Author: Ronald L. Conte Jr.

Abstract

Favipiravir is a Covid-19 medication which works as a nucleoside analog. However, Nsp14 functions to remove such analogs as part of its proofreading function. Therefore, a set of NSP14 inhibitors are considered for possible enhancement of the function and effectiveness of favipiravir. Remdesivir has a similar mechanism of action and many also benefit from combination with an NSP14 inhibitor.

Introduction

SARS-CoV-2 uses a protein called “replicase” (“RdRp”) to make copies of its viral RNA.

Other viruses use the same type of approach. Treatment of those viruses with an nucleoside analog can be effective. The analog is a fake RNA nucleotide (one of the four bases used in the RNA or DNA code: CGTU/A) which becomes incorporated into the viral RNA copy, causing it to fail to work.

However, SARS-CoV-2 has another protein, NSP14, called exonuclease (ExoN), which proofreads the RNA copy and kicks out any mistakes, including analogs. This causes drugs which work in this manner against SARS-CoV-2 to be less effective than they otherwise would be, at least in theory.

Another type of antiviral is called an inhibitor. Viral inhibitors bind to a location on a viral protein, causing the protein to be deactivated. If the ExoN proofreader is inactivated, then analog treatments like favipiravir might become more effective.

A study [1] titled “Combining SARS-CoV-2 proofreading exonuclease and RNA-dependent RNA polymerase inhibitors as a strategy to combat COVID-19: a highthroughput in silico screen”, by Dr. Shradha Khater, Dr. Nandini Dasgupta, and Dr. Gautam Das, from Mumbai, India first proposed this combination, a treatment for Replicase (RdRp) with an inhibitor of ExoN (Nsp14).

The question examined by this article is which ExoN inhibitors would be most effective? Here are the best Nsp14 inhibitors across several different molecular docking studies. I’ve exempted from this list any medications or chemicals which are not practical to use for treatment as they are toxic or have dangerous side effects.

Dexamethasone metasulfobenzoate (MSB)
Nsp14: -8.7 [1]
Spike: -10.4 [2]
Mpro: -8.7 [2]

Hesperidin
Nsp14: -8.6 [1]
Nsp14: mfScore -119.58, ICM score: -24.41 [3]
Mpro: -13.51 [7]
Spike: -9.61 [7]
ACE2: -9.50 [7]

Flavin adenine dinucleotide (FAD)
Nsp14: -8.5 [1]
Nsp14: -13.6 [5]
Nsp2: -11.8 [5]
RdRp: -12.8 [5]
Spike: -12.9 [5]
N-protein: -13.3 [5]
Helicase: -11.2 [5]
Mpro: -10.2 [6]

Rosmarinic acid
Nsp14: mfScore -143.36, ICM -23.63 [3]

Theaflavine digallate
Nsp14: mfScore -138.82, ICM -18.19 [3]
Mpro: -14.4 [8]

Curcumin
Nsp14: mfScore -133.50, ICM -33.47 [3]
Mpro: -11.82 [7]
Spike: -8.39 [7]
ACE2: -9.04 [7]

Myricetin
Nsp14: mfScore -117.61, ICM -31.93 [3]
Mpro: -7.9 [9]

Baicalein
Nsp14: mfScore -104.77, ICM -30.22 [3]
ACE2: -10.50 [10]
Mpro: -8.4 [10]

Famotidine
Nsp14: -6.50 [4]
PLpro: -7.9 [4]
Mpro: -6.0 [4]
RdRp: -7.0 [4]

All of the above medications or supplements are inhibitors of Nsp14 as well as other viral targets. Dexamethasone MSB is a good candidate for Covid-19 who have reached the stage of low viral load with high inflammation. As a steroid, it fights the inflammation; it is also a viral inhibitor. And it binds to Nsp14, to make any RdRp inhibitor (one that works as a nucleoside analog) more effective.

However, for mild to moderate, or early-stage Covid-19 patients, for whom steroids might not be appropriate, other Nsp14 inhibitors might be a better choice. Famotidine is only a mild inhibitor of Nsp14, but there are studies showing it may be effective against Covid-19 by other mechanisms of action. Curcumin is a strong Nsp14 inhibitor, and also effective at inhibiting other targets. Flavin adenine dinucleotide (FAD) might not be a viable treatment option as the body makes FAD and freely converts it into other molecules.

The best choices seem, at this point in time, to be dexamethasone MSB for severe or later stage patients, and for mild or early stage patients, hesperidin or curcumin might be used. Both of those compounds are only slightly soluble. Hesperidin is a not uncommon health supplement.

Proposed Studies

Hesperidin methyl chalcone (HMC) is sometimes used instead of hesperidin, as the former is highly soluble in water. A molecular docking study (unpublished) showed that HMC is a good inhibitor of several SARS-CoV-2 targets, including Spike, Mpro, N-protein, Nsp15, and ACE2. A new study is needed to determine if HMC might be effective against Nsp14, and to confirm the previously-described unpublished study.

A clinical trial to test Favipiravir with and without various NSP14 inhibitors is also proposed. The study should begin with a molecular docking study to consider the above NSP14 inhibitor candidates, and decide on 1 to 3 of them to test in a trial. Then the clinical trial would focus on moderate or early Covid-19 patients, and would have multiple arms:
1. Favipiravir alone
2. with Nsp14 inhibitor candidate A
3. with candidate B
4. with candidate C (optional)
5. placebo control

The placebo group should receive standard care, including other antivirals (those that are not nucleoside analogs). A similar study is proposed for Remdesivir, as it has a similar mechanism of action and many also benefit from combination with an NSP14 inhibitor.

Ronald L. Conte Jr.
Covid.us.org
Note: The author of this article is not a doctor, nurse, or healthcare provider, and this article does not offer medical advice.

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1. Khater, Shradha, Nandini Dasgupta, and Gautam Das. “Combining SARS-CoV-2 proofreading exonuclease and RNA-dependent RNA polymerase inhibitors as a strategy to combat COVID-19: a high-throughput in silico screen.” (2020).
PDF file

2. Arul, Murugan Natarajan, et al. “Searching for target-specific and multi-targeting organics for covid-19 in the drugbank database with a double scoring approach.” (2020).
PDF file

3. Wu, Canrong, et al. “Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods.” Acta Pharmaceutica Sinica B (2020).
Link to Study

4. Gupta, Parth Sarthi Sen, et al. “Molecular Mechanism of Clinically Oriented Drug Famotidine with the Identified Potential Target of SARS-CoV-2.”
PDF file

5. Anwar, Muhammad Umer, et al. “Combined Deep Learning and Molecular Docking Simulations Approach Identifies Potentially Effective FDA Approved Drugs for Repurposing Against SARS-CoV-2.” (2020).
PDF file

6. Mittal, Lovika, et al. “Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach.” Journal of Biomolecular Structure and Dynamics just-accepted (2020): 1-26.
Study Link

7. Utomo, Rohmad Yudi, and Edy Meiyanto. “Revealing the potency of citrus and galangal constituents to halt SARS-CoV-2 infection.” (2020).
PDF file

8. Manish, Manish. “Studies on computational molecular interaction between SARS-CoV-2 main protease and natural products.” (2020).
PDF file

9. Das, Sourav, et al. “An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study.” Journal of Biomolecular Structure and Dynamics just-accepted (2020): 1-18.
Study Link

10. Yong-Ming, Yan, et al. “Discovery of anti-2019-nCoV agents from 38 Chinese patent drugs toward respiratory diseases via docking screening.” Preprints (2020).
Study Link