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Virtual screening and evaluation of Ketol-Acid Reducto-Isomerase (KARI) as a putative drug target for Aspergillosis.

Morya VK, Kumari S, Kim EK - Clin Proteomics (2012)

Bottom Line: In our previous work, we have analyzed the various biochemical pathways, and we found Ketol Acid Reducto-Isomerase (KARI) an enzyme involves in the amino acid biosynthesis, could be a better target.This enzyme was found to be unique by comparing to host proteome through BLASTp analysis.The Zinc ID of the potential inhibitors is ZINC00720614, ZINC01068126, ZINC0923, ZINC02090678, ZINC00663057 and ZINC02284065 and found to be pharmacologically active agonist and antagonist of KARI.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Engineering, Inha University, Incheon, Republic of Korea, 402-751. moryavivek@gmail.com.

ABSTRACT
Aspergillus is a leading causative agent for fungal morbidity and mortality in immuno-compromised patients. To identify a putative target to design or identify new antifungal drug, against Aspergillus is required. In our previous work, we have analyzed the various biochemical pathways, and we found Ketol Acid Reducto-Isomerase (KARI) an enzyme involves in the amino acid biosynthesis, could be a better target. This enzyme was found to be unique by comparing to host proteome through BLASTp analysis. A homology based model of KARI was generated by Swiss model server. The generated model had been validated by PROCHECK and WHAT IF programs. The Zinc library was generated within the limitation of the Lipinski rule of five, for docking study. Based on the dock-score six molecules have been studied for ADME/TOX analysis and subjected for pharmacophore model generation. The Zinc ID of the potential inhibitors is ZINC00720614, ZINC01068126, ZINC0923, ZINC02090678, ZINC00663057 and ZINC02284065 and found to be pharmacologically active agonist and antagonist of KARI. This study is an attempt to Insilco evaluation of the KARI as a drug target and the screened inhibitors could help in the development of the better drug against Aspergillus.

No MeSH data available.


Ribbon representation of KARI model (A) with the ligand in green color (B). Important residues are shown (Ser, Arg and Val.) and the distance was calculated from the active site that is serine residue (ser-184) to N-terminal (31.97Å) and C- (30.57 Å) terminals of the model receptor as calculated by pymol are shown. The inset shows the length (12.49 Å) of (4R)-6-amino-3-(3,4-dimethoxyphenyl)-4-(5-(4-fluorophenyl)-1H-pyrazol-4-yl)-2,4 dihydropyrano(2,3-c)pyrazole-5-carbonitrile.
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Figure 3: Ribbon representation of KARI model (A) with the ligand in green color (B). Important residues are shown (Ser, Arg and Val.) and the distance was calculated from the active site that is serine residue (ser-184) to N-terminal (31.97Å) and C- (30.57 Å) terminals of the model receptor as calculated by pymol are shown. The inset shows the length (12.49 Å) of (4R)-6-amino-3-(3,4-dimethoxyphenyl)-4-(5-(4-fluorophenyl)-1H-pyrazol-4-yl)-2,4 dihydropyrano(2,3-c)pyrazole-5-carbonitrile.

Mentions: The 3D structural model of KARI gerenated by homology based model has been examined by their stereo-chemical quality, by Procheck. The phi/psi angles of 85.0% residues fell in the most favored regions, 13.4% residues lied in the additional allowed regions and 1% fell in the generously allowed regions; only 0.6% of residues lied in the disallowed conformations (Figure 2). Thus, statistical analysis suggests that the backbone conformation of our predicted model of KARI was almost as good as that of the template; the 3D conformation of the predicted model of KARI has been shown in Figure 3. In the Figure 4 main chain parameters are given. These graphs represent a comparison between the structures of the model with reference, at the similar resolution. Figure 3 and four shows various properties namely Ramachandran plot, peptide bond planarity, bad non bonded interaction's alpha tetrahedral distortion, main chain hydrogen bond energy and the overall G- factor. The overall G - factor is the measure of the overall normality of the structure. After that, residue which was present in the active site of the model found out manually and also with the help of molegro software mainly three residue of amino acid was found to be associated an active site of the model of KARI these are Arg.101-ser-184 and Val- 175. Figure 3b shows the distance from active site residue to N- terminal and C- terminal [34,35]. The residues involved in the active site as predicted by LIGSITEcsc and CASTp were Arg 101, lys 169, glu 233, Asp 223, Glu 269, ser 184 and val 175 are involved in formation of cavity for binding of ligands. A previous study on Spinach, E. coli and P. aeruginosa have shown a different active site than the prediction KARI from Aspergillus [36]. The proscane analysis for pattern elucidation was done according to Bairoch and coworkers [37]. Four patterns were found on the sequence of K.A.R.I. these patterns represent N-glycosylation site, Protein kinase C phosphorylation site, Casein kinase II phosphorylation site and N-myristoylation site. The above parametric comparison shows that the modeled structure is good for the further analysis like docking, to find some potential inhibitor.


Virtual screening and evaluation of Ketol-Acid Reducto-Isomerase (KARI) as a putative drug target for Aspergillosis.

Morya VK, Kumari S, Kim EK - Clin Proteomics (2012)

Ribbon representation of KARI model (A) with the ligand in green color (B). Important residues are shown (Ser, Arg and Val.) and the distance was calculated from the active site that is serine residue (ser-184) to N-terminal (31.97Å) and C- (30.57 Å) terminals of the model receptor as calculated by pymol are shown. The inset shows the length (12.49 Å) of (4R)-6-amino-3-(3,4-dimethoxyphenyl)-4-(5-(4-fluorophenyl)-1H-pyrazol-4-yl)-2,4 dihydropyrano(2,3-c)pyrazole-5-carbonitrile.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3298717&req=5

Figure 3: Ribbon representation of KARI model (A) with the ligand in green color (B). Important residues are shown (Ser, Arg and Val.) and the distance was calculated from the active site that is serine residue (ser-184) to N-terminal (31.97Å) and C- (30.57 Å) terminals of the model receptor as calculated by pymol are shown. The inset shows the length (12.49 Å) of (4R)-6-amino-3-(3,4-dimethoxyphenyl)-4-(5-(4-fluorophenyl)-1H-pyrazol-4-yl)-2,4 dihydropyrano(2,3-c)pyrazole-5-carbonitrile.
Mentions: The 3D structural model of KARI gerenated by homology based model has been examined by their stereo-chemical quality, by Procheck. The phi/psi angles of 85.0% residues fell in the most favored regions, 13.4% residues lied in the additional allowed regions and 1% fell in the generously allowed regions; only 0.6% of residues lied in the disallowed conformations (Figure 2). Thus, statistical analysis suggests that the backbone conformation of our predicted model of KARI was almost as good as that of the template; the 3D conformation of the predicted model of KARI has been shown in Figure 3. In the Figure 4 main chain parameters are given. These graphs represent a comparison between the structures of the model with reference, at the similar resolution. Figure 3 and four shows various properties namely Ramachandran plot, peptide bond planarity, bad non bonded interaction's alpha tetrahedral distortion, main chain hydrogen bond energy and the overall G- factor. The overall G - factor is the measure of the overall normality of the structure. After that, residue which was present in the active site of the model found out manually and also with the help of molegro software mainly three residue of amino acid was found to be associated an active site of the model of KARI these are Arg.101-ser-184 and Val- 175. Figure 3b shows the distance from active site residue to N- terminal and C- terminal [34,35]. The residues involved in the active site as predicted by LIGSITEcsc and CASTp were Arg 101, lys 169, glu 233, Asp 223, Glu 269, ser 184 and val 175 are involved in formation of cavity for binding of ligands. A previous study on Spinach, E. coli and P. aeruginosa have shown a different active site than the prediction KARI from Aspergillus [36]. The proscane analysis for pattern elucidation was done according to Bairoch and coworkers [37]. Four patterns were found on the sequence of K.A.R.I. these patterns represent N-glycosylation site, Protein kinase C phosphorylation site, Casein kinase II phosphorylation site and N-myristoylation site. The above parametric comparison shows that the modeled structure is good for the further analysis like docking, to find some potential inhibitor.

Bottom Line: In our previous work, we have analyzed the various biochemical pathways, and we found Ketol Acid Reducto-Isomerase (KARI) an enzyme involves in the amino acid biosynthesis, could be a better target.This enzyme was found to be unique by comparing to host proteome through BLASTp analysis.The Zinc ID of the potential inhibitors is ZINC00720614, ZINC01068126, ZINC0923, ZINC02090678, ZINC00663057 and ZINC02284065 and found to be pharmacologically active agonist and antagonist of KARI.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Engineering, Inha University, Incheon, Republic of Korea, 402-751. moryavivek@gmail.com.

ABSTRACT
Aspergillus is a leading causative agent for fungal morbidity and mortality in immuno-compromised patients. To identify a putative target to design or identify new antifungal drug, against Aspergillus is required. In our previous work, we have analyzed the various biochemical pathways, and we found Ketol Acid Reducto-Isomerase (KARI) an enzyme involves in the amino acid biosynthesis, could be a better target. This enzyme was found to be unique by comparing to host proteome through BLASTp analysis. A homology based model of KARI was generated by Swiss model server. The generated model had been validated by PROCHECK and WHAT IF programs. The Zinc library was generated within the limitation of the Lipinski rule of five, for docking study. Based on the dock-score six molecules have been studied for ADME/TOX analysis and subjected for pharmacophore model generation. The Zinc ID of the potential inhibitors is ZINC00720614, ZINC01068126, ZINC0923, ZINC02090678, ZINC00663057 and ZINC02284065 and found to be pharmacologically active agonist and antagonist of KARI. This study is an attempt to Insilco evaluation of the KARI as a drug target and the screened inhibitors could help in the development of the better drug against Aspergillus.

No MeSH data available.