Course Code Course Title Credits Type
CUBS2545 BIOVIA DISCOVERY STUDIO 4 (0+2+2)

Course Overview:
This course provides hands-on experience with BIOVIA Discovery Studio, a comprehensive suite for modeling and simulation in life sciences. Students will learn to handle enzyme properties, ligand and protein structures, drug-receptor interactions, and in silico data interpretation. Through practical exercises and projects, students will critically evaluate and apply computational tools in drug discovery processes.

Prerequisites:

  • Basic understanding of biochemistry and molecular biology.
  • Familiarity with basic computer operations and data handling.

Course Objectives: Students will be able to:

  1. Comprehend the general properties and mechanisms of enzymes. (L2)
  2. Demonstrate proficiency in handling ligand structures using BIOVIA Discovery Studio. (L3)
  3. Analyze protein structures and identify active sites using BIOVIA Discovery Studio. (L4)
  4. Evaluate drug-receptor interactions and perform molecular docking using BIOVIA Discovery Studio. (L5)
  5. Interpret in silico data and prepare reports for publication. (L6)

Course Outcomes: Students will:

  • CO1: Define the general properties of enzymes and their classification. (L2)
  • CO2: Sketch, import, and handle ligand structures in BIOVIA Discovery Studio. (L3)
  • CO3: Analyze protein structures and identify active sites using BIOVIA Discovery Studio. (L4)
  • CO4: Conduct molecular docking and lead identification through virtual screening using BIOVIA Discovery Studio. (L5)
  • CO5: Interpret docking scores and ADMET predictions and summarize data for publication. (L6)

CO-PO Mapping:

CO\PO PO1 PO2 PO3 PO4 PO5 PO6 PO7 PO8 PO9 PO10 PO11 PO12
CO1 3 2 2 2
CO2 3 3 2 2 3 2
CO3 2 3 3 3 3 2 2 2 3 3 2 3
CO4 2 3 3 3 3 2 2 2 3 3 2 3
CO5 2 3 3 3 3 2 2 2 3 2 3

Syllabus

Module 1: Enzymes

  • General properties
  • Classification
  • Mechanism of action
  • Michaelis & Menten and Line Weaver Burk equations and plots
  • Introduction to allosteric enzymes
  • Exercise:
    • Hypothesis: Allosteric enzymes exhibit the same kinetic behavior as Michaelis-Menten enzymes.
    • Exercise: Compare the kinetic plots of an allosteric enzyme and a Michaelis-Menten enzyme using BIOVIA Discovery Studio to highlight differences.

Module 2: 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 searches
  • Structure importing from chemical databases and handling of large databases
  • Exercise:
    • Hypothesis: Manual ligand sketching yields the same results as automated ligand importing.
    • Exercise: Compare manually sketched ligands with those imported from databases for accuracy and completeness using BIOVIA Discovery Studio.

Module 3: Protein Structure Handling in Discovery Studio

  • Study of various components of a receptor protein
  • Protein analysis and identification of active site cavities using Discovery Studio
  • Disease target search at various biological pathways
  • Study of various protein databases and identification of target proteins
  • Ligand preparation steps and algorithms
  • Automated ligand preparation using Discovery Studio
  • Theory of ligand filtration and screening
  • Ligand filtration of large chemical databases
  • Protein preparation steps and algorithms
  • Protein preparation using Discovery Studio
  • Exercise:
    • Hypothesis: Automated protein preparation is as thorough as manual preparation.
    • Exercise: Compare automated and manual protein preparation processes to identify active sites accurately and efficiently using BIOVIA Discovery Studio.

Module 4: 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
  • Exercise:
    • Hypothesis: Virtual screening is equally effective in identifying lead compounds as traditional laboratory methods.
    • Exercise: Perform virtual screening for a set of ligands and compare the identified leads with those found through experimental methods.

Module 5: In silico Data Interpretation and Publication

  • Data analysis of molecular docking scores and study of various docking interactions
  • Interpretation of ADMET prediction scores
  • Summarization of docking scores and molecular properties for publication
  • Exercise:
    • Hypothesis: In silico ADMET predictions are as reliable as in vitro ADMET assays.
    • Exercise: Compare ADMET predictions from BIOVIA Discovery Studio with experimental data to evaluate their reliability.

Projects:

  1. In Silico Screening of Natural and Synthetic Ligands Against Alzheimer’s Disease Target Proteins.
  2. Computational Evaluation of Antimicrobial Ligands Targeting Plant Pathogenic Bacterial Proteins.
  3. Molecular Docking-Based Identification of Ligand Candidates Against SARS-CoV-2 Proteins.
  4. In Silico Design of Ligands for Heavy Metal Detoxification via Protein–Ligand Interactions.

Textbook:

  • Waite, Gabi Nindle. Applied Cell and Molecular Biology for Engineers. McGraw-Hill Education, 2007.

SESSION-WISE LECTURE PLAN AND LEARNING OUTCOME

Module 1: Enzymes (10 Hours)

Hours Session Type Topic Name Learning Outcome/s
2 Practice General properties Understanding enzyme properties.
2 Practice Classification Learning enzyme classification.
2 Practice Mechanism of action Understanding enzyme mechanisms.
2 Practice Michaelis & Menten and Lineweaver-Burk equations and plots Learning kinetic equations and plotting.
2 Practice Introduction to allosteric enzymes Understanding allosteric regulation.

Module 2: Ligand Structure Handling in Discovery Studio (10 Hours)

Hours Session Type Topic Name Learning Outcome/s
2 Theory Introduction to Drug Discovery Processes Understanding the stages and role of ligand discovery.
2 Theory + Demo Introduction to BIOVIA Discovery Studio Familiarity with the interface and tools of Discovery Studio.
2 Hands-On Ligand sketching using BIOVIA Discovery Studio Creating molecular structures using sketching tools.
2 Hands-On Ligand importing and handling with BIOVIA Discovery Studio Learning import formats and manipulation of ligands.
1 Theory Study of chemical and ligand databases Familiarity with PubChem, ChEMBL, ZINC, and others.
1 Hands-On Structure import and large-scale handling Working with large sets of chemical structures efficiently.

Module 3: Protein Structure Analysis and Active Site Identification (10 Hours)

Hours Session Type Topic Name Learning Outcome/s
2 Theory Introduction to Protein Structure Understanding protein structure hierarchy and PDB file formats.
2 Theory + Demo Loading and Visualizing Protein Structures in Discovery Studio Navigating 3D structures and analyzing structural domains.
2 Hands-On Protein Preparation and Refinement Cleaning, optimizing, and preparing proteins for docking.
2 Hands-On Active Site Prediction and Identification Identifying binding pockets and druggable sites.
1 Theory Protein Structure-Function Relationship Correlating 3D structure with biological activity.
1 Hands-On Exploring Protein Databases Working with RCSB PDB and UniProt for structure retrieval.

Module 4: Molecular Docking and Virtual Screening (10 Hours)

Hours Session Type Topic Name Learning Outcome/s
2 Theory Introduction to Molecular Docking Understanding molecular recognition and docking strategies.
2 Theory + Demo Docking Protocols and Types Differentiating rigid, flexible, and induced-fit docking techniques.
2 Hands-On Ligand and Receptor Preparation Preparing molecules and defining binding sites in Discovery Studio.
2 Hands-On Performing Docking Simulation Running docking protocols and retrieving docking scores.
2 Hands-On Virtual Screening Techniques Conducting high-throughput virtual screening to identify lead candidates.

Module 5: Post-Docking Analysis and Reporting (8 Hours)

Hours Session Type Topic Name Learning Outcome/s
2 Theory Docking Score Interpretation Learn to analyze docking scores and understand binding affinity metrics.
2 Hands-On Visualization of Docked Complexes Use Discovery Studio to visualize binding poses and interactions (e.g., H-bond, hydrophobic).
2 Hands-On ADMET Prediction and Filtering Predict ADMET properties and filter unsuitable ligands.
2 Hands-On + Report Writing Result Interpretation and Report Compilation Compile in silico results into a scientific report suitable for publication or presentation.

Supplementary Learning Resources: BIOVIA Discovery Studio Tutorials

S. No. Title Link
1 BIOVIA Discovery Studio Overview Watch Video
2 Protein Preparation and Active Site Prediction Watch Video
3 Ligand Preparation and Visualization Watch Video
4 Docking Protocol Setup Watch Video
5 Post-Docking Analysis and Interactions Watch Video
6 Live Session: Discovery Studio Tutorial – Part 1 Watch Live
7 Live Session: Discovery Studio Tutorial – Part 2 Watch Live
8 Live Session: Complete Workflow Demonstration Watch Live