the United Kingdom were the leading countries in research output, with academic institutions, particularly the Chinese Academy of Sciences and the University of Cambridge, being the most productive. In addition, industrial companies, including both pharmaceutical and high-tech ones, also made significant contributions. Additionally, this paper thoroughly discussed the evolution and research frontiers of AIDD, which were uncovered through co-occurrence analyses of keywords using VOSviewer. Our findings highlight that AIDD is an interdisciplinary and promising research field that has the potential to revolutionize drug discovery. The comprehensive overview provided here will be of significant interest to researchers, practitioners, and policy-makers in related fields. The results emphasize the need for continued investment and collaboration in AIDD to accelerate drug discovery, reduce costs, and improve patient outcomes.

Keywords: Drug discovery, artificial intelligence, AI, bibliometric, Scopus, VOSviewer.

Graphical Abstract
[1]
Oeppen, J.; Vaupel, J.W. Demography. Broken limits to life expectancy. Science, 2002, 296(5570), 1029-1031.
[http://dx.doi.org/10.1126/science.1069675] [PMID: 12004104]
[2]
Economic UNDo. In: World population prospects 2022: Summary of results; United Nations: NY, USA, 2022.
[3]
Peters, M.A. Against death. Longevity forever! Educ. Philos. Theory, 2021, 53(6), 559-562.
[http://dx.doi.org/10.1080/00131857.2019.1684803]
[4]
Lao, J.I.; Montoriol, C.; Morer, I.; Beyer, K. Genetic contribution to aging: Deleterious and helpful genes define life expectancy. Ann. N. Y. Acad. Sci., 2005, 1057(1), 50-63.
[http://dx.doi.org/10.1196/annals.1356.003] [PMID: 16399887]
[5]
Wetle, T. The use of new information technologies in an aging population. Older adults, health information, and the World Wide Web; Psychology Press, 2001, pp. 15-24.
[6]
Downs, M.; Blackburn, T. The challenges of the changing drug discovery model; , 2012. Available from: https://www.ddw-online.com/the-challenges-of-the-changing-drug-discovery-model-1312-201210/
[7]
Harky, A.; Mishra, V.; Ansari, D.M.; Melamed, N. Are open-source approaches the most efficient way forward for COVID-19 drug discovery? Expert Opin. Drug Discov., 2021, 16(2), 115-117.
[http://dx.doi.org/10.1080/17460441.2020.1820983] [PMID: 32915657]
[8]
Guo, J.; Zhou, H.X. Allosteric activation of SENP1 by SU-MO1 β-grasp domain involves a dock-and-coalesce mechanism. eLife, 2016, 5, e18249.
[http://dx.doi.org/10.7554/eLife.18249] [PMID: 27576863]
[9]
Li, M.; Li, M.; Xie, Y.; Guo, J. Uncovering the molecular basis for the better gefitinib sensitivity of EGFR with complex mutations over single rare mutation: insights from molecular simulations. Molecules, 2022, 27(12), 3844.
[http://dx.doi.org/10.3390/molecules27123844] [PMID: 35744964]
[10]
Li, M.; Guo, J. Deciphering the T790M/L858R-selective inhibition mechanism of an allosteric inhibitor of EGFR: Insights from molecular simulations. ACS Chem. Neurosci., 2021, 12(3), 462-472.
[http://dx.doi.org/10.1021/acschemneuro.0c00633] [PMID: 33435671]
[11]
Guo, J.; Bao, Y.; Li, M. Application of computational approaches in biomembranes: From structure to function. In: Computational Molecular Science; Wiley, 2023.
[12]
Bai, Q.; Liu, S.; Tian, Y.; Xu, T.; Banegas-Luna, A.J.; Pérez-Sánchez, H.; Huang, J.; Liu, H.; Yao, X. Application advances of deep learning methods for de novo drug design and molecular dynamics simulation. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2022, 12(3), e1581.
[http://dx.doi.org/10.1002/wcms.1581]
[13]
Lin, Y.; Zhang, Y.; Wang, D.; Yang, B.; Shen, Y.Q. Computer especially AI-assisted drug virtual screening and design in traditional chinese medicine. Phytomedicine, 2022, 107, 154481.
[http://dx.doi.org/10.1016/j.phymed.2022.154481] [PMID: 36215788]
[14]
Martinelli, D.D. Generative machine learning for de novo drug discovery: A systematic review. Comput. Biol. Med., 2022, 145, 105403.
[http://dx.doi.org/10.1016/j.compbiomed.2022.105403] [PMID: 35339849]
[15]
Kaushal, K.; Sarma, P.; Rana, S.V.; Medhi, B.; Naithani, M. Emerging role of artificial intelligence in therapeutics for COVID-19: A systematic review. J. Biomol. Struct. Dyn., 2022, 40(10), 4750-4765.
[http://dx.doi.org/10.1080/07391102.2020.1855250] [PMID: 33300456]
[16]
Brasil, S.; Allocca, M.; Magrinho, S.C.M.; Santos, I.; Raposo, M.; Francisco, R.; Pascoal, C.; Martins, T.; Videira, P.A.; Pereira, F.; Andreotti, G.; Jaeken, J.; Kantautas, K.A.; Perlstein, E.O.; Ferreira, V.R. Systematic review: Drug repositioning for Congenital Disorders of Glycosylation (CDG). Int. J. Mol. Sci., 2022, 23(15), 8725.
[http://dx.doi.org/10.3390/ijms23158725] [PMID: 35955863]
[17]
Bijral, R.K.; Singh, I.; Manhas, J.; Sharma, V. Exploring artificial intelligence in drug discovery: A comprehensive review. Arch. Comput. Methods Eng., 2022, 29(4), 2513-2529.
[http://dx.doi.org/10.1007/s11831-021-09661-z]
[18]
Askr, H.; Elgeldawi, E.; Aboul Ella, H. Deep learning in drug discovery: An integrative review and future challenges. Artif. Intell. Rev., 2022, 1-63.
[PMID: 36415536]
[19]
Kim, H.; Kim, E.; Lee, I.; Bae, B.; Park, M.; Nam, H. Artificial intelligence in drug discovery: A comprehensive review of data-driven and machine learning approaches. Biotechnol. Bioprocess Eng.; BBE, 2020, 25(6), 895-930.
[http://dx.doi.org/10.1007/s12257-020-0049-y] [PMID: 33437151]
[20]
Karger, E.; Kureljusic, M. Using artificial intelligence for drug discovery: A bibliometric study and future research agenda. Pharmaceuticals, 2022, 15(12), 1492.
[http://dx.doi.org/10.3390/ph15121492] [PMID: 36558943]
[21]
To, W.M. A bibliometric analysis of world issues-social, political, economic, and environmental dimensions. WORLD, 2022, 3(3), 619-638.
[http://dx.doi.org/10.3390/world3030034]
[22]
Donthu, N.; Kumar, S.; Mukherjee, D.; Pandey, N.; Lim, W.M. How to conduct a bibliometric analysis: An overview and guidelines. J. Bus. Res., 2021, 133, 285-296.
[http://dx.doi.org/10.1016/j.jbusres.2021.04.070]
[23]
Scopus Database; Elsevier, 2023.
[24]
Baas, J.; Schotten, M.; Plume, A. Scopus as a curated, high-quality bibliometric data source for academic research in quantitative science studies. Quanti. Sci. Stud., 2020, 1(1), 377-86.
[http://dx.doi.org/10.1162/qss_a_00019]
[25]
Van Eck, N.; Waltman, L. Software survey: VOSviewer, a computer program for bibliometric mapping. Scientometrics, 2010, 84(2), 523-538.
[26]
Liberati, A.; Altman, D.G.; Tetzlaff, J.; Mulrow, C.; Gøtzsche, P.C.; Ioannidis, J.P.; Clarke, M.; Devereaux, P.J.; Kleijnen, J.; Moher, D. The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: Explanation and elaboration. Ann. Intern. Med., 2009, 151(4), W.
[http://dx.doi.org/10.7326/0003-4819-151-4-200908180-00136] [PMID: 19622512]
[27]
Moher, D.; Liberati, A.; Tetzlaff, J.; Altman, D.G. Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement. Ann. Intern. Med., 2009, 151(4), 264-269. W64
[http://dx.doi.org/10.7326/0003-4819-151-4-200908180-00135] [PMID: 19622511]
[28]
Page, MJ.; Moher, D.; Bossuyt, PM. PRISMA 2020 explana-tion and elaboration: Updated guidance and exemplars for reporting systematic reviews. BMJ, 2021, 372.
[29]
Donthu, N.; Kumar, S.; Pandey, N.; Pandey, N.; Mishra, A. Mapping the electronic word-of-mouth (eWOM) research: A systematic review and bibliometric analysis. J. Bus. Res., 2021, 135, 758-773.
[http://dx.doi.org/10.1016/j.jbusres.2021.07.015]
[30]
Dubois, J.E.; Sobel, Y. DARC system for documentation and artificial intelligence in chemistry. J. Chem. Inf. Comput. Sci., 1985, 25(3), 326-333.
[http://dx.doi.org/10.1021/ci00047a032]
[31]
Klopman, G.; Buyukbingol, E. An artificial intelligence approach to the study of the structural moieties relevant to drug-receptor interactions in aldose reductase inhibitors. Mol. Pharmacol., 1988, 34(6), 852-862.
[PMID: 3143909]
[32]
Mueller, K. Strategy and tactics in molecular modeling in drug design. J. Mol. Graphics Mod., 1989.
[33]
LeCun, Y.; Bengio, Y.; Hinton, G. Deep learning. Nature, 2015, 521(7553), 436-444.
[http://dx.doi.org/10.1038/nature14539] [PMID: 26017442]
[34]
Dietterich, T.G.; Lathrop, R.H.; Lozano-Pérez, T. Solving the multiple instance problem with axis-parallel rectangles. Artif. Intell., 1997, 89(1-2), 31-71.
[http://dx.doi.org/10.1016/S0004-3702(96)00034-3]
[35]
Pires, D.E.V.; Blundell, T.L.; Ascher, D.B. pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J. Med. Chem., 2015, 58(9), 4066-4072.
[http://dx.doi.org/10.1021/acs.jmedchem.5b00104] [PMID: 25860834]
[36]
Domingos, P. A few useful things to know about machine learning. Commun. ACM, 2012, 55(10), 78-87.
[http://dx.doi.org/10.1145/2347736.2347755]
[37]
Cherkasov, A.; Muratov, E.N.; Fourches, D.; Varnek, A.; Baskin, I.I.; Cronin, M.; Dearden, J.; Gramatica, P.; Martin, Y.C.; Todeschini, R.; Consonni, V.; Kuz’min, V.E.; Cramer, R.; Benigni, R.; Yang, C.; Rathman, J.; Terfloth, L.; Gasteiger, J.; Richard, A.; Tropsha, A. QSAR modeling: Where have you been? Where are you going to? J. Med. Chem., 2014, 57(12), 4977-5010.
[http://dx.doi.org/10.1021/jm4004285] [PMID: 24351051]
[38]
Sliwoski, G.; Kothiwale, S.; Meiler, J.; Lowe, E.W., Jr Computational methods in drug discovery. Pharmacol. Rev., 2014, 66(1), 334-395.
[http://dx.doi.org/10.1124/pr.112.007336] [PMID: 24381236]
[39]
Hammond, S.M. An overview of microRNAs. Adv. Drug Deliv. Rev., 2015, 87, 3-14.
[http://dx.doi.org/10.1016/j.addr.2015.05.001] [PMID: 25979468]
[40]
Ching, T.; Himmelstein, D.S.; Beaulieu-Jones, B.K.; Kalinin, A.A.; Do, B.T.; Way, G.P.; Ferrero, E.; Agapow, P.M.; Zietz, M.; Hoffman, M.M.; Xie, W.; Rosen, G.L.; Lengerich, B.J.; Israeli, J.; Lanchantin, J.; Woloszynek, S.; Carpenter, A.E.; Shrikumar, A.; Xu, J.; Cofer, E.M.; Lavender, C.A.; Turaga, S.C.; Alexandari, A.M.; Lu, Z.; Harris, D.J.; DeCaprio, D.; Qi, Y.; Kundaje, A.; Peng, Y.; Wiley, L.K.; Segler, M.H.S.; Boca, S.M.; Swamidass, S.J.; Huang, A.; Gitter, A.; Greene, C.S. Opportunities and obstacles for deep learning in biology and medicine. J. R. Soc. Interface, 2018, 15(141), 20170387.
[http://dx.doi.org/10.1098/rsif.2017.0387] [PMID: 29618526]
[41]
Vamathevan, J.; Clark, D.; Czodrowski, P.; Dunham, I.; Ferran, E.; Lee, G.; Li, B.; Madabhushi, A.; Shah, P.; Spitzer, M.; Zhao, S. Applications of machine learning in drug discovery and development. Nat. Rev. Drug Discov., 2019, 18(6), 463-477.
[http://dx.doi.org/10.1038/s41573-019-0024-5] [PMID: 30976107]
[42]
Chen, H.; Engkvist, O.; Wang, Y.; Olivecrona, M.; Blaschke, T. The rise of deep learning in drug discovery. Drug Discov. Today, 2018, 23(6), 1241-1250.
[http://dx.doi.org/10.1016/j.drudis.2018.01.039] [PMID: 29366762]
[43]
Sander, T.; Freyss, J.; von Korff, M.; Rufener, C. Data Warrior: An open-source program for chemistry aware data visualization and analysis. J. Chem. Inf. Model., 2015, 55(2), 460-473.
[http://dx.doi.org/10.1021/ci500588j] [PMID: 25558886]
[44]
Guo, J.; Wang, X.; Sun, H.; Liu, H.; Yao, X. The molecular basis of IGF-II/IGF2R recognition: A combined molecular dynamics simulation, free-energy calculation and computational alanine scanning study. J. Mol. Model., 2012, 18(4), 1421-1430.
[http://dx.doi.org/10.1007/s00894-011-1159-4] [PMID: 21761181]
[45]
Xue, W.; Pan, D.; Yang, Y.; Liu, H.; Yao, X. Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435. Antiviral Res., 2012, 93(1), 126-137.
[http://dx.doi.org/10.1016/j.antiviral.2011.11.007] [PMID: 22127068]
[46]
Wang, S.; Lin, H.; Huang, Z.; He, Y.; Deng, X.; Xu, Y.; Pei, J.; Lai, L. CavitySpace: A database of potential ligand binding sites in the human proteome. Biomolecules, 2022, 12(7), 967.
[http://dx.doi.org/10.3390/biom12070967] [PMID: 35883523]
[47]
Zhang, L.; Tan, J.; Han, D. From machine learning to deep learning: progress in machine intelligence for rational drug discovery. Drug Discov. Today, 2017, 22(11), 1680-1685.
[http://dx.doi.org/10.1016/j.drudis.2017.08.010]
[48]
Blaschke, T.; Olivecrona, M.; Engkvist, O.; Bajorath, J.; Chen, H. Application of generative autoencoder in de novo molecular design. Mol. Inform., 2018, 37(1-2), 1700123.
[http://dx.doi.org/10.1002/minf.201700123] [PMID: 29235269]
[49]
Kadurin, A.; Nikolenko, S.; Khrabrov, K.; Aliper, A.; Zhavoronkov, A. druGAN: An advanced generative adversarial autoencoder model for de novo generation of new molecules with desired molecular properties in silico. Mol. Pharm., 2017, 14(9), 3098-3104.
[http://dx.doi.org/10.1021/acs.molpharmaceut.7b00346] [PMID: 28703000]
[50]
Lam, H.Y.I.; Pincket, R.; Han, H.; Ong, X.E.; Wang, Z.; Hinks, J.; Wei, Y.; Li, W.; Zheng, L.; Mu, Y. Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design. Nat. Mach. Intell., 2023, 5(7), 754-764.
[http://dx.doi.org/10.1038/s42256-023-00683-9]
[51]
Yang, Y.; Hsieh, C.Y.; Kang, Y.; Hou, T.; Liu, H.; Yao, X. Deep generation model guided by the docking score for active molecular design. J. Chem. Inf. Model., 2023, 63(10), 2983-2991.
[http://dx.doi.org/10.1021/acs.jcim.3c00572] [PMID: 37163364]
[52]
Yang, Y.; Wu, Z.; Yao, X.; Kang, Y.; Hou, T.; Hsieh, C.Y.; Liu, H. Exploring low-toxicity chemical space with deep learning for molecular generation. J. Chem. Inf. Model., 2022, 62(13), 3191-3199.
[http://dx.doi.org/10.1021/acs.jcim.2c00671] [PMID: 35713712]
[53]
Putin, E.; Asadulaev, A.; Ivanenkov, Y.; Aladinskiy, V.; Sanchez-Lengeling, B.; Aspuru-Guzik, A.; Zhavoronkov, A. Reinforced adversarial neural computer for de novo molecular design. J. Chem. Inf. Model., 2018, 58(6), 1194-1204.
[http://dx.doi.org/10.1021/acs.jcim.7b00690] [PMID: 29762023]
[54]
Xiong, J.; Xiong, Z.; Chen, K.; Jiang, H.; Zheng, M. Graph neural networks for automated de novo drug design. Drug Discov. Today, 2021, 26(6), 1382-1393.
[http://dx.doi.org/10.1016/j.drudis.2021.02.011] [PMID: 33609779]
[55]
Fang, Y.; Pan, X.; Shen, H.B. De novo drug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment. Bioinformatics, 2023, 39(4), btad157.
[http://dx.doi.org/10.1093/bioinformatics/btad157] [PMID: 36961341]
[56]
Lee, K.; Kim, D. In-silico molecular binding prediction for human drug targets using deep neural multi-task learning. Genes, 2019, 10(11), 906.
[http://dx.doi.org/10.3390/genes10110906] [PMID: 31703452]
[57]
Zinner, M.; Dahlhausen, F.; Boehme, P.; Ehlers, J.; Bieske, L.; Fehring, L. Quantum computing’s potential for drug discovery: Early stage industry dynamics. Drug Discov. Today, 2021, 26(7), 1680-1688.
[http://dx.doi.org/10.1016/j.drudis.2021.06.003] [PMID: 34119668]
[58]
Cova, T.; Vitorino, C.; Ferreira, M. Artificial intelligence and quantum computing as the next pharma disruptors. Methods Mol. Biol., 2022, 2390, 321-347.
[http://dx.doi.org/10.1007/978-1-0716-1787-8_14]
[59]
Tian, Y.; Wang, X.; Yao, X.; Liu, H.; Yang, Y. Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism. Brief. Bioinform., 2023, 24(1), bbac534.
[http://dx.doi.org/10.1093/bib/bbac534] [PMID: 36526280]
[60]
Li, K.; Tong, H.H.Y.; Chen, Y.; Sun, Y.; Wang, J. The emerging roles of next-generation metabolomics in critical care nutrition. Crit. Rev. Food Sci. Nutr., 2022, 1-12.
[http://dx.doi.org/10.1080/10408398.2022.2113761] [PMID: 36004623]
[61]
Li, Y.; Hsieh, C.Y.; Lu, R.; Gong, X.; Wang, X.; Li, P.; Liu, S.; Tian, Y.; Jiang, D.; Yan, J.; Bai, Q.; Liu, H.; Zhang, S.; Yao, X. An adaptive graph learning method for automated molecular interactions and properties predictions. Nat. Mach. Intell., 2022, 4(7), 645-651.
[http://dx.doi.org/10.1038/s42256-022-00501-8]
[62]
Jin, J.; Wang, D.; Shi, G.; Bao, J.; Wang, J.; Zhang, H.; Pan, P.; Li, D.; Yao, X.; Liu, H.; Hou, T.; Kang, Y. FFLOM: A flow-based autoregressive model for fragment-to-lead optimization. J. Med. Chem., 2023, 66(15), 10808-10823.
[http://dx.doi.org/10.1021/acs.jmedchem.3c01009] [PMID: 37471134]
[63]
Wang, Z.; Zheng, L.; Wang, S.; Lin, M.; Wang, Z.; Kong, A.W.K.; Mu, Y.; Wei, Y.; Li, W. A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function. Brief. Bioinform., 2023, 24(1), bbac520.
[http://dx.doi.org/10.1093/bib/bbac520] [PMID: 36502369]
[64]
Zheng, L.; Meng, J.; Jiang, K.; Lan, H.; Wang, Z.; Lin, M.; Li, W.; Guo, H.; Wei, Y.; Mu, Y. Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term. Brief. Bioinform., 2022, 23(3), bbac051.
[http://dx.doi.org/10.1093/bib/bbac051] [PMID: 35289359]
[65]
Wang, Z.; Zheng, L.; Liu, Y.; Qu, Y.; Li, Y.Q.; Zhao, M.; Mu, Y.; Li, W. OnionNet-2: A convolutional neural network model for predicting protein-ligand binding affinity based on residue-atom contacting shells. Front. Chem., 2021, 9, 753002.
[http://dx.doi.org/10.3389/fchem.2021.753002] [PMID: 34778208]
[66]
Wang, Z.; Zhao, W. Hao, G-F Automated synthesis: Current platforms and further needs. Drug Discov. Today, 2020, 25(11), 2006-2011.
[http://dx.doi.org/10.1016/j.drudis.2020.09.009]
[67]
Martis, E; Radhakrishnan, R; Badve, R. High-throughput screening: The hits and leads of drug discovery-an overview. J. Appl. Pharmaceut. Sci., 2011, 211, 02-10.
[68]
Li, J.; Eastgate, M.D. Making better decisions during synthetic route design: Leveraging prediction to achieve greenness by design. React. Chem. Eng., 2019, 4(9), 1595-1607.
[http://dx.doi.org/10.1039/C9RE00019D]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy