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Coronavirus and SARS-CoV-2 Inhibitors

LSBio offers a range of research-use-only biochemicals that show potential inhibitory action against various coronaviruses such as SARS-CoV-2. These include direct inhibitors of coronavirus spike, nucleocapsid, protease, and polymerase proteins. We also offer various chemicals that block host proteins utilized by coronaviruses for infection and replication.

Spike (S) Protein Inhibitors Papain-like Protease Inhibitors Membrane (M) Protein Inhibitors NSP12 Polymerase Inhibitors Envelope (E) Protein Inhibitors Open Reading Frame 3 Inhibitors All Coronavirus Inhibitors Helicase Inhibitors

SARS-CoV-2 Spike (S) Protein Inhibitors

The spike (S) protein is responsible for attachment to and fusion with the host cell. For both SARS-CoV and SARS-CoV-2, the host receptor is known to be angiotensin converting enzyme 2 (ACE2) (Hoffmann, 2020). The spike protein is proteolytically cleaved into two subunits, S1 and S2. The S1 subunit binds to ACE2 presented on the host cell surface, and the S2 subunit is responsible for fusion with the host cell. Target cells include pneumocytes and macrophages expressing ACE2 in the lung, as well as ACE2-positive epithelial cells in the lung, gastrointestinal tract, and liver (cholangiocytes). The spike protein subunits are of interest as targets of vaccines; the S2 subunit is highly conserved and may be an effective pan-coronavirus target. SARS-CoV studies in monkeys immunized with full-length spike protein showed successful protection against subsequent infection (Shang, 2020).

Camostat Mesylate

Camostat mesylate is an inhibitor of the protease TMPRSS2. This host protease is used by SARS-CoV-2 for spike protein priming, and inhibition with camostat mesylate has been shown to block SARS-CoV-2 infection in lung cell lines (Hoffmann, 2020).

Emodin

Emodin is an anthraquinone derivative extracted from Rheum tanguticum. It has been found to inhibit the SARS-CoV ORF3a protein and also block interactions between the SARS-CoV spike protein and the ACE2 receptor. It is of interest as a potential inhibitor of SARS-CoV-2 infection (Zhou, Y., 2020).

All Spike (S) Protein 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).

Toremifene

Toremifene is a nonsteroidal selective estrogen receptor modulator (SERM) used in the treatment of metastatic breast cancer. It has also been found to block the fusion of viral and endosomal membranes by destabilizing the viral membrane glycoprotein and has been demonstrated to inhibit Ebola, MERS-CoV, and SARS-CoV viral replication in vitro using established cell lines. It is of interest as a potential inhibitor of SARS-CoV-2 infection (Zhou, Y., 2020).

All Membrane (M) Protein Inhibitors

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).

Lopinavir

Lopinavir is the most powerful inhibitor of CoV protease and Saquinavir is the least powerful. As per current guidelines, Lopinavir + Ritonavir is the recommended protease inhibitor combination for the treatment of COVID-19.

Mercaptopurine (6MP)

Mercaptopurine has been found to inhibit both SARS-CoV and MERS-CoV papain-like protease (PLpro), a protein necessary for viral maturation. Mercaptopurine acts as an anti-inflammatory agent by inhibiting interferon stimulation via proteases (Zhou, Y., 2020; Chen, X., 2009; Cheng, K.W., 2015).

Darunavir

Darunavir is a protease inhibitor. When used in combination with cobicistat it has been found to inhibit the 3CL-protease (3CLpro), thereby blocking viral replication.

Oseltamivir (Tamiflu)

Oseltamivir is a neuraminidase inhibitor, a competitive inhibitor of influenza's neuraminidase enzyme. The enzyme cleaves the sialic acid which is found on glycoproteins on the surface of human cells, which helps new virions to exit the cell. The use of oseltamivir in combination ASC09 or Ritonavir is currently under clinical study for treating coronavirus infections. (Harrison, C., 2020)

Nelfinavir

Nelfinavir is an HIV-1 protease inhibitor that has been demonstrated to also suppress SARS-CoV viral replication (Yamamoto, 2004). Nelfinavir is of interest in COVID-19 antiviral drug research, as it was found to inhibit the SARS-CoV-2 papain-like protease (plPro, mPro) when tested in Vero E6 cells (Xu, 2020). It has also been shown to inhibit inflammatory cytokines in vitro and may be effective in reducing the inflammatory response and severe innate immune activation resulting from COVID-19 and other viral diseases (Xu, 2020; Wallet, 2012).

All Papain-like Protease Inhibitors

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).

Acyclovir

Acyclovir is a synthetic nucleoside analog that serves as a polymerase inhibitor. Acyclovir fleximers have shown to inhibit HCov-NL63 and MERS-CoV (Creative Biolabs, 2020).

Baloxavir marboxil

Baloxavir marboxil is a Cap-dependent endonuclease inhibitor and is used in combination with favipiravir, a nucleoside analog RdRP polymerase inhibitor, for SARS-CoV-2 treatment (Harrison, C., 2020).

Favipiravir (T-705)

Favipiravir is an RNA polymerase inhibitor used for the treatment of Influenza A and B. Although it has not shown strong activity against SARS-CoV-2 (Wang, M., 2020), it is still in trial for use in combination with other therapies (Harrison, C., 2020).

Emtricitabine

Emtricitabine acts as a reverse transcriptase inbibitor. Although coronaviruses do not have reverse transcriptase, repurposing of these inhibitors is being explored in concert with other antivirals for treatment of COVID-19 (Harrison, C., 2020).

Tenofovir

Tenofovir acts as a guanosine analog reverse transcriptase inhibitor. In combination, Emtricitabine/Tenofovir inhibit viral RNA synthesis. These have been used in trials in combination with guanosine analogs and RNA synthesis inhibitors (Harrison, C., 2020).

Galidesivir (BCX4430, Immucillin-A)

Galidesivir tightly binds to RdRP and is used as a polymerase inhibitor (Elfiky, A.A., 2020).

Remdesivir

Remdesivir is a broad spectrum anti-viral developed against Ebola virus and is being tried as an anti-replicase.

Ribavirin

Ribavirin is an anti-polymerase drug which binds tightly to RdRP (Elfiky, A.A., 2020).

Sofosbuvir

Sofosbuvir is an anti-HCV drug which targets RdRP (Elfiky, A.A., 2020).

All NSP12 Polymerase Inhibitors

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).

Tranilast

Tranilast inhibits activation of the NLRP3 inflammasome pathway, which is activated by ORF3a.

All ORF3a Inhibitors

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.

All Helicase Inhibitors

References

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