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In silico Study on Inhibition of NS5 Protein of Dengue Virus

Shubham Raikar, Neha Patil, Madhusudhan Kulkarni, Nidhi Kulkarni, Deepak. A. Yaraguppi, Uday. M. Muddapur, Zabin. K. Bagewadi

Abstract


Abstract

Dengue fever is a flu-like illness. It is caused by a virus. The infection is passed to humans through mosquito bites. Statistical survey has revealed that every year 5,00,000 people get hospitalized due to dengue. Therefore there arises a serious necessity to find a drug molecule to cure this disease. At the first, we identified the proteins involved in the disease for which we obtained FASTA sequence using NCBI. Sequence alignment of the proteins was carried out by using BLAST (Basic Local Alignment Search Tool), this tool compares the query sequence with the sequences in database. For each comparison, it gives the E- value, identity, and score. Out of these parameters, we focus on 2 parameters - Identity, to be more than 85% and E- value to be -100. Those sequences which satisfy the required values of E-value and Identity are selected for analysis of structure by SWISS MODEL. Identification of the ligand was done by using RCSB database and the sequence obtained from NCBI was used to find PDB files for corresponding proteins by finding out there PDB id’s. Using these PDB id’s ligands where obtained from ‘ligand expo’ in SDF format and these SDF files were converted to PDB and these were further used for docking, by this two ligands were found out to be the most suitable lead molecules-7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-GUANOSINE and B-OCTYLGLUCOSIDE were found to have binding energy of -123.2 and -84.61 respectively for envelope protein and NS5 protein.

 

Keywords:Dengue fever, FASTA, BLAST, SWISS MODEL

Cite this Article

Shubham Raikar, Neha Patil, Madhusudhan Kulkarni et al. In silico study on Inhibition of NS5 Protein of Dengue Virus. Research & Reviews: A Journal of Bioinformatics. 2017; 4(2): 28–43p.


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