Hands-On CNS Drug Discovery: Molecular Docking, Binding-Site Analysis & Compound Prioritization
Analyze CNS drug targets, assess predicted blood–brain barrier penetration, and build a justified compound shortlist using practical computational tools.
Skills you will gain:
About Workshop:
This three-day workshop introduces a practical computational workflow for central nervous system (CNS) drug discovery. Participants will examine a selected CNS target, identify its ligand-binding site, perform molecular docking and assess predicted properties relevant to brain exposure.
Using one target and a small compound set, participants will combine structural observations, docking results and molecular-property predictions to prepare a justified shortlist for further investigation. Prepared files and guided notebooks will support the exercises.
Aim: To develop practical skills in binding-site analysis, molecular docking, and compound prioritization for CNS drug discovery, with attention to prediction limits and experimental validation.
Workshop Objectives:
- Understand the role of structure-based methods in central nervous system (CNS) drug discovery.
- Retrieve and examine CNS target structures and identify key ligand-binding residues.
- Understand receptor and ligand preparation requirements for molecular docking.
- Perform reference-ligand redocking and screen a small compound set using AutoDock Vina.
- Assess predicted binding poses, molecular interactions and docking scores.
- Interpret predicted blood–brain barrier penetration, P-glycoprotein substrate status and other CNS-relevant molecular properties.
- Combine structural and computational evidence to prepare a justified compound shortlist.
- Recognize prediction limitations and identify experimental validation needs.
What you will learn?
Day 1: CNS Target Structures & Binding-Site Analysis
- Introduction to structure-based CNS drug discovery.
- Overview of the selected target and reference ligand.
- Retrieving an experimental protein–ligand structure from RCSB PDB.
- Understanding structure quality, missing regions and binding-site uncertainty.
- Identifying the reference ligand and surrounding binding-site residues.
- Examining hydrogen bonds, hydrophobic contacts and steric features.
- Assessing binding-pocket suitability for molecular docking.
Hands-On Activity:
Visualize the selected target and reference ligand in ChimeraX, identify key binding-site residues and create an annotated binding-pocket image.
Tools: RCSB PDB, UCSF ChimeraX.
Output: Annotated binding-site image and pocket-assessment worksheet.
Day 2: Molecular Docking & Binding-Pose Assessment
- Fundamentals of receptor and ligand preparation.
- Considering protonation, relevant waters and essential cofactors.
- Defining the docking search box using the reference ligand.
- Performing reference-ligand redocking with AutoDock Vina.
- Comparing predicted and experimental poses using structural overlays and ligand RMSD where appropriate.
- Screening a prepared set of 3–5 compounds.
- Interpreting docking scores, molecular interactions and steric clashes.
Hands-On Activity:
Redock the reference ligand, assess pose recovery and dock the prepared compound set. Record docking scores and inspect predicted binding interactions.
Tools: AutoDock Vina, Google Colab, UCSF ChimeraX.
Output: Reference-pose comparison and docking-results table.
Day 3: Predicted CNS Properties & Compound Prioritization
- Understanding the difference between target binding and brain exposure.
- Assessing molecular weight, lipophilicity, polarity and hydrogen bonding.
- Interpreting predicted blood–brain barrier penetration and P-glycoprotein substrate status.
- Reviewing solubility, metabolism predictions and medicinal-chemistry alerts.
- Combining pose quality, interactions, docking scores and predicted properties.
- Building a compound comparison and prioritization matrix.
- Identifying limitations and experimental follow-up requirements.
Hands-On Activity:
Assess the screened compounds using SwissADME and complete a comparison matrix. Select up to 2–3 compounds for further investigation, or explain why none should progress.
Tools: SwissADME, Google Colab, Excel or Google Sheets.
Output: Compound-prioritization matrix with a brief written justification.
Mentor Profile
Fee Plan
Important Dates
11 Nov 2026 Indian Standard Timing 4:30 PM
09 Nov 2026 to 11 Nov 2026 Indian Standard Timing 5:00 PM
Get an e-Certificate of Participation!
Intended For :
- Undergraduate students in their final year and postgraduate students in pharmacy, biotechnology, biochemistry, bioinformatics, life sciences and related disciplines.
- PhD scholars and researchers in medicinal chemistry, computational biology, structural biology, neuroscience and neuropharmacology.
- Faculty members and professionals interested in structure-based CNS drug discovery.
Career Supporting Skills
Workshop Outcomes
- Retrieve and visualize a selected CNS target structure using RCSB PDB and UCSF ChimeraX.
- Identify ligand-binding sites, key residues and protein–ligand interactions.
- Perform guided reference-ligand redocking and screen a small compound set using AutoDock Vina.
- Compare predicted binding poses and interpret docking scores.
- Assess predicted blood–brain barrier penetration, P-glycoprotein substrate status and CNS-relevant molecular properties using SwissADME.
- Build a compound comparison matrix and justify a shortlist for further investigation.
- Recognize computational limitations and identify experimental validation requirements.