Limits...
Comparative Molecular docking analysis of DNA Gyrase subunit A in Pseudomonas aeruginosaPAO1.

Gupta A, Sharma V, Tewari AK, Surenderkumar V, Wadhwa G, Mathur A, Sharma SK, Jain CK - Bioinformation (2013)

Bottom Line: Till date no drug/ligand molecule has been reported against this targets.In our work we have identified the ligand /drug molecules, through Orthologous gene mapping against Bacillus subtilis subsp. subtilis str. 168 and performed modelling and docking analysis.The drugs cited for Bacillus sp. have been docked with PA genes and energy analyses have been made.Based on Orthologous gene mapping andin-silico studies, Nalidixic acid is reported as an effective drug against PA3168 gyrA for the treatment of CF and COPD.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P-201301, India.

ABSTRACT
Pseudomonas aeruginosa is an opportunistic bacterium known for causing chronic infections in cystic fibrosis and chronic obstructive pulmonary disease (COPD) patients. Recently, several drug targets in Pseudomonas aeruginosa PAO1 have been reported using network biology approaches on the basis of essentiality and topology and further ranked on network measures viz. degree and centrality. Till date no drug/ligand molecule has been reported against this targets.In our work we have identified the ligand /drug molecules, through Orthologous gene mapping against Bacillus subtilis subsp. subtilis str. 168 and performed modelling and docking analysis. From the predicted drug targets in PA PAO1, we selected those drug targets which show statistically significant orthology with a model organism and whose orthologs are present in all the selected drug targets of PA PAO1.Modeling of their structure has been done using I-Tasser web server. Orthologous gene mapping has been performed using Cluster of Orthologs (COGs) and based on orthology; drugs available for Bacillus sp. have been docked with PA PAO1 protein drug targets using MoleGro virtual docker version 4.0.2.Orthologous gene for PA3168 gyrA is BS gyrAfound in Bacillus subtilis subsp. subtilis str. 168. The drugs cited for Bacillus sp. have been docked with PA genes and energy analyses have been made. Based on Orthologous gene mapping andin-silico studies, Nalidixic acid is reported as an effective drug against PA3168 gyrA for the treatment of CF and COPD.

No MeSH data available.


Related in: MedlinePlus

Snapshots of docking and interaction between DNA Gyrase subunit A protein receptor and their respective drugNalidixic acid from Pseudomonas aeruginosa and Bacillus subtilis. (A) and (B) Red color represents ligands or drug molecules andwireform and amino acid residue represent protein structure; (C) The interaction of ligands with Bacillus subtilis subsp. subtilis str.168 proteins; (D) The interaction of ligands with Pseudomonas aeruginosa PAO1 proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3569597&req=5

Figure 1: Snapshots of docking and interaction between DNA Gyrase subunit A protein receptor and their respective drugNalidixic acid from Pseudomonas aeruginosa and Bacillus subtilis. (A) and (B) Red color represents ligands or drug molecules andwireform and amino acid residue represent protein structure; (C) The interaction of ligands with Bacillus subtilis subsp. subtilis str.168 proteins; (D) The interaction of ligands with Pseudomonas aeruginosa PAO1 proteins.

Mentions: Docking has been performed using Mole Gro virtual dockertool where the largest cavity in the target protein is identifiedon the basis of cavity volume. This could be done online vizcastP software [13]. The docking is represented by MolDockscoring function which has been derived from the PLP(Piecewise Linear Potential) scoring functions [14]. Docking ofligand / drug has been performed in the largest cavity based oncavity volume, and the results obtained are saved. From thedocking results, energy vs. conformations graph, the MolDockscore representing the binding energy and the hydrogenbonding energy score are of particular importance for analysis.These docking result as .MVD file format have been loaded onthe same workplace containing the ligand and the target cavityto visualise and analyse the docking in various poses orconformations of ligand as in Figure 1(A) & (B).


Comparative Molecular docking analysis of DNA Gyrase subunit A in Pseudomonas aeruginosaPAO1.

Gupta A, Sharma V, Tewari AK, Surenderkumar V, Wadhwa G, Mathur A, Sharma SK, Jain CK - Bioinformation (2013)

Snapshots of docking and interaction between DNA Gyrase subunit A protein receptor and their respective drugNalidixic acid from Pseudomonas aeruginosa and Bacillus subtilis. (A) and (B) Red color represents ligands or drug molecules andwireform and amino acid residue represent protein structure; (C) The interaction of ligands with Bacillus subtilis subsp. subtilis str.168 proteins; (D) The interaction of ligands with Pseudomonas aeruginosa PAO1 proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3569597&req=5

Figure 1: Snapshots of docking and interaction between DNA Gyrase subunit A protein receptor and their respective drugNalidixic acid from Pseudomonas aeruginosa and Bacillus subtilis. (A) and (B) Red color represents ligands or drug molecules andwireform and amino acid residue represent protein structure; (C) The interaction of ligands with Bacillus subtilis subsp. subtilis str.168 proteins; (D) The interaction of ligands with Pseudomonas aeruginosa PAO1 proteins.
Mentions: Docking has been performed using Mole Gro virtual dockertool where the largest cavity in the target protein is identifiedon the basis of cavity volume. This could be done online vizcastP software [13]. The docking is represented by MolDockscoring function which has been derived from the PLP(Piecewise Linear Potential) scoring functions [14]. Docking ofligand / drug has been performed in the largest cavity based oncavity volume, and the results obtained are saved. From thedocking results, energy vs. conformations graph, the MolDockscore representing the binding energy and the hydrogenbonding energy score are of particular importance for analysis.These docking result as .MVD file format have been loaded onthe same workplace containing the ligand and the target cavityto visualise and analyse the docking in various poses orconformations of ligand as in Figure 1(A) & (B).

Bottom Line: Till date no drug/ligand molecule has been reported against this targets.In our work we have identified the ligand /drug molecules, through Orthologous gene mapping against Bacillus subtilis subsp. subtilis str. 168 and performed modelling and docking analysis.The drugs cited for Bacillus sp. have been docked with PA genes and energy analyses have been made.Based on Orthologous gene mapping andin-silico studies, Nalidixic acid is reported as an effective drug against PA3168 gyrA for the treatment of CF and COPD.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, U.P-201301, India.

ABSTRACT
Pseudomonas aeruginosa is an opportunistic bacterium known for causing chronic infections in cystic fibrosis and chronic obstructive pulmonary disease (COPD) patients. Recently, several drug targets in Pseudomonas aeruginosa PAO1 have been reported using network biology approaches on the basis of essentiality and topology and further ranked on network measures viz. degree and centrality. Till date no drug/ligand molecule has been reported against this targets.In our work we have identified the ligand /drug molecules, through Orthologous gene mapping against Bacillus subtilis subsp. subtilis str. 168 and performed modelling and docking analysis. From the predicted drug targets in PA PAO1, we selected those drug targets which show statistically significant orthology with a model organism and whose orthologs are present in all the selected drug targets of PA PAO1.Modeling of their structure has been done using I-Tasser web server. Orthologous gene mapping has been performed using Cluster of Orthologs (COGs) and based on orthology; drugs available for Bacillus sp. have been docked with PA PAO1 protein drug targets using MoleGro virtual docker version 4.0.2.Orthologous gene for PA3168 gyrA is BS gyrAfound in Bacillus subtilis subsp. subtilis str. 168. The drugs cited for Bacillus sp. have been docked with PA genes and energy analyses have been made. Based on Orthologous gene mapping andin-silico studies, Nalidixic acid is reported as an effective drug against PA3168 gyrA for the treatment of CF and COPD.

No MeSH data available.


Related in: MedlinePlus