A Computational Approach to Design Potential Antiviral RNA for 3’UTR Post Transcriptional Gene Silencing of Different Strains of Zika Virus

    Published on:November 2016
    Journal of Young Pharmacists, 2017; 9(1):23-30
    Original Article | doi:10.5530/jyp.2017.9.5

    M.A Hashem*, Moinul Abedin Shuvo and Arifuzzaman

    Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy’s Lake, Chittagong-4202, Bangladesh


    Background: Zika virus is a flare-up mosquito-borne virus that manifests itself in sporadic human infections with Zika fever. It has a serious affect in pregnant women. Mother transmits Zika virus infection to her infant during the time of delivery which results in the birth of newborn with microcephaly and some neurological malformations. Molecular studies revealed that the 3’UTR of Zika virus genome plays a vital role in viral replication and pathogenicity. So, the 3’UTR can be a suitable target for the prevention of viral multiplications and degree of pathogenicity. The activity of the 3’ UTR of Zika virus genome can be controlled by blocking or down regulating its expression through RNAi technology. RNAi works by silencing or turning off target gene expression using siRNA. Hence there arises an urgent need to design potential siRNA against the target sequence of Zika virus genome to control its replication and pathogenicity. This study is aimed to predict potential siRNA based therapeutics that might be used for the treatment of Zika virus infection. Methods: Designing siRNA against the target region of different strains of Zika virus is difficult due to its genetic diversity. Therefore, the work is done on the basis of rational siRNA designing method by targeting the 3’UTR of Zika virus strains. The prediction of potential siRNA was done by using various computational tools as searching target sequences, multiple sequences alignment, secondary structure prediction, siRNA-Target sequence interaction prediction and finally the evaluation of effectiveness of predicted and depicted siRNA. Results: Out of sixty siRNA only four potential siRNA were predicted and depicted rationally for silencing 3’UTR of 37 different Zika virus genome used in the study through RNAi technology. Conclusion: The outcomes of this study are four potential siRNA molecules which might be used as a potential antiviral RNA based therapeutics to suppress the Zika virus mediated infection.

    Key words: Antiviral RNA, RNAi technology, siRNA, Zika virus, 3’ UTR region.

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