Computer simulation of molecular docking between methylene blue and some proteins of Porphyromonas gingivalis.
- Author:
Lin Tian YUAN
1
;
Li Sha MA
2
;
Run Yuan LIU
3
;
Wei QI
1
;
Lu Dan ZHANG
2
;
Gui Yan WANG
2
;
Yu Guang WANG
2
Author Information
1. Department of General Medicine, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China.
2. Center for Digital Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China.
3. Department of Endodontics, College of Stomatology, Dalian Medical University, Dalian 116044, Liaoning, China.
- Publication Type:Journal Article
- Keywords:
Methylene blue;
Molecular docking;
Photodynamic;
Porphyromonas gingivalis;
Target prediction
- MeSH:
Computer Simulation;
Methylene Blue;
Molecular Docking Simulation;
Photosensitizing Agents;
Porphyromonas gingivalis
- From:
Journal of Peking University(Health Sciences)
2022;54(1):23-30
- CountryChina
- Language:Chinese
-
Abstract:
OBJECTIVE:To study the binding target of photosensitizer and bacteria in antimicrobial photodynamic therapy with computer-simulated target prediction and molecular docking research methods and to calculate the binding energy.
METHODS:The protein names of Porphyromonas gingivalis (Pg) were obtained and summarized in Uniprot database and RCSB PDB database; the structure diagrams of methy-lene blue were screened in SciFinder database, PubChem database, ChemSpider database, and Chemical Book, and ChemBioDraw software was used to draw and confirm the three-dimensional structure for target prediction and Cytoscape software was used to build a visual network diagram; a protein interaction network was searched and built between the methylene blue target and the common target of Pg in the String database; then we selected FimA, Mfa4, RgpB, and Kgp K1 proteins, used AutoDock software to calculate the docking energy of methylene blue and the above-mentioned proteins and performed molecular docking.
RESULTS:The target prediction results showed that there were 19 common targets between the 268 potential targets of methylene blue and 1 865 Pg proteins. The 19 targets were: groS, radA, rplA, dps, fabH, pyrG, thyA, panC, RHO, frdA, ileS, bioA, def, ddl, TPR, murA, lepB, cobT, and gyrB. The results of the molecular docking showed that methylene blue could bind to 9 sites of FimA protein, with a binding energy of -6.26 kcal/mol; with 4 sites of Mfa4 protein and hydrogen bond formation site GLU47, and the binding energy of -5.91 kcal/mol, the binding energy of LYS80, the hydrogen bond forming site of RgpB protein, was -5.14 kcal/mol, and the binding energy of 6 sites of Kgp K1 protein and the hydrogen bond forming site GLY1114 of -5.07 kcal/mol.
CONCLUSION:Computer simulation of target prediction and molecular docking technology can initially reveal the binding, degree of binding and binding sites of methylene blue and Pg proteins. This method provides a reference for future research on the screening of binding sites of photosensitizers to cells and bacteria.
