In silico EsxG EsxH rational epitope selection: Candidate epitopes for vaccine design against pulmonary tuberculosis

Constanza Estefania Martinez-Olivares; Rogelio Hernández-Pando; Edgar Mixcoha

doi:10.1371/journal.pone.0284264

Peer Review History

Original SubmissionJune 27, 2022
25 Oct 2022 Decision Letter - Angelo A. Izzo, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-22-18255 In silico EsxG·EsxH Rational Epitope Selection: Candidate Epitopes for Vaccine Design against Pulmonary Tuberculosis PLOS ONE Dear Dr. Mixcoha, 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. Please submit your revised manuscript by Dec 08 2022 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Angelo A. Izzo Academic Editor PLOS ONE Journal requirements: When submitting your revision, we need you to address these additional requirements. 1.Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf. 2. Thank you for stating the following financial disclosure: “This paper was supported by grant 413957, CVU 406611 from the National Council for Science and Technology of Mexico (Consejo Nacional de Ciencia y Tecnología-CONACyT). Project number 21-2019 and 13-2020 by LANCAD supercomputing center.” Please state what role the funders took in the study. If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."" If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This paper was supported by grant 413957, CVU 406611 from the National Council for Science and Technology of Mexico (Consejo Nacional de Ciencia y Tecnología-CONACyT). Project number 21-2019 and 13-2020 by LANCAD supercomputing center. We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “This paper was supported by grant 413957, CVU 406611 from the National Council for Science and Technology of Mexico (Consejo Nacional de Ciencia y Tecnología-CONACyT). Project number 21-2019 and 13-2020 by LANCAD supercomputing center.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [Note: HTML markup is below. Please do not edit.] 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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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: Yes ****** 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 ****** 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: The following manuscript describes the rational design of novel vaccine epitopes targeting pulmonary tuberculosis through a suite of predictive servers and molecular dynamics simulations. As a proof of concept, the authors used the EsxG:EsxH complex as template, an heterodimer involved into the bacteria viability and homeostasis (i.e. zinc uptake). The two proteins are also involved into antibiotic resistance mechanisms. The group first selected 21 epitopes from the proteins EsxG and EsxH that could bind to MHC class II using ProPred and NetMHCII 2.3 platforms. They predicted additional 13 linear B cell epitopes from the same protein complex using BepiPred 2.0 (8 continuous epitopes) and DiscoTope 2.0 (5 discontinuous epitopes) - Figure 1. The epitopes were subjected to peptide-protein docking experiments using CABS-Dock and FlexPepDock to predict their binding conformations into MHC class II molecules, in particular HLA-DRB1. Only seven out of all epitopes were selected for further studies (Table 1), namely G1, G2, H1 and H2. On the second large section of the manuscript, the authors evaluated the predicted folding and structural stability of (1) the heterodimeric complex and the two distinct monomers EsxG and EsxH [Figures 2-4, 7 and S1-S6] and (2) the epitopes and HLA-DRB1-epitope complexes [Figures 5-6, S7-S11, and Table 2] using multiple molecular dynamics simulations. The four epitopes did not fold into specific secondary structures in solution or in complex. They identified the 4 epitopes forming complexes with HLA-DRB1. In their discussion, the authors supported their bioinformatic observations for epitopes G1, H1, H2 (Table 3) with external experimental validation throughout the scientific literature. The manuscript is well-documented and information-rich. Some sentences throughout the manuscript are hard to grasp and should be re-written for clarity (e.g. lines 49-51). I encourage the authors to review and edit the document. Please consider the following minor corrections; (1) Mycobacterium tuberculosis should be italicized. (2) Typo – line 453 RMFS Reviewer #2: The paper by Martinez-Olivares et al. describes a rational design of epitope-based peptide vaccines by using bioinformatics and structural vaccinology tools, focusing on the testing of EsxG·EsxH complex. The ESX systems from Mycobacterium tuberculosis are very well-known factors for the secretion of highly immunogenic proteins that seem of key importance for bacterial survival and growth. I appreciated the fact that, even if the authors use already investigated tools and approaches, they explore the fusion of EsxG and EsxH proteins as candidate target for TB vaccine development, never tested before in this conjugated version, especially for the presence of EsxH protein. The pipeline is well described and the results appropriately report the potentiality to be considered as subunit vaccine candidates or conjugated vaccines, even if the validation phase is mandatory for the evaluation of the immunogenicity. The conclusions convey the main points of the manuscript and the methodology is exhaustively described in the Methods section. I would recommend the authors to address my concerns here below before final pubblication in order to provide to the scientific community this further step in the field of TB vaccine development. - Inside the Introduction part, the authors should integrate the bibliography related to the rational vaccine design through immunobioinformatics tools and computational chemistry approaches. They report only two references (not so recent) while the literature offers more innovative and updated examples of new vaccine development pipeline such as the one reported in Sunita et al., 2019 (doi:10.1080/21645515.2019.1670035) and some specific examples applied for example to COVID-19 vaccine (doi: 10.1093/bib/bbab403). - In Results section, the authors mention the role of the MTB in provoking intracellular infection, justifying the importance of MHC class II epitope prediction. For the sake of completeness, the authors should also report specific results related also to the extracellular infection that Mtb is able to cause and the consequent main immunological actors dynamics involved in this perspective. I would suggest then to insert new plots or piece of evidence in such view, for example focusing on MHC class I epitope prediction. - The "Thermal unfolding simulations" is missing the bibliography. Please insert it. - Even if the Methods are well described, I would suggest the authors to insert inside the manuscript a summary figure reporting all the steps of the rational design approach applied. ****** 6. 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: Giulia Russo ******** [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. Attachments Attachment Submitted filename: Review_PLOSONE.pdf https://doi.org/10.1371/journal.pone.0284264.r001
Revision 1
17 Nov 2022 Author Response Reviwer #1. Thank you for all your valuable comments about our work, these are helpful to improve the quality of our work. 1. Reviewer #1 Suggest checking in detail sentences that are difficult to follow. Author response: We revised our manuscript in detail to find sentences that were difficult to follow, as you suggested. In the reviewed manuscript, we found some sentences that are already changed and highlighted in yellow in the file named “Revised Manuscript with Track Changes” 2. Reviewer #1 recommend check all typos throughout the manuscript. Author response: After reviewing the text, all the typos found are already corrected. Reviewer #2 We want to thank all your comments, we found them helpful to make our clearer and more objective in the submitted manuscript. 1. Reviewer #2 recommended incorporating recent articles related to rational vaccine design in Introduction Section. Author response: We have incorporated a new bibliography in the Introduction Section. In the file named “Revised Manuscript with Track Changes,” you can corroborate it. 2. Reviewer #2 advises incorporating reports related to extracellular infection and evidence of epitopes MHC-I prediction. Author response: As required, information about the results related to the extracellular Mtb infection related to the humoral immune response was added in the Results section with three references that support this information 3. Reviewer #2 pointed out a missed bibliography in Thermal unfolding simulations. Author response: We have checked that missed cite and incorporated it in the indicated section. 4. Reviewer #2 suggests inserting a summary figure inside the manuscript reporting all the steps of the rational design approach applied. Author response: We have designed a summary figure as the reviewer suggested. (Fig 1 in the file “Revised Manuscript with Track Changes”) https://doi.org/10.1371/journal.pone.0284264.r002
2 Jan 2023 Decision Letter - Angelo A. Izzo, Editor PONE-D-22-18255R1In silico EsxG·EsxH Rational Epitope Selection: Candidate Epitopes for Vaccine Design against Pulmonary TuberculosisPLOS ONE Dear Dr. Mixcoha, 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. Please submit your revised manuscript by Feb 16 2023 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Angelo A. Izzo 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. [Note: HTML markup is below. Please do not edit.] 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: (No Response) Reviewer #3: All comments have been addressed ******** 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: (No Response) Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: (No Response) Reviewer #3: N/A ****** 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: (No Response) Reviewer #3: 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 #2: (No Response) Reviewer #3: 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 #2: Dear Authors, it's a bit hard for me to catch the new advancements and revisions to indicate if you have adequately addressed my comments. Could you please provide a new version with highlighted or marked in bold parts concerning my comments? Thank you. Reviewer #3: Please add the full name of" EsxG·EsxH" protein complex in the beginning of the study and then through out the manuscript the abbreviation can be used ****** 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: Yes: Giulia Russo 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.] 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. https://doi.org/10.1371/journal.pone.0284264.r003
Revision 2
3 Feb 2023 Author Response Reviewer #2: Dear Authors, it's a bit hard for me to catch the new advancements and revisions to indicate if you have adequately addressed my comments. Could you please provide a new version with highlighted or marked in bold parts concerning my comments? Thank you. Author response Reviewer #2. We regret being unclear in our previous response. In order to make all suggestions easier to understand and read, we are currently underlining and highlighting them in the "Revised Manuscript with Track Changes" file. On October 25th, we received the very first comments and advice from Reviewers of our submitted work titled “In silico EsxG·EsxH Rational Epitope Selection: Candidate Epitopes for Vaccine Design against Pulmonary Tuberculosis” . In this way, reviewer #2's comments stated: Reviewer #2: The paper by Martinez-Olivares et al. describes a rational design of epitope-based peptide vaccines by using bioinformatics and structural vaccinology tools, focusing on the testing of EsxG·EsxH complex. The ESX systems from Mycobacterium tuberculosis are very well-known factors for the secretion of highly immunogenic proteins that seem of key importance for bacterial survival and growth. I appreciated the fact that, even if the authors use already investigated tools and approaches, they explore the fusion of EsxG and EsxH proteins as candidate target for TB vaccine development, never tested before in this conjugated version, especially for the presence of EsxH protein. The pipeline is well described and the results appropriately report the potentiality to be considered as subunit vaccine candidates or conjugated vaccines, even if the validation phase is mandatory for the evaluation of the immunogenicity. The conclusions convey the main points of the manuscript and the methodology is exhaustively described in the Methods section. I would recommend the authors to address my concerns here below before final pubblication in order to provide to the scientific community this further step in the field of TB vaccine development. - Inside the Introduction part, the authors should integrate the bibliography related to the rational vaccine design through immunobioinformatics tools and computational chemistry approaches. They report only two references (not so recent) while the literature offers more innovative and updated examples of new vaccine development pipeline such as the one reported in Sunita et al., 2019 (doi:10.1080/21645515.2019.1670035) and some specific examples applied for example to COVID-19 vaccine (doi: 10.1093/bib/bbab403). Author response We modified the manuscript in order to update cites about new techniques and immunoinformatics, also we mentioned both cite that Reviewer #2 advised to us. That changes are present in Pag. 2 lines 32 to 38 in the Introduction section of the final Manuscript. It is worth mentioning that references 5, 6, 7, 8, 9, 10 and, 39 were added as recommended by Reviewer #2. - In Results section, the authors mention the role of the MTB in provoking intracellular infection, justifying the importance of MHC class II epitope prediction. For the sake of completeness, the authors should also report specific results related also to the extracellular infection that Mtb is able to cause and the consequent main immunological actors dynamics involved in this perspective. I would suggest then to insert new plots or piece of evidence in such view, for example focusing on MHC class I epitope prediction. Author response We have included the reports that reviewer #2 pointed out. These modifications are present in the final Manuscript, Pag. 10, lines 218 to 224 in the Results section. - The "Thermal unfolding simulations" is missing the bibliography. Please insert it. Author response This reference is placed already in Pag. 7, line 148. - Even if the Methods are well described, I would suggest the authors to insert inside the manuscript a summary figure reporting all the steps of the rational design approach applied. Author response A new figure (Fig 1 in the final manuscript) was made for this proposal. In Pag. 9, lines 195 to 201 contain explanation about that Summary Figure. -----------------* Reviewer #3: Please add the full name of" EsxG·EsxH" protein complex in the beginning of the study and then through out the manuscript the abbreviation can be used Author response Thank you very much for your comments, we addressed the new change that you suggested to us this time. We have completed the name of the EsxG·EsxH" protein complex in the abstract section (Pag. 1, lines 3 and 4) and, in the Introduction section, Pag. 3, lines 60 and 61 in the final Manuscript. Attachments Attachment Submitted filename: response_reviewers.pdf https://doi.org/10.1371/journal.pone.0284264.r004
29 Mar 2023 Decision Letter - Angelo A. Izzo, Editor In silico EsxG·EsxH Rational Epitope Selection: Candidate Epitopes for Vaccine Design against Pulmonary Tuberculosis PONE-D-22-18255R2 Dear Dr. Mixcoha, 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Angelo A. Izzo 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 #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 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 Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes ****** 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 Reviewer #2: 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 Reviewer #2: 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: The authors have addressed the comments I made in the first round of reviews, and those of other reviews in the subsequent forms. Reviewer #2: I'm quite satisfied about the author response and edits to my comments provided by the authors. Hence, I would recommend the manuscrupit for final publication. ****** 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: No Reviewer #2: Yes: Giulia Russo ******** https://doi.org/10.1371/journal.pone.0284264.r005
Formally Accepted
10 Apr 2023 Acceptance Letter - Angelo A. Izzo, Editor PONE-D-22-18255R2 In silico EsxG·EsxH Rational Epitope Selection: Candidate Epitopes for Vaccine Design against Pulmonary Tuberculosis Dear Dr. Mixcoha: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Angelo A. Izzo Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0284264.r006

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