Course Objectives

• To know about the  tools of discovery studio Biovia software
• Ligand-protein interaction
• Drug designing

Learning Outcomes

• Prediction of drug by molecular docking
• Pharmacophore modelling
• Publication/product

Course Syllabus

Module I: Discovery of phytochemicals as potential drug substitute (18 hrs)

Practice: Use of discovery studio for drug design
Practice: Phytochemicals present in a particular plant and download its mol file
Practice: Identification of enzyme molecules of a microbe using Brenda enzyme database
Practice: Downloads PDB file of different enzymes
Practice: Study of different parts of an enzyme molecule in a molecular window.
Practice: Ligand-protein molecular docking.

Module 11: Identification of pharmacophore (Automatic/Manually) (9 hrs)

Practice: Automatic identification of structural feature of a pharmacophore

Practice: Identification of a pharmacophore manually

Practice: ADMET and Toxicity report analysis of a drug molecule.

Module 111: Functionalisation of a molecule and study its potential as a drug (3hrs)

Practice: Forcefield of a protein molecule using simulation.

Reference Books :

1. Textbook of Drug Design and Discovery. Edited By Kristian Stromgaard, Povl Krogsgaard-Larsen, Ulf Madsen. 2017. CRC Press
2. Drug Discovery and Development, Third Edition. Edited By James J. O'Donnell, John Somberg, Vincent Idemyor, James T. O'Donnell. 2020. CRC Press

Projects [30hrs]
(1) Identification of a specific phytochemical for a disease.
(2)Identification of a chemical drug based on structural similarity with a phytochemical for a specific disease.
(Two publications from this projects)

Session Plan

Session 1

WEB-LINKS : Use of discovery studio

BIOVIA information pdf

Session 2

WEB-LINKS : How to download ligand ?

sdf file pdf

Session 3

WEB-LINKS : Brenda enzyme database

Enzymes classification

Session 4

WEB-LINKS : Download of PDB file of an enzyme

PDB number for a protein or enzyme pdf

Session 5

WEB-LINKS : Parts of enzyme molecules

Session 6

WEB-LINKS : Molecular docking

Molecular docking 2 video

Session 7

WEB-LINKS : Drugs and molecular interactions

Session 8

WEB-LINKS : Pharmacophore model

Pharmacophore search pdf

Session 9

WEB-LINKS : ADMET link

Video on ADME

flow chart ADMET

ADMET tutorial pdf

Session 10

simulation tool pdf

Session 11

Project-1 Identification of a specific phytochemical for a disease

Session 12

Project-1 Identification of a specific phytochemical for a disease

Session 13

Project-1 Identification of a specific phytochemical for a disease

Session 14

Project-1 Identification of a specific phytochemical for a disease

Session 15

Project-2 Identification of a chemical drug based on structural similarity with a phytochemical for a specific disease

Session 16

Project-2 Identification of a chemical drug based on structural similarity with a phytochemical for a specific disease

Session 17

Project-2 Identification of a chemical drug based on structural similarity with a phytochemical for a specific disease

Session 18

Project-2 Identification of a chemical drug based on structural similarity with a phytochemical for a specific disease

Session 19

Project presentation

Journal paper for reference

Session 20

Project presentation

Journal link

Case Studies