Repurposing of Four Drugs as Anti-SARS-CoV-2 Agents and Their Interactions with Protein Targets

Round 1

Reviewer 1 Report

The manuscript ID scipharm-1618222 entitled "Repurposing of four drugs as anti- SARS-CoV-2 and their interaction with protein targets" is a good study. The summary of the study expresses that existing vaccines against SARS-CoV-2, new COVID 19 cases are increasing due to low immunization coverage and the emergence of new variants. For this reason, new drugs to treat and prevent severe COVID-19 are needed. Here we provided four different FDA-approved drugs against SARS-CoV-2 proteins involved in the entry and replication process, aiming to identify potential drugs to treat COVID-19 disease. We use the main protease (Mpro), spike glycoprotein (S protein), and RNA-dependent RNA polymerase (RdRp) as protein targets for anti- SARS-CoV-2 drugs. Within our constructed database, drugs mainly used to treat cancers, HIV, malaria, and others are included. Besides, a review of previously predicted drugs against SARS-CoV-2 is shown. From these, we show 31 drugs that are predicted to work against COVID-19 infection; moreover, we selected different drugs against each target (Mpro, S protein, and RdRp) based on their common interactions with relevant residues involved in viral entry at host cell and replication. Furthermore, their stability inside the binding pocket, as well as their predicted free binding energy, allow us to provide new insight into the possible drug repurposing of viomycin (interacting with S-protein), elvitegravir (interacting with Mpro), nystatin, and hesperidin (interacting with RdRp) to inhibit the viral life cycle of SARS-CoV-2 and some of its variants of concern (VOC). However, the following points need to be addressed,

1. The abstract lack key results of the study. The authors may revise it accordingly.
2. What is the ratio of selecting three different proteins? why not all the proteins? how about ACE2 and TMPRSS2?
3. The subsection "Visualization" instead of "Figures"
4. In figures 2, 5, 10; how the frequency was calculated for the different interaction types? is there any reference?
5. In figures 2F, 5F, 10F, is it RMSD of ligand or complex? What are R1, R2, and R3?
6. The discussion and conclusion needs to be improved

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

VDP- Revision comments

Article

Repurposing of four drugs as anti- SARS-CoV-2 and their in-2 teraction with protein targets

In this research article, Vesga et al. detect four antiviral drugs as anti-SARS-CoV-2: viomycin (interacting with S-protein), hesperidin (interacting with Mpro), nystatin and elvitegravir (interacting with RdRp) to treat COVID-19 including new emerging SARS-CoV-2 variants.

The research item is clearly explained, the methodology is well stated in line with other similar computational pharmacology studies and the results were reported and discussed properly. I have only minor comments and one issue that it is of interest to discuss.

Minor comments:

-           It's unclear in the abstract if the selection of 31 and after 4 drugs of interest was performed choosing among the drugs mainly used to treat cancers, HIV, malaria and others previously predicted drugs against SARS-CoV-2 or only from one of these drug collection. At the same time, it’s unclear in the abstract if the final selection of 4 drugs anti-SARS-CoV-2 is derived by the results about the interactions with relevant residues involved in viral entry at host cell and replication and/or by the stability inside the binding pocket, as well as by their predicted free binding energy. Please, I suggest to reframe these sentence to improve their meaning.

-           In the line 50, I suggest to change “The” with “the” and in the line 51 to remove “of SARS-CoV and”.

-           In the line 200, it was reported a docking scores -10.319 and -74.39 Kcal/mol but in the table 1 was reported -10.319 and -74.63 Kcal/mol. In addition, it will be more clear to specify that -10.319 is docking score and -74,.. is free binding energy. Similar errors were observed in the lines 256-257. Please you to check about this in the all text.

-           In the line 445 and 468, please you correct “Addiottionally…”.

It may be of interest to discuss if there are or are not clinical trials ongoing or pubblished case report about these drugs of interest.

Comments for author File: Comments.pdf

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

The authors have conducted in silico analyses via molecular docking and molecular dynamics to investigate the potential binding interactions and stability between different, potential inhibitors against proteins vital for complete replication of SARS-CoV-2. While this study provides useful information to predict the efficacies of possible inhibitors targeting specific SARS-CoV-2 proteins, this study lack novelty as several inhibitors focused in this manuscript have been studied in the past. The following are my comments on this manuscript:

1) Why were specific compounds which did not exhibit the most promising molecular docking scores in this study, selected for further investigation via molecular dynamics and given a more focused discussion in the manuscript? What do they provide that makes them more interesting to be studied in comparison with the other listed compounds? Eg. Viomycin, Hesperidin, Nystatin and Elvitegravir were not the best performing compounds in their respective sets of experiments. 

2) In silico study including molecular docking and molecular dynamics simulation have been reported in the past for viomycin against SARS-CoV-2 Mpro, hence the findings reported here lack novelty.

Mahanta, Saurov, Purvita Chowdhury, Neelutpal Gogoi, Nabajyoti Goswami, Debajit Borah, Rupesh Kumar, Dipak Chetia, Probodh Borah, Alak K. Buragohain, and Bhaskarjyoti Gogoi. "Potential anti-viral activity of approved repurposed drug against main protease of SARS-CoV-2: an in silico based approach." Journal of Biomolecular Structure and Dynamics 39, no. 10 (2021): 3802-3811.

3) Although the molecular docking and molecular dynamics simulation in this study showed promising findings on hesperidin, the similar compound has been shown via in vitro enzymatic assay and pseudovirus system to be ineffective in suppressing the interaction between the virus S protein and ACE2. In general, in vitro findings are more conclusive than in silico predictions.

Cheng, Fang-Ju, Thanh-Kieu Huynh, Chia-Shin Yang, Dai-Wei Hu, Yi-Cheng Shen, Chih-Yen Tu, Yang-Chang Wu et al. "Hesperidin is a potential inhibitor against SARS-CoV-2 infection." Nutrients 13, no. 8 (2021): 2800.

4) Line 359: I do not see the significance of ref# 95 with SARS-CoV-2 studies.

5)  Line 143-144: Reference(s) need to be added regarding the parameters used to generate the docking box for remdesivir.

6) Line 184: "Variant of concern" was misspelled.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Accept after minor revision (corrections to minor methodological errors and text editing)

Author Response

We want to thank the reviewer.
We checked the methodology and corrected mistype.

Reviewer 3 Report

The authors have addressed my concerns and made the necessary ammendments. However, there are some sentences which need to be restructured to better portray the authors' actual idea.

Page 15: Since N3 derivatives that interact with these residues have higher inhibitory activity compared with N3

Page 26: Due to the hesperidin interactions with relevant residues involved in SARS-CoV-2 entry within the host cells mediated by interaction with the ACE2 and TMPRSS2 receptors as shown by Cheng et al.,2021[97]

Author Response

The authors have addressed my concerns and made the necessary ammendments. However, there are some sentences which need to be restructured to better portray the authors' actual idea.

Page 15: Since N3 derivatives that interact with these residues have higher inhibitory activity compared with N3

We changed the sentence to “similar to shown by N3 derivatives, which have higher inhibitory Mpro activity compared with N3”.

Page 26: Due to the hesperidin interactions with relevant residues involved in SARS-CoV-2 entry within the host cells mediated by interaction with the ACE2 and TMPRSS2 receptors as shown by Cheng et al.,2021[97]

We changed the sentence to “Due to hesperidin interacting with relevant residues involved in SARS-CoV-2 infection mediated by interaction with the ACE2 and TMPRSS2 receptors, as shown by Cheng et al.,2021[97], we evaluated the hesperidin stability in the proposed pocket by molecular dynamics simulation”.

We thank the reviewer for all suggestions to improve this manuscript.