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Nirmatrelvir Against SARS-CoV-2 Mutants

SARS-CoV-2 continues to cause death and illness across the world. We need both vaccines and an arsenal of antiviral drugs to combat this virus.

One drug that was recently developed to treat SARS-CoV-2 is nirmatrelvir. Nirmatrelvir targets the main protease (Mpro) of SARS-CoV-2, which it needs to replicate. This molecule binds to the active site of Mpro and permanently alters it.

A recent study by Ullrich et al. sought to test whether nirmatrelvir still works when SARS-CoV-2 accumulates mutations in its Mpro. Epidemiologists have identified many mutations in this protease, so Ullrich et al. chose a selection of the most common mutations to study. They expressed mutant copies of Mpro and measured their proteolytic activity. The mutant Mpro has similar activity to wild-type.

Next, the researchers added nirmatrelvir to the mutant Mpro and calculated its inhibitory concentration. Nirmatrelvir inhibitory concentration against the mutant Mpro was similar to the wild-type.

This encouraging result suggests that nirmatrelvir will continue to work against SARS-CoV-2 in the near future, even if the virus mutates. However, in the long term we should consider developing drug cocktails to prevent resistance from evolving.

 

Ullrich S, Ekanayake KB, Otting G, Nitsche C. Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Bioorg Med Chem Lett. 2022 Apr 15;62:128629. doi.org/10.1016/j.bmcl.2022.128629. PMID: 35182772

Mayaro Virus Antiviral EIDD-1931

Mayaro virus is a mosquito-borne virus endemic to forests in South America. It causes acute illness with fever, headache, rash, and long-lasting joint pain. Mayaro’s range could spread in the future because of climate change. No vaccines or antiviral drugs are currently available although there are some candidates under development.

Therefore, a concerned team of scientists from the Rega Institute for Medical Researchin Belgium wanted to do exploratory research on antivirals that might treat this disease. They chose a panel of molecules that are known to treat other mosquito-borne viruses, some of which block early stages of the virus life cycle (arbidol, chloroquine, suramin, and ribavirin), and some that inhibit virus genome replication (favipiravir, 7DMA, 2’CMC, EIDD-1931, galidesivir and remdesivir).

They then applied these selected molecules to a model of cell culture that was infected with Mayaro virus. The researchers measured the 50% effective concentration, or the amount of molecule that inhibits 50% of the virus infectivity. They optimized the antiviral screening assay to be reproducible and reliable.

The assay described in this paper can be useful to test future antiviral drugs against this virus. Furthermore, the three molecules that performed well in cell culture are worth further study with in vivo models. Although the range of Mayaro virus is limited for now, we should study it and other neglected diseases to proactively prevent suffering in the future.

 

Langendries L, Abdelnabi R, Neyts J, Delang L. Repurposing drugs for Mayaro virus: identification of EIDD-1931, Favipiravir, and Suramin as Mayaro virus inhibitors. Microorganisms. 2021 Mar 31;9(4):734. PMID: 33807492

Molnupiravir Against COVID-19

Molnupiravir is an antiviral drug that has recently been approved by the FDA for the treatment of COVID-19. This drug is especially exciting because it is the first approved COVID-19 drug that can be taken as a pill, and also because it reduces the risk of hospitalization and death by 30%. Two recent research papers give us insight into the molecular biology of how molnupiravir works.

In order to reproduce, the virus SARS-CoV-2 needs to synthesize RNA. Usually, the enzyme it uses to do this, RNA-dependent RNA polymerase (RdRp), is an attractive target for makers of antiviral drugs. At present, many antiviral drugs block RdRp by mimicking RNA nucleotides. When such a drug gets incorporated into a new RNA strand, synthesis stops. Unfortunately, this drug strategy is not effective against SARS-CoV-2 because it has proofreading enzymes that allow synthesis to continue.

Two research teams in Germany and Canada recently showed that molnupiravir mimics cytidine and uridine, two RNA nucleotides. Molnupiravir incorporates into new RNA strands, like other antiviral drugs. But interestingly, RdRp continues to synthesize RNA. How, then, does molnupiravir prevent severe COVID-19?

Both teams addressed this question by combining RNA that contained molnupiravir with RdRp in vitro. They found that when RdRp uses this RNA to synthesize new RNA, molnupiravir causes mutations. After several generations, mutations build up to a lethal level and the virus can no longer reproduce.

Molnupiravir’s mechanism of action evades viral proofreading enzymes. Because of this, it may also find use in treating a broad variety of other viruses that also have these enzymes.

 

Kabinger F, Stiller C, Schmitzova J, et al. Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nature Structural & Molecular Biology. 2021 Sep;28(9):740-746. PMID: 34381216

Gordon CJ, Tchesnokov EP, Schinazi RF, et al. Molnupiravir promotes SARS-CoV-2 mutagenesis via the RNA template. Journal of Biological Chemistry. 2021 Jul;297(1):100770. PMID: 33989635

FDA News Release: FDA authorizes additional oral antiviral for treatment of COVID-19 in certain adults

Protease Inhibitors: Saquinavir and Boceprevir

The COVID-19 pandemic continues to cause death and severe illness around the world. As many countries still experience vaccine shortages and the virus evolves to be more contagious, we need to develop better treatments for this disease.

A Possible Target:

The SARS-CoV2 main protease (Mpro) is an attractive target for drug treatment. The coronavirus needs this protease to process its proteins, an important step in its life cycle. Protease inhibitors are already in clinical use to treat other viral infections, such as HIV and hepatitis C. Repurposed existing drugs can get approval to treat disease faster than new drugs because their safety and pharmacokinetics are already known. Can we repurpose known protease inhibitors to treat SARS-CoV2 infection?

Two recent scientific studies address this question.

Docking and Molecular Dynamics Simulations:

Bello et al. built a computer model of Mpro and twelve promising protease inhibitors: darunavir, indinavir, saquinavir, tipranavir, diosmin, hesperidin, rutin, raltegravir, velpatasvir, ledipasvir, rosuvastatin, and bortezomib. The model predicts that of the twelve, saquinavir should bind to Mpro the best. Interestingly, saquinavir has long been used as part of drug cocktails to treat HIV. Although a computer study is limited, saquinavir is worth following up in vitro.

Enzyme Assays:

Another team of researchers, Ma et al., used an enzyme assay to screen for drugs that might inhibit the activity of Mpro. Out of a library of known inhibitors, they found that boceprevir inhibited Mpro the most. Formerly, boceprevir was used to treat hepatitis C before more effective protease inhibitors were developed. Boceprevir might find new life now as a treatment for COVID-19, and is worth further study.

 

Bello M, Martinez-Muñoz A, Balbuena-Rebolledo I. Identification of saquinavir as a potent inhibitor of dimeric SARS-CoV2 main protease through MM/GBSA. Journal of Molecular Modeling. 2020 Nov 12; 26(12):340. PMID: 33184722

Ma C, Sacco MC, Hurst B, et al. Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV2 viral replication by targeting the viral main protease. Cell Research. 2020 Aug; 30(8):678-692. PMID: 32541865

Remdesivir Synergy Against COVID-19

Currently, remdesivir is the only antiviral drug approved to treat COVID-19. Its effects on the course of disease are moderate. Many viral diseases, such as HIV and hepatitis C, are treated with drug cocktails. Existing antiviral drugs might make remdesivir more effective in combination.

Two research teams recently screened for antiviral drugs that might increase the effectiveness of remdesivir.

Lo et al. screened a library of drugs for its ability to reduce SARS-CoV-2 viral load in kidney epithelial cells. They found that simeprevir reduces viral load in vitro. Simeprevir is a protease inhibitor that is often combined with sofosbuvir to treat hepatitis C. Simeprevir was even more effective in the in vitro experiment when combined with remdesivir.

Nguyenla et al. added remdesivir to cell cultures of kidney epithelial cells and human lung cells and infected these cells with SARS-CoV-2. They used this remdesivir-treated culture to screen a large library of FDA-approved drugs for compounds that reduce a proxy measure of viral load. The team chose the twenty most promising drugs to validate in human lung cell culture, which they tested for viral load.

The drugs velpatasvir and elbasvir reduced viral load. Both velpatasvir and elbasvir are used as parts of drug cocktails to treat hepatitis C. Velpatasvir is used with sofosbuvir and elbasvir is used with grazoprevir. The research team then tested the velpatasvir/sofosbuvir and elbasvir/grazoprevir cocktails with remdesivir in lung cell culture; the three-drug cocktails were even more effective that the pairs.

These results support the idea that COVID-19 could be better treated with cocktails of antiviral drugs.

 

Lo HS, Hui KPY, Lai HM, et al. Simeprevir potently suppresses SARS-CoV-2 replication and synergizes with remdesivir. ACS Central Science. 2021 May 26;7(5): 792-802. doi: 10.1021/acscentsci.0c01186. PMID: 34075346

Nguyenla X, Wehri E, Dis EV, et al. Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells. BiorXiv. Preprint. 2020 Sept. http://doi.org/10.1101/2020.09.18.302398

Baloxavir Antiviral to Shorten and Prevent Influenza

Baloxavir is an antiviral drug that was FDA approved in 2018 for the treatment of influenza. It works by inhibiting an enzyme that influenza needs to replicate its DNA. When taken early, it can shorten the course of influenza by a day.

But can it also prevent influenza?

Researchers working for Shionogi, the manufacturer of baloxavir, set up a clinical trial in Japan to test this question. During the 2018-2019 flu season, they identified patients with influenza when they went to see their primary care doctor.

The researchers offered the household contacts of these patients either baloxavir or a placebo. Ten days later, the researchers tested the household contacts for influenza RNA (clinical influenza) using RT-PCR.

1.9% of household contacts who took the active treatment had clinical influenza whereas 13.6% of household contacts who took the placebo had clinical influenza. This is a successful demonstration that Baloxavir is effective at preventing influenza and as such was recently FDA approved for this use.

The authors of this study were not able to rule out whether this chemical can contribute to the rise of drug-resistant influenza. Further research is needed on this topic.

 

Baloxavir

Baloxavir Marboxil

 

Ikematsu H, Hayden FG, Kawaguchi K, et al. Baloxavir marboxil for prophylaxis against influenza in household contacts. N Engl J Med. 2020 Jul 23; 383(4):309-320. doi 10.1056/NEJMoa1915341. PMID: 32640124.