Drug Docking in the Organic Chemistry Curriculum

This article presents a feasible 3-week lab project that introduces drug docking with proteins to undergraduate Organic Chemistry students. In week 1, students are briefly introduced to docking by demonstrating the use of Autodock, OpenBabel, Protox, PyMol, and Protein Ligand Interaction Profiler. In week 2, students use a known drug of their choice and study its docking to a protein known to bind to the drug from literature searches. In week 3, students modify the structure of the drug and study the modified drug’s docking to the same protein. The toxicity and hydrophobicity of both drugs are predicted using ProTox. Based on binding energies, students predict the drug that is likely to bind better to the binding site.