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A New Method for Mapping the Molecular Surface of a Protein Structure Using a Spherical Self-Organizing Map
Kiyoshi Hasegawa1, Kimito Funatsu2
1Chugai Pharmaceutical Company, Kamakura Research Laboratories, Kajiwara 200, Kamakura, Kanagawa 247-8530, Japan.
Molecular Informatics
|August 2, 2016
Summary
A novel spherical self-organizing map (SSOM) effectively mapped protein active sites and their electrostatic potentials. This method showed a negative correlation between strong β2 receptor ligands and the protein
Area of Science:
- Computational chemistry and structural biology.
- Application of artificial intelligence in molecular modeling.
Background:
- Understanding protein-ligand interactions is crucial for drug discovery.
- Representing complex molecular surfaces and their electrostatic properties geometrically is challenging.
Purpose of the Study:
- To develop and validate a Spherical Self-Organizing Map (SSOM) for mapping protein active sites.
- To analyze the molecular electrostatic potential (MEP) distribution on the protein surface and its ligands.
- To assess the correlation between the MEP of the β2 receptor active site and its ligands.
Main Methods:
- Utilized an X-ray crystal structure of the β2 receptor protein's active site.
- Applied SSOM to map molecular surface points and their associated MEP values.
- Mapped twenty β2 ligands onto the established SSOM sphere for comparison.
Main Results:
- The SSOM successfully reproduced the 3D structure of the β2 receptor active site.
- MEP values were mapped onto the spherical representations of both the protein and its ligands.
- A moderate negative correlation was observed between the MEP of the β2 receptor and strong β2 ligands.
Conclusions:
- SSOM is a viable method for geometrically representing and analyzing protein active sites and MEP.
- The observed MEP correlation provides insights into β2 receptor-ligand binding.
- This approach can aid in the design and screening of novel drug candidates.
Keywords:
ChemogenomicsMolecular electrostatic potentialMolecular surfaceSpherical self-organizing mapβ2 Receptor proteinMore Related Videos
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