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Updated: Jan 16, 2026

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

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Structure Modeling and Virtual Screening with HCAR3 to Discover Potential Therapeutic Molecules.

Yulan Liu¹, Yunlu Peng¹, Zhihao Zhao¹

¹Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong-Shenzhen, Shenzhen 518172, China.

Pharmaceuticals (Basel, Switzerland)

|September 27, 2025

Summary

Researchers identified six novel compounds that bind to Hydroxycarboxylic acid receptor 3 (HCAR3), a key target for treating dyslipidemia. These potential drug candidates show promising binding affinities, offering new avenues for lipid regulation therapies.

Keywords:

hydroxycarboxylic acid receptor 3 molecular dynamics simulations virtual screening

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Area of Science:

Biochemistry and Pharmacology
Computational Chemistry and Drug Discovery

Background:

Hydroxycarboxylic acid receptor 3 (HCAR3) is primarily expressed in human adipose tissue and plays a role in regulating lipid metabolism by inhibiting lipolysis.
HCAR3 is a significant therapeutic target for dyslipidemia due to its role in lipid regulation.
Existing HCAR3 active compounds are carboxylic acids, consistent with ARG111 being a key residue for ligand binding in the homologous HCAR2 protein.

Purpose of the Study:

To discover novel chemical entities with potential binding activity against HCAR3 using virtual screening.
To identify promising drug candidates for the development of novel therapeutics for dyslipidemia.

Main Methods:

Cross-docking was utilized to determine the optimal receptor conformation for screening.
Virtual screening of the ZINC20 database using molecular docking identified potential ligands.
Molecular dynamics (MD) simulations and umbrella sampling were employed to assess binding stability and estimate binding affinities.

Main Results:

A homology model (HCAR3_homology) was selected as the most suitable receptor conformation.
Prospective docking identified 30 candidate compounds that interacted favorably with ARG111.
MD simulations confirmed the stability of six selected complexes, which exhibited negative binding affinities via umbrella sampling.

Conclusions:

The six identified compounds demonstrate negative binding affinities, indicating their potential as novel ligands for HCAR3.
These compounds represent promising candidates for the development of new drugs to treat dyslipidemia.
The study validates a computational approach for identifying HCAR3 modulators.