Department of Biotechnology and Bioinformatics

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Browsing Department of Biotechnology and Bioinformatics by Subject "3D modeling"
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    3D modeling of dengue virus NS4B and Chikungunya virus nsP4: Identification of a common drug target and designing a single antiviral inhibitor
    ( 2014-01-01) Satheesh, Garisekurthi ; Prabhu, Nagu P. ; Venkataramana, Musturi
    Dengue and chikungunya virus infections are one of the major causes of morbidity and mortality in tropical and sub-tropical regions of the world. These two viruses belong to two different families with many similarities and dissimilarities. Both are enveloped viruses and the mode of transmission is also by the same mosquito species. Especially in case of symptom expression, there is confusion between these two viruses. Reports indicate the overlapping endemic areas and co-infections of both viruses in a single patient. The above factors indicate that there is a need for developing a single drug/vaccine for both the viruses. As a first report in this direction, we have used the bioinformatics tools to identify a common target in both the viruses for a single inhibitor molecule. Phylogenetic and distance based analyses using the nucleotide sequences of arthropod and non-arthropod borne viruses indicated a common origin of evolutionary point for mosquito borne viruses, irrespective of their families. Similarly, the amino acid sequences of non-structural protein-4B (NS4B) of dengue virus and non-structural protein-P4 (nsP4) of chikungunya virus showed a common evolutionary origin. Modeled and superimposed 3D-structures of above two proteins showed a common alpha helix. Virtual screening of selected molecules was done to identify the molecules which can bind to the identified common helix and found that N-(p-tolylmethyl)-3-[(3-pyridylmethylamino)methyl]benzamide (TPB) has significant binding characteristics to the common helix. Molecular simulations indicated that both the protein-TPB complexes were stable. Therefore, we propose that TPB or its analogues could act as antiviral agents against both the viruses.
  • Item
    3D modeling of dengue virus NS4B and Chikungunya virus nsP4: Identification of a common drug target and designing a single antiviral inhibitor
    ( 2014-01-01) Satheesh, Garisekurthi ; Prabhu, Nagu P. ; Venkataramana, Musturi
    Dengue and chikungunya virus infections are one of the major causes of morbidity and mortality in tropical and sub-tropical regions of the world. These two viruses belong to two different families with many similarities and dissimilarities. Both are enveloped viruses and the mode of transmission is also by the same mosquito species. Especially in case of symptom expression, there is confusion between these two viruses. Reports indicate the overlapping endemic areas and co-infections of both viruses in a single patient. The above factors indicate that there is a need for developing a single drug/vaccine for both the viruses. As a first report in this direction, we have used the bioinformatics tools to identify a common target in both the viruses for a single inhibitor molecule. Phylogenetic and distance based analyses using the nucleotide sequences of arthropod and non-arthropod borne viruses indicated a common origin of evolutionary point for mosquito borne viruses, irrespective of their families. Similarly, the amino acid sequences of non-structural protein-4B (NS4B) of dengue virus and non-structural protein-P4 (nsP4) of chikungunya virus showed a common evolutionary origin. Modeled and superimposed 3D-structures of above two proteins showed a common alpha helix. Virtual screening of selected molecules was done to identify the molecules which can bind to the identified common helix and found that N-(p-tolylmethyl)-3-[(3-pyridylmethylamino)methyl]benzamide (TPB) has significant binding characteristics to the common helix. Molecular simulations indicated that both the protein-TPB complexes were stable. Therefore, we propose that TPB or its analogues could act as antiviral agents against both the viruses.