Conceptualizing the Essence of Protein–Ligand Interaction at Undergraduate Level : Reinforcing Computational Skills (Journal Article)

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Abstract: The introduction of Computational Chemistry via “Molecular Modelling and Drug Design” course at undergraduate level has opened wide possibilities for students to expand their knowledge of quantum chemistry, organic reaction mechanisms, protein–ligand interactions, drug design, and probable in vivo behavior of drug candidates. Learning the use of various freely available molecular modeling software and web tools can further help in building a strong foundation for this course. The present work deals with the molecular docking study on inhibition of beta-trypsin with para-substituted benzamidine derivatives. The students were introduced to freely available software like ChemSketch, ArgusLab, UCSF Chimera, and SwissADME. The study involves docking of 12 ligands into the binding site of beta-trypsin, aiding the students in visualizing various factors responsible for protein–ligand interactions. The HOMO–LUMO plots, electrostatic potential (ESP) maps, and Mulliken charge analysis facilitated reactivity prediction of the ligands. To complement the docking studies, drug-likeness, physicochemical properties, and pharmacokinetics of the docked ligands were also analyzed.