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New findings on ligand series used as SARS-CoV-2 virus inhibitors within the frameworks of molecular docking, molecular quantum similarity and chemical reactivity indices

Morales-Bayuelo et al., F1000Research, doi:10.12688/f1000research.123550.3

Dec 2023

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Vitamin C for COVID-19

6th treatment shown to reduce risk in September 2020, now with p = 0.00000002 from 73 studies, recognized in 12 countries.

Lower risk for mortality, ICU admission, hospitalization, and recovery.

No treatment is 100% effective. Protocols combine treatments.

5,100+ studies for 109 treatments. c19early.org

In Silico analysis showing that vitamin C can stably bind within the SARS-CoV-2 RNA-dependent RNA polymerase binding pocket. Notable stabilizing interactions were seen between vitamin C and residue lysine 621, similar to the antiviral remdesivir.

14 preclinical studies support the efficacy of vitamin C for COVID-19:

6 In Silico studies1-6

7 In Vitro studies5,7-12

1 In Vivo animal study10

Vitamin C has been identified by the European Food Safety Authority (EFSA) as having sufficient evidence for a causal relationship between intake and optimal immune system function13-15. Vitamin C plays a key role in the immune system, supporting the production and function of leukocytes, or white blood cells, which defend against infection and disease, including the production of lymphocytes, which make antibodies, and enhancing phagocytosis, the process by which immune system cells ingest and destroy viruses and infected cells. Vitamin C is an antioxidant, protecting cells from damage caused by free radicals. Vitamin C inhibits SARS-CoV-2 3CL^pro5,9, inhibits SARS-CoV-2 infection by reducing ACE2 levels in a dose-dependent manner10, and may limit COVID-19 induced cardiac damage by acting as an antioxidant and potentially reducing the reactive oxygen species (ROS) production induced by the spike protein that contributes to the activation of profibrotic pathways16. Vitamin C reduces inflammation, oxidative stress, and NETosis, supporting immune function and vascular protection17. Intracellular levels of vitamin C decline during COVID-19 hospitalization suggesting ongoing utilization and depletion of vitamin C18. Threonic acid, a metabolite of vitamin C, is lower in mild and severe cases, consistent with increased need for and metabolization of vitamin C with moderate infection, but more limited ability to produce threonic acid in severe infection due to depletion or existing lower levels of vitamin C19. Symptomatic COVID-19 is associated with a lower frequency of natural killer (NK) cells, and vitamin C has been shown to improve NK cell numbers and functioning20,21.

Important missing comments or errors? Let us know.

Study covers vitamin D and vitamin C.

1. Agamah et al., Network-based multi-omics-disease-drug associations reveal drug repurposing candidates for COVID-19 disease phases, ScienceOpen, doi:10.58647/DRUGARXIV.PR000010.v1.scienceopen.com, doi.org.

2. Morales-Bayuelo et al., New findings on ligand series used as SARS-CoV-2 virus inhibitors within the frameworks of molecular docking, molecular quantum similarity and chemical reactivity indices, F1000Research, doi:10.12688/f1000research.123550.3.f1000research.com, doi.org.

3. Alkafaas et al., A study on the effect of natural products against the transmission of B.1.1.529 Omicron, Virology Journal, doi:10.1186/s12985-023-02160-6.biomedcentral.com, doi.org.

4. Pandya et al., Unravelling Vitamin B12 as a potential inhibitor against SARS-CoV-2: A computational approach, Informatics in Medicine Unlocked, doi:10.1016/j.imu.2022.100951.sciencedirect.com, doi.org.

5. Malla et al., Vitamin C inhibits SARS coronavirus-2 main protease essential for viral replication, bioRxiv, doi:10.1101/2021.05.02.442358.biorxiv.org, doi.org.

6. Kumar et al., In silico virtual screening-based study of nutraceuticals predicts the therapeutic potentials of folic acid and its derivatives against COVID-19, VirusDisease, doi:10.1007/s13337-020-00643-6.springer.com, doi.org.

7. Van Tin et al., Spike Protein of SARS-CoV-2 Activates Cardiac Fibrogenesis through NLRP3 Inflammasomes and NF-κB Signaling, Cells, doi:10.3390/cells13161331.mdpi.com, doi.org.

8. Moatasim et al., Potent Antiviral Activity of Vitamin B12 against Severe Acute Respiratory Syndrome Coronavirus 2, Middle East Respiratory Syndrome Coronavirus, and Human Coronavirus 229E, Microorganisms, doi:10.3390/microorganisms11112777.mdpi.com, doi.org.

9. Đukić et al., Inhibition of SARS-CoV-2 Mpro with Vitamin C, L-Arginine and a Vitamin C/L-Arginine Combination, Frontiers in Bioscience-Landmark, doi:10.31083/j.fbl2801008.imrpress.com, doi.org.

10. Zuo et al., Vitamin C promotes ACE2 degradation and protects against SARS‐CoV‐2 infection, EMBO reports, doi:10.15252/embr.202256374.wiley.com, doi.org.

11. Hajdrik et al., In Vitro Determination of Inhibitory Effects of Humic Substances Complexing Zn and Se on SARS-CoV-2 Virus Replication, Foods, doi:10.3390/foods11050694.mdpi.com, doi.org.

12. Goc et al., Inhibitory effects of specific combination of natural compounds against SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants, European Journal of Microbiology and Immunology, doi:10.1556/1886.2021.00022.akjournals.com, doi.org.

13. Galmés et al., Suboptimal Consumption of Relevant Immune System Micronutrients Is Associated with a Worse Impact of COVID-19 in Spanish Populations, Nutrients, doi:10.3390/nu14112254.mdpi.com, doi.org.

14. Galmés (B) et al., Current State of Evidence: Influence of Nutritional and Nutrigenetic Factors on Immunity in the COVID-19 Pandemic Framework, Nutrients, doi:10.3390/nu12092738.mdpi.com, doi.org.

15. EFSA, Scientific Opinion on the substantiation of health claims related to vitamin C and protection of DNA, proteins and lipids from oxidative damage (ID 129, 138, 143, 148), antioxidant function of lutein (ID 146), maintenance of vision (ID 141, 142), collagen formation (ID 130, 131, 136, 137, 149), function of the nervous system (ID 133), function of the immune system (ID 134), function of the immune system during and after extreme physical exercise (ID 144), non-haem iron absorption (ID 132, 147), energy-yielding metabolism (ID 135), and relief in case of irritation in the upper respiratory tract (ID 1714, 1715) pursuant to Article 13(1) of Regulation (EC) No 1924/2006, EFSA Journal, doi:10.2903/j.efsa.2009.1226.europa.eu, doi.org.

16. Van Tin (B) et al., Spike Protein of SARS-CoV-2 Activates Cardiac Fibrogenesis through NLRP3 Inflammasomes and NF-κB Signaling, Cells, doi:10.3390/cells13161331.mdpi.com, doi.org.

17. Xie et al., The role of reactive oxygen species in severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infection-induced cell death, Cellular & Molecular Biology Letters, doi:10.1186/s11658-024-00659-6.biomedcentral.com, doi.org.

18. Boerenkamp et al., Low Levels of Serum and Intracellular Vitamin C in Hospitalized COVID-19 Patients, Nutrients, doi:10.3390/nu15163653.mdpi.com, doi.org.

19. Albóniga et al., Differential abundance of lipids and metabolites related to SARS-CoV-2 infection and susceptibility, Scientific Reports, doi:10.1038/s41598-023-40999-5.nature.com, doi.org.

20. Graydon et al., High baseline frequencies of natural killer cells are associated with asymptomatic SARS-CoV-2 infection, Current Research in Immunology, doi:10.1016/j.crimmu.2023.100064.sciencedirect.com, doi.org.

21. Vojdani et al., In vivo effect of ascorbic acid on enhancement of human natural killer cell activity, Nutrition Research, doi:10.1016/S0271-5317(05)80799-7.sciencedirect.com, doi.org.

Morales-Bayuelo et al., 11 Dec 2023, peer-reviewed, 2 authors. Contact: amorales@unisinucartagena.edu.co.

In Silico studies are an important part of preclinical research, however results may be very different in vivo.

This Paper Vitamin C All

New findings on ligand series used as SARS-CoV-2 virus inhibitors within the frameworks of molecular docking, molecular quantum similarity and chemical reactivity indices

Alejandro Morales-Bayuelo, Jesús Sánchez-Márquez

F1000Research, doi:10.12688/f1000research.123550.1

Background The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 virus causes an infectious illness named coronavirus disease 2019 (COVID-19). SARS-CoV is a positive-sense single-stranded RNA virus from the Betacoronavirus genus. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) has an important role in the viral life cycle and its active site is a very accessible region, thus a potential therapeutic approach may be to target this region to study the inhibition of viral replication. Various preexisting drugs have been proposed for the treatment of COVID-19 and the use of existing antiviral agents may reduce the time and cost of new drug discoveries, but the efficacy of these drugs is limited. Therefore, the aim of the present study was to evaluate a number of ligands used as SARS-CoV-2 virus inhibitors to determine the suitability of them for potential COVID-19 treatment. Methods In this study, we selected a series of ligands used as SARS-CoV-2 virus inhibitors such as: abacavir, acyclovir, amprenavir, ascorbic acid vitamin C, azithromycin, baloxavir, boceprevir, cholecalciferol vitamin D, cidofovir, edoxudine, emtricitabine, hydroxychloroquine and

Open Peer Review Is the study design appropriate and is the work technically sound? Yes Are sufficient details of methods and provided to allow replication by others? Yes If applicable, is the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required. Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Partly Competing Interests: No competing interests were disclosed. Reviewer Expertise: Computational chemistry; DFT; Nanotechnology; Docking simulation I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Author Response 17 Jul 2023 Alejandro Morales-Bayuelo 1. What are the novelties of the manuscript? What's new in this manuscript compared to similar papers? Answer: There is currently no effective treatment for Covid-19. Therefore, there are a series of drugs such as those listed in this article that have been used for the treatment of this disease, however they have not been associated as solutions for covid-19. That is why carrying out studies that show that the drugs used are directly related to the Covid-19 proteins is pertinent. 2. The introduction section should be written in a higher quality way, i.e. more up-to-date references. The..

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SARS-CoV is a positive-sense ' 'single-stranded RNA virus from the <ns3:italic>Betacoronavirus</ns3:italic> genus. The ' 'SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) has an important role in the viral life cycle ' 'and its active site is a very accessible region, thus a potential therapeutic approach may be ' 'to target this region to study the inhibition of viral replication. Various preexisting drugs ' 'have been proposed for the treatment of COVID-19 and the use of existing antiviral agents may ' 'reduce the time and cost of new drug discoveries, but the efficacy of these drugs is limited. ' 'Therefore, the aim of the present study was to evaluate a number of ligands used as ' 'SARS-CoV-2 virus inhibitors to determine the suitability of them for potential COVID-19 ' 'treatment. Methods In this study, we selected a series of ligands used as SARS-CoV-2 virus ' 'inhibitors such as: abacavir, acyclovir, amprenavir, ascorbic acid vitamin C, azithromycin, ' 'baloxavir, boceprevir, cholecalciferol vitamin D, cidofovir, edoxudine, emtricitabine, ' 'hydroxychloroquine and remdesivir. These ligands were analyzed using molecular docking, ' 'molecular quantum similarity, and chemical reactivity indices defined within a conceptual ' 'density functional theory framework. Results The analysis of molecular quantum similarity ' 'indices on inhibitors showed a high number of differences from a structural point of view. ' 'However, they are quite similar in their electronic density, obtaining the highest values in ' 'the electronic similarity index. Global and local chemical reactivity indices were analyzed. ' 'Conclusions These studies allowed for the identification of the main stabilizing interactions ' 'using the crystal structure of SARS-CoV-2 RdRp. 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The ' 'funders had no role in study design, data collection and analysis, decision to ' 'publish, or preparation of the manuscript.', 'order': 1, 'name': 'grant-information', 'label': 'Grant Information'}, { 'value': 'This is an open access article distributed under the terms of the Creative ' 'Commons Attribution Licence, which permits unrestricted use, distribution, and ' 'reproduction in any medium, provided the original work is properly cited.', 'order': 0, 'name': 'copyright-info', 'label': 'Copyright'}]}

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