Coronavirus and SARS-CoV-2 Inhibitors

SARS-CoV-2 Membrane (M) Protein Inhibitors

The membrane (M) protein determines the shape of the SARS-CoV-2 viral envelope and organizes viral assembly through interaction with each additional structural protein (Chang, 2014).

SARS-CoV-2 Envelope (E) Protein Inhibitors

The envelope (E) protein is the smallest of the SARS-CoV-2 structural proteins, and it is incorporated into the virion envelope, though this represents only a small amount of total expressed envelope protein. A high proportion is also expressed inside the infected cell, where it is involved in viral assembly, budding, maturation, and propagation (Schoeman, 2019; Chang, 2020). The E protein sequence of SARS-CoV-2 has 90% amino acid overlap with other human coronavirus envelope proteins, which may allow for the development or repurposing of pan-coronavirus antiviral drugs that target this protein.

Belachinal, Macaflavanone E, and Vibsanol B are phytochemicals which have been shown in in silico models to potentially inhibit the activity of E protein (Gupta, M.G., 2020).

SARS-CoV-2 Papain-like Protease Inhibitors

There are two types of proteases expressed by SARS-CoV and SARS-CoV-2, the papain-like protease (PLpro, NSP3), and the CL-like protease (NSP5A & B, 3CLpro, Mpro). These proteases are responsible for cleaving the viral polyprotein and releasing nonstructural proteins (NSPs). These NSPs are vital for SARS-CoV-2 viral replication, maturation, and its overall life-cycle. In SARS-CoV, the papain-like protease (PLpro) inhibits type I interferon (IFN) by blocking IRF3 phosphorylation, which results in downstream inhibition of interferon induction and a reduction in the host’s innate immune response. This is thought to contribute to higher viral titer and leads to an increase in cell death and damage to infected and surrounding tissue (Matthews, 2014). The SARS-CoV-2 papain-like protease is thus of interest as a drug target to prevent viral replication and potentially reduce tissue damage (Báez-Santos, 2015).

SARS-CoV-2 NSP12 Polymerase Inhibitors

NSP12 RNA-dependent RNA polymerase (RdRP, RDR, RNA replicase) is an enzyme that catalyzes the replication of RNA from an RNA template. RdRP is a crucial viral enzyme in the life cycle of RNA viruses. In all positive-strand RNA viruses including SARS-CoV and SARS-CoV-2, RdRP constitutes the central catalytic subunit of the machinery involved in RNA synthesis and catalyzes the replication and transcription of the RNA genome (te Velthuis, 2010).

SARS-CoV-2 Open Reading Frame 3 (ORF3a) Inhibitors

The ORF3a protein expressed by SARS-CoV-2 has 72% sequence homology with SARS-CoV ORF3a. In SARS-CoV, the ORF3a protein activates NF-κB and the NLRP3 inflammasome by inducing TRAF3-dependent ubiquitination of p105 and ASC (Kam-Leung Siu, 2019). There is evidence that the SARS-CoV-2 virus is less effective in activating the NLRP3 inflammasome and in suppressing the antiviral response when compared to SARS-CoV. More studies are needed to fully understand how the SARS-CoV-2 ORF3a protein influences the immune and inflammatory response as it pertains to COVID-19 disease progression (Yuen, 2020; Zeng, 2004).

Helicase Inhibitors

The coronavirus helicase protein (nsp13) is conserved among coronavirus species, in contrast to structural proteins (e.g. spike) that show high sequence variability. Given the 70-80% sequence similarity of helicases among MERS, SARS, and SARS-CoV-2, and the effectiveness of drugs targeting protease and polymerase enzymes of MERS and SARS (Indinavir, Remdesivir), the helicase protein is therefore an attractive potential target for COVID-19 therapy.

Helicase enzymes are motor proteins that use energy derived from ATP hydrolysis (Briguglio I, 2010). Nsp13 helicase has been demonstrated to catalyze NTP-dependent unwinding of duplex oligonucleotides (RNA or DNA) into single strands, a step that is required for viral replication (Jia Z, 2019; Singleton MR, 2007).

Helicase inhibitors can have the following mechanisms of action:

• 1)   Interfere with ATP binding to limit energy required from ATP hydrolysis
• 2)   Inhibit NTPase activity by allosteric mechanisms
• 3)   Inhibit nucleic acid binding to the helicase
• 4)   Inhibit coupling of hydrolysis to unwinding

In silico studies on MERS and SARS-CoV have shown helicase domain 1A to have a direct effect on unwinding (Mirza MU, 2020). Small compounds that have the potential to inhibit ATP binding or direct NTPase activity include benzotriazole, imidazole, imidazodiazepine, phenothiazine, quinoline, anthracycline, triphenylmethane, tropolone, pyrrole, acridone, small peptide, and bananin derivatives (Briguglio I, 2010). Such compounds have been demonstrated to inhibit ATPase activity, leading to inhibition of viral replication in vitro, and may prove to be of benefit in vivo.

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