Molecular Docking and Dynamics Simulation of Protein β-Tubulin and Antifungal Cyclic Lipopeptides
| Autor: | Daniel Cerqueda-García, Luz America Chi-Uluac, Esaú Ruiz-Sánchez, Filiberto Ortiz-Chi, Emanuel Hernández-Núñez, Nubia Noemi Cob-Calan, Gabriel Navarrete-Vázquez |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
animal structures
Stereochemistry Protein Data Bank (RCSB PDB) Pharmaceutical Science macromolecular substances Molecular Dynamics Simulation 01 natural sciences Peptides Cyclic Homology (biology) Article Analytical Chemistry lcsh:QD241-441 03 medical and health sciences chemistry.chemical_compound Lipopeptides lcsh:Organic chemistry Tubulin Drug Discovery Fusarium oxysporum Physical and Theoretical Chemistry Root-mean-square deviation 030304 developmental biology 0303 health sciences biology Chemistry fungi Organic Chemistry antifungal activity computer.file_format molecular docking biology.organism_classification Protein Data Bank molecular dynamics 0104 chemical sciences Molecular Docking Simulation 010404 medicinal & biomolecular chemistry cyclic lipopeptides Chemistry (miscellaneous) biology.protein Molecular Medicine lipids (amino acids peptides and proteins) β-tubulin Surfactin computer Fusarium solani |
| Zdroj: | Molecules Volume 24 Issue 18 Molecules, Vol 24, Iss 18, p 3387 (2019) |
| ISSN: | 1420-3049 |
| Popis: | To elucidate interactions between the antifungal cyclic lipopeptides iturin A, fengycin, and surfactin produced by Bacillus bacteria and the microtubular protein &beta tubulin in plant pathogenic fungi (Fusarium oxysporum, Colletrotrichum gloeosporioides, Alternaria alternata, and Fusarium solani) in molecular docking and molecular dynamics simulations, we retrieved the structure of tubulin co-crystallized with taxol from the Protein Data Bank (PDB) (ID: 1JFF) and the structure of the cyclic lipopeptides from PubChem (Compound CID: 102287549, 100977820, 10129764). Similarity and homology analyses of the retrieved &beta tubulin structure with those of the fungi showed that the conserved domains shared 84% similarity, and the root mean square deviation (RMSD) was less than 2 Å In the molecular docking studies, within the binding pocket, residues Pro274, Thr276, and Glu27 of &beta tubulin were responsible for the interaction with the cyclic lipopeptides. In the molecular dynamics analysis, two groups of ligands were formed based on the number of poses analyzed with respect to the RMSD. Group 1 was made up of 10, 100, and 500 poses with distances 0.080 to 0.092 nm and RMSDs of 0.10 to 0.15 nm. For group 2, consisting of 1000 poses, the initial and final distance was 0.1 nm and the RMSDs were in the range of 0.10 to 0.30 nm. These results suggest that iturin A and fengycin bind with higher affinity than surfactin to &beta tubulin. These two lipopeptides may be used as lead compounds to develop new antifungal agents or employed directly as biorational products to control plant pathogenic fungi. |
| Databáze: | OpenAIRE |
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