Question

According to the website, molecular docking is the "corner stone of structure-based drug design and well-suited to learn and teach the strategies for small molecule discovery and optimization." In your own words, what is molecular docking and why would we study it for drug design?

Answer 1

Molecular docking is a kind of bioinformatic modelling which involves the interaction of two or more molecules to give the stable adduct.It is a well established computational technique which predicts the interaction energy between two molecules.This technique mainly incorporates algorithms like molecular dynamics,Monte Carlo stimulation,fragment based research methods.Depending upon the binding properties of ligand and target,it predicts the three dimensional structure of any complex.Mutiple stages of molecular docking method consist of preparation of 3D structure of proteins,preparation of ligands,estimation of binding energy of protein-ligand complex and analysis of results.

Molecular docking study is extermely significant in a wide range of applications in computer aided drug designing.The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as protein,which results in therapeutic benefit to the patient.

Docking can be used to predict in where and in which relative orientation a ligand binds to a protein,and this information can be used to design more potent and selective analogs.

Molecular docking leads to discovery of many therapeutic drugs by various ways like:

1) Identification of potential target

2) Screening of potent drugs as activators/inhibitors against certain diseases.

3) Designing of novel drug by lead optimization.

4) Prediction of binding mode and nature of active site.

5) Synthesis of chemical compounds with less time consumption.

This technique can be implemented in medicinal chemistry.protein engineering,chemo informatics,bioremediation and many other biological and medical fields.