CIENCIA LIFE SCIENCES

Syllabus for certification Course

Computational Aided Drug Designing

Concept and Approaches used in Computer Aided Drug Discovery

1. Basics in Drug Discovery and Development

  • Introduction about Known Drug and Diseases
  • The role of drugs in the practice of medicine
  • The role of Pharmaceutical Chemistry
  • Natural substances as drugs
  • The process of drug discovery and development (DDD)
  • Stages and cost of modern The process of DDD
  • Tools and teams involve in the DDD
  • The role of Computational Chemistry in the DDD
  • Rational approaches in the DDD

2. Ligand Preparation/Virtual databases generation using Cheminformatics Tools

  • Introduction about compound/ligand
  • The role of ligand as Drugs
  • The meaning 2D and 3D structure of compounds
  • File format, conversion of file format, sketching compounds
  • Molecular mechanics (MM) and quantum mechanics (QM)representation of Molecule
  • Force filed and Energy expression – Local and Global minima
  • Minimization of molecule using MM
  • Preparation of virtual small molecule databases
  • Calculation of Drug like properties and applying of Lipinski rule

3. Target Protein Preparation using Bioinformatics Tools

  • Bioinformatics technical tool box, Biological data.
  • File format, conversion of file format, Sketching compounds.
  • Data retrieval system.
  • Databases: Bioinformatics databases, Types of databases, Nucleotide
  • sequence databases,
  • Primary nucleotide sequence databases-EMBL, Gene Bank, DDBJ;
  • Secondary nucleotide databases,
  • Protein sequence databases-SwissProt/ TrEMBL.
  • Amino acids, Functional classification of proteins.
  • Structural organization of proteins: Primary, Secondary, Tertiary and
  • Quaternary structure of proteins; Protein folding
  • The Protein Data Bank (PDB)
  • Relationship between sequence and 3D structure of a protein
  • Alignment of protein sequences
  • Needleman-Wunsch alignment method
  • Multiple sequence alignments (MSA)
  • Homology modelling of proteins
  • Construction of loops and turns
  • Construction of the Side chains
  • Refinement of the homology model
  • Prediction of protein structures by threading
  • Comparison of various strategies in homology modelling
  • Analysis PDB structures (RCSB databank)
  • Active site or binding site analysis

4. Virtual library screening and Structure based drug design

  • Protein and Ligand Preparation
  • Binging site analysis and identifying of important amino acids
  • Known compound docking for understanding crucial binding pattern
  • Docking of virtual library using standard and precision methods
  • Understanding of interaction profiles of top compounds
  • Dock score analysis and Filter of compounds
  • Molecular docking for Top compounds
  • Selection of compounds for biological screening

5. Virtual library screening and Ligand based drug design approaches

  • The Active Analogue Approach (AAA) and patent bursting
  • Sub structure, Bioisoster and similarity based screening
  • 2D and 3D Pharmacophore generation and screening
  • Introduction to SAR and QSAR studies
  • ADMET models and screening
  • Basics in AI and Ml tools and their applications in DDD

6. Practical sessions for above methodologies will apply for 10 hours

  • ACD/ChemSketch,
  • Editor and viewer- CSFChimera.
  • Biology Databases
  • Small compound Databases
  • 2D to 3D conversion
  • Protein Modelling (Homology modelling)
  • Molecular Docking
  • Virtual screening
  • Sub and similar structure screening using VS

Microbiology Lab Syllabus


  • Study of differ equipment (Biosafety Cabinet BSL-II, Laminar, Autoclave, Incubator, Hot Air Oven)
  • Sterilization Procedures
  • Sub-Culturing of bacteria and fungus
  • Staining Methods- gram staining and acid-fasting staining
  • Pure culture techniques-spread plates, pour plates, streak plate
  • Isolation of pure-culture of microorganism
  • Biochemical tests
  • Media Preparations
  • Inoculation methods
  • Bacterial Growth Curve
  • Isolation of bacteria
  • Identification of bacteria
  • Heamocytometer
  • Types of Industrial fermentation processes
  • Antibacterial Activity
  • Antifungal activity
  • Biofilm assay
  • Minimum Inhibitory Concentration(MIC)

Biochemistry Lab Syllabus


  • Thin Layer Chromatography
  • Column Chromatography
  • Enzyme Estimations
  • Qualitative and Quantitative Analysis of proteins and enzymes
  • UV Spectrophotometer
  • Colorimeter
  • pH Optimization
  • SDS-PAGE
  • Protein Purification
  • Preparation of Standard Curves
  • Agarose Gel Electrophoresis
  • ELISA Reader
  • IC50 calculations for binding assay

Molecular Biology Lab Syllabus


  • Isolation of DNA and RNA
  • Isolation of RNA
  • Isolation of Plasmid DNA
  • Agarose Gel Electrophoresis
  • Primer designing
  • Optimization of PCR
  • Polymerase Chain Reaction
  • Gradient and multiplex PCR
  • Agarose Gel Electrophoresis with ladder
  • Primer designing and tools in bioinformatics
  • SDS-PAGE
  • Restriction of Plasmid DNA
  • Quantification of DNA & RNA and Protein
  • Chromatography
  • Biomarkers
  • Statistical analysis (Ex: Epiinfo)
  • Sardarpatel Nagar, Nizampet X Roads, Kukatpally, Hyderabad. India - 500085
  • Phone: +918247307129; +91 9966239797
  • www.ciencialifesciences.com