Title: In silico prediction of effective small interfering RNA (siRNA) against major structural genes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
In the city of Wuhan of Hubei Province, China, by the end of December 2019, suddenly, a large number of severe pneumonia cases of unknown etiology in adults were reported by Wuhan Municipal Health Commission (Li, Q. et al. .2020; Wang et al., 2020). In further investigations, a novel coronavirus (nCoV) was found responsible for this outbreak and provisionally termed the disease caused by it as infectious coronavirus disease 2019 (COVID-19). The novel coronavirus was shown significant homology with severe acute respiratory syndrome-Coronavirus (SARS-CoV); therefore, The International Committee on Taxonomy of Viruses (ICTV) classified it as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (Abdo, 2020; Wrapp2020).
Like other highly pathogenic viruses against humans such as Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV, SARS-CoV-2 is also a β-Coronavirus (Cui, 2019; Hui, 2020; Forni, 2017). The genome is a positive sense, RNA molecule of about 29.8 kb to 29.9 kb in size with a nucleocapsid of helical symmetry (Zumla 2016). The 5′ end of the genome comprises more than two-thirds of the genome and encloses an open reading frame “ab” (orf1ab), which encodes for orf1ab polyproteins. The 3′ end of the genome contains one-third part of the genome and encodes for major structural proteins- surface (S), envelope (E), membrane (M), and nucleocapsid N proteins. Besides this, genes of other ORFs such as ORF3a, ORF6, ORF7a, ORF7b, and ORF8 encode for six accessory proteins (Li et al., 2005; Oostra et al., 2007).
S protein facilitates the entry of coronavirus into the host cell by binding with the host cell receptors, responsible for the host tropism (Millet, 2015). S, M, and E proteins are mainly involved in the viral coat formation, and N proteins work in viral packaging (Wu C, 2020). Hence, these proteins provide structural integrity to the coronavirus; consequently, they may act as potent targets for discovering novel antiviral drug candidates.
According to the World health organization (WHO), there have been 13,824,739 confirmed cases of COVID-19, including 591,666 deaths, till 20 July 2020 (https://covid19.who.int/). Still, the number of confirmed positive cases is increasing drastically. Coronavirus infected persons may be asymptomatic (Song et al., 2020) or may undergo mild to severe pyrexia, tiredness, dry cough, muscle spasm, dyspnea, and sometimes severe pneumonia (Hussin, 2020; Cynthia, 2020). The disease swept across the world in just a few months and attained the Pandemic status (Sohrabi et al., 2020).
Scientists are attempting to develop vaccines and drugs for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), but no vaccine or specific drug is available in the market for it. Currently, COVID-19 patients are being treated with the administration of convalescent donor’s plasma and by the use of repurposed drugs-including antimalarial (hydroxychloroquine), anticancerous (Siltuximab, Tocilizumab, Enoxaparin), and antivirals (Lopinavir, Ritonavir, Remdesivir). However, clinical trials of these repurposed drugs are going on still not the crucial data available on the efficacy of these drugs against SARS-CoV-2. Direct therapeutic approaches will be more efficient in treating the patients; therefore, there is a need for the rapid development of an effective drug to treat COVID-19 patients.
RNA interference (RNAi) is a gene-silencing process that acts by cleaving the target RNA via 19-23 mer long small interfering RNA (siRNA) molecules. RNAi is not a new process. It is an old remedy for the new curse and has already been shown the optimum level of silencing for other coronaviruses. Since 2003, many patents on Coronavirus siRNA are filed by inventors, and trials are still going on (Excli). Many pharmaceutical companies such as- Biogen, Vir Biotechnology, Alnylam Pharmaceuticals, etc. are trying to identify competent siRNA candidates targeting SARS-CoV-2.
To develop effective siRNA candidates for all the available strains of SARS-CoV-2, Vir Biotechnology is also planning to conduct the in vitro and in vivo testing of all 350 synthesized siRNA by Alnylam pharmaceuticals (John Hodgson., 2020).
Taking these facts into account, the attempt is made for the in silico prediction and validation of effective siRNA/s targeting essential structural proteins- surface (S), envelope (E), membrane (M), and nucleocapsid N proteins of SARS-CoV-2.