MOLECULAR DOCKING: AN EXPLANATORY APPROACH IN STRUCTURE-BASED DRUG DESIGNING AND DISCOVERY

Manish Dev Sharma,Vaishali Vaishali,Vaishali Agarwal,Neha Chauhan,Saloni Kunwar,Aditi Sharma,Chhaya Singh

doi:10.22159/ijpps.2021v13i6.40830

Manish Dev Sharma, Vaishali Vaishali + Show 5 more

Open Access

https://doi.org/10.22159/ijpps.2021v13i6.40830

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Abstract

Molecular docking is a modeling tool of Bioinformatics which includes two or more molecules which interact to provide a stable product in the form of a complex. Molecular docking is helpful in predicting the 3-d structure of a complex which depends on the binding characteristics of Ligand and target. Also, it is a structure-based virtual screening (SBVS) utilized to keep the 3-d structures of small molecule which are generated by computers into a target structure in various types of conformations, positions and orientations. This molecular docking has come out to be a novel concept with various types of advantages. It behaves as a highly exploring domain due to its significant structure-based drug design (SBDD), Assessment of Biochemical pathways, Lead Optimization and in De Novo drug design. In spite of all potential approaches, there are certain challenges which are-scoring function (differentiate the true binding mode), ligand chemistry (tautomerism and ionization) and receptor flexibility (single conformation of rigid receptor). The area of computer-aided drug design and discovery (CADDD) has achieved large favorable outcomes in the past few years. CADD has been adopted by various big pharmaceutical companies for leading discoveries of drugs. Many researchers have worked in order to examine different docking algorithms and to predict molecules' active site. Hence, this Review article depicts the whole sole of Molecular Docking.

Highlights

Molecular Docking involves the anticipation of the recommended conformation of the ligand against receptor (Protein) to achieve a complex which is stable [1]
These recommended orientations are used in predicting the affinity of binding amongst the ligand and protein by the help of scoring functions
Different conformations are adopted by a protein which depends on the binding ligand

Summary

INTRODUCTION

Molecular Docking involves the anticipation of the recommended conformation of the ligand against receptor (Protein) to achieve a complex which is stable [1] These recommended orientations are used in predicting the affinity of binding amongst the ligand and protein by the help of scoring functions. There exist many relevant algorithms for analyzing docking procedures like Point complementary, Monte Carlo, Fragment-based, Genetic algorithms, Systematic searches, Distance geometry etc., [19, 20] This approach is beneficial in generating an initial orientation of a ligand at the active site which possesses translation, random conformation rotation. It is beneficial in the rapid and accurate methods for docking of smaller molecule ligands into the active sites of protein This approach aims at evaluating the shape and chemical complementarity between the molecules forming specific interactions. Prediction of optimized conformation of ligand on its target [62, 63]

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CONCLUSION