Course Title: 
Computer Aided Drug Design - Theory
Course Code: 
Year Taught: 
Undergraduate (UG)
School of Pharmacy

'Computer Aided Drug Design - Theory' is a course offered in the eighth semester of B. Pharm program at School of Pharmacy, Health Sciences campus, Amrita Vishwa Vidyapeetham.

Course Duration: 45 Hours


This subject is designed to provide detailed knowledge of rational drug design process and various techniques used in rational drug design process.


Upon completion of the course, the student shall be able to understand

  1. Design and discovery of lead molecules
  2. The role of drug design in drug discovery process
  3. The concept of QSAR and docking
  4. Various strategies to develop new drug like molecules.
  5. The design of new drug molecules using molecular modeling software.

Unit I (10 Hours)

Introduction to Drug Discovery and Development: Stages of drug discovery and development

Lead discovery and Analog Based Drug Design: Rational approaches to lead discovery based on traditional medicine, Random screening, Non-random screening, serendipitous drug discovery, lead discovery based on drug metabolism, lead discovery based on clinical observation.

Analog Based Drug Design: Bioisosterism, Classification, Bioisosteric replacement. Any three case studies

Unit II (10 Hours)

Quantitative Structure Activity Relationship (QSAR) : SAR versus QSAR, History and development of QSAR, Types of physicochemical parameters, experi- mental and theoretical approaches for the determination of physicochemical parameters such as Partition coefficient, Hammet’s substituent constant and Tafts steric constant. Hansch analysis, Free Wilson analysis, 3D-QSAR approaches like COMFA and COMSIA.

Unit III (10 Hours)

Molecular Modeling and virtual screening techniques

Virtual Screening techniques: Drug likeness screening, Concept of pharmacophore mapping and phar- macophore based Screening,

Molecular docking: Rigid docking, flexible docking, manual docking, Docking based screening. De novo drug design.

Unit IV (08 Hours)

Informatics & methods in drug design Introduction to Bioinformatics, chemoinformatics. ADME databases, chemical, biochemical and pharma- ceutical databases.

Unit V (07 Hours)

Molecular Modeling: Introduction to molecular mechanics and quantum mechanics. Energy Minimiza- tion methods and Conformational Analysis, global conformational minima determination.

Recommended Books (Latest Editions)

  1. Robert GCK, ed., Drug Action at the Molecular Level University Prak Press Baltimore.
  2. Martin YC. Quantitative Drug Design Dekker, New York.
  3. Delgado JN, Remers WA eds Wilson & Gisvolds’s Text Book of Organic Medicinal & Pharmaceutical Chemistry Lippincott, New York.
  4. Foye WO Principles of Medicinal chemistry ‘Lea & Febiger.
  5. Koro lkovas A, Burckhalter JH. Essentials of Medicinal Chemistry Wiley Interscience.
  6. Wolf ME, ed The Basis of Medicinal Chemistry, Burger’s Medicinal Chemistry JohnWiley& Sons, New York.
  7. Patrick Graham, L., An Introduction to Medicinal Chemistry, Oxford University Press.
  8. Smith HJ, Williams H, eds, Introduction to the principles of Drug Design Wright Boston.
  9. Silverman R.B. The organic Chemistry of Drug Design and Drug Action Academic Press New York.