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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding Sites

Ligand Binding Sites

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

Ligand Binding and Linkage

Ligand Binding and Linkage

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Updated: Mar 3, 2026

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

Benchmarking the Ligand-HER2 Interactions Using Machine Learning and Molecular Dynamics Simulations.

Duc Toan Truong^1,2, Quang Tung Dao³, Thi Thuy Mai Tran⁴

¹Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City 70000, Vietnam.

|March 2, 2026

Summary

This summary is machine-generated.

Researchers identified key interactions between breast cancer's HER2 protein and inhibitors. A novel compound, lig233, shows significantly stronger binding than lapatinib, offering new avenues for HER2 inhibitor drug development.

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Area of Science:

Biochemistry
Computational Biology
Pharmacology

Background:

HER2 tyrosine kinase is a critical target in breast cancer therapy.
Understanding inhibitor-HER2 interactions is vital for developing effective treatments.
Existing therapies face challenges, necessitating novel inhibitor strategies.

Purpose of the Study:

To elucidate the molecular mechanism of inhibitor-HER2 interactions.
To identify novel potent anti-HER2 compounds.
To establish a benchmark for ligand-HER2 binding strength.

Main Methods:

Machine learning predictive regression model.
Atomistic molecular dynamics (MD) simulations.
Umbrella sampling MD method for binding free energy calculations.
Systematic mining of 8 million chemical compounds.

Main Results:

Identified 13 novel anti-HER2 candidate compounds.
Established electrostatic interactions with key residues (Lys753, Leu796, Thr798, Asp863, Asp880) as crucial for inhibitor strength.
Compound lig233 demonstrated exceptional binding free energy (-47 kcal/mol), exceeding that of lapatinib (-21 kcal/mol).
Lig233 forms hydrogen bonds with Asp863 and Asp880, indicating strong chemical bonds.

Conclusions:

Novel insights into inhibitor-HER2 binding mechanisms.
Lig233 represents a promising lead compound for next-generation HER2 inhibitors.
Findings can guide experimental development of more effective breast cancer therapies.