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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Steered Molecular Dynamics Simulations Study on FABP4 Inhibitors.

Rosario Tomarchio¹, Vincenzo Patamia¹, Chiara Zagni¹

¹Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy.

Molecules (Basel, Switzerland)

|March 29, 2023

Summary

Steered molecular dynamics (SMD) simulations were first used to assess small molecule binding to fatty acid binding protein 4 (FABP4). This computational method accelerates drug discovery for FABP4 inhibitors, which show promise for treating cancer and metabolic diseases.

Keywords:

FABP4 FABP4 inhibitors computer-aided drug design drug design fatty acid binding protein molecular modeling steered molecular dynamics

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Area of Science:

Computational chemistry
Drug discovery
Molecular modeling

Background:

Traditional de novo drug design is slow and costly.
Computational tools, including molecular dynamics (MD) simulations, accelerate drug discovery.
Fatty acid binding protein 4 (FABP4) is a therapeutic target for various diseases.

Purpose of the Study:

To apply steered molecular dynamics (SMD) for the first time to evaluate small molecule binding to FABP4.
To investigate the potential of SMD in rational drug design for FABP4 inhibitors.

Main Methods:

Utilized steered molecular dynamics (SMD) simulations.
Evaluated binding properties of small molecules targeting FABP4.

Main Results:

Demonstrated the first application of SMD for assessing small molecule interactions with FABP4.
Provided insights into the binding characteristics of potential FABP4 inhibitors.

Conclusions:

SMD is a promising computational tool for accelerating the rational design of FABP4 inhibitors.
FABP4 inhibitors hold therapeutic potential for cancer, metabolic syndrome, and diabetes.