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Md. Anayet Hasan,Md. Habibul Hasan Mazumder,Md. Arif Khan,Mohammad Uzzal Hossain,A. S. M. Homaun Kabir Chowdhury 한국유전체학회 2014 Genomics & informatics Vol.12 No.4
The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire’s disease. The increasingdevelopment of drug resistance against legionellosis has led to explore new novel drug targets. It has been found thatphosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the mostprobable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugarand nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this,the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means ofhomology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structurevalidation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondarystructural features were determined through self-optimized prediction method with alignment (SOPMA) and interactingnetworks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showedthat 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in thegenerously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 forERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorablebinding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensiveinvestigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
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Hasan, Md. Anayet,Mazumder, Md. Habibul Hasan,Khan, Md. Arif,Hossain, Mohammad Uzzal,Chowdhury, A.S.M. Homaun Kabir Korea Genome Organization 2014 Genomics & informatics Vol.12 No.4
The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire's disease. The increasing development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this, the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
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Habib, Abdul Musaweer,Islam, Md. Saiful,Sohel, Md.,Mazumder, Md. Habibul Hasan,Sikder, Mohd. Omar Faruk,Shahik, Shah Md. Korea Genome Organization 2016 Genomics & informatics Vol.14 No.4
The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.
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Abdul Musaweer Habib,Md. Saiful Islam,Md. Sohel,Md. Habibul Hasan Mazumder,Mohd. Omar Faruk Sikder,Shah Md. Shahik 한국유전체학회 2016 Genomics & informatics Vol.14 No.4
The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog’s in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.
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