Course Name: Drug Design Using Biovia

Course Credit: ABC01(2-2-0)

Course Description

Description: Computer-Aided drug design accelerates and economizes drug discovery and drug manufacturing processes; it is considered an effective strategy. With the significant rise in the availability of information on small molecule and biological macromolecule, the efficiency of computer-aided drug discovery has been enhanced and is being extensively applied to almost every phase in drug discovery and manufacturing activities such as detecting targets, validation, lead discovery, and optimization & preclinical tests. Since the last few years, substantial developments have been observed in computer-aided drug discovery techniques including molecular similarity calculation, de novo design, pharmacophore modeling and mapping, molecular docking, and sequence-based virtual screening, etc. Industries and also Government laboratories and Research centers are utilizing ampoule funding after computer-aided drug discovery.

Eligibility: Minimum Qualification required to get into this program is Bachelor of Medicine, Bachelor of Pharmacy or Bachelor of Science or equivalent program in the Life Science or Healthcare sector.

Prerequisite: Before joining the program a student must have adequate knowledge of the organic and bio-molecules and a thorough understanding of biological pathways and life processes in the living organisms. A brief knowledge about the pathophysiology of diseases and drug therapy for various diseases are advantageous

Duration of the course: One-month training and 15 days' practice.

Key highlights: After getting the certification a student will get more preference to various job roles at the Pharma and Biotech industries, Research and Development Organization, etc.

Course Objectives

To understand

• The Molecular Modeling Process used in Drug Discovery.
• The concept of Structure and Ligand-based Drug Designing.
• The Molecular Docking processes and their use in drug discovery.
• The Drug-likeness properties of various chemical entities.
• The application of Pharmacophore Modeling in drug discovery.
• To identify potential drug candidates through Virtual Screening of biological compounds.

Learning Outcomes

• Students will understand the Biovia Tools and their application in drug discovery processes.
• Identify potential biological molecules from synthetic and natural sources by using Biovia.
• Recognize and comprehend various disease targets and select an ideal target for drug discovery.
• Design novel drug candidates for various diseases by using Biovia Discovery Studio.
• Repurpose the already existing drugs for safe and effective medication for various diseases.

Course Syllabus

Module 1: Ligand Structure Handling in Discovery Studio

Introduction to Drug Discovery Processes. Introduction to Biovia Discovery Studio.  Ligand sketching using Biovia Discovery Studio. Ligand importing and Handling with Biovia Discovery Studio. Study of Various Chemical and Ligand databases and structure search in the databases. Structure importing from chemical databases and Handling of Large chemical databases.

Practice 1: Create your own Ligand Database using at least 10 natural product molecules and 10 synthetic compounds from published literature with appropriate references enlisted in a word document file.

Module 2: Protein Structure Handling in Discovery Studio

Study of various components of a receptor protein. Protein analysis and identification of active site cavities by using Discovery Studio. Diseases target search at various biological pathways. Study of Various protein databases and identification of desired protein for study. Ligand preparation steps and algorithms. Automated Ligand preparation using Discovery Studio. Theory of Ligand Filtration and screening. Ligand Filtration of Large chemical database. Protein preparation steps and algorithms. Protein preparation using Discovery Studio.

Practice 2: Identify a disease protein from plant or animal origin and prepare the suitable protein using Biovia.

Module 3: Drug Receptor Interaction study in Discovery Studio

Theory of Receptor - Ligand Interaction and Molecular Docking. Molecular Docking using Discovery Studio. Lead Identification through Virtual screening. Structure-based virtual screening using Discovery Studio.

Practice 3: Perform the Molecular docking of ligands prepared in Practice 1 with Protein prepared in Practice 2.

Module 4: Prediction of Ligand properties and Pharmacophore in Discovery Studio

ADMET Descriptors and their theories. Prediction of ADMET properties of Ligands using Discovery Studio. Introduction to pharmacophore model and their use in drug discovery. Pharmacophore modeling using Discovery Studio (Auto Pharmacophore Generation). Pharmacophore modeling using Discovery Studio (Common Feature Pharmacophore Generation). Pharmacophore modeling using Discovery Studio (3D QSAR Pharmacophore Generation). Virtual screening using Pharmacophore model using Discovery Studio.

Practice 4: Perform the preparation of the Pharmacophore model of the ligands prepared in Practice 1.

Module 5: In silico data interpretation and publication

Data Analysis of Molecular Docking Score and study of various docking interactions. Interpretation of ADMET Prediction Score. Summarization of Docking Score and Molecular properties for Publication.

Practice 5: Prepared a docking report for the molecular docking study performed in Module 3.

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

Session Plan

Session 1

Introduction to Drug Discovery Processes.

Text Note: Introduction to drug discovery processes

Session 2

Introduction to Biovia Discovery Studio.

Text Note: Introduction to Biovia Discovery Studio.

Video Tuotorial:

1_Introduction to Biovia Discovery Studio,

 2_Downloading and Installing Discovery Studio Visualizer

3_Graphic User Interface of Biovia Discovery Studio

Session 3

Ligand sketching and ligand importing to Biovia Discovery Studio.

Text Note: Ligand sketching and ligand importing to Biovia Discovery Studio.

Video Tutorial:

 1. Ligand Sketching and Importing in Discovery Studio Visualizer_1

1. Ligand Sketching and Importing in Discovery Studio Visualizer_2

Session 4

Ligand importing and Handling with Biovia Discovery Studio.

Text Note: Ligand sketching and ligand importing to Biovia Discovery Studio.

Video Tutorial: Ligand Importing and Handling Large Library

Session 5

Study of Various Chemical and Ligand databases and structure search in the databases.

Text Note: Study of Various Ligand databases and structure importing from chemical databases,

Video Tutorial: Study of various chemical and Ligand databases

Session 6

Assessment 1

Session 7

Study of Various Chemical and Ligand databases and structure search in the databases.

Video Tutorial: Structure search through the Various ligand databases

Session 8

Study of various components of a receptor protein.

Video Tutorial: Study of components of a receptor protein

Session 9

Protein analysis and identification of active site cavities by using Discovery Studio.

Video Tutorial: Identification of SBD Site sphere in Receptor Protein

Session 10

Diseases target search at various biological pathways.

Video Tutorial: Identifying the Diseases target through various biological pathways

Session 11

Study of Various protein databases and identification of desired protein for study.

Video Tutorial: Identification of desired Protein Structure for in silico study

Session 12

Assessment 2

Session 13

Ligand preparation steps and algorithms.

Text Note: Ligand preparation Theory and Protocol.

Session 14

Automated Ligand preparation using Discovery Studio.

Video Tutorial: Preparation of Ligand

Session 15

Theory of Ligand Filtration and screening.

Text Note: Theory of Ligand Filtration.

Video Tutorial: Ligand Filtration Theory

Session 16

Ligand Filtration of Large chemical database.

Video Tutorial: Ligand Filteration Protocol

Session 17

Protein preparation steps and algorithms.

Theory: Theory of Protein Preparation,

Video Tutorial: Preparation Of Protein Algorithm

Session 18

Protein preparation using Discovery Studio.,

Video Tutorial: Preparation 0f Protein using Biovia

Session 19

Assessment 3

Session 20

Theory of Receptor - Ligand Interaction and Molecular Docking.

Text Note: Theory of Receptor Ligand Interaction

Session 21

Molecular Docking using Discovery Studio.

Video Tutorial: Molecular Docking Using Discovery Studio

Session 22

Lead Identification through Virtual screening

Text Note: Structure Based Virtual Screening

Session 23

Structure based virtual screening using Discovery Studio.

Video Tutorial: Virtual Screening of Large Chemical Library

Session 24

Assessment 4

Session 25

ADMET Descriptors and their theories.

Text Note: Prediction of ADMET properties of Ligands

Session 26

Prediction of ADMET properties of Ligands using Discovery Studio.

Video Tutorial: Prediction of ADMET properties of ligands

Session 27

Introduction to pharmacophore model and their use in drug discovery.

Text Notes: Introduction to pharmacophore model and its use in drug discovery Pharmacophore modeling using Discovery Studio

Session 28

Pharmacophore modeling using Discovery Studio (Auto Pharmacophore Generation).

Video Tutorial: Autopharmacophore Generation

Session 29

Pharmacophore modeling using Discovery Studio (Common Feature Pharmacophore Generation).

Video Tutorial: Common Feature Pharmacophore Generation

Session 30

Assessment 5

Session 31

Pharmacophore modelling using Discovery Studio (3D QSAR Pharmacophore Generation).

Video Tutorial: 3D Qsar Pharmacophoregeneration

Session 32

Virtual screening using Pharmacophore model using Discovery Studio.

Text Notes: 3D-Pharmacophore Based Virtual Screening

Video Tutorial: 3D Pharmacophore Based Virtual Screening

Session 33

Data Analysis of Molecular Docking Score and study of various docking interactions.

Case Study: Result Interpretation of Molecular Docking and ADMET study

Session 34

Interpretation of ADMET prediction Score.

Case Study: Result Interpretation of Molecular Docking and ADMET study

Session 35

Summarization of Docking Score and Molecular properties for Publication.

Case Study: Result Interpretation of Molecular Docking and ADMET study

Session 36

Assessment 6