Investigation of the inhibitory potential of secondary metabolites isolated from Fernandoa adenophylla against Beta-glucuronidase via molecular docking and molecular dynamics simulation studies

Abdur Rauf; Rahaf Ajaj; Zuneera Akram; Majid Khan; Abdul Wadood; Maryam Zulfat; Zafar Ali Shah; Abdulhakeem S. Alamri; Walaa F. Alsanie; Majid Alhomrani; Humaira Hussain; Dorota Formanowicz

doi:10.1371/journal.pone.0324100

Peer Review History

Original SubmissionJanuary 27, 2025
27 Jan 2025 Author Response https://doi.org/10.1371/journal.pone.0324100.r001
12 Feb 2025 Decision Letter - Viet Phong Nguyen, Editor PONE-D-25-04376Investigation of the inhibitory potential of secondary metabolites isolated from Fernandoa adenophylla against Beta-glucuronidase via molecular docking and molecular dynamics simulation studiesPLOS ONE Dear Dr. Rauf, 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. ============================== ACADEMIC EDITOR: In this study: " Investigation of the inhibitory potential of secondary metabolites isolated from Fernandoa adenophylla against Beta-glucuronidase via molecular docking and molecular dynamics simulation studies" The authors provide report about the inhibitory activities of compounds isolated from Fernandoa adenophylla against β-glucuronidase via in vitro and in silico studies. However, there are many concerns in this study, and major revision is required. ============================== Please submit your revised manuscript by Mar 29 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 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, Viet Phong Nguyen, Ph.D. 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. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. 3. Please provide a complete Data Availability Statement in the submission form, ensuring you include all necessary access information or a reason for why you are unable to make your data freely accessible. If your research concerns only data provided within your submission, please write "All data are in the manuscript and/or supporting information files" as your Data Availability Statement. Additional Editor Comments : 1. Abstract: Avoid non-standard or uncommon abbreviations. If any are essential to include, ensure they are defined within your abstract at first mention. 2. Section 2.1: - Details on chromatographic separation techniques are missing (type of chromatographic column, stationary/mobile phase used, elution conditions, detection). - Details of spectroscopic techniques to determine the structure of the isolated compound (type of NMR spectroscopy, mass, equipment used). 3. Section 2.3: check again the writing here. There are many grammar and presentation issues. Additionally, all NMR data along with Chemical properties and spectra are mandatory in Supplemental materials. 4. Section 2.5: references of enzyme structures downloaded from Protein Data Bank are required. In addition, was a grid box defined around the binding site to specify the docking region, or was blind docking used in this study? Please clearly indicate the grid box parameters (grid size, grid position) for each target protein. How was the 3D structure of the inhibitor constructed? Was the structure of the test compounds minimized before the docking process? Please indicate. 5. Section 3.1: Please provide the IC50 graphs of all test compounds. The β-glucuronidase enzyme has multiple ligand binding sites (e.g., catalytic and allosteric sites). Without conducting enzyme kinetics analysis, it is unclear which binding site is relevant for the inhibitors. Therefore, to validate the binding site and confirm the docking results, enzyme kinetics experiments are mandatory. 6. Section 3.2 Molecular docking analysis: There is much literature reporting the inhibition mode and binding site of β-glucuronidase inhibitors. Please compare your compounds with reported inhibitors. What is the difference between the binding sites? Please clearly describe. 7. Section 3.3 MD simulation: A molecular dynamics simulation of 20 ns is not meaningful and does not yield any significant scientific results. In fact, the protein-ligand complex tends to exhibit many fluctuations during the initial 20 ns equilibration of simulations. Therefore, a prolonged molecular dynamics simulation of at least 100 ns is required. 8. It would be beneficial to report the RMSD of the ligand after fitting to the protein backbone, along with the distance between the centers of mass of the protein and ligand. These parameters can reveal any potential internal motions, particularly interdomain motion, within the protein. 9. How about the binding affinity of bound ligand conformations? MM/PB(GB)SA calculations are required. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: [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: comments.pdf https://doi.org/10.1371/journal.pone.0324100.r002
Revision 1
17 Mar 2025 Author Response Dear Viet Phong Nguyen, Ph.D. Academic Editor PLOS ONE Thank you very much for the reviewers’ comments concerning our manuscript. We have studied the reviewer comments carefully and have made several revisions to the text. We would like to express our appreciation to you and the reviewers for your many suggestions, which have greatly improved our manuscript. All changes are shown in yellow, highlighted in the revised manuscript, and are outlined below on a point-by-point basis (red color). We hope these corrections and revisions are satisfactory and that the manuscript now meets the requirements for publication. We look forward to hearing from you at your earliest convenience. 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 Response: Done 2. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. Response: Done 3. Please provide a complete Data Availability Statement in the submission form, ensuring you include all necessary access information or a reason for why you are unable to make your data freely accessible. If your research concerns only data provided within your submission, please write "All data are in the manuscript and/or supporting information files" as your Data Availability Statement. Response: Done Additional Editor Comments : 1. Abstract: Avoid non-standard or uncommon abbreviations. If any are essential to include, ensure they are defined within your abstract at first mention. Response: Corrected as suggested. 2. Section 2.1: - Details on chromatographic separation techniques are missing (type of chromatographic column, stationary/mobile phase used, elution conditions, detection). Response: Details on chromatographic separation techniques, including column specifications, stationary and mobile phases, elution conditions, and detection methods, have now been incorporated. - Details of spectroscopic techniques to determine the structure of the isolated compound (type of NMR spectroscopy, mass, equipment used). Response: Details of the spectroscopic data, along with the corresponding spectra, are provided in the supplementary file. 3. Section 2.3: check again the writing here. There are many grammar and presentation issues. Additionally, all NMR data along with Chemical properties and spectra are mandatory in Supplemental materials. Response: All grammatical issues have been addressed. The NMR data, physical data, and spectra are now provided in the Supplemental Materials. Section 2.5: references of enzyme structures downloaded from Protein Data Bank are required. In addition, was a grid box defined around the binding site to specify the docking region, or was blind docking used in this study? Response: Dear Reviewer, Thank you for your valuable comments. We have incorporated the suggested references and followed the docking procedure as reported in a previous study. (https://doi.org/10.3390/pr11030880, doi:10.5281/zenodo.3576583). Please clearly indicate the grid box parameters (grid size, grid position) for each target protein. How was the 3D structure of the inhibitor constructed? Was the structure of the test compounds minimized before the docking process? Please indicate. Response: The requested details have now been incorporated into the revised manuscript and have been highlighted for clarity. Section 3.1: Please provide the IC50 graphs of all test compounds. Response: We sincerely appreciate the reviewer's insightful comment. In response, we have incorporated the IC₅₀ graphs for all tested compounds (AA: Lapachol, DD: Alpha-lapachone, CC: Indanone derivatives, and D-Saccharic acid 1,4-lactone) as requested. The IC₅₀ values were determined using nonlinear regression analysis in GraphPad Prism, and the corresponding dose-response curves are now provided below. The β-glucuronidase enzyme has multiple ligand binding sites (e.g., catalytic and allosteric sites). Without conducting enzyme kinetics analysis, it is unclear which binding site is relevant for the inhibitors. Therefore, to validate the binding site and confirm the docking results, enzyme kinetics experiments are mandatory. Response: Thank you for your valuable comment. We acknowledge that β-glucuronidase has multiple ligand-binding sites, including catalytic and allosteric sites, and that enzyme kinetics experiments are essential for definitive validation. In our study, molecular docking was employed as an initial approach to predict potential interactions. However, to further substantiate our findings, we plan to conduct enzyme kinetics experiments in future studies to confirm the binding site and validate the docking results experimentally. Section 3.2 Molecular docking analysis: There is much literature reporting the inhibition mode and binding site of β-glucuronidase inhibitors. Please compare your compounds with reported inhibitors. What is the difference between the binding sites? Please clearly describe. Response: The compounds have now been compared with the reported inhibitors, and the updates are highlighted in the revised manuscript. Section 3.3 MD simulation: A molecular dynamics simulation of 20 ns is not meaningful and does not yield any significant scientific results. In fact, the protein-ligand complex tends to exhibit many fluctuations during the initial 20 ns equilibration of simulations. Therefore, a prolonged molecular dynamics simulation of at least 100 ns is required. Response: The MD simulation has been extended to 100 ns, and the updates have been highlighted in the revised manuscript. It would be beneficial to report the RMSD of the ligand after fitting to the protein backbone, along with the distance between the centers of mass of the protein and ligand. These parameters can reveal any potential internal motions, particularly interdomain motion, within the protein. Response: As per the suggestions, the RMSD and distance analysis have been incorporated and highlighted in the revised manuscript. How about the binding affinity of bound ligand conformations? MM/PB(GB)SA calculations are required Response: The required details have now been added and appropriately highlighted in the revised manuscript. Attachments Attachment Submitted filename: Reply-comments.docx https://doi.org/10.1371/journal.pone.0324100.r003
9 Apr 2025 Decision Letter - Viet Phong Nguyen, Editor PONE-D-25-04376R1Investigation of the inhibitory potential of secondary metabolites isolated from Fernandoa adenophylla against Beta-glucuronidase via molecular docking and molecular dynamics simulation studiesPLOS ONE Dear Dr. Rauf, 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 May 24 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 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, Viet Phong Nguyen, 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. [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 #1: All comments have been addressed Reviewer #2: All comments have been addressed 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 #1: Yes Reviewer #2: Partly Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes Reviewer #3: (No Response) ****** 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 Reviewer #3: (No Response) ****** 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 Reviewer #3: (No Response) ****** 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 adequately responded to all comments and suggestions raised to improve their manuscript. Reviewer #2: In my opinion, the manuscript “Investigation of the inhibitory potential of secondary metabolites isolated from Fernandoa adenophylla against Beta-glucuronidase via molecular docking and molecular dynamics simulation studies” is well written and presents interesting information. But I would like to point out some issues which can be revised: Abstract: Revise the abstract to align with conventional standards of clarity, logical flow, and objectivity. Introduction: The introduction section should be rewritten in a more focused manner, in concise paragraphs. The statement of the problem and the rationale of this study is unclear. Although the authors have included some studies, it is needed to include additional literature on this plant, and a justification of its choice for the current investigation. According to this study, isolated chemical constituents (1-5) of Fernandoa adenophylla exhibited remarkable antidiabetic activity. Additionally, what are all the major phytocompounds have been reported and so on can be added. Result: Appropriate inferential statistics are missing, especially for results. This is particularly important in interpreting the results, appraising their validity, and drawing appropriate conclusions. Discussion : The discussion section should be revised and focused on interpretation, relationships with reports from other scholars in the field, and implication of the obtained results. Reviewer #3: I recommend the acceptance of the manuscript. One additional comment I just mention that author should write the unit of binding energy in the manuscript. ****** 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: Khaled M. Darwish Reviewer #2: No Reviewer #3: Yes: Shashank Shekher Mishra ******** [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.0324100.r004
Revision 2
14 Apr 2025 Author Response Dear Viet Phong Nguyen, Ph.D. Academic Editor PLOS ONE Thank you very much for the reviewers’ comments concerning our manuscript. We have carefully reviewed the comments from the reviewers and made several revisions to the text. We would like to express our appreciation to you and the reviewers for your many suggestions, which have greatly improved our manuscript. All changes are highlighted in yellow in the revised manuscript and are outlined below on a point-by-point basis (in red). We hope these corrections and revisions are satisfactory and that the manuscript now meets the requirements for publication. We look forward to hearing from you at your earliest convenience. 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. Response: The reference list has been checked and found to be corrected. 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 Reviewer #3: All comments have been addressed Response: Thank you. ________________________________________ 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: Partly Reviewer #3: Yes Response: The necessary corrections have been made. ________________________________________ 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes Reviewer #3: (No Response) Response: Thank you. ________________________________________ 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 Reviewer #3: (No Response) Response: Thank you. ________________________________________ 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 Reviewer #3: (No Response) Response: Thank you. ________________________________________ 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 adequately responded to all comments and suggestions raised to improve their manuscript. Response: Thank you. Reviewer #2: In my opinion, the manuscript “Investigation of the inhibitory potential of secondary metabolites isolated from Fernandoa adenophylla against Beta-glucuronidase via molecular docking and molecular dynamics simulation studies” is well written and presents interesting information. But I would like to point out some issues which can be revised: Abstract: Revise the abstract to align with conventional standards of clarity, logical flow, and objectivity. Response: Dear reviewer, thank you for your suggestion. We have revised the abstract to make it more concise and clear. Introduction: The introduction section should be rewritten in a more focused manner, in concise paragraphs. The statement of the problem and the rationale of this study is unclear. Although the authors have included some studies, it is needed to include additional literature on this plant, and a justification of its choice for the current investigation. According to this study, isolated chemical constituents (1-5) of Fernandoa adenophylla exhibited remarkable antidiabetic activity. Additionally, what are all the major phytocompounds have been reported and so on can be added. Response: Dear reviewer, thank you for your suggestion. The introduction has been revised as per the suggestions. Result: Appropriate inferential statistics are missing, especially for results. This is particularly important in interpreting the results, appraising their validity, and drawing appropriate conclusions. Response: We thank the reviewer for the comment. The results were presented as mean ± SEM from triplicate experiments, analyzed using ANOVA to ensure consistency. Due to the limited sample size (n=3), further inferential statistics (e.g., p-values) were not applied to avoid overinterpretation. However, conclusions were supported through complementary molecular docking, MD simulations, and MM-GBSA analyses, providing robust validation of the findings. Discussion : The discussion section should be revised and focused on interpretation, relationships with reports from other scholars in the field, and implication of the obtained results. Response: Dear reviewer, we have revised the discussion as per the suggestions Reviewer #3: I recommend the acceptance of the manuscript. One additional comment I just mention that author should write the unit of binding energy in the manuscript. Response: We thank the reviewer for the suggestion. The unit of binding energy (kcal/mol) has been added in the text and Table 4. ________________________________________ 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: Khaled M. Darwish Reviewer #2: No Reviewer #3: Yes: Shashank Shekher Mishra Response: It okay Attachments Attachment Submitted filename: Comments reply.docx https://doi.org/10.1371/journal.pone.0324100.r005
22 Apr 2025 Decision Letter - Viet Phong Nguyen, Editor Investigation of the inhibitory potential of secondary metabolites isolated from Fernandoa adenophylla against Beta-glucuronidase via molecular docking and molecular dynamics simulation studies PONE-D-25-04376R2 Dear Dr. Rauf, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Viet Phong Nguyen, Ph.D. Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0324100.r006
Formally Accepted
Acceptance Letter - Viet Phong Nguyen, Editor PONE-D-25-04376R2 PLOS ONE Dear Dr. Rauf, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Viet Phong Nguyen Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0324100.r007

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .