In-Silico Prediction of Common siRNA Targeting Protein Coding Sequence of NS5 Gene of West Nile and Japanese Encephalitis Virus siRNAs against West Nile and Japanese Encephalitis viruses

Trends in Peptide and Protein Sciences, Vol. 8 No. 1 (2023), 24 December 2023 , Page 1-12(e6)
https://doi.org/10.22037/tpps.v8i1.42723

Abstract

West Nile virus (WNV) and Japanese Encephalitis virus (JEV) are two major mosquito-borne flaviviruses that share almost similar symptoms after infection, e.g., flu-like symptoms. Though JEV is the most common cause of encephalitis (brain inflammation), recent studies have discovered approximately 30% involvement of the WNV in this. Furthermore, both viruses share similar genetic constituents with more than 70% homology. Therefore, these two viruses sometimes cause misdiagnosis due to their co-circulation with the same vector, and no solid protective treatment has yet been discovered against them. As a result, in this study, we used small interfering RNAs to provide dual protection against both viruses. The siRNAs have high demand as a potential treatment option for genetic treatments, and antiviral or antibacterial therapeutics for many diseases. In this study, we concluded that a single highly potent siRNA (5'-UCUCUUUCCCAUCAUGUUGUA-3') could be effective in silencing the coding sequences (CDS) of both WNV and JEV by utilizing several computational assays such as GC content, free energy of binding, free energy of folding, melting temperature, siRNA efficacy prediction, and molecular docking. After structural analysis (molecular modeling and docking), we found that this siRNA effectively binds with the human Argonaute-2 (AGO2) protein. Consequently, this siRNA could be a potential therapeutic development target against both viruses by silencing the CDS. Our research aims to develop genome-level therapies. The results can be applied to develop RNA molecules as a drug against WNV and JEV.

HIGHLIGHTS

  • Promising siRNA target identified for dual protection against WNV and JEV.
  • Efficient siRNA molecule S2 shows high binding affinity with human AGO2 protein.
  • siRNA targeting NS5 gene shows promise for treating WNV and JEV-mediated infections.
Keywords:
  • In silico analysis
  • Japanese Encephalitis virus
  • siRNA
  • Small interfering RNA
  • West Nile virus

How to Cite

1.
Islam R, Shahriar A, Siddiquee MF-R, Fatema N, Uddin MR, Acharjee M, et al. In-Silico Prediction of Common siRNA Targeting Protein Coding Sequence of NS5 Gene of West Nile and Japanese Encephalitis Virus : siRNAs against West Nile and Japanese Encephalitis viruses . Trends Pept. Protein Sci. [Internet]. 2023 Nov. 4 [cited 2026 Jul. 8];8(1):1-12(e6). Available from: https://journals.sbmu.ac.ir/protein/article/view/42723

References

Amarzguioui, M. and H. Prydz, (2004). ″An algorithm for selection of functional siRNA sequences.″ Biochemical and Biophysical Research Communications, 316(4): 1050-1058. DOI: https://doi.org/10.1016/j.bbrc.2004.02.157.

Anderson, R.J., Weng, Z., Campbell, R.K. and X. Jiang, (2005). ″Main‐chain conformational tendencies of amino acids.″ Proteins: Structure, Function, and Bioinformatics, 60(4): 679-689. DOI: https://doi.org/10.1002/prot.20530.

Bellaousov, S., Reuter, J.S., Seetin, M.G. and D.H. Mathews, (2013). ″RNAstructure: web servers for RNA secondary structure prediction and analysis.″ Nucleic Acids Research, 41(W1): W471-W474. DOI: https://doi.org/10.1093/nar/gkt290.

Campbell, G.L., Hills, S.L., Fischer, M., Jacobson, J.A., Hoke, C.H., Hombach, J.M., Marfin, A.A., Solomon, T., Tsai, T.F., Tsu, V.D. and A.S. Ginsburg, (2011). ″Estimated global incidence of Japanese encephalitis: a systematic review.″ Bulletin of the World Health Organization, 89(10): 766-774. DOI: https://doi.org/10.2471/BLT.10.085233.

Chen, Y., Cheng, G. and R.I. Mahato, (2008). ″RNAi for treating hepatitis B viral infection.″ Pharmaceutical Research, 25: 72-86. DOI: https://doi.org/10.1007/s11095-007-9504-0.

Chowdhury, U.F., Shohan, M.U.S., Hoque, K.I., Beg, M.A., Siam, M.K.S. and M.A. Moni, (2021). ″A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2.″ Genomics, 113(1): 331-343.

DOI: https://doi.org/10.1016/j.ygeno.2020.12.021.

Daep, C. A., Muñoz-Jordán, J. L. and E. A. Eugenin, (2014). ″Flaviviruses, an expanding threat in public health: focus on dengue, West Nile, and Japanese encephalitis virus.″ Journal of Neurovirology, 20: 539-560. DOI: https://doi.org/10.1007/s13365-014-0285-z.

Dana, H., Chalbatani, G.M., Mahmoodzadeh, H., Karimloo, R., Rezaiean, O., Moradzadeh, A., Mehmandoost, N., Moazzen, F., Mazraeh, A., Marmari, V. and M. Ebrahimi, (2017). ″Molecular mechanisms and biological functions of siRNA.″ International Journal of Biomedical Science, 13(2): 48. PMID: 28824341.

Dar, S. A., Gupta, A. K., Thakur, A. and M. Kumar, (2016). ″SMEpred workbench: a web server for predicting efficacy of chemically modified siRNAs.″ RNA Biology, 13(11): 1144-1151. DOI: https://doi.org/10.1080/15476286.2016.1229733.

ElHefnawi, M., Kim, T., Kamar, M.A., Min, S., Hassan, N.M., El-Ahwany, E., Kim, H., Zada, S., Amer, M. and M.P. Windisch, (2016). ″In silico design and experimental validation of siRNAs targeting conserved regions of multiple hepatitis C virus genotypes.″ Plos One, 11(7): e0159211. DOI: https://doi.org/10.1371/journal.pone.0159211.

Gaunt, M.W., Sall, A.A., Lamballerie, X.D., Falconar, A.K., Dzhivanian, T.I. and E.A. Gould, (2001). ″Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography.″ Journal of General Virology, 82(8): 1867-1876. DOI: https://doi.org/10.1099/0022-1317-82-8-1867.

Goverdhan, M., Kulkarni, A., Gupta, A., Tupe, C. and J. J. A. v. Rodrigues, (1992). ″Two-way cross-protection between West Nile and Japanese encephalitis viruses in bonnet macaques.″ Acta Virologica, 36(3): 277-283. PMID: 1360756.

Guy, B., Guirakhoo, F., Barban, V., Higgs, S., Monath, T. P. and J. J. V. Lang, (2010). ″Preclinical and clinical development of YFV 17D-based chimeric vaccines against dengue, West Nile and Japanese encephalitis viruses.″ Vaccine, 28(3): 632-649. DOI: https://doi.org/10.1016/j.vaccine.2009.09.098.

Halstead, S.B., Jacobson, J. and K. Dubischar-Kastner, (2012). ″Japanese encephalitis vaccines.″ Vaccines, 6th ed.; Plotkin, SA, Orenstein, WA, Offit, PA, Eds: 312-351.

Hasan, M., Ashik, A. I., Chowdhury, M. B., Tasnim, A. T., Nishat, Z. S., Hossain, T. and S. Ahmed, (2021). ″Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2.″ Informatics in Medicine Unlocked, 24: 100569. DOI: https://doi.org/10.1016/j.imu.2021.100569.

Heinz, F. X. and K. Stiasny, (2012). ″Flaviviruses and flavivirus vaccines.″ Vaccine, 30(29): 4301-4306. DOI: https://doi.org/10.1016/j.vaccine.2011.09.114.

Hoque, H., Islam, R., Ghosh, S., Rahaman, M. M., Jewel, N. A. and M. A. Miah, (2021). ″Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses.″ Heliyon, 7(3): e06396. DOI: https://doi.org/10.1016/j.heliyon.2021.e06396.

Islam, R., Parvez, M. S. A., Anwar, S. and M. J. Hosen, (2020). ″Delineating blueprint of an epitope-based peptide vaccine against the multiple serovars of dengue virus: A hierarchical reverse vaccinology approach.″ Informatics in Medicine Unlocked, 20: 100430. DOI: https://doi.org/10.1016/j.imu.2020.100430.

Islam, R., Rahaman, M., Hoque, H., Hasan, N., Prodhan, S. H., Ruhama, A. and N. A. Jewel, (2021). ″Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene.″ Plos One, 16(11): e0259691. DOI: https://doi.org/10.1371/journal.pone.0259691.

Jana, S., Chakraborty, C. and S. Nandi, (2004). ″Mechanisms and roles of the RNA-based gene silencing.″ Electronic Journal of Biotechnology, 7(3): 321-332.

Khan, M. T., Islam, M. J., Parihar, A., Islam, R., Jerin, T. J., Dhote, R., Ali, M. A., Laura, F. K. and M. A. Halim, (2021)A. ″Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2.″ Informatics in Medicine Unlocked, 24: 100578. DOI: https://doi.org/10.1016/j.imu.2021.100578.

Khan, M. T., Islam, R., Jerin, T. J., Mahmud, A., Khatun, S., Kobir, A., Islam, M. N., Akter, A. and S. I. Mondal, (2021)B. ″Immunoinformatics and molecular dynamics approaches: next generation vaccine design against West Nile virus.″ Plos One, 16(6): e0253393. DOI: https://doi.org/10.1016/j.imu.2021.100578.

Kibbe, W.A. (2007). ″OligoCalc: an online oligonucleotide properties calculator.″ Nucleic Acids Research, 35(suppl_2): W43-W46. DOI: https://doi.org/10.1093/nar/gkm234.

Kim, D.E., Chivian, D. and D. Baker, (2004). ″Protein structure prediction and analysis using the Robetta server.″ Nucleic Acids Research, 32(suppl_2): W526-W531. DOI: https://doi.org/10.1093/nar/gkh468.

Lam, J.K., Chow, M.Y., Zhang, Y. and S.W. Leung, (2015). ″siRNA versus miRNA as therapeutics for gene silencing.″ Molecular Therapy. Nucleic Acids, 4: e252-e252. DOI: https://doi.org/10.1038/mtna.2015.23.

Laskowski, R.A., Jabłońska, J., Pravda, L., Vařeková, R.S. and J.M. Thornton, (2018). ″PDBsum: structural summaries of PDB entries.″ Protein Science, 27(1): 129-134. DOI: https://doi.org/10.1002/pro.3289.

Levanova, A. and M.M. Poranen, (2018). ″RNA interference as a prospective tool for the control of human viral infections.″ Frontiers in Microbiology, 9: 2151. DOI: https://doi.org/10.3389/fmicb.2018.02151.

Lindsey, N.P., Kuhn, S., Campbell, G.L. and E.B. Hayes, (2008). ″West Nile virus neuroinvasive disease incidence in the United States, 2002–2006.″ Vector-Borne and Zoonotic Diseases, 8(1): 35-40. DOI: https://doi.org/10.1089/vbz.2007.0137.

Markham, N.R. and M. Zuker, (2005). ″DINAMelt web server for nucleic acid melting prediction.″ Nucleic Acids Research, 33(suppl_2): W577-W581. DOI: https://doi.org/10.1093/nar/gki591.

Méndez, C., Ahlenstiel, C.L. and A.D. Kelleher, (2015). ″Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus.″ World Journal of Virology, 4(3): 219. DOI: https://doi.org/10.5501/wjv.v4.i3.219.

Motavaf, M., Safari, S. and S.M. Alavian, (2012). ″Therapeutic potential of RNA interference: a new molecular approach to antiviral treatment for hepatitis C.″ Journal of Viral Hepatitis, 19(11): 757-765. DOI: https://doi.org/10.1111/jvh.12006.

Murray, K.O., Baraniuk, S., Resnick, M., Arafat, R., Kilborn, C., Shallenberger, R., York, T.L., Martinez, D., Malkoff, M., Elgawley, N. and W. McNeely, (2008). ″Clinical investigation of hospitalized human cases of West Nile virus infection in Houston, Texas, 2002–2004.″ Vector-Borne and Zoonotic Diseases, 8(2): 167-174. DOI: https://doi.org/10.1089/vbz.2007.0109.

Naito, Y., Yamada, T., Ui-Tei, K., Morishita, S. and K. Saigo, (2004). ″siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference.″ Nucleic Acids Research, 32(suppl_2): W124-W129. DOI: https://doi.org/0.1093/nar/gkh442.

Naito, Y., Yoshimura, J., Morishita, S. and K. Ui-Tei, (2009). ″siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics, 10(1): 1-8. DOI: https://doi.org/10.1186/1471-2105-10-392.

Popenda, M., Szachniuk, M., Antczak, M., Purzycka, K.J., Lukasiak, P., Bartol, N., Blazewicz, J. and R.W. Adamiak, (2012). ″Automated 3D structure composition for large RNAs.″ Nucleic Acids Research, 40(14): e112. DOI: https://doi.org/10.1093/nar/gks339.

Rahaman, M.M., Islam, R., Jewel, G.N.A. and H. Hoque, (2022). ″Implementation of computational approaches to explore the deleterious effects of non-synonymous SNPs on pRB protein.″ Journal of Biomolecular Structure and Dynamics, 40(16): 7256-7273. DOI: https://doi.org/10.1080/07391102.2021.1896385.

Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W.S. and A. Khvorova, (2004). ″Rational siRNA design for RNA interference.″ Nature Biotechnology, 22(3): 326-330. DOI: https://doi.org/10.1038/nbt936.

Rivas, F.V., Tolia, N.H., Song, J.J., Aragon, J.P., Liu, J., Hannon, G.J. and L. Joshua-Tor, (2005). ″Purified Argonaute2 and an siRNA form recombinant human RISC.″ Nature Structural & Molecular Biology, 12(4): 340-349. DOI: https://doi.org/10.1038/nsmb918.

Safari, F., Barouji, S.R. and A.M. Tamaddon, (2017). ″Strategies for improving siRNA-induced gene silencing efficiency.″ Advanced Pharmaceutical Bulletin, 7(4): 603. DOI: https://doi.org/10.15171/apb.2017.072.

Saxena, S., Jónsson, Z.O. and A. Dutta, (2003). ″Small RNAs with imperfect match to endogenous mRNA repress translation: implications for off-target activity of small inhibitory RNA in mammalian cells.″ Journal of Biological Chemistry, 278(45): 44312-44319. DOI: https://doi.org/10.1074/jbc.M307089200.

Shawan, M.M.A.K., Sharma, A.R., Bhattacharya, M., Mallik, B., Akhter, F., Shakil, M.S., Hossain, M.M., Banik, S., Lee, S.S., Hasan, M.A. and C. Chakraborty, (2021). ″Designing an effective therapeutic siRNA to silence RdRp gene of SARS-CoV-2.″ Infection, Genetics and Evolution, 93: 104951. DOI: https://doi.org/10.1016/j.meegid.2021.104951.

Singh, S., Gupta, S.K., Nischal, A., Khattri, S., Nath, R., Pant, K.K. and P.K. Seth, (2012). ″Design of potential siRNA molecules for hepatitis delta virus gene silencing.″ Bioinformation, 8(16): 749. DOI: https://doi.org/10.6026/97320630008749.

Su, H., Trombly, M.I., Chen, J. and X. Wang, (2009). ″Essential and overlapping functions for mammalian Argonautes in microRNA silencing.″ Genes & Development, 23(3): 304-317. DOI: https://doi.org/10.1101/gad.1749809.

Takasaki, T., Yabe, S., Nerome, R., Ito, M., Yamada, K.I. and I. Kurane, (2003). ″Partial protective effect of inactivated Japanese encephalitis vaccine on lethal West Nile virus infection in mice.″ Vaccine, 21(31): 4514-4518. DOI: https://doi.org/10.1016/S0264-410X(03)00507-3.

Tanaka, K., Kanazawa, T., Ogawa, T., Takashima, Y., Fukuda, T. and H. Okada, (2010). ″Disulfide crosslinked stearoyl carrier peptides containing arginine and histidine enhance siRNA uptake and gene silencing.″ International Journal of Pharmaceutics, 398(1-2): 219-224. DOI: https://doi.org/10.1016/j.ijpharm.2010.07.038.

Tesh, R.B., da Rosa, A.P.T., Guzman, H., Araujo, T.P. and S.Y. Xiao, (2002). ″Immunization with heterologous flaviviruses protective against fatal West Nile encephalitis.″ Emerging Infectious Diseases, 8(3): 245. DOI: https://doi.org/10.3201/eid0803.010238.

Ui‐Tei, K., Naito, Y., Takahashi, F., Haraguchi, T., Ohki‐Hamazaki, H., Juni, A., Ueda, R. and K. Saigo, (2004). ″Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference.″ Nucleic Acids Research, 32(3): 936-948. DOI: https://doi.org/10.1093/nar/gkh247.

Ui-Tei, K., Naito, Y., Nishi, K., Juni, A. and K. Saigo, (2008). ″Thermodynamic stability and Watson–Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.″ Nucleic Acids Research, 36(22): 7100-7109. DOI: https://doi.org/10.1093/nar/gkn902.

Van den Hurk, A.F., Ritchie, S.A., Johansen, C.A., Mackenzie, J.S. and G.A. Smith, (2008). ″Domestic pigs and Japanese encephalitis virus infection, Australia.″ Emerging Infectious Diseases, 14(11): 1736. DOI: https:// doi.org/ 10.3201/eid1411.071368.

Van den Hurk, A.F., Ritchie, S.A. and J.S. Mackenzie, (2009). ″Ecology and geographical expansion of Japanese encephalitis virus.″ Annual Review of Entomology, 54: 17-35. DOI: https://doi.org/10.1146/annurev.ento.54.110807.090510.

Vickers, T.A., Wyatt, J.R. and S.M. Freier, (2000). ″Effects of RNA secondary structure on cellular antisense activity.″ Nucleic Acids Research, 28(6):1340-1347.

DOI: https://doi.org/10.1093/nar/28.6.1340.

Williams, D.T., Daniels, P.W., Lunt, R.A., Wang, L.F., Newberry, K.M. and J.S. Mackenzie, (2001). ″Experimental infections of pigs with Japanese encephalitis virus and closely related Australian flaviviruses.″ The American Journal of Tropical Medicine and Hygiene, 65(4): 379-387.

DOI: https://doi.org/10.4269/ajtmh.2001.65.379.

Xu, W., Jiang, X. and L., Huang, (2019). ″RNA interference technology.″ Comprehensive Biotechnology, 5: 560-575. DOI: https;//doi.org/10.1016/B978-0-444-64046-8.00282-2.

Yan, Y., Tao, H., He, J. and S.Y. Huang, (2020). ″The HDOCK server for integrated protein–protein docking.″ Nature Protocols, 15(5): 1829-1852. DOI: https://doi.org/10.1038/s41596-020-0312-x.

Zuker, M. (2003). ″Mfold web server for nucleic acid folding and hybridization prediction.″ Nucleic Acids Research, 31(13): 3406-3415. DOI: https://doi.org/10.1093/nar/gkg595.

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