PONE-D-20-34651

A comprehensive SARS-CoV-2 genomic analysis identifies potential targets for drug repurposing

PLOS ONE

Dear Dr. Pradhan,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

While one reviewer found it acceptable at the current form, the others found some concerning issues or misleading/vague/improvable sentences.

As suggested, please describe the docking results with hsp10-16 dimer, and refer to other phylogenetic studies instead of redoing them in this. 

In addition to what the reviewers have asked, please review the manuscript yourself and correct or fix anything that you think would improve the readers understanding with minimum navigation within the manuscript. You can add these as additional edits.

Please submit your revised manuscript by Jan 24 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Malaya Kumar Sahoo, Ph.D

Academic Editor

PLOS ONE

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https://www.biorxiv.org/content/10.1101/2020.10.30.362764v1

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

Reviewer #3: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: I Don't Know

Reviewer #3: No

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In this Manuscript Anand et al. provide the important findings such as identification of conserved genes and the drugs candidates to target the conserved genes. This approach of identifying stable genes and targeting stable genes with drugs would provide a better therapeutic approach and possible hope in the successive clinical trials.

The manuscript was well written, the experiments well designed, and the conclusions are appropriate. I believe that the findings of the manuscript are of sufficient novelty and breadth to merit publication in PLOS ONE.

Below are suggestions for minor revision of the manuscript:

1. Sentences are too long in the abstract section, I would like to recommend split the sentences in abstract.

One of the recent studies suggests the existence of three central variants of SARS-CoV-2 distinguished by amino acid changes 13. We urgently need therapeutic options to combat this virus infection.

2. The sentences above are important for the introduction part but it would sound better, if the authors can bring some coherence.

3. “This approach of targeting the stable genes for drug discovery would provide a better therapeutic approach and confidence in the successive clinical trials”.

Please check the bioavailability of the identified drugs (in plasma and organ tissues) whether the drug candidates has possible therapeutic efficacy at MTD drug doses. However I have no major concerns with this paper in its current form.

Reviewer #2: In the presented manuscript, Anand et al. authors performed a phylogenetic analysis of SASR-COV-2 variants to determine the most conserved region of the virus and performed a virtual screening against determined proteins FDA-approved drugs. Further, they performed molecular docking and determined the drugs Darifenacin, Nebivolol, Bictegravir, Alvimopan, and Irbesartan as the most promising candidates.

In the first part of the paper, the phylogenetic analyses are unnecessary and misleading. There is a number of high-quality publications (e.g. doi.org/10.1101/2020.04.17.046086 ., DOI: 10.1002/jmv.25902, DOI: 10.1002/jmv.25699) and publicly available resource for phylogenetic analysis of SARS-COV-2 variants https://nextstrain.org/. Therefore, to avoid controversial and unsupported conclusions of coronavirus's potential origin and transmission roads, I recommend focusing on virtual screening and docking of the FDA-approved drugs, presented in the second part of the manuscript.

With the modifications, the paper could be suitable for publication

Reviewer #3: This paper presents a very standard approach to both the phylogenetic analysis of SARS-CoV2 and the homology modeling building and virtual ligand screening. There are a number of issues that preclude publication in the following form:

1. The paper is disjoint. What insights does the phylogenetic analysis provide with respect to the drug repurposing aspect of the algorithm?

2.There are numerous technical and conceptual problems with the ligand screening/homology modeling. 25 ns or so simulations are too short to see significant structural changes. How were the the particular drugs chosen? What is the point of doing a Lipinski analysis on FDA approved drugs?

3. The paper targets nsp10. But nsp10 forms a complex with nsp16 which is likely to be a biologically relevant conformation. How does the dimer affect the putative ligand binding with nsp10? Why not simulate the dimer since there is a crystal structure of the nsp10/nsp16 complex?

4. What is the false positive rate of the docking approach that is used? How confident are the binding predictions?

5. The authors need to perform experimental validation that their predictions are correct.

Overall, this paper represents an incremental contribution to a very important and difficult problem.

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Reviewer #1: Yes: Raja Sab Kalluru

Reviewer #2: No

Reviewer #3: No

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PONE-D-20-34651R1

A comprehensive SARS-CoV-2 genomic analysis identifies potential targets for drug repurposing

PLOS ONE

Dear Dr. Pradhan,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

I went over your responses to the queries to the reviewers and agree that they have been addressed appropriately. The manuscript is basically acceptable.

However, I have the following additional suggestions to improve the palatability of the manuscript to broader reader base.  There is no  major change to the methodology, or interpretation of the results, or conclusions. 

@Abstract:

Plpro and 3CLpro : please use their common names NSP## in addition, and mark the second names in figure 1.

Please remove "a novel approach for drug targeting". This is the standard approach to design/develop new drugs.

Please remove " This approach of targeting the stable genes for drug discovery would provide a better therapeutic approach and confidence in the successive clinical trials. We also identified the

mutation frequencies across the viral genome". This is only a projection, and the mutation frequencies are used from other more comprehensive mutation tracking databases.

@heading :Viral clusters identified via haplotype network

Please add a statement at the end of this paragraph that, this haplotype network may be incomplete because of the origin of the sequences from specific regions. This limitation is intended to reflect that there might be more haplotypes in other parts of the world which are under-reported due to limited access to sequencing. Can you also add a rough date here representing the time of this analysis? Also in materials and methods. This will help the manuscript serve as a guide when the mutation landscape changes in future and someone tries to repeat the steps.

@"Nucleotide positions 240, 3036, 8781, 11082, 14407, 23402, 28143, with reference to NC_045512"

Please add the version number as NC_045512.2. And ensure that these numbers match to this specific version. The previous version had ~30 bases less, so the positions would be incorrect if those were the positions at the time of study. No correction needed if these numbers already come from the version 2.

@results section. I notice that the findings are arranged by the methods followed by the genes and drugs.

Root Mean Square Deviation (RMSD)

The radius of Gyration (Rg)

Intermolecular Hydrogen Bonding

Root Mean Square Fluctuations (RMSF)

Solvent Accessible Surface Area analysis (SASA)

While this approach is fine for those who have a deeper understanding over these methodologies, it is hard for broader reader-base to collate the information. I suggest you to re-arrange them by the gene/protein; then in each, one drug at a time, then describe all the finer aspects above (RMSD, Rg, IHB, RMSF, and SASA). There is no need to change the figures or numbering. That way, the first interaction would be more comprehensive with some brief information about the methods, then the remaining would be easier for the reader because of the same pattern of description. It also helps if someone wants to focus a specific gene or drug.

I believe this is increase the palatability of the manuscript..

Please submit your revised manuscript by Apr 09 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Malaya Kumar Sahoo, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: I Don't Know

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: I was satisfied with the corrections they have made. I have no major concerns with this paper in its current form.

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: raja sab kalluru

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

A comprehensive SARS-CoV-2 genomic analysis identifies potential targets for drug repurposing

PONE-D-20-34651R2

Dear Dr. Pradhan,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Malaya Kumar Sahoo, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: