Identification of Potential Trypanosoma cruzi Trans-Sialidase Inhibitors by Computational Drug Repositioning Approaches

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I have reviewed the manuscript and would like to express some concerns and suggestions for improvement:

Minor Changes:

Abstract and Introduction: The statement “Through the enzyme trans-salidase, the parasite invades, infects, and multiplies intracellularly in the host cell” lacks precision. I suggest the authors be more specific and/or cite relevant studies to support this claim or change it accordingly.

Abstract: The phrase “represents an epidemiological in the world” is unclear. Is missing burden?

Line 186 and others: The energy value should be given as “Kcal/mole”.

Line 337. A potential anti-TS candidate in a TcTS-inactive form is a non-sense.

The statement, "Our in silico study predicts that a single compound can influence the enzymatic activity of TcTS in T. cruzi or a combination of these drugs," appears twice, in both the Discussion and Conclusion sections. However, this interpretation seems to overstate the results, which are purely predictive and lack empirical validation.

Major changes:

1. The clarity is lacking on whether the compounds chosen from the docking analysis interact with crucial residues that are known to facilitate the transfer of sialic acid, stabilize transition states, and adapt the lactosyl moiety to the donor/acceptor substrates. Elaborating on this could enhance the study’s robustness. It’s puzzling why the authors concentrated only on the four potential new hits yet omitted the analysis of the known drugs available in the market. Even more puzzling is the fact they do not focused only on those hits specifically found to interact with the active TS (in red in the Table).

2. The study's findings are rooted in in silico analysis, which, while intriguing, renders the study more speculative than definitive. It would be beneficial if the authors could corroborate their predictions with empirical data. Although testing the impact of potential drugs on cell cultures might need additional time and effort, assessing the influence of these drugs on TS activity in vitro could add to all those predictions, more value.

3. Clarify whether the hits found are sugar-based as it could have implications for the mechanism of action of these compounds.

 

Comments on the Quality of English Language

It is clear enough for me, a non-native english speaker. 

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

Uc-Chuc et al., present a virtual screening for novel theraputic agents against human trypanosomiasis. While the proposed target is compelling, the overall methodology relatively simple and straightforward.

Major comments

While the homology modelling is well conducted. I think that a more robust validation of the obtained is due. In addition, I ponder on the omission of other tools such as Robetta or Alphafold. This is not to say that SWISSMODEL is bad or something similar. Then again, for better or worse these tools have proven accuracy and pertinence in several contexts. Thus, the authors' insight in this regard would be appreciated.

Detailed description of the docking protocol and general process of pruning is needed.

Considering that one of the identified hits is peptidic in nature. It must be acknowledged that any derived result from it is dubious. Unless the protocol or selected software accounts for these difficulties.

Finally, as there is no experimental validation of any of the hits, the authors must provide further evidence. Molecular docking results by themselves are not enough, and this has been proved time and again by several studies. Therefore, a robust characterization using MM/PBSA would be a reasonable choice.

 

Minor comments

In section 4, the authors develop on the advantages and success cases of molecular docking. However, the chosen example is a very controversial one to say the least. While it is true that molecular modelling has proven to be a very powerful tool in the search for threapies against COVID-19. There is no denying that the literature was overflowed with fruitless results coming mostly from docking. Thus, I strongly suggest the omission of this example in favor of another.

 

 

 

Comments on the Quality of English Language

There are some long and/or confusing sentences. Please revise

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

This article covers the identification of potential Trypanosoma cruzi  trans-sialidase inhibitors by computational drug repositioning approaches and molecular docking. 

This specific strategy is designed to combat Chagas disease, for which there is no efficient treatment.  As this parasitic infection is exploiting trans-sialidase for infection and intracellular proliferation in the host cell, consequently this enzyme is logical target to combat the disease.

The potential inhibitors were developed by in silico analysis by computational drug repositioning approaches. Authors were able to identify 49 potential compounds to act as effective inhibitors.

This study constitutes crucially important developments, and accomplished the goals and novelty of this very important paper.

The compiled data are supported with 4 figures and 4 tables. Particularly important is Table 2 with identified compound and their inserted Lipinski’s rule of 5 data such as number of H-bond donors and H-Bond acceptors along with their structures. The article concludes with 49 very recent literature references.

 

The following suggested changes and recommendations should be introduced before the publication of the manuscript:

    •     Page 8, Table 3. Please insert the structures of five compounds in additional column on the right. 

• Page 12, Line 335. Replace “macromolecular” with real compound name. 

• Page 14, Line 415. Replace “analyzes” with “Analysis” 

• Page 14, Line 442. Insert the chemical name of “first” and “last” compounds. 

• Page 14, Line 433. Conclusions. This section must be expanded. In its present format, the authors do not fully describe the desired/anticipated effect of consolidated data. Authors should include comparative data of all analyzed compounds and highlight why their methodology proves to be the best tool to identify the best potential inhibitor. 

 

The manuscript is of good quality, well-written, and meets the standard for articles published in Scientia Pharmaceutica. I recommend it for publication after the correction of these minor suggested changes. 

Author Response

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Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

I have two comments to make:

1. When describes tran-sialidase bological function please include this reference. PMID: 35073735. It may provide the most up to date description of its activity and may force some rewritting of the ms. 

2. Why do the authors pick potential inhibitors, via docking, that would act on both inactive and active ones. I understand structures are pretty much similar but I doubt that compounds binding both structures woud block TS activity. So, interesting candidates to check would be the ones specific for the active TS not present in the inactive form. Since this is not explicit in the manuscript, I may be missing somehting. Please clarify it.

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

The work has been improved. Yet there are still some style and / or writing errors.

More importantly, I think that the addition of MD simulations is necessary. The presented protocol by itself is very presumptive, results solely based on docking are not encouraged in most journals.

Comments on the Quality of English Language

There are persisting issues in some of the wording or style.

Author Response

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Author Response File: Author Response.pdf

Round 3

Reviewer 2 Report

Comments and Suggestions for Authors

No further comment

Comments on the Quality of English Language

...

Author Response

Thank you very much for the comments/suggestions and for your valuable time to reviewing this manuscript entitled “Identification of potential Trypanosoma cruzi trans-sialidase inhibitors by computational drug repositioning approaches”.
Without a doubt, their support is very valuable because it improved the manuscript.