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Sathyabama Institute of Science and Technology B.Tech - BioTechnology SBTA3009 Molecular Modelling and Drug design Syllabus

SATHYABAMA INSTITUTE OF SCIENCE AND TECHNOLOGY SCHOOL OF BIO AND CHEMICAL ENGINEERING

SBTA3009 MOLECULAR MODELLING AND DRUG DESIGN
L T P Credits Total Marks
3 0 0 3 100

UNIT 1 CONCEPTS IN MOLECULAR MODELING 9 Hrs.
Introduction, Coordinate systems, Energy surfaces. Introduction to Quantum mechanics - Schrodinger wave equation, Born-
Oppenheimer Approximation.

UNIT 2 MOLECULAR MECHANICS 9 Hrs.
Force field - Bond Stretching, Angle bending and Torsion angle, Covalent bond, Non-bonding interactions. Introduction to
Energy minimization, Computer simulations, Conformational analysis.

UNIT 3 DRUGS 9 Hrs.
Hard drugs, Soft drugs. Prodrugs. Drug targets - Enzymes, Receptors, Proteins, Nucleic acids, Lipids. Drug solubility, Drug
Metabolism.

UNIT 4 DRUG DISCOVERY AND DESIGN 9 Hrs.
Steps in drug Development, Computer aided drug design- structure based, Ligand based, Lead discovery, Pharmacophore.
Molecular docking, QSAR

UNIT 5 COMPUTATIONAL REPRESENTATION OF MOLECULES 9 Hrs.
Chemical Databases - PDB LIGAND, PUBCHEM, ZINC. Sources of data for 3D structures - PDB, PDB Sum. SMILES
Notation.
Max.45 Hrs.

COURSE OUTCOMES
On completion of course, student will able to
CO1 - Provide an overview of the basic concepts of molecular modelling and analyse on the different types of input
provided to generate 3D models along with the stability of a model based on the energy of the system
CO2 - Enumerate on the various force fields responsible for the energy of a system and assess the significance of
energy minimisation for the stability of a system
CO3 - List out the different aspects of drugs like soft drugs and pro drugs and comprehend the various parameters
involved in the solubility of the drugs
CO4 - Summarise the steps involved in the development of drugs and ponder on the important aspects of
pharmacophore analysis and lead molecule identification in the process of drug design
CO5 - Describe the docking mechanism and analyse its importance in the development of drugs and thereby understand
the nuances involved in the development of drugs
CO6 - Look into the various databases of molecules and analyse them by giving the appropriate input system like
SMILES notation and analyse the three dimensional structures of molecules

END SEMESTER EXAMINATION QUESTION PAPER PATTERN
Max. Marks: 100 Exam Duration: 3 Hrs.
Part A: 10 Questions of 2 marks each - No choice 20 Marks
Part B: 2 Questions from each unit of internal choice, each carrying 16 marks 80 Marks