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:
- Comprehend the general properties and mechanisms of enzymes. (L2)
- Demonstrate proficiency in handling ligand structures using BIOVIA Discovery Studio. (L3)
- Analyze protein structures and identify active sites using BIOVIA Discovery Studio. (L4)
- Evaluate drug-receptor interactions and perform molecular docking using BIOVIA Discovery Studio. (L5)
- 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:
- In Silico Screening of Natural and Synthetic Ligands Against Alzheimer’s Disease Target Proteins.
- Computational Evaluation of Antimicrobial Ligands Targeting Plant Pathogenic Bacterial Proteins.
- Molecular Docking-Based Identification of Ligand Candidates Against SARS-CoV-2 Proteins.
- 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 |