Computational transformation in drug discovery: A comprehensive study on molecular docking and quantitative structure activity relationship (QSAR)

Manan Shah, Maanit Patel, Monit Shah, Monali Patel, Mitul Prajapati

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Intelligent Pharmacy ›› 2024, Vol. 2 ›› Issue (5) : 589-595. DOI: 10.1016/j.ipha.2024.03.001
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Computational transformation in drug discovery: A comprehensive study on molecular docking and quantitative structure activity relationship (QSAR)

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Abstract

The procedure for learning and creating a new medicine is widely seen as a drawn-out and costly endeavor. Different rational strategies are considered, depending on their requirements, as potential ways; nevertheless, techniques to designing drugs based on structure and ligands are well acknowledged as very practical and potent tactics in drug discovery. Computational approaches help decrease the need for Medicinal research with animals, helping to develop fresh, safe therapeutic concepts via rational design and positioning of existing products and supporting pharmaceutical scientists and medicinal chemists during the medication development process. Computer-aided drug discovery (CADD) methods are useful for reducing the time and cost of drug discovery and development and understanding the molecular mechanisms of drug action and toxicity. Molecular docking is a technique that predicts a ligand’s binding mode and affinity to a target protein. At the same time, QSAR is a technique that establishes mathematical relationships between the structural features and biological activities of a series of compounds. This study reviews the current state and applications of CADD methods, focusing on molecular docking and quantitative structure–activity relationship (QSAR) techniques. This study reviews the principles, advantages, limitations, and challenges of these methods, as well as some recent advances and examples of their applications in drug discovery for various diseases. The study also discusses the future prospects and directions of CADD methods in the era of big data and artificial intelligence.

Keywords

Docking / Drug discovery / Computer aided methods

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Manan Shah, Maanit Patel, Monit Shah, Monali Patel, Mitul Prajapati. Computational transformation in drug discovery: A comprehensive study on molecular docking and quantitative structure activity relationship (QSAR). Intelligent Pharmacy, 2024, 2(5): 589‒595 https://doi.org/10.1016/j.ipha.2024.03.001

References

[1]
Singh AR. 2010 Undefined. Modern Medicine: Towards Prevention, Cure, Well-Being and Longevity. NcbiNlmNihGovAR SinghMens Sana Monographs;2010, 2010•ncbiNlmNihGov.
[2]
Hughes JP, Rees SS, Kalindjian SB, Philpott KL. Principles of early drug discovery. Br J Pharmacol. 2011;162:1239–1249.
CrossRef Google scholar
[3]
Mohs RC, Greig NH. Drug discovery and development: role of basic biological research. Alzheimer’s Dementia: Translational Research and Clinical Interventions. 2017;3. 651–7.
CrossRef Google scholar
[4]
Lombardino JG, Lowe JA. The role of the medicinal chemist in drug discovery - then and now. Nat Rev Drug Discov. 2004;3:853–862.
CrossRef Google scholar
[5]
Guido R VC, Oliva G DAndricopulo A. Modern drug discovery technologies: opportunities and challenges in lead discovery. Comb Chem High Throughput Screen. 2011;14:830–839.
CrossRef Google scholar
[6]
Augen J. The evolving role of information technology in the drug discovery process. Drug Discov Today. 2002;7:315–323.
CrossRef Google scholar
[7]
Davidov EJ, Holland JM, Marple EW, Naylor S. Advancing drug discovery through systems biology. Drug Discov Today. 2003;8:175–183.
CrossRef Google scholar
[8]
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.
CrossRef Google scholar
[9]
Song CM, Lim SJ, Tong JC. Recent advances in computer-aided drug design. Brief Bioinform. 2009;10:579–591.
CrossRef Google scholar
[10]
Ain Q, Batool M, Molecules SC-. 2020 undefined. TLR4-targeting therapeutics: structural basis and computer-aided drug discovery approaches. MdpiComQ Ain, M Batool, S ChoiMolecules, 2020•mdpiCom. 2020. https://doi.org/10.3390/molecules25030627.
[11]
Kapetanovic IM. Computer-aided drug discovery and development (CADDD): in silico-chemico-biological approach. Chem Biol Interact. 2008;171:165–176.
CrossRef Google scholar
[12]
Rudrapal M, Chetia D. Virtual screening, molecular docking and QSAR studies in drug discovery and development programme. J Drug Deliv Therapeut. 2020;10:225–233.
CrossRef Google scholar
[13]
Tripathi A, Misra K. Molecular Docking: a structure-based drug designing approach. J Bioinform. 2017;2:1015.
[14]
Cheng K-C, Korfmacher WA, White RE, Njoroge FG. Lead optimization in discovery drug metabolism and pharmacokinetics/case study: the hepatitis C virus (HCV) protease inhibitor SCH 503034. Perspect Med Chem. 2007;1. 1177391X0700100.
CrossRef Google scholar
[15]
Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:1–13.
CrossRef Google scholar
[16]
Vyas VK, Ukawala RD, Ghate M, Chintha C. Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives. vol. 74. 2012. [Online]. Available.
CrossRef Google scholar
[17]
Lionta E, Spyrou G, Vassilatis D, Cournia Z. Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances. vol. 14. 2014.
CrossRef Google scholar
[18]
Aminpour M, Montemagno C, Tuszynski JA. An overview of molecular modeling for drug discovery with specific illustrative examples of applications. Molecules. 2019;24:9.
CrossRef Google scholar
[19]
Jain A. Computer aided drug design. J Phys Conf Ser. 2017;884:504–509.
CrossRef Google scholar
[20]
Torres PHM, Sodero ACR, Jofily P, Silva-Jr FP. Key topics in molecular docking for drug design. Int J Mol Sci. 2019;20:1–29.
CrossRef Google scholar
[21]
de Ruyck J, Brysbaert G, Blossey R, Lensink MF. Molecular docking as a popular tool in drug design, an in silico travel. Comput Biol Chem Adv Appl. 2016;9:1–11.
CrossRef Google scholar
[22]
Forli S, Huey R, Pique ME, Sanner M, Goodsell DS, Arthur J. 00006565-201002000-00017 2016;11:905–19. Computational.
CrossRef Google scholar
[23]
Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov. 2004;3:935–949.
CrossRef Google scholar
[24]
Nguyen PTV, Yu H, Keller PA. Molecular docking studies to explore potential binding pockets and inhibitors for chikungunya virus envelope glycoproteins. Interdiscip Sci. 2018;10:515–524.
CrossRef Google scholar
[25]
Mendie LE, Hemalatha S. Molecular docking of phytochemicals targeting GFRs as therapeutic sites for cancer: an in silico study. Appl Biochem Biotechnol. 2022;194:215–231.
CrossRef Google scholar
[26]
Sharma V, Sharma PC, Kumar V. In silico molecular docking analysis of natural pyridoacridines as anticancer agents. Advances in Chemistry. 2016;2016:1–9.
CrossRef Google scholar
[27]
Factor I. Impact Factor:4.41. vol. 16. 2010:24.
[28]
Winkler DA. The role of quantitative structure-activity relationships (QSAR) in biomolecular discovery. Brief Bioinform. 2002;3:73–86.
CrossRef Google scholar
[29]
Abdel-Ilah L, Veljović E, Gurbeta L, Badnjević A. Applications of QSAR study in. Drug Design. 2017;6:582–587.
[30]
Neves BJ, Braga RC, Melo-Filho CC, Moreira-Filho JT, Muratov EN, Andrade CH. QSAR-based virtual screening: advances and applications in drug discovery. Front Pharmacol. 2018;9:1–7.
CrossRef Google scholar
[31]
Kleandrova VV, Scotti L, Bezerra Mendonça Junior FJ, Muratov E, Scotti MT, Speck-Planche A. QSAR modeling for multi-target drug discovery: designing simultaneous inhibitors of proteins in diverse pathogenic parasites. Front Chem. 2021;9.
CrossRef Google scholar
[32]
Wang W, Kim MT, Sedykh A, Zhu H. Developing enhanced blood-brain barrier permeability models: integrating external bio-assay data in QSAR modeling. Pharm Res (N Y). 2015;32:3055–3065.
CrossRef Google scholar
[33]
Kwon S, Bae H, Jo J, Yoon S. Comprehensive ensemble in QSAR prediction for drug discovery. BMC Bioinf. 2019;20:1.
CrossRef Google scholar
[34]
Zhang S, Golbraikh A, Oloff S, Kohn H, Tropsha A. A novel Automated Lazy Learning QSAR (ALL-QSAR) approach: method development, applications, and virtual screening of chemical databases using validated ALL-QSAR models. J Chem Inf Model. 2006;46:1984. -95.
CrossRef Google scholar
[35]
Pinzi L, Rastelli G. Molecular docking: shifting paradigms in drug discovery. Int J Mol Sci. 2019;20:18.
CrossRef Google scholar
[36]
Perkins R, Fang H, Tong W, Welsh WJ. Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology. Environ Toxicol Chem. 2003;22:1666–1679.
CrossRef Google scholar

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2024 2024 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd.
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