Introduction
Molecular docking is a computational method used to predict how small molecules, such as drugs and inhibitors, interact with target proteins. It is widely applied in structure-based drug discovery to investigate protein–ligand interactions, identify potential binding sites, and predict favorable ligand-binding conformations.
In this exercise, each student will investigate a different protein–inhibitor pair associated with a specific disease or therapeutic application. Students will retrieve an experimentally determined protein–inhibitor complex from the Protein Data Bank (PDB), perform molecular docking using AutoDock Vina, and visualize the results using PyMOL.
By comparing the predicted binding pose with the experimentally determined structure, students will evaluate the accuracy of molecular docking and gain an understanding of protein–ligand interactions and their relevance to drug development.
Protein-inhibitor complexes
Student will be assigned to analyze one of the following examples.
| No. | Protein | Inhibitor | Disease/Application | PDB ID |
|---|---|---|---|---|
| 1 | EGFR | Erlotinib | Lung cancer | 1M17 |
| 2 | DHFR | Trimethoprim | Bacterial infections | 6XG5 |
| 3 | Neuraminidase | Oseltamivir | Influenza | 2HU4 |
| 4 | HIV-1 protease | Darunavir | HIV/AIDS | 4HLA |
| 5 | DPP-4 | Sitagliptin | Type 2 diabetes | 1X70 |
| 6 | c-Abl kinase | Imatinib | Chronic myeloid leukemia | 1IEP |
Tasks
For your assigned task, perform a protein–ligand interaction analysis and write a report summarizing your findings. Finally, prepare a 10-minute presentation to present your results.
Step 1. Biological Background
Investigate the biological function of the assigned protein, its relationship to the associated disease, and the mechanism of action of its inhibitor.
Step 2. Protein Structure Analysis
Retrieve the experimentally determined protein–inhibitor complex from the Protein Data Bank (PDB). Identify the protein structure, inhibitor, and ligand-binding site.
Step 3. Molecular Docking
Prepare the protein and ligand structures and perform molecular docking using AutoDock Vina. Remove the inhibitor from the experimental complex before docking and predict its binding pose.
Step 4. Molecular Visualization Using PyMOL
Use PyMOL to visualize and analyze:
- The overall protein structure and inhibitor-binding site.
- Important amino acid residues interacting with the inhibitor.
- The experimentally determined and docking-predicted ligand conformations.
Step 5. Docking Validation
Compare the predicted ligand-binding pose with the experimentally determined structure. Calculate the root-mean-square deviation (RMSD) between the ligand conformations and report the docking score.
Step 6. Discussion
Interpret the docking results, identify important protein–ligand interactions, and discuss the accuracy and limitations of molecular docking.
Expected outcome
Each student will prepare a brief presentation summarizing the biological background, docking procedure, molecular visualizations, and validation results. The presentation should demonstrate how structural information and molecular docking can be used to understand protein–inhibitor interactions in the context of disease treatment and drug discovery.