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A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7
Malaria is a major public health concern, and malarial parasites have developed resistance against the commonly available drugs. So now a days it is a major concern to find out a new target for drug therapy. Plasmodium falciparum 3D7, one of the strains of plasmodium species also lacks in a function...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Medknow Publications & Media Pvt Ltd
2012
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3573378/ https://www.ncbi.nlm.nih.gov/pubmed/23492818 http://dx.doi.org/10.4103/0975-1483.104370 |
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author | Ullah, M Hira, J Ghosh, T Ishaque, N Absar, N |
author_facet | Ullah, M Hira, J Ghosh, T Ishaque, N Absar, N |
author_sort | Ullah, M |
collection | PubMed |
description | Malaria is a major public health concern, and malarial parasites have developed resistance against the commonly available drugs. So now a days it is a major concern to find out a new target for drug therapy. Plasmodium falciparum 3D7, one of the strains of plasmodium species also lacks in a functional tricarboxylic acid cycle and solely dependent on glycolysis for its energy supply like other plasmodium species. Although enzymes of malarial parasite have been considered as potential antimalarial drug targets, a little is known about their structural biology. The tertiary structure of triose phosphate isomerase of P. falciparum 3D7 was determined by means of homology modeling through multiple alignment followed by intensive optimization and validation. The modeling was done by Swiss-Model Workspace. The obtained model was verified with the structure validation programs such as, PROCHECK, Verify3D, and QMEAN for reliability. The verify3D value of 0.69 indicates that the environment profile of the model is good. A self-optimized prediction method with alignment or SOPMA is employed for calculation of the secondary structural features of triose phosphate isomerase. The secondary structure indicates that the predicted 3D structure of triosephosphate isomerase of P. falciparum 3D7 contains 48.37% α-helix, 29.27% random coil, and 16.67% extended strand. Active site determination through CASTp suggests that this protein can be utilized as a potential drug target. However, these will further be tested by wet lab studies for a targeted vaccine design against P. falciparum 3D7. |
format | Online Article Text |
id | pubmed-3573378 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Medknow Publications & Media Pvt Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-35733782013-03-14 A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7 Ullah, M Hira, J Ghosh, T Ishaque, N Absar, N J Young Pharm Pharmaceutical Chemistry Malaria is a major public health concern, and malarial parasites have developed resistance against the commonly available drugs. So now a days it is a major concern to find out a new target for drug therapy. Plasmodium falciparum 3D7, one of the strains of plasmodium species also lacks in a functional tricarboxylic acid cycle and solely dependent on glycolysis for its energy supply like other plasmodium species. Although enzymes of malarial parasite have been considered as potential antimalarial drug targets, a little is known about their structural biology. The tertiary structure of triose phosphate isomerase of P. falciparum 3D7 was determined by means of homology modeling through multiple alignment followed by intensive optimization and validation. The modeling was done by Swiss-Model Workspace. The obtained model was verified with the structure validation programs such as, PROCHECK, Verify3D, and QMEAN for reliability. The verify3D value of 0.69 indicates that the environment profile of the model is good. A self-optimized prediction method with alignment or SOPMA is employed for calculation of the secondary structural features of triose phosphate isomerase. The secondary structure indicates that the predicted 3D structure of triosephosphate isomerase of P. falciparum 3D7 contains 48.37% α-helix, 29.27% random coil, and 16.67% extended strand. Active site determination through CASTp suggests that this protein can be utilized as a potential drug target. However, these will further be tested by wet lab studies for a targeted vaccine design against P. falciparum 3D7. Medknow Publications & Media Pvt Ltd 2012 /pmc/articles/PMC3573378/ /pubmed/23492818 http://dx.doi.org/10.4103/0975-1483.104370 Text en Copyright: © Journal of Young Pharmacists http://creativecommons.org/licenses/by-nc-sa/3.0 This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Pharmaceutical Chemistry Ullah, M Hira, J Ghosh, T Ishaque, N Absar, N A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7 |
title | A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7 |
title_full | A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7 |
title_fullStr | A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7 |
title_full_unstemmed | A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7 |
title_short | A Bioinformatics Approach for Homology Modeling and Binding Site Identification of Triosephosphate Isomerase from Plasmodium falciparum 3D7 |
title_sort | bioinformatics approach for homology modeling and binding site identification of triosephosphate isomerase from plasmodium falciparum 3d7 |
topic | Pharmaceutical Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3573378/ https://www.ncbi.nlm.nih.gov/pubmed/23492818 http://dx.doi.org/10.4103/0975-1483.104370 |
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