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Viral replication is an essential process for viruses to propagate. Upon viral host cell entry, the viral genome is released, replicated and packaged into new viral particles. These may then be released by the host cell and go on to infect further cells. Viral replication is a key target for development of effective antivirals and requires significant understanding of the associated molecular and cellular mechanisms. In the COVID-19 pandemic viral replication has been a key focus for therapeutic and prophylactic intervention.
SARS-CoV-2 is a positive sense RNA virus with a >30 kb genome. This contains 3' and 5' untranslated regions with cis-acting secondary RNA structures essential for RNA synthesis. The genome contains two open reading frames (ORF), namely ORF1a and ORF1b. These are translated into two large polyproteins pp1a and pp1ab, respectively. Processing of these pp1a and pp1ab by the viral proteases, papain-like protease (PLpro) and the coronavirus main protease (Mpro, also known as 3CLpro), releases 16 non-structural proteins (nsp1-16). These nsps have a range of functions. Nsp1 targets the host cell machinery and nsp2-16 make up the viral replication and transcription complex (RTC). The viral proteases PLpro and Mpro reside within nsp3 and nsp5, respectively. PLpro proteolytically releases nsp1, nsp2, nsp3 and the amino terminus of nsp4, while the carboxy terminus of nsp4 and the remaining nsps 5-16 are cleaved by Mpro. Nsps2-11 are associated with RTC support functions, such as host immune evasion and providing cofactors for replication. Nsp12-16 are involved in the RNA synthesis process. For example, nsp12 is an RNA-dependent RNA polymerase (RdRP), and nsp7 and nsp8 comprise RdRP cofactors.
Downstream of ORF1A and ORF1B are genes encoding four structural proteins that form the virus coat: spike (S), envelope (E), membrane (M), and nucleocapsid (N).
The viral replication process offers several targets for intervention, including the proteases PLpro and Mpro. Inhibitors developed against the previous SARS-CoV proteases have also proven effective against their SARS-CoV-2 homologues; GRL 0617 (Cat. No. 7280) and Mpro N3 (Cat. No. 7230) have both shown low micromolar potency (IC50) against PLpro and Mpro, respectively.
Viral RdRPs in RNA viruses are also a target for antiviral compounds. The first approved drug against SARS-CoV-2, Remdesivir (Cat. No. 7226), targets RdRP through its metabolite GS 441524 (a nucleotide phosphate; Cat. No. 7227) competes with ATP for incorporation into the forming RNA strand. This results in premature termination of transcription of viral RNA and inhibition of viral reproduction.
Research has also highlighted host proteins that interact with viral proteins as potential targets. For example, SARS-CoV-2 RNA-dependent RNA polymerase has been found to interact with receptor interacting protein kinase 1 (RIPK1), while 3' - 5'-exonuclease has been found to interact with inosine monophosphate dehydrogenase 2 (IMPDH2).