Applied Chemical Engineering

Applications of artificial intelligence in the synthesis, docking, and pharmacological profiling of coumarins

Yasser Fakri Mustafa

Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, 41001, Iraq

DOI: https://doi.org/10.59429/ace.v8i2.5678

Keywords: artificial intelligence; drug discovery; machine learning; molecular docking; pharmacological profiling

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Abstract

Coumarins, a diverse class of benzopyrone derivatives, have long captivated researchers due to their broad spectrum of pharmacological activities and synthetic versatility. In recent years, the convergence of artificial intelligence (AI) with pharmaceutical sciences has redefined how researchers approach the synthesis, molecular docking, and pharmacological profiling of such bioactive compounds. This review explores the transformative potential of AI in the context of coumarin research, presenting a holistic view of how machine learning algorithms, deep learning models, and data-driven design strategies are reshaping drug discovery. Traditional synthesis of coumarins, often constrained by multistep protocols and environmental concerns, is now being revolutionized through AI-assisted reaction predictions and retrosynthetic analyses. AI enables the generation of synthetically accessible molecules with optimized structural features, significantly reducing time and resource investment. Furthermore, molecular docking, critical to understanding structure-activity relationships, is increasingly benefiting from AI-enhanced scoring functions and predictive modeling, thus improving the accuracy of ligand-receptor interaction predictions. Pharmacological profiling, both in vitro and in vivo, is becoming more streamlined with AI models capable of predicting bioactivity, toxicity, and pharmacokinetics, making the lead optimization process more efficient and reliable. Public databases, curated datasets, and integrative cheminformatics platforms now provide a rich foundation for data mining and drug-target interaction studies. This review not only highlights the successes of AI in coumarin-based drug design but also discusses existing challenges, including algorithm interpretability, data quality, and regulatory considerations. Ultimately, the synergy between AI and coumarin research presents an exciting frontier that holds immense promise for accelerating drug discovery and advancing personalized therapeutics.

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[123]. Mustafa YF, Hassan DA, Faisal AF, Alshaher MM. Synthesis of novel skipped diene-3-halocoumarin conjugates as potent anticancer and antibacterial biocompatible agents. Results in Chemistry. 2024;11:101846.

[124]. Mustafa YF, Khalil RR, Mohammed ET. Antimicrobial activity of aqueous extracts acquired from the seeds of two apples ’ cultivars. Systematic Reviews in Pharmacy. 2020;11(2):382–7.

[125]. Batran RZ, Ebaid MS, Nasralla SN, Son NT, Ha NX, Abdelsattar Ibrahim HA, Alkabbani MA, Kasai Y, Imagawa H, Al-Sanea MM, Ibrahim TM, Elshamy AI, Bekhit AA, Eldehna WM, Sabt A. Synthesis and mechanistic insights of Coumarinyl-Indolinone hybrids as potent inhibitors of Leishmania major. European Journal of Medicinal Chemistry. 2025;288:117392.

[126]. Zeki MN, Mustafa YF. Synthesis and evaluation of novel ring-conjugated coumarins as biosafe broad-spectrum antimicrobial candidates. Journal of Molecular Structure. 2024;1309:138192.

[127]. Wang Z, Pan F, Zhang M, Liang S, Tian W. Discovery of potential anti- Staphylococcus aureus natural products and their mechanistic studies using machine learning and molecular dynamic simulations. Heliyon. 2024;10(9):e30389.

[128]. Mustafa YF, Bashir MK, Oglah MK, Khalil RR, Mohammed ET. Bioactivity of some natural and semisynthetic coumarin derived compounds. NeuroQuantology. 2021;19(6):129–38.

[129]. Abdelbasset WK, Jasim SA, Sharma SK, Margiana R, Bokov DO, Obaid MA, Hussein BA, Lafta HA, Jasim SF, Mustafa YF. Alginate-Based Hydrogels and Tubes, as Biological Macromolecule-Based Platforms for Peripheral Nerve Tissue Engineering: A Review. Annals of Biomedical Engineering. 2022;50(6):628–53.

[130]. Mustafa YF, Ismael RN, Jebir RM. Natural coumarins from two cultivars of watermelon seeds as biosafe anticancer agents, an algorithm for their isolation and evaluation. Journal of Molecular Structure. 2024;1295(P1):136644.

[131]. Mustafa YF. Nutraceutical-based telomerase inhibitors: Renewed hope for cancer therapy. Phytomedicine Plus. 2024;4(2):100537.

[132]. McKay K, Hamilton NB, Remington JM, Schneebeli ST, Li J. Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery. Frontiers in Molecular Biosciences. 2022;9:879212.

[133]. Mustafa YF. Coumarins from toxic phenol: An algorithm of their synthesis and assessment as biosafe, wide-spectrum, potent antimicrobial prospects. Applied Chemical Engineering. 2024;7(3):5527.

[134]. Mustafa YF. Classical approaches and their creative advances in the synthesis of coumarins: A brief review. Journal of Medicinal and Chemical Sciences. 2021;4(6):612–25.

[135]. Mustafa YF, Mohammed NA alwahab. A promising oral 5-fluorouracil prodrug for lung tumor: Synthesis, characterization and release. Biochemical and Cellular Archives. 2021;21(Supp 1):1991–9.

[136]. Wang K, Huang Y, Wang Y, You Q, Wang L. Recent advances from computer-aided drug design to artificial intelligence drug design. RSC Medicinal Chemistry. 2024;15(12):3978–4000.

[137]. Trachtenberg A, Akabayov B. From Patterns to Pills: How Informatics Is Shaping Medicinal Chemistry. Pharmaceutics. 2025;17(5):612.

[138]. Zeki NM, Mustafa YF. Coumarin hybrids for targeted therapies: A promising approach for potential drug candidates. Phytochemistry Letters. 2024;60:117–33.

[139]. Douka MD, Sigala IM, Gabriel C, Nikolakaki E, Hadjipavlou-Litina DJ, Litinas KE. Pharmacochemical Studies of Synthesized Coumarin–Isoxazole–Pyridine Hybrids. Molecules. 2025;30(7):1592.

[140]. Correa de Moraes M, Frassini R, Roesch-Ely M, Reisdorfer de Paula F, Barcellos T. Novel Coumarin–Nucleobase Hybrids with Potential Anticancer Activity: Synthesis, In Vitro Cell-Based Evaluation, and Molecular Docking. Pharmaceuticals. 2024;17(7):956.

[141]. Zeki NM, Mustafa YF. Coumarin hybrids: a sighting of their roles in drug targeting. Chemical Papers. 2024;78:5753–5772.

[142]. Mustafa YF, Mohammed ET, Khalil RR. Antioxidant and antitumor activities of methanolic extracts obtained from Red Delicious and Granny Smith apples’ seeds. Systematic Reviews in Pharmacy. 2020;11(4):570–6.

[143]. Atia YA, Bokov DO, Zinnatullovich KR, Kadhim MM, Suksatan W, Abdelbasset WK, Hammoodi HA, Mustafa YF, Cao Y. The role of amino acid functionalization for improvement of adsorption Thioguanine anticancer drugs on the boron nitride nanotubes for drug delivery. Materials Chemistry and Physics. 2022;278:125664.

[144]. Abdelbasset WK, Savina SV, Mavaluru D, Shichiyakh RA, Bokov DO, Mustafa YF. Smartphone based aptasensors as intelligent biodevice for food contamination detection in food and soil samples: Recent advances. Talanta. 2023;252:123769.

[145]. David L, Thakkar A, Mercado R, Engkvist O. Molecular representations in AI-driven drug discovery: a review and practical guide. Journal of Cheminformatics. 2020;12(1):56.

[146]. Wan Z, Sun X, Li Y, Chu T, Hao X, Cao Y, Zhang P. Applications of Artificial Intelligence in Drug Repurposing. Advanced Science. 2025;12(14):2411325.

[147]. Khalil RR, Mohammed ET, Mustafa YF. Various promising biological effects of Cranberry extract: A review. Clinical Schizophrenia and Related Psychoses. 2021;15(S6):1–9.

[148]. Visan AI, Negut I. Integrating Artificial Intelligence for Drug Discovery in the Context of Revolutionizing Drug Delivery. Life. 2024;14(2):233.

[149]. Mustafa YF. Chemotherapeutic applications of folate prodrugs: A review. NeuroQuantology. 2021;19(8):99–112.

[150]. Mustafa YF, Abdulaziza NT, Jasima MH. 4-Methylumbelliferone and its derived compounds: A brief review of their cytotoxicity. Egyptian Journal of Chemistry. 2021;64(4):1807–16.

[151]. Maashi MS, Al-Mualm M, Al-Awsi GRL, Opulencia MJC, Al-Gazally ME, Abdullaev B, Abdelbasset WK, Ansari MJ, Jalil AT, Alsaikhan F, Shalaby MN, Mustafa YF. Apigenin alleviates resistance to doxorubicin in breast cancer cells by acting on the JAK/STAT signaling pathway. Molecular Biology Reports. 2022;49(9):8777–84.

[152]. Patil VM, Gupta SP, Masand N, Balasubramanian K. Experimental and computational models to understand protein-ligand, metal-ligand and metal-DNA interactions pertinent to targeted cancer and other therapies. European Journal of Medicinal Chemistry Reports. 2024;10:100133.

[153]. Vasilev B, Atanasova M. A (Comprehensive) Review of the Application of Quantitative Structure–Activity Relationship (QSAR) in the Prediction of New Compounds with Anti-Breast Cancer Activity. Applied Sciences. 2025;15(3):1206.

[154]. Rodrigo-Ginés FJ, Carrillo-de-Albornoz J, Plaza L. A systematic review on media bias detection: What is media bias, how it is expressed, and how to detect it. Expert Systems with Applications. 2024;237:121641.

[155]. Mustafa YF, Oglah MK, Bashir MK. Conjugation of sinapic acid analogues with 5- Fluorouracil: Synthesis, preliminary cytotoxicity, and release study. Systematic Reviews in Pharmacy. 2020;11(3):482–9.

[156]. Bashir MK, Mustafa YF, Oglah MK. Antitumor, antioxidant, and antibacterial activities of glycosyl-conjugated compounds: A review. Systematic Reviews in Pharmacy. 2020;11(4):175–87.

[157]. Wu WT, Li YJ, Feng AZ, Li L, Huang T, Xu AD, Lyu J. Data mining in clinical big data: the frequently used databases, steps, and methodological models. Military Medical Research. 2021;8(1):44.

[158]. Sovacool BK, Hess DJ, Amir S, Geels FW, Hirsh R, Rodriguez Medina L, Miller C, Alvial Palavicino C, Phadke R, Ryghaug M, Schot J, Silvast A, Stephens J, Stirling A, Turnheim B, van der Vleuten E, van Lente H, Yearley S. Sociotechnical agendas: Reviewing future directions for energy and climate research. Energy Research & Social Science. 2020;70:101617.

[159]. Suksatan W, Chupradit S, Valerievich Yumashev A, Ravali S, Nader Shalaby M, Fakri Mustafa Y, Kurochkin A, Siahmansouri H. Immunotherapy of multisystem inflammatory syndrome in children (MIS-C) following COVID-19 through mesenchymal stem cells. International Immunopharmacology. 2021;101(PB):108217.

[160]. Mustafa YF, Kasim SM, Al-Dabbagh BM, Al-Shakarchi W. Synthesis, characterization and biological evaluation of new azo-coumarinic derivatives. Applied Nanoscience (Switzerland). 2023;13:1095–1102.

[161]. Mahmudiono T, Singhal S, Mohammad AA, Failoc-Rojas VE, Catalan Opulencia MJ, Haro AS, Salam Karim Y, Qurbonov N, Kamal Abdelbasset W, Mahdi AB, Fakri Mustafa Y. The impact of aerosol box on tracheal intubation during the COVID‐19 pandemic: a systematic review. Expert Review of Medical Devices. 2022;19(10):779–89.

[162]. Hu A, Li J, Tang W, Liu G, Zhang H, Liu C, Chen X. Anthralin Suppresses the Proliferation of Influenza Virus by Inhibiting the Cap-Binding and Endonuclease Activity of Viral RNA Polymerase. Frontiers in Microbiology. 2020;11:00178.

[163]. Lai Y, Han T, Zhan S, Jiang Y, Liu X, Li G. Antiviral Activity of Isoimperatorin Against Influenza A Virus in vitro and its Inhibition of Neuraminidase. Frontiers in Pharmacology. 2021;12:657826.

[164]. Zan N, Li J, Yao J, Wu S, Li J, Chen F, Song B, Song R. Rational design of phytovirucide inhibiting nucleocapsid protein aggregation in tomato spotted wilt virus. Nature Communications. 2025;16(1):2034.

[165]. Mustafa YF, Zain Al-Abdeen SH, Khalil RR, Mohammed ET. Novel functionalized phenyl acetate derivatives of benzo [e]-bispyrone fused hybrids: Synthesis and biological activities. Results in Chemistry. 2023;5:100942.

[166]. Mustafa YF, Abdulaziz NT. Biological potentials of hymecromone-based derivatives: A systematic review. Systematic Reviews in Pharmacy. 2020;11(11):438–52.

[167]. Abdulaziz NT, Al-bazzaz FY, Mustafa YF. Natural products for attenuating Alzheimer’s disease: A narrative review. Eurasian Chemical Communications. 2023;5(4):358–70.

[168]. Mahmood AAJ, Mustafa YF, Abdulstaar M. New coumarinic azo-derivatives of metoclopramide and diphenhydramine: Synthesis and in vitro testing for cholinesterase inhibitory effect and protection ability against chlorpyrifos. International Medical Journal Malaysia. 2014;13(1):3–12.

[169]. Salamanova E, Atanasova M, Doytchinova I. A Novel Galantamine–Curcumin Hybrid Inhibits Butyrylcholinesterase: A Molecular Dynamics Study. Chemistry. 2024;6(6):1645–57.

[170]. Abu-Aisheh MN, Al-Aboudi A, Mustafa MS, El-Abadelah MM, Ali SY, Ul-Haq Z, Mubarak MS. Coumarin derivatives as acetyl- and butyrylcholinestrase inhibitors: An in vitro, molecular docking, and molecular dynamics simulations study. Heliyon. 2019;5(4):e01552.

[171]. Widjaja G, Doewes R iqbal, Rudiansyah M, Sultan MQ, Ansari MJ, Izzat SE, Al Jaber MS, Kzar HH, Mustafa YF, Hammid AT, Turki Jalil A, Aravindhan S. Effect of tomato consumption on inflammatory markers in health and disease status: A systematic review and meta-analysis of clinical trials. Clinical Nutrition ESPEN. 2022;50:93–100.

[172]. Hussein HK, Aubead NM, Kzar HH, Karim YS, Amin AH, Al-Gazally ME, Ahmed TI, Jawad MA, Hammid AT, Jalil AT, Mustafa YF, Saleh MM, Heydari H. Association of cord blood asprosin concentration with atherogenic lipid profile and anthropometric indices. Diabetology & Metabolic Syndrome. 2022;14(1):74.

[173]. Aldewachi H, Mustafa YF, Najm R, Ammar F. Adulteration of Slimming Products and its Detection Methods. Systematic Reviews in Pharmacy. 2020;11(3):289–96.

[174]. Kasim SM, Abdulaziz NT, Jasim MH, Mustafa YF. Resveratrol in cancer chemotherapy: Is it a preventer, protector, or fighter? Eurasian Chemical Communications. 2023;5(7):576–87.

[175]. Li G, Chen W, Liu D, Tang S. Recent advances in medicinal chemistry strategies for the development of METTL3 inhibitors. European Journal of Medicinal Chemistry. 2025;290:117560.

[176]. Robison AD, Finkelstein IJ. High‐throughput single‐molecule studies of protein–DNA interactions. FEBS Letters. 2014;588(19):3539–46.

[177]. Firoozeh AZ, Bokov DO, Salahdin OD, Abdelbasset WK, Jawad MA, Kadhi MM, Qasim MT, Kzar HH, Al-Gazally ME, Mustafa YF, Khatami M. Cytotoxicity evaluation of environmentally friendly synthesis Copper/Zinc bimetallic nanoparticles on MCF7 cancer cells. Rendiconti Lincei Scienze Fisiche e Naturali. 2022;33:441–7.

[178]. Javed M, Saade A, Jasim A, Zeedan T, Dmitry T, Bokov O, Shalaby MNMEAG, Kzar HH, Qasim MT, Mustafa YF, Khatami M. Anticancer Drug-Loading Capacity of Green Synthesized Porous Magnetic Iron Nanocarrier and Cytotoxic Effects Against Human Cancer Cell Line. Journal of Cluster Science. 2022;4:44–7.

[179]. Askr H, Elgeldawi E, Aboul Ella H, Elshaier YAMM, Gomaa MM, Hassanien AE. Deep learning in drug discovery: an integrative review and future challenges. Artificial Intelligence Review. 2023;56(7):5975–6037.

[180]. Addis P, Bali U, Baron F, Campbell A, Harborne S, Jagger L, Milne G, Pearce M, Rosethorne EM, Satchell R, Swift D, Young B, Unitt JF. Key aspects of modern GPCR drug discovery. SLAS Discovery. 2024;29(1):1–22.

[181]. Kasim SM, Abdulaziz NT, Mustafa YF. Synthesis and biomedical activities of coumarins derived from natural phenolic acids. Journal of Medicinal and Chemical Sciences. 2022;5(4):546–60.

[182]. Khalil RR, Mohammed ET, Mustafa YF. Evaluation of in vitro antioxidant and antidiabetic properties of Cydonia Oblonga seeds’ extracts. Journal of Medicinal and Chemical Sciences. 2022;5(6):1048–58.

[183]. Vázquez J, López M, Gibert E, Herrero E, Luque FJ. Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches. Molecules. 2020;25(20):4723.

[184]. Hage DS. Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications. Clinical Chemistry. 2017;63(6):1083–93.

[185]. Mustafa YF, Khalil RR, Mohammed ET, Bashir MK, Oglah MK. Effects of structural manipulation on the bioactivity of some coumarin-based products. Archives of Razi Institute. 2021;76(5):1297–305.

[186]. Mohammed ET, Mustafa YF. Coumarins from Red Delicious apple seeds: Extraction, phytochemical analysis, and evaluation as antimicrobial agents. Systematic Reviews in Pharmacy. 2020;11(2):64–70.

[187]. Song J. Applications of the Cellular Thermal Shift Assay to Drug Discovery in Natural Products: A Review. International Journal of Molecular Sciences. 2025;26(9):3940.

[188]. Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J, Wang L, Yang X, Yang M, Liu G. Applications of multi‐omics analysis in human diseases. MedComm. 2023;4(4):e315.

[189]. Budi HS, Younus LA, Lafta MH, Parveen S, Mohammad HJ, Al-qaim ZH, Jawad MA, Parra RMR, Mustafa YF, Alhachami FR, Karampoor S, Mirzaei R. The role of miR-128 in cancer development, prevention, drug resistance, and immunotherapy. Frontiers in Oncology. 2023;12:1067974.

[190]. Fu L, Jia G, Liu Z, Pang X, Cui Y. The applications and advances of artificial intelligence in drug regulation: A global perspective. Acta Pharmaceutica Sinica B. 2025;15(1):1–14.

[191]. Margiana R, Hammid AT, Ahmad I, Alsaikhan F, Turki Jalil A, Tursunbaev F, Umar F, Romero Parra RM, Fakri Mustafa Y. Current Progress in Aptasensor for Ultra-Low Level Monitoring of Parkinson’s Disease Biomarkers. Critical Reviews in Analytical Chemistry. 2024;54(3):617–32.

[192]. Mustafa YF. Modern Developments in the Application and Function of Metal/Metal Oxide Nanocomposite–Based Antibacterial Agents. BioNanoScience. 2023;13:840–52.

[193]. Mustafa YF. Synthesis, characterization, and biomedical assessment of novel bisimidazole–coumarin conjugates. Applied Nanoscience (Switzerland). 2023;13(3):1907–18.

[194]. Fu C, Chen Q. The future of pharmaceuticals: Artificial intelligence in drug discovery and development. Journal of Pharmaceutical Analysis. 2025;101248.

[195]. Mustafa YF, Khalil RR, Mohammed ET. Synthesis and antitumor potential of new 7-halocoumarin-4-acetic acid derivatives. Egyptian Journal of Chemistry. 2021;64(7):3711–6.

[196]. Oglah MK, Mustafa YF. Curcumin analogs: synthesis and biological activities. Medicinal Chemistry Research. 2020;29(3):479–86.

[197]. Khalil RR, Mustafa YF. Phytochemical, antioxidant and antitumor studies of coumarins extracted from Granny Smith apple seeds by different methods. Systematic Reviews in Pharmacy. 2020;11(2):57–63.

[198]. Vijayan RSK, Kihlberg J, Cross JB, Poongavanam V. Enhancing preclinical drug discovery with artificial intelligence. Drug Discovery Today. 2022;27(4):967–84.

[199]. Sadeghi Z, Alizadehsani R, CIFCI MA, Kausar S, Rehman R, Mahanta P, Bora PK, Almasri A, Alkhawaldeh RS, Hussain S, Alatas B, Shoeibi A, Moosaei H, Hladík M, Nahavandi S, Pardalos PM. A review of Explainable Artificial Intelligence in healthcare. Computers and Electrical Engineering. 2024;118:109370.

[200]. Ocana A, Pandiella A, Privat C, Bravo I, Luengo-Oroz M, Amir E, Gyorffy B. Integrating artificial intelligence in drug discovery and early drug development: a transformative approach. Biomarker Research. 2025;13(1):45.

[201]. Niazi SK, Mariam Z. Artificial intelligence in drug development: reshaping the therapeutic landscape. Therapeutic Advances in Drug Safety. 2025;16.

[202]. Gangwal A, Lavecchia A. Artificial intelligence in anti-obesity drug discovery: unlocking next-generation therapeutics. Drug Discovery Today. 2025;30(4):104333.

[203]. Jiang W, Ye W, Tan X, Bao YJ. Network-based multi-omics integrative analysis methods in drug discovery: a systematic review. BioData Mining. 2025;18(1):27.

[204]. Jasim SF, Mustafa YF. Synthesis, ADME Study, and antimicrobial evaluation of novel naphthalene-based derivatives. Journal of Medicinal and Chemical Sciences. 2022;5(5):793–807.

[205]. Sorokina M, Merseburger P, Rajan K, Yirik MA, Steinbeck C. COCONUT online: Collection of Open Natural Products database. Journal of Cheminformatics. 2021;13(1):2.

[206]. Freshour SL, Kiwala S, Cotto KC, Coffman AC, McMichael JF, Song JJ, Griffith M, Griffith OL, Wagner AH. Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Research. 2021;49(D1):D1144–51.

[207]. Mustafa YF. New Coumarin-Metronidazole Composites: Synthesis, Biocompatibility, and Anti-anaerobic Bacterial Activity. Russian Journal of Bioorganic Chemistry. 2024;50(1):201–10.

[208]. Hassija V, Chamola V, Mahapatra A, Singal A, Goel D, Huang K, Scardapane S, Spinelli I, Mahmud M, Hussain A. Interpreting Black-Box Models: A Review on Explainable Artificial Intelligence. Cognitive Computation. 2024;16(1):45–74.

[209]. Saarela M, Podgorelec V. Recent Applications of Explainable AI (XAI): A Systematic Literature Review. Applied Sciences. 2024;14(19):8884.

[210]. Kibriya H, Siddiqa A, Khan WZ, Khan MK. Towards safer online communities: Deep learning and explainable AI for hate speech detection and classification. Computers and Electrical Engineering. 2024;116:109153.

[211]. Antoniadi AM, Du Y, Guendouz Y, Wei L, Mazo C, Becker BA, Mooney C. Current Challenges and Future Opportunities for XAI in Machine Learning-Based Clinical Decision Support Systems: A Systematic Review. Applied Sciences. 2021;11(11):5088.

[212]. Kamal IK, Mahmood AT, Mustafa YF. Synthesis of Eugenol-Derived Coumarins as Broad-Spectrum Biosafe Antimicrobial Agents. Russian Journal of Bioorganic Chemistry. 2024;50(6):2240–51.