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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'abstract': '<ns3:p>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 <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. The molecular quantum similarity and chemical '
'reactivity descriptors provide novel insights into these ligands that can be used in the '
'design of new COVID-19 treatments.</ns3:p>',
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