PONE-D-24-33214Immunoinformatic Strategy for Developing Multi-Epitope Subunit Vaccine Against Helicobacter pyloriPLOS ONE

Dear Dr. Nahian,

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.

The study presents valuable insights, but to further strengthen the findings, I recommend conducting molecular dynamics (MD) simulations of at least 100 ns using the GROMACS platform. This extended simulation will offer deeper insights into the stability and interactions of the studied complexes. Additionally, a more comprehensive analysis of the simulation data should be included, such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (RG), principal component analysis (PCA), and binding free energy calculations using MM/PBSA. These analyses will provide a more detailed evaluation of the system's behavior.

Moreover, the reviewers have recommended that the authors enhance the analysis of the MD simulations to better support the manuscript's conclusions. It may be beneficial for the authors to extend their study, either through potential collaboration or by adopting similar methodologies. This enhancement could lead to a more thorough understanding and provide stronger validation of the molecular dynamics results presented.

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Abu Tayab Moin

Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

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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: No

Reviewer #2: Partly

Reviewer #3: Yes

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

Reviewer #1: No

Reviewer #2: N/A

Reviewer #3: Yes

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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: No

Reviewer #2: Yes

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: No

Reviewer #2: No

Reviewer #3: Yes

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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: Thank you for the opportunity to review the manuscript. The work presented is of high quality and addresses an important area of research. However, after careful consideration, I regret to inform you that the manuscript, in its current form, is not suitable for publication in PLOS ONE.

Comments:

Docking and Dynamics Simulations:

The manuscript presents docking and dynamics simulation studies that are critical to the conclusions drawn. However, the current simulation is limited and lacks the extensive analysis required for robust conclusions. To strengthen the study, I recommend performing molecular dynamics (MD) simulations of at least 200 ns using the GROMACS platform. This extended simulation will provide deeper insights into the stability and interactions of the studied complexes. Additionally, more comprehensive analyses of the simulation data, such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and binding free energy calculations using MM/PBSA, should be included.

Data Interpretation and Analysis:

While the results presented are interesting, the interpretation of the data could be improved. The authors should provide a more detailed discussion of how the results from the extended simulations support the conclusions. This should include a comparison with existing literature and a clear explanation of the relevance of the findings.

I am sorry to deliver this decision, but please do not be discouraged. Your work is valuable, and with the suggested enhancements, I am confident it will find a suitable publication outlet.

Reviewer #2: 1. In the methods section, the authors should briefly explain the algorithms used in the used servers

2. The authors should perform disulfide engineering of the vaccine construct

3. In the manuscript, the authors should provide a logical reason for using this type of linkers in the structure of the vaccine by citing a valid reference.

4. . The authors should present the results of the "Molecular Dynamic Simulation" and "Immune Simulation" sections in more detail.

5. The authors should further discuss why the current vaccine constructs is more advantageous than the previous ones. How do you see the future steps for your vaccine? What are your next planned steps? Add a discussion regarding the next needed steps, Limitation, and etc.?

6. Please provide the MM-PBSA calculations of the simulated trajectory.

7. Please explain why you selected the pET28a plasmid for cloning your vaccine construct.

8. Please revise the English language of your manuscript.

9. For the richness of the article, the authors should compare their study with other vaccine design studies. For this, the authors please use the following studies and cite them.

https://doi.org/10.2174/1573409919666230612125440

https://doi.org/10.1080/07391102.2023.2258403

https://doi.org/10.1007/s12033-023-00949-y

https://doi.org/10.1016/j.ijbiomac.2024.131517

Reviewer #3: Reviewer’s Feedback to the Authors:

I have had the opportunity to review the study titled " Immunoinformatic Strategy for Developing Multi-Epitope Subunit Vaccine Against Helicobacter pylori", (Manuscript Number: PONE-D-24-33214). This study describes a comprehensive immunoinformatic strategy that targets the BabA, CagA, and VacA proteins in order to create a multi-epitope subunit vaccine against Helicobacter pylori. The study is well-done; it employs a variety of computational techniques to assess the vaccine's population coverage, antigenicity, allergenicity, and binding interactions with human TLRs. The work has a lot of potential to advance the H. pylori vaccine field. However, there are a few places in which the paper may be improved with more clarification, data visualization.

1. There are some minor grammatical errors and awkward phrasings throughout the manuscript. For instance, the sentence "this bacterium has successfully adapted to survive in the highly acidic environment" (Introduction) could be rephrased for clarity. A thorough proofread is recommended.

2. The methods section provides detailed computational analyses, but it can be overwhelming due to the technical density. Consider streamlining the descriptions of the servers and algorithms used to focus on the key aspects of the workflow, or placing detailed descriptions of the tools in supplementary materials.

3. In the methodology a flowchart summarizing the vaccine design and evaluation pipeline could significantly enhance understanding for readers unfamiliar with immunoinformatics approaches.

4. However, the presentation of the simulation data (Figure 10) could be improved. It would be beneficial to provide more detailed insights into the immune responses, particularly regarding the longevity of immune memory and the balance between humoral and cell-mediated responses.

5. Some figures (such as Figures 7 and 8 on molecular docking) are highly technical. Consider adding explanatory captions to make the data more accessible to a broader audience. In particular, explaining what the negative ΔG values represent in practical terms would be helpful.

6. The picture quality should be improved.

7. Table 1 (epitope predictions) contains important data, but the layout could be clearer. Grouping the data more effectively (e.g., by protein or epitope type) might improve readability.

This manuscript provides a valuable contribution to H. pylori vaccine research through a robust immunoinformatic framework. With minor revisions to improve clarity, data presentation, and additional discussions on experimental validation, this work could make a substantial impact in the field. After addressing these concerns, the manuscript would likely be suitable for publication in PLOS ONE.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes: Shahina Akter, PhD

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Submitted filename: 5.Reviewer-comments to the author-Plos one.docx

Immunoinformatic Strategy for Developing Multi-Epitope Subunit Vaccine Against Helicobacter pylori

PONE-D-24-33214R1

Dear Dr. Acharjee,

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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If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Abu Tayab Moin

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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 #2: All comments have been addressed

Reviewer #3: 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 #2: Yes

Reviewer #3: (No Response)

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

Reviewer #2: N/A

Reviewer #3: Yes

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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 #2: Yes

Reviewer #3: Yes

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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 #2: Yes

Reviewer #3: Yes

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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 #2: All comments have been considered correctly and I hope this article will be used by many researchers.

Reviewer #3: I am pleased to recommend that the research article titled “Immunoinformatic Strategy for Developing Multi-Epitope 1 Subunit Vaccine Against Helicobacter pylori" to be accepted after the second round of review. The authors made the necessary corrections. The manuscript is now much clearer and better organized, particularly with the added of experimental design with flowchart. They explained all the queries that were asked in the review. The manuscript provides a stronger foundation by incorporating relevant recent studies, which enhances the context of this new species' discovery. Additionally, the expanded methods section improves reproducibility, especially with the clarification on the changes they had made. Overall, this version is greatly improved, and I believe it is nearing readiness for publication.

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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 #2: No

Reviewer #3: Yes: Shahina Akter, Ph.D

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Attachments

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Submitted filename: Reviewer-comments-docx.docx