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The interaction pattern between a homology model of 40S ribosomal S9 protein of Rhizoctonia solani and 1-hydroxyphenaize by docking study.

Dharni S - Biomed Res Int (2014)

Bottom Line: 1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani.In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein.Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

View Article: PubMed Central - PubMed

Affiliation: Agronomy and Soil Science Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India.

ABSTRACT
1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani. In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein. Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

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Docking of 1-OH-PHZ with 40S ribosomal S9 protein.
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fig7: Docking of 1-OH-PHZ with 40S ribosomal S9 protein.

Mentions: The Autodock 4.2 program was used for the molecular docking analysis [24]. The three-dimensional structure of 1-OH-PHZ was considered as ligand molecule (Figure 7). The interaction of this ligand with modeled protein was performed. The Lamarckian genetic algorithm was used in Autodock to perform the automated molecular dockings [33] and default parameters were used. In the process a large grid map was created by AutoGrid to cover the whole surface of protein. By performing the rigid docking, a total of 10 conformations of interaction were obtained having variation in their energies, that is, free energy of binding, predicted inhibition constant, and ligand efficiency (Table 1). From all the docking conformations of ligand, conformation 3 was selected for having −5.84 kcal/mol binding energy and 1 hydrogen bond. The ligand, 1-OH-PHZ, was found to be bound with two residues of protein by polar contacts. These contacts are present at VAL81 and Arg69 positions of the protein.


The interaction pattern between a homology model of 40S ribosomal S9 protein of Rhizoctonia solani and 1-hydroxyphenaize by docking study.

Dharni S - Biomed Res Int (2014)

Docking of 1-OH-PHZ with 40S ribosomal S9 protein.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016899&req=5

fig7: Docking of 1-OH-PHZ with 40S ribosomal S9 protein.
Mentions: The Autodock 4.2 program was used for the molecular docking analysis [24]. The three-dimensional structure of 1-OH-PHZ was considered as ligand molecule (Figure 7). The interaction of this ligand with modeled protein was performed. The Lamarckian genetic algorithm was used in Autodock to perform the automated molecular dockings [33] and default parameters were used. In the process a large grid map was created by AutoGrid to cover the whole surface of protein. By performing the rigid docking, a total of 10 conformations of interaction were obtained having variation in their energies, that is, free energy of binding, predicted inhibition constant, and ligand efficiency (Table 1). From all the docking conformations of ligand, conformation 3 was selected for having −5.84 kcal/mol binding energy and 1 hydrogen bond. The ligand, 1-OH-PHZ, was found to be bound with two residues of protein by polar contacts. These contacts are present at VAL81 and Arg69 positions of the protein.

Bottom Line: 1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani.In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein.Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

View Article: PubMed Central - PubMed

Affiliation: Agronomy and Soil Science Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India.

ABSTRACT
1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani. In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein. Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

Show MeSH
Related in: MedlinePlus