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Related Experiment Video

Updated: Jun 18, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Trypsin-ligand binding free energy calculation with AMOEBA.

Yue Shi¹, Dian Jiao, Michael J Schnieders

¹Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

|December 8, 2009

Summary

Benzamidine-like inhibitors bind effectively to trypsin, driven by electrostatic interactions. Molecular polarizability, not dipole moment, strongly correlates with binding affinity, validated by molecular mechanics and simulations.

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Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Published on: September 13, 2014

Area of Science:

Biochemistry and Molecular Biology
Computational Chemistry
Drug Discovery

Background:

Trypsin is a key serine protease involved in various physiological processes.
Benzamidine derivatives are known inhibitors of trypsin.
Understanding inhibitor binding mechanisms is crucial for drug development.

Purpose of the Study:

To investigate the binding free energies of benzamidine-like inhibitors to trypsin.
To elucidate the driving forces behind inhibitor-trypsin interactions.
To explore the relationship between inhibitor properties and binding affinity.

Main Methods:

Polarizable molecular mechanics potential calculations.
Molecular dynamics (MD) simulations.
Free energy decomposition analysis.

Main Results:

Computed binding free energies closely matched experimental data.
Electrostatic interactions identified as the primary driving force for binding.
Ligands formed competitive hydrogen bonds with trypsin and surrounding water molecules.
Binding free energy showed a strong correlation with ligand molecular polarizability, independent of dipole moment.

Conclusions:

Polarizable molecular mechanics accurately predicts inhibitor-trypsin binding.
Electrostatic forces and molecular polarizability are key factors in benzamidine-like inhibitor efficacy.
These findings inform the rational design of novel trypsin inhibitors.