View Article

Abstract

The field of computer-aided drug design and discovery (CADD) has been growing rapidly in recent years, with many successes. Both large pharmaceutical companies and academia use CADD for drug lead discovery. Advances in structural informatics, genomics, and proteomics have been vital in modern drug discovery and development. Research over the past two decades has focused on studying different docking algorithms to predict the active site of a molecule. Various docking programs have been developed to visualize the 3D structure of a molecule, and docking scores can be analysed using different computational methods. Molecular Docking is a structure-based virtual screening (SBVS) technique used to position computer-generated three-dimensional structures of small molecules into a target structure in various positions, conformations, and orientations. Protein-ligand docking is a new concept that has various applications and is significant in structure-based drug design (SBDD), Lead Optimization, and Evaluation of Biochemical pathways, as well as in De Novo drug design. This review provides a comprehensive explanation of Molecular Docking and how it helps in the Molecular Recognition Process towards the discovery of new drug leads by estimating the binding mode and affinity of the complex formed.

Keywords

Molecular Docking, Computer-aided drug design [CADD], Structure-based drug design [SBDD], Structure-based virtual screening [SBVS], Protein data bank [PDB], Three-dimensional [3D]

Reference

  1. DiMasi J. A., Grabowski H. G., & Hansen R. W. Innovation in the pharmaceutical industry: new estimates of R&D costs. Journal of Health Economics 2016; 47:20-33.
  2. Lengauer T., & Rarey M. Computational methods for biomolecular docking. Current opinion in structural biology 1996; 6(3):402-406.
  3. Kitchen D. B., Decornez H., Furr, J. R., & Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nature reviews Drug discovery 2004; 3(11): 935-949.
  4. Kuntz I. D., Blaney J. M., Oatley S. J., Langridge R., & Ferrin T. E. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology 1982; 161(2):269-288.
  5. Stanzione F., Giangreco I., & Cole J. C. Use of molecular docking computational tools in drug discovery. Progress in Medicinal Chemistry 2021; 60:273-343.
  6. Rarey M., Kramer B., & Lengauer T. Multiple automatic base selection: Protein–ligand docking based on incremental construction without manual intervention. Journal of computer-aided molecular design 1997; 11:369-384.
  7. Schulz-Gasch T., & Stahl M. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. Journal of Molecular Modelling 2003; 9: 47-57.
  8. Friesner R. A., Banks J. L., Murphy R. B., Halgren T. A., Klicic J. J., Mainz D. T., et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of medicinal chemistry 2004; 47(7):1739-1749.
  9. Jones G., Willett P., Glen R. C., Leach A. R., & Taylor R. Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology 1997; 267(3):727-748.
  10. Huang, N., Shoichet, B. K., & Irwin, J. J. Benchmarking sets for molecular docking. Journal of medicinal chemistry 2006; 49(23):6789-6801.
  11. Hernández-Santoyo A., Tenorio-Barajas A. Y., Altuzar V., Vivanco-Cid H., & Mendoza-Barrera C: Protein engineering-technology and application. IntechOpen, Rijeka, Edition 1 2013:63-81.
  12. Trosset J. Y., & Scheraga H. A. PRODOCK: software package for protein modeling and docking. Journal of Computational Chemistry 1999; 20(4):412-427.
  13. McMartin C., & Bohacek R. S. QXP: powerful, rapid computer algorithms for structure-based drug design. Journal of computer-aided molecular design 1997; 11:333-344.
  14. Schnecke V., & Kuhn L. A. Virtual screening with solvation and ligand-induced complementarity. Perspectives in Drug Discovery and Design 2000; 20:171-190.
  15. Agarwal, S., & Mehrotra, R. J. J. C. An overview of molecular docking. JSM chem 2016; 4(2):1024-1028.
  16. Kumalo H. M., Bhakat S., & Soliman M. E. Theory and applications of covalent docking in drug discovery: merits and pitfalls. Molecules 2015; 20(2):1984-2000.
  17. Li Y., Zhang, X., & Cao D. The role of shape complementarity in the protein-protein interactions. Scientific reports 2013; 3(1):3271.
  18.  Johnson D. S., Weerapana E., & Cravatt B. F. Strategies for discovering and derisking covalent, irreversible enzyme inhibitors. Future medicinal chemistry 2010; 2(6): 949-964.
  19. Bianco G., Forli, S., Goodsell D. S., & Olson A. J. Covalent docking using autodock: Two?point attractor and flexible side chain methods. Protein Science 2016; 25(1):295-301.
  20. Dias R., de Azevedo J., & Walter F. Molecular docking algorithms. Current drug targets 2008; 9(12):1040-1047.
  21. Yuriev E., & Ramsland P. A. Latest developments in molecular docking: 2010–2011 in review. Journal of Molecular Recognition 2013; 26(5):215-239.
  22.  Alonso H., Bliznyuk A. A., & Gready J. E.  Combining docking and molecular dynamic simulations in drug design. Medicinal research reviews 2006; 26(5): 531-568.
  23. Goodsell D. S., & Olson A. J. Automated docking of substrates to proteins by simulated annealing. Proteins: Structure, Function, and Bioinformatics 1990; 8(3):195-202.
  24. Kuntz I. D., Blaney J. M., Oatley S. J., Langridge R., & Ferrin T. E. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology 1982; 161(2): 269-288
  25. Venkatachalam C. M., Jiang X., Oldfield T., & Waldman M. Ligand Fit: a novel method for the shape-directed rapid docking of ligands to protein active sites. Journal of Molecular Graphics and Modelling 2003; 21(4):289-307.
  26.  Kellenberger E., Rodrigo J., Muller P., & Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins: Structure, Function, and Bioinformatics 2004; 57(2): 225-242.
  27. David, L., Nielsen, P. A., Hedstrom, M., & Norden, B. Scope and limitation of ligand docking: methods, scoring functions, and protein targets. Current Computer-Aided Drug Design 2005; 1(3): 275-306.
  28. Lee H. S., & Zhang Y. BSP?SLIM: A blind low?resolution ligand?protein docking approach using predicted protein structures. Proteins: Structure, Function, and Bioinformatics 2012; 80(1):93-110.
  29. Singh J., Petter R. C., Baillie T. A., & Whitty A. The resurgence of covalent drugs. Nature reviews Drug discovery 2011; 10(4): 307-317.
  30. Li Q., Wang Z., Zheng Q., & Liu S. Potential clinical drugs as covalent inhibitors of the priming proteases of the spike protein of SARS-CoV-2. Computational and structural biotechnology journal 2020; 18:2200-2208.
  31. Sotriffer C. Docking of covalent ligands: challenges and approaches. Molecular Informatics 2018; 37(9-10):1-14:1800062.
  32. Kharkar P. S., Warrier S., & Gaud R. S. Reverse docking: a powerful tool for drug repositioning and drug rescue. Future medicinal chemistry 2014; 6(3): 333-342.
  33. Terrett N. K., Bell A. S., Brown D., & Ellis P. Sildenafil (VIAGRATM), a potent and selective inhibitor of type 5 cGMP phosphodiesterase with utility for the treatment of male erectile dysfunction. Bioorganic & Medicinal Chemistry Letters 1996; 6(15):1819-1824.
  34. Pinzi L., & Rastelli G. Molecular docking: shifting paradigms in drug discovery. International journal of molecular sciences 2019; 20(18):4331.
  35. Ferreira L. G., Dos Santos R. N., Oliva G., & Andricopulo A. D.  Molecular docking and structure-based drug design strategies. Molecules 2015; 20(7):13384-13421.
  36. Shoichet B. K., McGovern S. L., Wei B., & Irwin J. J. Lead discovery using molecular docking. Current opinion in chemical biology 2002; 6(4): 439-446.
  37. Pagadala N. S., Syed K., & Tuszynski J. Software for molecular docking: a review. Biophysical reviews 2017; 9: 91-102.

Photo
Shubhangi H. Bhowate
Corresponding author

Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India- 440016

Photo
Dr. Dinesh R. Chaple
Co-author

Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India- 440016

Photo
Dr. Alpana J. asnani
Co-author

Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India- 440016

Photo
Pranita I. Rathod
Co-author

Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India- 440016

Photo
Aishwarya V. Lichade
Co-author

Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India- 440016

Photo
Vaishnavi S. Bhure
Co-author

Department of Pharmaceutical Chemistry, Priyadarshini J. L. College of Pharmacy, Nagpur, Maharashtra, India- 440016

Shubhangi H. Bhowate*, Dr. Dinesh R. Chaple, Dr. Alpana J. asnani, Pranita I. Rathod, Aishwarya V. Lichade, Vaishnavi S. Bhure, Molecular Docking: A Powerful Tool In Modern Drug Discovery And Its Approaches, Int. J. in Pharm. Sci., 2023, Vol 1, Issue 10, 170-181. https://doi.org/10.5281/zenodo.10017630

More related articles
Sexual Dysfunction among drug naive anxiety disord...
Swagnik Roy, Lalhriatpuia, Raj Kumar Lenin Singh, Rajesh Rongpi, ...
Antimicrobial Activity Of Adhatoda Vasica Against...
Aditya Sunil Balchanne , Shubham S. Gannewar , Priya P. Sarkar , ...
Antioxidant And Acetylcholinesterase Inhibitory Po...
Ruchi Solanki, Prof. Vijay Juyal, ...
Evaluation Parameters For Mouth Dissolving Films...
Avinash Bichave, Somesh Phate, Vaishnavi Naik, Anushka Gaikwad, Lalit Choudhary, Uttam Choudhary, Sh...
Review on 'Polycystic kidney disease pathophysiology and prognosis'...
Seema Kashyap, Eshu Sahu, Bignesh Pradhan, Dali Kanwar, Chhabi Lal, ...
Related Articles
A Detailed Pythopharmacological And Biochemical Review On Mimosa Pudica (Laajvan...
Syed Mohammad Abdullah, Anuska Shivani, Raushan Kumar, Aditya Kumar, Raunak Kumar Singh, ...
A Review On Pharmacovigilance And Its Important ...
Asane Varad Arun, VISHAL SURESH RASKAR, RUSHIKESH ADINATH KALE, VIKAS BABASAHEB JORI, DIPAK KAILAS J...
Karkatshringi Pistacia Integerrima Significant Role In Cancer Treatment...
Vaidhshiromani.Dheeraj Sharma, Pransu gupta , Tanishka Gupta , Rajesh K. Mishra, M. K. Yadav , Ramak...
An Overview of Her 2 Neu Positive Breast Cancer...
K. Sireesha, P. Shivani Naidu, P. Lakshmi Prasanna, A. Renuka, G. Manas Kumar, ...
Sexual Dysfunction among drug naive anxiety disorder patient in a multidisciplin...
Swagnik Roy, Lalhriatpuia, Raj Kumar Lenin Singh, Rajesh Rongpi, ...
More related articles
Sexual Dysfunction among drug naive anxiety disorder patient in a multidisciplin...
Swagnik Roy, Lalhriatpuia, Raj Kumar Lenin Singh, Rajesh Rongpi, ...
Antimicrobial Activity Of Adhatoda Vasica Against Pathogens...
Aditya Sunil Balchanne , Shubham S. Gannewar , Priya P. Sarkar , Gayatri A. Narule, Snehal B. Hemane...
Sexual Dysfunction among drug naive anxiety disorder patient in a multidisciplin...
Swagnik Roy, Lalhriatpuia, Raj Kumar Lenin Singh, Rajesh Rongpi, ...
Antimicrobial Activity Of Adhatoda Vasica Against Pathogens...
Aditya Sunil Balchanne , Shubham S. Gannewar , Priya P. Sarkar , Gayatri A. Narule, Snehal B. Hemane...