This project investigates the binding potential of Capsaicin — a bioactive compound found in chili peppers with known anti-inflammatory and analgesic properties — against a protein target identified via SwissTargetPrediction. Molecular docking was performed using AutoDock Vina, and binding poses were visualized in PyMOL.
- SwissTargetPrediction — target identification
- AutoDock Vina — molecular docking
- PyMOL — 3D visualization of binding interactions
- Protein Data Bank (PDB) — protein structure source
- PubChem — ligand structure source
- Retrieved Capsaicin SMILES from PubChem; converted to MOL2 and PDBQT format
- Identified top protein targets using SwissTargetPrediction
- Downloaded target protein (PDB ID: 7LR0) and prepared structure (removed water molecules, added polar hydrogens)
- Defined docking grid box around the active site
- Ran molecular docking using AutoDock Vina with defined parameters
- Visualized top binding pose and interactions in PyMOL
- Target protein: 7LR0 (TRPV1 — Transient Receptor Potential Vanilloid 1), a well-known receptor for Capsaicin
- Docking performed and binding poses generated
- Best binding pose visualized using PyMOL showing ligand placement within the active site
| File | Description |
|---|---|
7lr0_modified.pdb |
Prepared protein structure |
ligand.pdbqt |
Capsaicin ligand file for docking |
system.pdbqt |
Receptor file for docking |
vina_dock.pdbqt |
Docking output with binding poses |
parameters |
AutoDock Vina configuration file |
- Binding energy values to be updated after full AutoDock Vina run
- Future: run MD simulation to validate docking stability
- Expand to screen multiple Capsaicin analogues
- AutoDock Vina: https://vina.scripps.edu
- SwissTargetPrediction: http://www.swisstargetprediction.ch
- RCSB PDB: https://www.rcsb.org