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Journal of Peking University (Health Sciences) ›› 2022, Vol. 54 ›› Issue (1): 23-30. doi: 10.19723/j.issn.1671-167X.2022.01.005

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Computer simulation of molecular docking between methylene blue and some proteins of Porphyromonas gingivalis

YUAN Lin-tian1,2,MA Li-sha2,LIU Run-yuan3,QI wei1,2,ZHANG Lu-dan2,4,WANG Gui-yan2,5,WANG Yu-guang2,△()   

  1. 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
    4. First Clinical Division, Peking University School and Hospital of Stomatology, Beijing 100081, China
    5. Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing 100081, China
  • Received:2020-10-10 Online:2022-02-18 Published:2022-02-21
  • Contact: Yu-guang WANG E-mail:wangyuguang@bjmu.edu.cn
  • Supported by:
    National Natural Science Foundation of China(51972003);National Key Research and Development Plan(2018YFE0192500);Capital Characteristic Clinical Research(Z181100001718186);Fundamental Research Funds for the Central Universities: Peking University Medicine Seed Fund for Interdisciplinary Research(BMU2020MX013);Smart Medical Project of Peking University Health Science Center(BMU2019ZHYL003)

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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.

Key words: Target prediction, Molecular docking, Photodynamic, Methylene blue, Porphyromonas gingivalis

CLC Number: 

  • R781.4

Figure 1

Visual network diagram of drug components-targets"

Figure 2

PPI network diagram of drug-bacterial PPI diagram"

Figure 3

Molecule docking diagram of methylene blue and target protein FimA A, methylene blue structure; B, FimA protein structure; C, methylene blue and FimA protein docking (overall); D, methylene blue and FimA protein docking (partial)."

Figure 4

The molecular docking diagram of methylene blue and the target protein Mfa4 protein A, methylene blue structure; B, Mfa4 protein structure; C, methylene blue and Mfa4 protein docking (overall); D, methylene blue and Mfa4 protein docking (partial)."

Figure 5

Molecule docking model diagram of methylene blue and RgpB protein A, methylene blue structure; B, RgpB protein structure; C, methylene blue and RgpB protein docking (overall); D, methylene blue and RgpB protein docking (partial)."

Figure 6

The molecular docking diagram of methylene blue and Kgp K1 protein A, methylene blue structure; B, Kgp K1 protein structure; C, methylene blue and Kgp K1 protein docking (overall); D, methylene blue and Kgp K1 protein docking (partial)."

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