Computer Aided Drug Design (Pharmaceutical chemistry) M.Pharm Second Semester

Syllabus

MPC 203T

Computer Aided Drug Design

Theory                                                                                          (60 Hours)

Unit-1                                                                                                                                  (12 hours)

Introduction to Computer Aided Drug Design (CADD):  History, different techniques and applications. Quantitative Structure Activity Relationships: Basics History and development of QSAR: Physicochemical parameters and methods to calculate physicochemical parameters: Hammett equation and electronic parameters (sigma), lipophilicity effects and parameters (log P, pi-substituent constant), steric effects (Taft steric and MR parameters) Experimental and theoretical approaches for the determination of these physicochemical parameters.

Unit-2                                                                                                                                 (12 hours)

Quantitative Structure Activity Relationships: Applications Hansch analysis, Free Wilson analysis and relationship between them, Advantages and disadvantages; Deriving 2D-QSAR equations. 3D-QSAR approaches and contour map analysis. Statistical methods used in QSAR analysis and importance of statistical parameters. 

Unit-3                                                                                                                                 (12 hours)

Molecular Modeling and Docking:  

a)       Molecular and Quantum Mechanics in drug design.

b)       Energy Minimization Methods: Comparison between global minimum conformation and bioactive conformation.

c)       Molecular Docking and Drug Receptor Interactions: Rigid docking, flexible docking and extra-precision docking. Agents acting on enzymes such as DHFR, HMG-CoA reductase and HIV protease, choline esterase (AChE & BChE).

Unit-4                                                                                                                                 (12 hours)

Molecular Properties and Drug Design: 

a)       Prediction and analysis of ADMET properties of new molecules and its importance in drug design.

b)       De novo Drug Design: Receptor/enzyme-interaction and its analysis, Receptor/enzyme cavity size prediction, predicting the functional components of cavities, Fragment based drug design.

c)       Homology modeling and generation of 3D-structure of protein.

Unit-5                                                                                                                                  (12 hours)

Pharmacophore Mapping and Virtual Screening: Concept of pharmacophore, pharmacophore mapping, identification of Pharmacophore features and Pharmacophore modeling; Conformational search used in pharmacophore mapping.

In Silico Drug Design and Virtual Screening Techniques: Similarity based methods and Pharmacophore based screening, structure based In-silico virtual screening protocols.