Prediction of micro RNAs against H5N1 and H1N1 NS1 Protein: a Window to Sequence Specific Therapeutic Development

Abstract

Motivation: Conventional Influenza drugs might result in failure of action due to highly variable nature of influenza antigenic proteins. in silico prediction of sequence specific therapeutics is less time consuming and cost effective. Most of the miRNA target prediction platforms differ in their specificity and sensitivity in prediction. Here we propose a bioinformatics approach to predict micro RNAs against non-structural protein 1 of avian influenza H5N1 virus and against segment 8 swine influenza H1N1 virus. Results: hsa-miR-138, hsa-miR-525-5p and hsa-miR-124 were sorted out as potential sequence specific therapeutic agents against NS1 protein of H5N1 virus. Similar studies on different H1N1 segment 8 genomes resulted in the prediction of miRNAs which can be used as anti-influenza agents. The predicted micro RNAs also possess roles in regulatory processes of host cell, stress related pathways including MAPK pathway, mTOR pathway and are found to be involved in pathways related to cancer.

Identification of Chicken Pulmonary miRNAs Targeting PB1, PB1-F2, and N40 Genes of Highly Pathogenic Avian Influenza Virus H5N1 in Silico

“…Some researchers have used a cutoff free energy of −17 kcal/mol for predicting miRNA targets in PB1 gene of H1 N1 21 and some have used a threshold free energy of −15 kcal/mol while predicting the binding site of miRNA to NS1 gene of H1 N1 and H5N1. 33 The complete length of ORFs. 22,23 The mRNA and protein expression of genes containing target sites both in coding regions and 3′-UTRs are reported to be mildly but significantly more regulated than those containing target sites in 3′-UTRs only.…”

“…Some researchers have used a cutoff free energy of −17 kcal/mol for predicting miRNA targets in PB1 gene of H1 N1 21 and some have used a threshold free energy of −15 kcal/mol while predicting the binding site of miRNA to NS1 gene of H1 N1 and H5N1. 33 The complete length of segment 2 was screened for target sites of the miRNAs as three different proteins were expressed from the same segment and the same target site may have a different impact on the different proteins. Although most investigation into metazoan miRNA function has been for sites in 3′-UTRs, experiments using artificial sites show that targeting can occur in 5′-UTRs and open ORFs.…”

The screening of the functional microRNA binding site SNPs in sporadic colorectal cancer genes

“…15 However, these predictions frequently yield false-positive candidates, and experimental validation of the predicted miRNAs is essential to understand miRNA regulation fully. 16 Thus, we combined the predicted results from RegRNA and the RNAhybrid database with a luciferase reporter to screen possible functional SNPs in the miRNA target sites of the 3 0 -UTRs of 31 sCRC-related genes.…”

MicroRNA expression in mice infected with seasonal H1N1, swine H1N1 or highly pathogenic H5N1

“…miR-141 has also been implicated in the infection process utilized by enteroviruses and picornaviruses, and the upregulation of miR-141 has been shown to facilitate viral propagation by promoting cap-independent translation (Ho et al , 2011). Moreover, miR-141 has been predicted as an miRNA target in H5N1 infection utilizing a bioinformatics approach (Koparde & Singh, 2010). However, the involvement of miR-141 in the influenza virus infection cycle has yet to be determined.…”