Molecular docking in the study of the interaction between cholera toxin subunit B and lipid raft components
https://doi.org/10.18699/SSMJ20250106
Abstract
The aim of this study was to predict, using molecular docking, the formation of complexes between cholera toxin subunit B (CTB) and lipid raft components – gangliosides GM1 and GM3, lactosylceramide (LacCer), and cholesterol.
Material and methods. The study involved modeling the three-dimensional structure of the lipid raft–CTB complex to obtain information on ligand coordinates and binding energy, analysis of the amino acid sequences of the CTB D-chain, and molecular docking.
Results. Three-dimensional structures of the complexes were obtained using molecular docking. The topology of ligands GM1, GM3, and cholesterol in the molecular pocket of the CTB D-chain was proposed. It was shown that the conformations of CTB with GM1, GM3, and cholesterol ligands exhibited negative binding energy, indicating the potential formation of stable complexes. LacCer was an exception, as its chemical characteristics, associated with the formation of unstable conformers, rendered it unsuitable for docking analysis.
Conclusions. The proposed algorithms lay a scientific foundation for solving important applied problems in bioinformatics and pharmacology, specifically in the study of the pathogenesis and treatment of diseases related to lipid raft dysfunction.
Supporting agencies: The research was carried out with the financial support of the Russian Science Foundation (Agreement No. 23-25-00049 dated 12. 01. 2023).
About the Authors
I. A. Andrievskaya
Far Eastern Research Center for Physiology and Pathology of Respiration
Russian Federation
Russian Federation
Irina A. Andrievskaya, doctor of biological sciences, professor of the RAS
675004; Kalinina st., 22; Blagoveshchensk
P. D. Timkin
All-Russian Research Institute of Soybean
Russian Federation
Russian Federation
Pavel D. Timkin
675028; Ignatievskoye highw., 19; Blagoveshchensk
E. M. Ustinov
Far Eastern Research Center for Physiology and Pathology of Respiration
Russian Federation
Russian Federation
Egor M. Ustinov
675004; Kalinina st., 22; Blagoveshchensk
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