PCOMPBIOL-D-24-01488

Viral Escape-Inspired Framework for Precision Structure-guided Protein Biosensor Development

PLOS Computational Biology

Dear Dr. Chowdhury,

Thank you for submitting your manuscript to PLOS Computational Biology. After careful consideration, we feel that it has merit but does not fully meet PLOS Computational Biology'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.

Please submit your revised manuscript within 60 days Mar 25 2025 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 ploscompbiol@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pcompbiol/ 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 editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. This file does not need to include responses to formatting updates and technical items listed in the 'Journal Requirements' section below.

* 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, competing interests statement, or data availability statement, please make these updates within the submission form at the time of resubmission. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter

We look forward to receiving your revised manuscript.

Kind regards,

Claudio José Struchiner, M.D., Sc.D.

Academic Editor

PLOS Computational Biology

Arne Elofsson

Section Editor

PLOS Computational Biology

Additional Editor Comments:

The review process highlights the necessity for significant revisions in the methodology description, validation, and presentation to enhance clarity, reproducibility, and scientific rigor.

Journal Requirements:

1) We ask that a manuscript source file is provided at Revision. Please upload your manuscript file as a .doc, .docx, .rtf or .tex. If you are providing a .tex file, please upload it under the item type u2018LaTeX Source Fileu2019 and leave your .pdf version as the item type u2018Manuscriptu2019.

2) Please provide an Author Summary. This should appear in your manuscript between the Abstract (if applicable) and the Introduction, and should be 150-200 words long. The aim should be to make your findings accessible to a wide audience that includes both scientists and non-scientists. Sample summaries can be found on our website under Submission Guidelines:

https://journals.plos.org/ploscompbiol/s/submission-guidelines#loc-parts-of-a-submission

3) Please upload all main figures as separate Figure files in .tif or .eps format. For more information about how to convert and format your figure files please see our guidelines:

https://journals.plos.org/ploscompbiol/s/figures

4) We have noticed that you have uploaded Supporting Information files, but you have not included a list of legends. Please add a full list of legends for your Supporting Information files after the references list.

5) Please ensure that the funders and grant numbers match between the Financial Disclosure field and the Funding Information tab in your submission form. Note that the funders must be provided in the same order in both places as well.

- State the initials, alongside each funding source, of each author to receive each grant. For example: "This work was supported by the National Institutes of Health (####### to AM; ###### to CJ) and the National Science Foundation (###### to AM)."

- State what role the funders took in the study. If the funders had no role in your study, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.".

If you did not receive any funding for this study, please simply state: u201cThe authors received no specific funding for this work.u201d

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: Teoh et al have presented a manuscript that describes the mechanistic design of a high specificity biosensor protein. They describe use cases of 3 versions of differing versions of the program (CTRL-V) benchmarked against known experimental data on SARS-CoV-2 spike antigen, a monoclonal antibody, a human receptor and data from a DMS experiment and 30 circulating variants emerging from Spike. The manuscript covers the performance of the 3 iterations of the model in predicting true variants compared to false variants. CTRL-V-3 performs the best amongst the 3 when compared to these experimentally derived datasets and is beneficial in that it requires no training phase. I believe that this study is suitable for publication with the caveat, that this is not my exact field of expertise. The experimental design appears to be sound, although parts of the paper the relevance of the method should be clarified.

Reviewer #2: The paper shows a potential method that can be used to make a biosensor. However, I have following concerns and suggestions:

1. Is it safe to use the COVID-19 virus to construct a bio sensor (we hate the virus). Please justify this choice and state the measurement for guarantee the safety for the public.

2. Why the specific commercial LY-CoV1404 antibody is used, will other brand or other antibodies also fit in the method along with the framework?

3. Why only hydrophobicity is considered important here? Are there any other indexes that is also important?

4. The presentation of the entire paper needs a major modification, please separate the discussion on biological termed analysis (for biologist) with the method explanation used like integer optimization formulation (for engineer), and simulation procedures (for programmer) as well.

5. It looks the entire paper is comparing pro and con for the gradually improved platforms, from which, the reader can neither gain inside of the virus mutation escaping antibody, nor the inside of a potential flexible sensor design, or the appreciation of the accuracy of the Python model.

5. Please explain the importance of electrostatic contact, how it is compared with hydrophobicity?

6. Please number all the formulae.

7. Why there are a number of 0% in the simulation table, is it caused by the particular virus sequence or computer code/model design?

Reviewer #3: Recommendations to Authors

Highlight Novelty: Emphasize how CTRL-V differs from existing escape-prediction and biosensor design frameworks. Include quantitative comparisons to establish its advantage.

Enhance Methodological Clarity: Provide detailed descriptions of integer programming, PyRosetta, and ProteinMPNN steps. Ensure all methods are reproducible by detailing parameter choices and workflow configurations.

Improve Validation:

Strengthen computational validation by comparing CTRL-V outputs with experimental datasets from other viral escape studies or biosensor applications.

Consider including wet-lab validation to support computational predictions.

Focus on Presentation:

Use clearer, high-resolution images for structural results and create more descriptive legends.

Reorganize tables to facilitate comparisons across CTRL-V versions.

Expand Generalizability: Provide examples or mock results to demonstrate CTRL-V's potential applications beyond SARS-CoV-2.

Address Scalability: Discuss computational resource requirements and how CTRL-V can be scaled or optimized for broader adoption.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

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: No

Reviewer #2: Yes:  Jun Steed Huang

Reviewer #3: No

[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.]

Figure resubmission:

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. If there are other versions of figure files still present in your submission file inventory at resubmission, please replace them with the PACE-processed versions.

Reproducibility:

To enhance the reproducibility of your results, we recommend that authors of applicable studies deposit laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Dear Mr Chowdhury,

We are pleased to inform you that your manuscript 'Viral Escape-Inspired Framework for Precision Structure-guided Dual Bait Protein Biosensor Development' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Claudio José Struchiner, M.D., Sc.D.

Academic Editor

PLOS Computational Biology

Arne Elofsson

Section Editor

PLOS Computational Biology

***********************************************************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #2: Good revision.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

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 #2: Yes:  Jun Steed Huang