In Silico Analysis of the Multi-Targeted Mode of Action of Ivermectin and Related Compounds

Round 1

Reviewer 1 Report

Here my counter-responses to the authors:

1) We modified the manuscript to meet the suggestions of the referee.

I have not seen any changes. The "Keywords" section is the same of the first version of the paper as for uppercase and lowercase letters. Several acronyms are still not expanded (SARS-CoV-2, ACE2, SPR, Co-IP, ELISA, MERS, TNF, IL-1, Ach, and so on), and there are other various typos [e.g.: "CA++" (line 136)]. The whole manuscript still needs a revision in this sense because as it stands it is not scientifically acceptable.

2) We appreciate the reviewer’s suggestion, but we kindly disagree with just this point. Consideration of Lipinski’s rule is standard in molecular modeling studies, and this paragraph was quite short. Paragraph 3.5 is relevant because if SARS-CoV-2 spike protein binds strongly to the α7nAChr receptor, given the indicated viral pathologies that could result, then the indicated binding of Ivermectin to α7nAChr could competitively inhibit those spike-α7nAChr bindings and alleviate those pathologies.

I apologize to the authors: rereading it, the paragraph 3.4 is certainly of interest for the reader. I remain somehow convinced that 3.5 is not necessary, but if the authors think it is useful for a better understanding of the research, then it is fine for me too.

Author Response

Reviewer#1

We thank the reviewer for the constructive feedback. We considered the feedback from the reviewer in detail and further improved the paper as the reviewer suggested. Our detailed responses to the comments and questions are below.

I have not seen any changes. The "Keywords" section is the same of the first version of the paper as for uppercase and lowercase letters. Several acronyms are still not expanded (SARS-CoV-2, ACE2, SPR, Co-IP, ELISA, MERS, TNF, IL-1, Ach, and so on), and there are other various typos [e.g.: "CA++" (line 136)]. The whole manuscript still needs a revision in this sense because as it stands it is not scientifically acceptable.

Answer: We modified the Keywords part and we used uppercase for all of them.

“Keywords: Alpha-7 nicotinic receptor; CD147; Docking; Ivermectin; Molecular modeling; SARS CoV-2”

We added many entries to the abbreviations table per reviewer’s note. There are so many acronyms used in this paper, and many are well-known, and we didn’t want to make it too cumbersome by also inserting every definition in parentheses after first usage, and thus we didn’t add those also for most of the new abbreviation entries added.

Here is the new abbreviation table:

2) I apologize to the authors: rereading it, the paragraph 3.4 is certainly of interest for the reader. I remain somehow convinced that 3.5 is not necessary, but if the authors think it is useful for a better understanding of the research, then it is fine for me too.

Answer:

We appreciate the reviewer’s understanding and we would like to keep part 3.5 if it is OK for her/him.

Reviewer 2 Report

It is a complex research that is based on extensive documentation.

Ivermectin is a compound that has been used in some forms of infection caused by SARS-CoV-2, but it is not an ideal medicine.

But the research undertaken aims to elucidate the mode of action of ivermectin and related compounds.

In my opinion, some additions are needed; for example:

- for a better understanding, in subchapter 1.5 the explanations should also be accompanied by a suggestive image.

- in the case of experimental research, no conclusions resulting from the bibliographic data will be submitted.

I agree with the publication of the article with minor revision.

Author Response

Reviewer#2

It is a complex research that is based on extensive documentation. Ivermectin is a compound that has been used in some forms of infection caused by SARS-CoV-2, but it is not an ideal medicine. But the research undertaken aims to elucidate the mode of action of ivermectin and related compounds.

In my opinion, some additions are needed; for example:

1) for a better understanding, in subchapter 1.5 the explanations should also be accompanied by a suggestive image.

Answer: We added a new figure to subchapter 1.5 as Figure 1 to elaborate on the structure of spike protein.

Figure 1 (A, B) Side view of SARS-CoV-2 spike protein trimer, open (PDB: 6VSB) and closed (PDB: 6VXX) configurations, respectively. (C) Spike protein monomer color coded by subdomain. (D) Sequence of full-length spike protein with domain assignments, with N-terminal end to the left and C-terminal (stalk) end to the right. (E) N-linked glycans are shown, localized in the schematic representation by arrows, for the NTD and RBD domains only. (F) A key to the monosaccharides depicted in (E). C-E are from Aminpour et al., 2021 [1], used with permission; added glycan representations in E and the glycan key, F, are from Sikora et al., 2021 [2] (CC-BY 4.0).

2) in the case of experimental research, no conclusions resulting from the bibliographic data will be submitted.

Answer:

We removed this sentence from conclusions: “, which agrees with in vitro experimental results obtained with chick and human cells [3]”

I agree with the publication of the article with minor revision.

1. Aminpour, M.; Cannariato, M.; Zucco, A.; Di Gregorio, E.; Israel, S.; Perioli, A.; Tucci, D.; Rossi, F.; Pionato, S.; Marino, S., et al. Computational Study of Potential Galectin-3 Inhibitors in the Treatment of COVID-19. Biomedicines 2021, 9, 1208.
2. Sikora, M.; von Bülow, S.; Blanc, F.E.C.; Gecht, M.; Covino, R.; Hummer, G. Computational epitope map of SARS-CoV-2 spike protein. PLOS Computational Biology 2021, 17, e1008790, doi:10.1371/journal.pcbi.1008790.
3. Krause, R.M.; Buisson, B.; Bertrand, S.; Corringer, P.J.; Galzi, J.L.; Changeux, J.P.; Bertrand, D. Ivermectin: a positive allosteric effector of the alpha7 neuronal nicotinic acetylcholine receptor. Mol Pharmacol 1998, 53, 283-294, doi:10.1124/mol.53.2.283.