Volume : 13, Issue : 04, April – 2026
Title:
RECENT ADVANCES IN STRUCTURE-BASED DRUG DESIGN AND COMPUTATIONAL APPROACHES IN MEDICINAL CHEMISTRY FOR NOVEL THERAPEUTIC DEVELOPMENT
Authors :
Mr. Saurabh V. Kaulagi*, Mr. Baliram B. Saravade, Dr. Amit N. Panaskar, Dr. Bhayashri A. Panaskar, Dr. Kotresh Yaligar
Abstract :
Structure-Based Drug Design (SBDD) and computational approaches have revolutionized modern medicinal chemistry by enabling the rational and efficient development of novel therapeutic agents. Traditional drug discovery methods, which largely rely on trial-and-error strategies, are often time-consuming, costly, and associated with high failure rates. In contrast, SBDD utilizes the three-dimensional structural information of biological targets to design molecules with enhanced specificity, affinity, and pharmacological activity. The integration of computational techniques such as molecular docking, molecular dynamics simulations, quantitative structure–activity relationship (QSAR) modeling, pharmacophore mapping, and virtual screening has significantly accelerated the identification and optimization of lead compounds. Recent advancements, including cryo-electron microscopy (cryo-EM), fragment-based drug design, covalent inhibitor development, allosteric targeting, and the incorporation of multi-omics data, have further expanded the scope and applicability of SBDD. Additionally, the emergence of artificial intelligence (AI), machine learning (ML), big data analytics, and high-performance computing (HPC) has transformed drug discovery into a data-driven and predictive process. These technologies facilitate accurate prediction of drug–target interactions, pharmacokinetic properties, and toxicity profiles, thereby reducing late-stage failures. Despite these advancements, challenges such as data quality, computational limitations, and the gap between in silico predictions and in vivo outcomes remain. This review provides a comprehensive overview of recent advances in SBDD and computational drug design, highlighting their principles, applications, advantages, and limitations. Furthermore, it emphasizes the future potential of integrating computational and experimental approaches to develop safe, effective, and personalized therapeutics.
Keywords: Structure-Based Drug Design; Computational Drug Discovery; Molecular Docking; Molecular Dynamics; QSAR; Pharmacophore Modeling; Artificial Intelligence; Machine Learning; Fragment-Based Drug Design; Cryo-EM; Drug–Target Interaction; ADMET Prediction; Medicinal Chemistry
Cite This Article:
Please cite this article in press Saurabh V. Kaulagi et al., Recent Advances In Structure-Based Drug Design And Computational Approaches In Medicinal Chemistry For Novel Therapeutic Development., Indo Am. J. P. Sci, 2026; 13(04).
REFERENCES:
1. Lionta E, Spyrou G, Vassilatis DK, Cournia Z. Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem. 2014;14(16):1923–38.
2. Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery. Nat Rev Drug Discov. 2004;3(11):935–49.
3. Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies. Molecules. 2015;20(7):13384–421.
4. Meng XY, Zhang HX, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011;7(2):146–57.
5. Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4. J Comput Chem. 2009;30(16):2785–91.
6. Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for docking. J Med Chem. 2004;47(7):1739–49.
7. Hollingsworth SA, Dror RO. Molecular dynamics simulation for all. Neuron. 2018;99(6):1129–43.
8. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002;9(9):646–52.
9. Trott O, Olson AJ. AutoDock Vina: improving docking speed. J Comput Chem. 2010;31(2):455–61.
10. Lavecchia A, Di Giovanni C. Virtual screening strategies in drug discovery. Curr Med Chem. 2013;20(23):2839–60.
11. Cherkasov A, Muratov EN, Fourches D, et al. QSAR modeling: where have you been? J Med Chem. 2014;57(12):4977–5010.
12. Todeschini R, Consonni V. Molecular descriptors for chemoinformatics. Wiley-VCH; 2009.
13. Guner OF. Pharmacophore perception, development and use. Int Univ Line; 2000.
14. Leach AR, Gillet VJ. An introduction to chemoinformatics. Springer; 2007.
15. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational methods in drug discovery. Pharmacol Rev. 2014;66(1):334–95.
16. Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583–9.
17. Senior AW, Evans R, Jumper J, et al. Improved protein structure prediction. Nature. 2020;577:706–10.
18. Schneider P, Walters WP, Plowright AT, et al. Rethinking drug design with AI. Nat Rev Drug Discov. 2020;19:353–64.
19. Vamathevan J, Clark D, Czodrowski P, et al. Applications of ML in drug discovery. Nat Rev Drug Discov. 2019;18:463–77.
20. Zhavoronkov A, Ivanenkov YA, Aliper A, et al. Deep learning enables rapid drug discovery. Nat Biotechnol. 2019;37:1038–40.
21. Stokes JM, Yang K, Swanson K, et al. Deep learning approach to antibiotic discovery. Cell. 2020;180(4):688–702.
22. Walters WP, Murcko MA. Assessing generative models. J Med Chem. 2020;63:8651–62.
23. Brown N, Fiscato M, Segler MHS, Vaucher AC. GuacaMol benchmarking. J Chem Inf Model. 2019;59:1096–108.
24. Elton DC, Boukouvalas Z, Fuge MD, Chung PW. Deep learning for molecular design. Mol Syst Des Eng. 2019;4:828–49.
25. Zhavoronkov A. Artificial intelligence for drug discovery. Nat Biotechnol. 2018;36:546–7.
26. Shoichet BK. Virtual screening in drug discovery. Nature. 2004;432:862–5.
27. Irwin JJ, Shoichet BK. ZINC database. J Chem Inf Model. 2005;45:177–82.
28. Kim S, Chen J, Cheng T, et al. PubChem update. Nucleic Acids Res. 2021;49:D1388–95.
29. Wishart DS, Feunang YD, Guo AC, et al. DrugBank update. Nucleic Acids Res. 2018;46:D1074–82.
30. Gaulton A, Bellis LJ, Bento AP, et al. ChEMBL database. Nucleic Acids Res. 2012;40:D1100–7.
31. Congreve M, Carr R, Murray C, Jhoti H. Fragment-based drug discovery. Drug Discov Today. 2003;8:876–7.
32. Erlanson DA, McDowell RS, O’Brien T. Fragment-based drug discovery. J Med Chem. 2004;47:3463–82.
33. Murray CW, Rees DC. Fragment-based drug discovery. Nat Chem. 2009;1:187–92.
34. Hajduk PJ, Greer J. Fragment-based drug discovery. Nat Rev Drug Discov. 2007;6:211–9.
35. Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-based approaches. Biochemistry. 2012;51:4990–5003.
36. Singh J, Petter RC, Baillie TA, Whitty A. Covalent drugs. Nat Rev Drug Discov. 2011;10:307–17.
37. Bauer RA. Covalent inhibitors. Drug Discov Today. 2015;20:1061–73.
38. London N, Miller RM, Krishnan S, et al. Covalent docking. Nat Chem Biol. 2014;10:1066–72.
39. Lu S, Zhang J. Allosteric drug discovery. Drug Discov Today. 2019;24:1657–64.
40. Nussinov R, Tsai CJ. Allostery in disease. Cell. 2013;153:293–305.
41. Cheng Y, LeGall T, Oldfield CJ, et al. Cryo-EM in drug discovery. Trends Pharmacol Sci. 2021;42:199–213.
42. Nogales E, Scheres SH. Cryo-EM revolution. Mol Cell. 2015;58:677–89.
43. Bai XC, McMullan G, Scheres SH. Cryo-EM advances. Trends Biochem Sci. 2015;40:49–57.
44. Hasin Y, Seldin M, Lusis A. Multi-omics approaches. Genome Biol. 2017;18:83.
45. Karczewski KJ, Snyder MP. Multi-omics in medicine. Nat Rev Genet. 2018;19:299–310.
46. Hood L, Flores M. Big data in biology. Cell. 2012;150:1133–5.
47. Marx V. Biology big data. Nature. 2013;498:255–60.
48. Stephens ZD, Lee SY, Faghri F, et al. Big data challenges. PLoS Biol. 2015;13:e1002195.
49. Buyya R, Yeo CS, Venugopal S. Cloud computing. Future Gener Comput Syst. 2009;25:599–616.
50. Dean J, Ghemawat S. MapReduce. Commun ACM. 2008;51:107–13.
51. Kuntz ID. Structure-based strategies. Science. 1992;257:1078–82.
52. Anderson AC. Structure-based drug design. Chem Biol. 2003;10:787–97.
53. Blundell TL. Structure-based drug design. Nature. 1996;384:23–6.
54. Klebe G. Applying thermodynamics. Nat Rev Drug Discov. 2015;14:95–110.
55. Jorgensen WL. Efficient drug discovery. Science. 2004;303:1813–8.
56. Lipinski CA. Rule of five. Adv Drug Deliv Rev. 2001;46:3–26.
57. Veber DF, Johnson SR, Cheng HY, et al. Molecular properties. J Med Chem. 2002;45:2615–23.
58. DiMasi JA, Grabowski HG, Hansen RW. Drug development cost. J Health Econ. 2016;47:20–33.
59. Paul SM, Mytelka DS, Dunwiddie CT, et al. Drug discovery productivity. Nat Rev Drug Discov. 2010;9:203–14.
60. Hughes JP, Rees S, Kalindjian SB, Philpott KL. Drug discovery process. Br J Pharmacol. 2011;162:1239–49.
61. Waring MJ, Arrowsmith J, Leach AR, et al. Drug attrition. Nat Rev Drug Discov. 2015;14:475–86.
62. Ekins S, Mestres J, Testa B. ADMET prediction. Drug Discov Today. 2007;12:81–9.
63. Kirchmair J, Göller AH, Lang D, et al. Predicting drug metabolism. Nat Rev Drug Discov. 2015;14:387–404.
64. Pammolli F, Magazzini L, Riccaboni M. Pharma R&D productivity. Nat Rev Drug Discov. 2011;10:428–38.
65. Schneider G. De novo design. Nat Rev Drug Discov. 2018;17:97–113.
66. Walters WP, Namchuk M. Designing screens. Nat Rev Drug Discov. 2003;2:259–66.
67. Macalino SJY, Gosu V, Hong S, Choi S. Role of computer-aided drug design. Arch Pharm Res. 2015;38:1686–701.
68. Lionta E, Spyrou G. Advances in docking. Curr Top Med Chem. 2014;14:1923–38.
69. Sadybekov AA, Katritch V. Computational approaches. Trends Pharmacol Sci. 2021;42:747–60.




