Abstract
Given the time criticality of finding treatments for the novel COVID-19 pandemic disease, drug repurposing has proved to be a vital strategy as the first response while de novo drug and vaccine developments are underway. Furthermore, Artificial Intelligence (AI) has also accelerated drug development in general. Key desirable features of AI that support a rapid and sustained response along the pandemic timeline include technical flexibility and efficiency (i.e. speed, resource-efficiency, algorithm adaptability), and clinical applicability and acceptability (i.e. scientific rigor, physiological applicability and practical implementation of proposed drugs). This chapter reviews a selection of AI-based applications used in drug development targeting COVID-19, including IDentif.AI—a small data platform for a rapid identification of optimal drug combinations, to illustrate the potential of AI in drug repurposing. The benefits and limitations of using Real-World Data are also discussed. The response to the COVID-19 pandemic has offered multiple learnings which highlight the need to strengthen both short- and long-term strategies in developing AI technologies, scientific and regulatory frameworks as well as worldwide collaborations to enable effective preparedness for future epidemic and pandemic risks.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Beck BR, Shin B, Choi Y, et al. Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug–target interaction deep learning model. Comput Struct Biotechnol J. 2020;18:784–90. https://doi.org/10.1016/j.csbj.2020.03.025.
Kadioglu O, Saeed M, Greten HJ, et al. Identification of novel compounds against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Comput Biol Med. 2021;133:104359. https://doi.org/10.1016/j.compbiomed.2021.104359.
Richardson P, Griffin I, Tucker C, et al. Baricitinib as potential treatment for 2019-nCoV acute respiratory disease. Lancet (London, England). 2020;395(10223):e30. https://doi.org/10.1016/S0140-6736(20)30304-4.
Abdulla A, Wang B, Qian F, et al. Project IDentif. AI: harnessing artificial intelligence to rapidly optimize combination therapy development for infectious disease intervention. Adv Ther. 2020;3(7):2000034. https://doi.org/10.1002/adtp.202000034.
Blasiak A, Lim JJ, Seah SGK, et al. IDentif. AI: Rapidly optimizing combination therapy design against severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) with digital drug development. Bioeng Transl Med. 2021a;6(1):e10196. https://doi.org/10.1002/btm2.10196.
Blasiak A, Truong AT, Remus A, et al. The IDentif. AI 2.0 pandemic readiness platform: rapid prioritization of optimized COVID-19 combination therapy regimens. medRxiv. 2021b;2021:9321. https://doi.org/10.1038/s41746-022-00627-4.
Belyaeva A, Cammarata L, Radhakrishnan A, et al. Causal network models of SARS-CoV-2 expression and aging to identify candidates for drug repurposing. Nat Commun. 2021;12:1024. https://doi.org/10.1101/2021.06.23.21259321.
Gysi DM, Do Valle Í, Zitnik M, et al. Network medicine framework for identifying drug-repurposing opportunities for COVID-19. Proc Natl Acad Sci. 2021;118(19):e2025581118. https://doi.org/10.1073/pnas.2025581118.
Zhou Y, Hou Y, Shen J, et al. Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov. 2020a;6:14. https://doi.org/10.1038/s41421-020-0153-3.
Zhou Y, Wang F, Tang J, et al. Artificial intelligence in COVID-19 drug repurposing. Lancet Digit Health. 2020c;2(12):e667–76. https://doi.org/10.1016/S2589-7500(20)30192-8.
Segler MH, Preuss M, Waller MP. Planning chemical syntheses with deep neural networks and symbolic AI. Nature. 2018;555(7698):604–10. https://doi.org/10.1038/nature25978.
Stebbing J, Phelan A, Griffin I, et al. COVID-19: combining antiviral and anti-inflammatory treatments. Lancet Infect Dis. 2020b;20(4):400–2. https://doi.org/10.1016/S1473-3099(20)30132-8.
Zeng X, Song X, Ma T, et al. Repurpose open data to discover therapeutics for COVID-19 using deep learning. J Proteome Res. 2020;19(11):4624–36. https://doi.org/10.1021/acs.jproteome.0c00316.
Galindez G, Matschinske J, Rose TD, et al. Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies. Nat Comput Sci. 2021;1:33–41. https://doi.org/10.1038/s43588-020-00007-6.
Ge Y, Tian T, Huang S, et al. An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. Signal Transduct Target Ther. 2021;6(1):165. https://doi.org/10.1038/s41392-021-00568-6.
Stebbing J, Krishnan V, de Bono S, et al. Mechanism of baricitinib supports artificial intelligence-predicted testing in COVID-19 patients. EMBO Mol Med. 2020a;12(8):e12697. https://doi.org/10.15252/emmm.202012697.
Kalil AC, Patterson TF, Mehta AK, et al. Baricitinib plus remdesivir for hospitalized adults with Covid-19. N Engl J Med. 2021;384(9):795–807. https://doi.org/10.1056/NEJMoa2031994.
Marconi VC, Ramanan AV, de Bono S, et al. Efficacy and safety of baricitinib for the treatment of hospitalised adults with COVID-19 (COV-BARRIER): a randomised, double-blind, parallel-group, placebo-controlled phase 3 trial. Lancet Respir Med. 2021;9(12):1407–18. https://doi.org/10.1016/S2213-2600(21)00331-3.
Khan M, Mehran MT, Haq ZU, et al. Applications of artificial intelligence in COVID-19 pandemic: a comprehensive review. Expert Syst Appl. 2021;185:115695. https://doi.org/10.1016/j.eswa.2021.115695.
Lv H, Shi L, Berkenpas JW, et al. Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design. Brief Bioinform. 2021;22(6):bbab320. https://doi.org/10.1093/bib/bbab320.
Cheng F, Desai RJ, Handy DE, et al. Network-based approach to prediction and population-based validation of in silico drug repurposing. Nat Commun. 2018;9(1):1–12. https://doi.org/10.1038/s41467-018-05116-5.
Guney E, Menche J, Vidal M, et al. Network-based in silico drug efficacy screening. Nat Commun. 2016;7:10331. https://doi.org/10.1038/ncomms10331.
Zhou Y, Hou Y, Shen J, et al. A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PLoS Biol. 2020b;18(11):e3000970. https://doi.org/10.1371/journal.pbio.3000970.
Sun W, Sanderson PE, Zheng W. Drug combination therapy increases successful drug repositioning. Drug Discov Today. 2016;21(7):1189–95. https://doi.org/10.1016/j.drudis.2016.05.015.
Ellinger B, Bojkova D, Zaliani A, et al. A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection. Sci Data. 2021;8(1):1–10. https://doi.org/10.1038/s41597-021-00848-4.
RECOVERY Collaborative Group. Dexamethasone in hospitalized patients with Covid-19. N Engl J Med. 2021;384(8):693–704. https://doi.org/10.1056/NEJMoa2021436.
Peele KA, Durthi CP, Srihansa T, et al. Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: a computational study. Inform Med Unlocked. 2020;19:100345. https://doi.org/10.1016/j.imu.2020.100345.
Muralidharan N, Sakthivel R, Velmurugan D, et al. Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. J Biomol Struct Dyn. 2021;39(7):2673–8. https://doi.org/10.1080/07391102.2020.1752802.
Batra R, Chan H, Kamath G, et al. Screening of therapeutic agents for COVID-19 using machine learning and ensemble docking studies. J Phys Chem Lett. 2020;11(17):7058–65. https://doi.org/10.1021/acs.jpclett.0c02278.
Mohapatra S, Nath P, Chatterjee M, et al. Repurposing therapeutics for COVID-19: rapid prediction of commercially available drugs through machine learning and docking. PLoS One. 2020;15(11):e0241543. https://doi.org/10.1371/journal.pone.0241543.
Anwaar MU, Adnan F, Abro A, et al. Combined deep learning and molecular docking simulations approach identifies potentially effective FDA approved drugs for repurposing against SARS-CoV-2. Comput Biol Med. 2022;141:105049. https://doi.org/10.1016/j.compbiomed.2021.105049.
Gimeno A, Ojeda-Montes MJ, Tomás-Hernández S, et al. The light and dark sides of virtual screening: what is there to know? Int J Mol Sci. 2019;20(6):1375. https://doi.org/10.3390/ijms20061375.
Marklund EG, Benesch JL. Weighing-up protein dynamics: the combination of native mass spectrometry and molecular dynamics simulations. Curr Opin Struct Biol. 2019;54:50–8. https://doi.org/10.1016/j.sbi.2018.12.011.
Al-Shyoukh I, Yu F, Feng J, et al. Systematic quantitative characterization of cellular responses induced by multiple signals. BMC Syst Biol. 2011;5(88):1–17. https://doi.org/10.1186/1752-0509-5-88.
Ding X, Sanchez DJ, Shahangian A, et al. Cascade search for HSV-1 combinatorial drugs with high antiviral efficacy and low toxicity. Int J Nanomedicine. 2012;7:2281. https://doi.org/10.2147/IJN.S27540.
Honda Y, Ding X, Mussano F, et al. Guiding the osteogenic fate of mouse and human mesenchymal stem cells through feedback system control. Sci Rep. 2013;3:3420. https://doi.org/10.1038/srep03420.
Liu Q, Zhang C, Ding X, et al. Preclinical optimization of a broad-spectrum anti-bladder cancer tri-drug regimen via the Feedback System Control (FSC) platform. Sci Rep. 2015;5:11464. https://doi.org/10.1038/srep11464.
Tekin E, White C, Kang TM, et al. Prevalence and patterns of higher-order drug interactions in Escherichia coli. NPJ Syst Biol Appl. 2018;4(1):1–10. https://doi.org/10.1038/s41540-018-0069-9.
Tsutsui H, Valamehr B, Hindoyan A, et al. An optimized small molecule inhibitor cocktail supports long-term maintenance of human embryonic stem cells. Nat Commun. 2011;2:167. https://doi.org/10.1038/ncomms1165.
Valamehr B, Tsutsui H, Ho C-M, et al. Developing defined culture systems for human pluripotent stem cells. Regen Med. 2011;6(5):623–34. https://doi.org/10.2217/rme.11.54.
Wang H, Silva A, Ho C-M. When medicine meets engineering—paradigm shifts in diagnostics and therapeutics. Diagnostics. 2013;3(1):126–54. https://doi.org/10.3390/diagnostics3010126.
Wei F, Bai B, Ho C-M. Rapidly optimizing an aptamer based BoNT sensor by feedback system control (FSC) scheme. Biosens Bioelectron. 2011;30(1):174–9. https://doi.org/10.1016/j.bios.2011.09.014.
Weiss A, Berndsen RH, Ding X, et al. A streamlined search technology for identification of synergistic drug combinations. Sci Rep. 2015;5:14508. https://doi.org/10.1038/srep14508.
Wong PK, Yu F, Shahangian A, et al. Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm. Proc Natl Acad Sci. 2008;105(13):5105–10. https://doi.org/10.1073/pnas.0800823105.
Yu F, Al-Shyoukh I, Feng J, et al. Control of Kaposi’s sarcoma-associated herpesvirus reactivation induced by multiple signals. PLoS One. 2011;6(6):e20998. https://doi.org/10.1371/journal.pone.0020998.
Yu H, Zhang WL, Ding X, et al. Optimizing combinations of flavonoids deriving from astragali radix in activating the regulatory element of erythropoietin by a feedback system control scheme. Evid Based Complement Alternat Med. 2013;2013:1436. https://doi.org/10.1155/2013/541436.
Xu H, Jaynes J, Ding X. Combining two-level and three-level orthogonal arrays for factor screening and response surface exploration. Stat Sin. 2014;24(1):269–89. https://www.jstor.org/stable/26432543
de Mel S, Rashid MB, Zhang XY, et al. Application of an ex-vivo drug sensitivity platform towards achieving complete remission in a refractory T-cell lymphoma. Blood Cancer J. 2020;10(9):1–5. https://doi.org/10.1038/s41408-020-0276-7.
Rashid MBMA, Toh TB, Hooi L, et al. Optimizing drug combinations against multiple myeloma using a quadratic phenotypic optimization platform (QPOP). Sci Transl Med. 2018;10(453):eaan0941. https://doi.org/10.1126/scitranslmed.aan0941.
Clemens DL, Lee B-Y, Silva A, et al. Artificial intelligence enabled parabolic response surface platform identifies ultra-rapid near-universal TB drug treatment regimens comprising approved drugs. PLoS One. 2019;14(5):e0215607. https://doi.org/10.1371/journal.pone.0215607.
Lee B-Y, Clemens DL, Silva A, et al. Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time. Nat Commun. 2017;8:14183. https://doi.org/10.1038/ncomms14183.
Lee B-Y, Clemens DL, Silva A, et al. Ultra-rapid near universal TB drug regimen identified via parabolic response surface platform cures mice of both conventional and high susceptibility. PLoS One. 2018;13(11):e0207469. https://doi.org/10.1371/journal.pone.0207469.
Shen Y, Liu T, Chen J, et al. Harnessing artificial intelligence to optimize long-term maintenance dosing for antiretroviral-naive adults with HIV-1 infection. Adv Ther. 2020;3(4):1900114. https://doi.org/10.1002/adtp.201900114.
Sun J, Wang B, Warden AR, et al. Overcoming multidrug-resistance in bacteria with a two-step process to repurpose and recombine established drugs. Anal Chem. 2019;91(21):13562–9. https://doi.org/10.1021/acs.analchem.9b02690.
Jarow JP, LaVange L, Woodcock J. Multidimensional evidence generation and FDA regulatory decision making: defining and using “real-world” data. JAMA. 2017;318(8):703–4. https://doi.org/10.1001/jama.2017.9991.
Makady A, de Boer A, Hillege H, et al. What is real-world data? A review of definitions based on literature and stakeholder interviews. Value Health. 2017;20(7):858–65. https://doi.org/10.1016/j.jval.2017.03.008.
Chen Z, Liu X, Hogan W, et al. Applications of artificial intelligence in drug development using real-world data. Drug Discov Today. 2021;26(5):1256–64. https://doi.org/10.1016/j.drudis.2020.12.013.
Wichniak A, Kania A, Siemiński M, et al. Melatonin as a potential adjuvant treatment for COVID-19 beyond sleep disorders. Int J Mol Sci. 2021;22(16):8623. https://doi.org/10.3390/ijms22168623.
Cave A, Kurz X, Arlett P. Real-world data for regulatory decision making: challenges and possible solutions for Europe. Clin Pharmacol Ther. 2019;106(1):36–9. https://doi.org/10.1002/cpt.1426.
Li Q, Lin J, Chi A, et al. Practical considerations of utilizing propensity score methods in clinical development using real-world and historical data. Contemp Clin Trials. 2020;97:106123. https://doi.org/10.1038/srep11464.
Prats-Uribe A, Sena AG, Lai LYH, et al. Use of repurposed and adjuvant drugs in hospital patients with Covid-19: multinational network cohort study. BMJ. 2021;373:n1038. https://doi.org/10.1136/bmj.n1038.
World Health Organization. WHO, Germany open hub for pandemic and epidemic intelligence in Berlin. 2021. https://www.who.int/news/item/01-09-2021-who-germany-open-hub-for-pandemic-and-epidemic-intelligence-in-berlin. Accessed 12 Jan 2022.
Blasiak A, Kee TW, Rashid MBM, et al. CURATE.AI-optimized modulation for multiple myeloma: an N-of-1 randomized trial [abstract]. AACR. Cancer Res. 2020a;80:CT268. https://doi.org/10.1158/1538-7445.am2020-ct268.
Blasiak A, Khong J, Kee T. CURATE.AI: optimizing personalized medicine with artificial intelligence. SLAS Technol. 2020b;25(2):95–105. https://doi.org/10.1177/2472630319890316.
Ho D. Artificial intelligence in cancer therapy. Science. 2020a;367(6481):982–3. https://doi.org/10.1126/science.aaz3023.
Ho D. Addressing COVID-19 drug development with artificial intelligence. Adv Intell Syst. 2020b;2(5):2000070. https://doi.org/10.1002/aisy.202000070.
Pantuck AJ, Lee D-K, Kee T, et al. Modulating BET bromodomain inhibitor ZEN-3694 and enzalutamide combination dosing in a metastatic prostate cancer patient using CURATE.AI, an artificial intelligence platform. Adv Ther. 2018;1(6):1800104. https://doi.org/10.1002/adtp.201800104.
Tan BKJ, Teo CB, Tadeo X, et al. Personalised, rational, efficacy-driven cancer drug dosing via an artificial Intelligence SystEm (PRECISE): a protocol for the PRECISE CURATE. AI pilot clinical trial. Front Digit Health. 2021;3(16):5524. https://doi.org/10.3389/fdgth.2021.635524.
Truong AT, Tan LW, Chew KA, et al. Harnessing CURATE. AI for N-of-1 optimization analysis of combination therapy in hypertension patients: a retrospective case series. Adv Ther. 2021;4(10):2100091. https://doi.org/10.1002/adtp.202100091.
Zarrinpar A, Lee D-K, Silva A, et al. Individualizing liver transplant immunosuppression using a phenotypic personalized medicine platform. Sci Transl Med. 2016;8(333):333ra49. https://doi.org/10.1126/scitranslmed.aac5954.
Gentile F, Agrawal V, Hsing M, et al. Deep docking: a deep learning platform for augmentation of structure based drug discovery. ACS Cent Sci. 2020;6(6):939–49. https://doi.org/10.1021/acscentsci.0c00229.
WHO Rapid Evidence Appraisal for COVID-19 Therapies (REACT) Working Group, Sterne JA, Murthy S, et al. Association between administration of systemic corticosteroids and mortality among critically ill patients with COVID-19: a meta-analysis. JAMA. 2020;324(13):1330–41. https://doi.org/10.1001/jama.2020.17023.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this chapter
Cite this chapter
Truong, A.T.L., Blasiak, A., Egermark, M., Ho, D. (2022). AI for Drug Repurposing in the Pandemic Response. In: Lidströmer, N., Eldar, Y.C. (eds) Artificial Intelligence in Covid-19. Springer, Cham. https://doi.org/10.1007/978-3-031-08506-2_3
Download citation
DOI: https://doi.org/10.1007/978-3-031-08506-2_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-08505-5
Online ISBN: 978-3-031-08506-2
eBook Packages: MedicineMedicine (R0)