- PII
- S30345278S0006302925050035-1
- DOI
- 10.7868/S3034527825050035
- Publication type
- Article
- Status
- Published
- Authors
- Volume/ Edition
- Volume 70 / Issue number 5
- Pages
- 864-876
- Abstract
- The aim of this work was to analyze the interactions of methyl-β-cyclodextrin and amphotericin B (AmB) with spectrin, actin, and hemoglobin by the method of molecular docking. The protein structures were taken from PDB. The full-atom models of proteins were "cleaned" from water molecules and buffer components, surface charge arrangement was performed, and cells were selected for "blind" docking. The structural formula of methyl-β-cyclodextrin and amphotericin B were taken from PubChem and converted to HyperChem. Geometry optimization was performed using the MM+ model potential, rigid/fixed structures were optimized using the semi-empirical quantum chemical method PM3. The protein-ligand complex interactions were described using PLIP. The total binding energy for all complexes ranged from –4.4 to –10.3 kcal/mol. The complexes were formed due to hydrogen, van der Waals bonds, and salt bridges. Visualization of the most energetically advantageous positions confirmed that both amphotericin B and methyl-β-cyclodextrin localized in the central cavities of hemoglobin and actin, and in the distal sites of α- and β-subunits of spectrin. Amphotericin B formed more stable complexes with each of the proteins: the strength of hydrogen bonds and the number of hydrophobic contacts with the proteins were higher than for complexes with methyl-β-cyclodextrin.
- Keywords
- молекулярный докинг спектрин актин гемоглобин метил-β-циклодекстрин амфотерицин В
- Date of publication
- 13.12.2025
- Year of publication
- 2025
- Number of purchasers
- 0
- Views
- 26
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