A Brief Review on Smart Drug Design in Favor of Improving Health Indicator
Abstract
The drug is a vital need in contemporary scenarios. Relevant to the traditional methods of drug designing like structural-based drug design and computer-aided drug design, Molecular Docking (MD) is a more complicated and intelligent tool. Approaching the precise three-dimensional binding site or pose of the drug candidate with the receptor is the target of ligand-receptor docking. It calculates the preciseness of drug candidates with receptors. Lead optimisation is assessed by the combinatorial libraries and provides the beneficial or harmful consequences of drug-receptor interaction. It can be difficult to interpret the outcomes of stochastic search methods and establishing the input structures for docking is just as important as docking itself. Based on the system’s overall energy, docking simulations forecast an optimum docked conformer. Despite all viable strategies, the difficulties still lay in ligand chemistry like tautomerism and ionisation, the rigidity of receptors like multi-confirmation of the drug candidate for the same receptor, and the interaction of the drug with the precise binding site. This article briefly discusses a few significant features of MD, including its techniques, kinds, applications, and problems.
How to cite this article:
Kumar V, Dobhal K, Guleria I, Bhawna, Rautela J. A Brief Review on Smart Drug Design in Favor of Improving Health Indicator. Chettinad Health City Med J. 2024;13(3):87-98.
DOI: https://doi.org/10.24321/2278.2044.202449
References
Meng XY, Zhang HX, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011 Jun;7(2):146-57. [PubMed] [Google Scholar]
Kaur T, Madgulkar A, Bhalekar M, Asgaonkar K. Molecular docking in formulation and development. Curr Drug Discov Technol. 2019;16(1):30-9. [PubMed] [Google Scholar]
Lengauer T, Rarey M. Computational methods for biomolecular docking. Curr Opin Struct Biol. 1996;6(3):402-6. [PubMed] [Google Scholar]
Shay JW, Homma N, Zhou R, Naseer MI, Chaudhary AG, Al-Qahtani M , et al. Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015. BMC Genomics. 2016;17 Suppl 6(Suppl 6):487. [PubMed] [Google Scholar]
Vera J, Lischer C, Nenov M, Nikolov S, Lai X, Eberhardt M. Mathematical modelling in biomedicine: a primer for the curious and the skeptic. Int J Mol Sci. 2021;22(2):547. [PubMed] [Google Scholar]
Jensen F. Using atomic charges to model molecular polarization. Phys Chem Chem Phys. 2022;24(4):1926-43. [PubMed] [Google Scholar]
Fang X, Wang S. A web-based 3D-database pharmacophore searching tool for drug discovery. J Chem Inf Comput Sci. 2002;42(2):192-8. [PubMed] [Google Scholar]
Li G, Lin P, Wang K, Gu CC, Kusari S. Artificial intelligenceguided discovery of anticancer lead compounds from plants and associated microorganisms. Trends Cancer. 2022;8(1):65-80. [PubMed] [Google Scholar]
Shaker B, Ahmad S, Lee J, Jung C, Na D. In silico methods and tools for drug discovery. Comput Biol Med. 2021;137:104851. [PubMed] [Google Scholar]
Wankowicz SA, de Oliveira SH, Hogan DW, van den Bedem H, Fraser JS. Ligand binding remodels protein side-chain conformational heterogeneity. Elife. 2022;11:e74114. [PubMed] [Google Scholar]
Qiu C, Shi W, Wu H, Zou S, Li J, Wang D, Liu G, Song Z, Xu X, Hu J, Geng H. Identification of molecular subtypes and a prognostic signature based on inflammationrelated genes in colon adenocarcinoma. Front Immunol. 2021;12:769685. [PubMed] [Google Scholar]
Naderi M, Lemoine JM, Govindaraj RG, Kana OZ, Feinstein WP, Brylinski M. Binding site matching in rational drug design: algorithms and applications. Brief Bioinform. 2019;20(6):2167-84. [PubMed] [Google Scholar]
Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies. Molecules. 2015 Jul 22;20(7):13384-421. [PubMed] [Google Scholar]
Torres PH, Sodero AC, Jofily P, Silva-Jr FP. Key topics in molecular docking for drug design. Int J Mol Sci. 2019;20(18):4574. [PubMed] [Google Scholar]
Miller MD, Kearsley SK, Underwood DJ, Sheridan RP. FLOG: a system to select ‘quasi-flexible’ ligands complementary to a receptor of known threedimensional structure. J Comput Aided Mol Des. 1994;8(2):153-74. [PubMed] [Google Scholar]
Shinn P, Chen L, Ferrer M, Itkin Z, Klumpp-Thomas C, McKnight C, Michael S, Mierzwa T, Thomas C, Wilson K, Guha R. High-throughput screening for drug combinations. Methods Mol Biol. 2019;1939:11-35. [PubMed] 17. Entzeroth M, Flotow H, Condron P. Overview of high-throughput screening. Curr Protoc Pharmacol. 2009;Chapter 9:Unit 9.4. [PubMed] [Google Scholar]
King E, Aitchison E, Li H, Luo R. Recent developments in free energy calculations for drug discovery. Front Mol Biosci. 2021;8:712085. [PubMed] [Google Scholar]
Rathore RS, Sumakanth M, Reddy MS, Reddanna P, Rao AA, Erion MD, Reddy MR. Advances in binding free energies calculations: QM/MM-based free energy perturbation method for drug design. Curr Pharm Des. 2013;19(26):4674-86. [PubMed] [Google Scholar]
Jespers W, Åqvist J, Gutiérrez-de-Terán H. Free energy calculations for protein-ligand binding prediction. Methods Mol Biol. 2021;2266:203-26. [PubMed]
Velmurugan D, Pachaiappan R, Ramakrishnan C. Recent trends in drug design and discovery. Curr Top Med Chem. 2020;20(19):1761-70. [PubMed] [Google Scholar]
Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR structures on drug discovery. Cell. 2020;181(1):81-91. [PubMed] [Google Scholar]
Yang C, Zhang Y. Lin_F9: a linear empirical scoring function for protein-ligand docking. J Chem Inf Model. 2021 Sep 27;61(9):4630-44. [PubMed] [Google Scholar]
Ramírez-Velásquez I, Bedoya-Calle ÁH, Vélez E, Caro-Lopera FJ. Shape theory applied to molecular docking and automatic localization of ligand binding pockets in large proteins. ACS Omega. 2022;7(50):45991-6002. [PubMed] [Google Scholar]
Hopkins PM, Cooke PJ, Clarke RC, Guttormsen AB, Platt PR, Dewachter P, Ebo DG, Garcez T, Garvey LH, Hepner DL, Khan DA, Kolawole H, Kopac P, Kroigaard M, Laguna JJ, Marshall SD, Mertes PM, Rose MA, Sabato V, Savic LC, Savic S, Takazawa T, Volcheck GW, Voltolini S, Sadleir PH. Consensus clinical scoring for suspected perioperative immediate hypersensitivity reactions. Br J Anaesth. 2019;123(1):e29-37. [PubMed] [Google Scholar]
Yau MQ, Loo JS. Consensus scoring evaluated using the GPCR-Bench dataset: reconsidering the role of MM/GBSA. J Comput Aided Mol Des. 2022;36(6):427-41. [PubMed] [Google Scholar]
Zeng C, Scott L, Malyutin A, Zandi R, Van der Schoot P, Dragnea B. Virus mechanics under molecular crowding. J Phys Chem B. 2021;125(7):1790-8. [PubMed] [Google Scholar]
Huang N, Kalyanaraman C, Bernacki K, Jacobson MP. Molecular mechanics methods for predicting proteinlig and binding. Phys Chem Chem Phys. 2006;8(44):5166-77. [PubMed] [Google Scholar]
Allinger NL. Understanding molecular structure from molecular mechanics. J Comput Aided Mol Des. 2011;25(4):295-316. [PubMed] [Google Scholar]
Zhong F, Xing J, Li X, Liu X, Fu Z, Xiong Z, Lu D, Wu X, Zhao J, Tan X, Li F, Luo X, Li Z, Chen K, Zheng M, Jiang H. Artificial intelligence in drug design. Sci China Life Sci. 2018;61(10):1191-204. [PubMed] [Google Scholar]
Morris GM, Lim-Wilby M. Molecular docking. Methods Mol Biol. 2008;443:365-82. [PubMed]
Ferrari AM, Wei BQ, Costantino L, Shoichet BK. Soft docking and multiple receptor conformations in virtual screening. J Med Chem. 2004;47(21):5076-84. [PubMed] [Google Scholar]
Jiang F, Kim SH. “Soft docking”: matching of molecular surface cubes. J Mol Biol. 1991;219(1):79-102. [PubMed] [Google Scholar]
Fernández-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci. 2002;11(2):280-91. [PubMed] [Google Scholar]
Banack HR, Hayes-Larson E, Mayeda ER. Monte Carlo simulation approaches for quantitative bias analysis: a tutorial. Epidemiol Rev. 2022;43(1):106-17. [PubMed] [Google Scholar]
Rimac H, Grishina M, Potemkin V. Use of the complementarity principle in docking procedures: a new approach for evaluating the correctness of binding poses. J Chem Inf Model. 2021 Apr 26;61(4):1801-13. [PubMed] [Google Scholar]
van den Berg MP, Scamman WC, Stubbs JM. Monte Carlo molecular simulation of solution and surfacebound DNA hybridization of short oligomers at varying surface densities. Biophys Chem. 2022;284:106784. [PubMed] [Google Scholar]
Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc. 2016;11(5):905-19. [PubMed] [Google Scholar]
Ivanova L, Karelson M. The impact of software used and the type of target protein on molecular docking accuracy. Molecules. 2022;27(24):9041. [PubMed] [Google Scholar]
Rosell M, Fernández-Recio J. Docking approaches for modeling multi-molecular assemblies. Curr Opin Struct Biol. 2020;64:59-65. [PubMed] [Google Scholar]
Bitencourt-Ferreira G, de Azevedo WF Jr. Molecular docking simulations with ArgusLab. Methods Mol Biol. 2019;2053:203-20. [PubMed]
Silakari O, Singh PK. Molecular docking analysis: basic technique to predict drug-receptor interactions. In:
Silakari O, Singh PK, editors. Concepts and experimental protocols of modelling and informatics in drug design. Academic Press; 2021. p. 131-55.
Pinzi L, Rastelli G. Molecular docking: shifting paradigms in drug discovery. Int J Mol Sci. 2019;20(18):4331. [PubMed] [Google Scholar]
Gurung AB, Ali MA, Lee J, Farah MA, Al-Anazi KM. An updated review of computer-aided drug design and its application to COVID-19. Biomed Res Int. 2021;2021:8853056. [PubMed] [Google Scholar]
Lin X, Li X, Lin X. A review on applications of cotational methods in drug screening and design. Molecules. 2020;25(6):1375. [PubMed] [Google Scholar]
Baig MH, Ahmad K, Roy S, Ashraf JM, Adil M, Siddiqui MH, Khan S, Kamal MA, Provaznik I, Choi I. Computer aided drug design: success and limitations. Curr Pharm Des. 2016;22(5):572-81. [PubMed] [Google Scholar]
Jiao X, Jin X, Ma Y, Yang Y, Li J, Liang L, Liu R, Li Z. A comprehensive application: molecular docking and network pharmacology for the prediction of bioactive constituents and elucidation of mechanisms of action in component-based Chinese medicine. Comput Biol Chem. 2021;90:107402. [PubMed] [Google Scholar]
Vilar S, Cozza G, Moro S. Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Curr Top Med Chem. 2008;8(18):1555-72. [PubMed] [Google Scholar]
Abagyan R, Totrov M, Kuznetsov D. ICM—a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem. 1994;15(5):488-506. [Google Scholar]
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47(7):1739-49. [PubMed] [Google Scholar]
Yuliana D, Bahtiar FI, Najib A. In silico screening of chemical compounds from roselle (Hibiscus sabdariffa) as angiotensin-I converting enzyme inhibitor used PyRx program. ARPN J Sci Technol. 2013;3(12):1158-60. [Google Scholar]
Kellenberger E, Rodrigo J, Muller P, Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins. 2004;57(2):225-42. [PubMed] [Google Scholar]
Corbeil CR, Englebienne P, Moitessier N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model. 2007;47(2):435-49. [PubMed] [Google Scholar]