PONE-D-23-41424Unveiling Kemuning’s (Murraya paniculata) Anti-Obesity Potential: A Network Pharmacology ApproachPLOS ONE

Dear Dr. Kusuma,

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.

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ACADEMIC EDITOR: The authors must address all concerns raised by the reviewers, particularly by providing molecular dynamics simulation data to substantiate the molecular docking studies, and presenting in vitro and in vivo experimental data to support the stated claims. 

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Md. Ashraful Hasan, Ph.D.

Academic Editor

PLOS ONE

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"The initials author: WAK

Grant numbers: This research was supported by Ministry of Research, Technology and Higher Education, Indonesia, under Competitive Research Grant from Directorate of Higher Education, Indonesia, 2023 No. 102/E5/PG.02.00.PL/2023

URL: https://dikti.kemdikbud.go.id/"

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

Reviewer #4: No

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2. Has the statistical analysis been performed appropriately and rigorously

Reviewer #1: Yes

Reviewer #2: N/A

Reviewer #3: Yes

Reviewer #4: No

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

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: No

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5. Review Comments to the Author

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

Reviewer #1: Murraya paniculata leaves water and ethanol extracts, active compounds were identified and protein targets for obesity, wherein molecular docking where done for PPARG and EP300 protein in the study.

The study has been well structured and results have been elucidated well.

However, the following points has to be considered:-

1) Ten compounds have been identified to have good binding affinity to both the proteins but does all the compounds have anti-obesity properties in other studies.

2) To confirm the molecular docking studies, a molecular dynamics simulation has to done to elucidate it.

Reviewer #2: Although LC-MS results are given in tabular form, the chromatogram is missing, which may be provided.

A molecular dynamics study for understanding the stability of compound-target interaction could add further support.

In-vitro or in-vivo studies to support predicted bioactivity would add value.

Line #42 INSTEAD OF energy entering the body is lower than the energy expended CONSIDER energy entering the body is higher than the energy expended

Line #75 INSTEAD OF drenergic receptor agonists CONSIDER adrenergic receptor agonists

Line #94 INSTEAD OF The anti-obesity effect of M. paniculata as been reported CONSIDER The anti-obesity effect of M. paniculata has been reported

Line # 95 INSTEAD OF 800 mg/kg bb CONSIDER 800 mg/kg

Line #96 INSTEAD OF L-glutamate 2 g/kgbb CONSIDER L-glutamate 2 g/kg

Line # 97 INSTEAD OF An effective dose of 200 mg/kg CONSIDER An effective dose of 200 mg/kg

Line # 366 INSTEAD OF ten active compounds CONSIDER Ten potentially active compounds

Line # 370 INSTEAD OF Various methods have been used for obesity treatment, including drug discovery from herbal….. CONSIDER Various methods have been used for obesity treatment, including herbal..

Line # 468 INSTEAD OF possible mechanism of the active compounds of M. paniculata CONSIDER possible mechanism of the compounds of M. paniculata

Line # 469 INSTEAD OF in curing obesity CONSIDER in treatment/management of obesity.

Reviewer #3: The authors seem to present a in silico analysis of the Kemuning’s (Murraya paniculata) Anti-Obesity Potential. however I would recommed major revision of the manuscript in its present form :-

1.Lack of Novelty:

- The integration method described in the paper does not seem to introduce any novel approach or technique. Similar methodologies have been employed in previous studies, and the paper fails to highlight any substantial advancement in the field.

2. Ambiguity in Results Interpretation:

- The paper lacks clarity in interpreting the results obtained from network pharmacology and molecular docking. The significance of the identified targets (EP300, PPARG, and PPARGC1A) is not well-established, and the connections between these targets and the treatment of obesity are inadequately explained.

3. Incomplete Validation:

- The paper lacks experimental validation of the proposed targeting mechanism. While molecular docking results are presented, there is a lack of in vitro or in vivo experiments to support the claims made regarding the binding affinity and the effectiveness of the active compounds from M. paniculata.

4. Limited Scope of Study with Over generalizations

- The scope of the study appears to be limited to the identification of potential targets and molecular interactions. However, a comprehensive understanding of the biological mechanisms involved in treating obesity requires additional investigations, such as cellular assays and animal model studies, which are lacking in this paper. he conclusions drawn from the study, particularly the statement that M. paniculata treats obesity by targeting PPARG and EP300 proteins, seem overly generalized. The results should be cautiously interpreted and discussed within the context of the study's limitations and uncertainties.

7. Inadequate Comparative Analysis:

- The paper lacks a comprehensive comparison with existing literature on the topic. A thorough review and discussion of similar studies would provide a clearer understanding of how the current work contributes to the existing body of knowledge. Some statements lack proper citation to support the claims made. It is essential to provide a robust foundation for the research by referencing relevant studies and findings in the field.

8. Language and Writing Style:

- The manuscript suffers from issues related to language and writing style. The narrative is convoluted at times, making it challenging for readers to follow the logical flow of the research.

Recommendation for Major Revisions:

- Given the aforementioned concerns, it is recommended that the paper undergoes major revisions to address the identified issues and strengthen the overall quality and validity of the study.

Reviewer #4: This manuscript is very unorganized and unplanned, and it is very hard to understand what authors actually want to show from their study. There is no alignment between the study flow they showed in Figure 3 and what they described in the results section.

First of all, network pharmacology should be made based on the M. paniculata metabolites identified from the LC-MS, and then the relevant targets and signaling pathways must be validated by experimental studies. but authors made their network based on the metabolites found in IJAH Analytics database, which makes their network prediction technically and scientifically not sound. Writing in both the result and discussion sections is also very crude, and docking is not enough to prove interaction. Furthermore, the authors did not prove any relationship between the M. paniculata network and obesity. The roles of their identified targets in obesity pathology and whether those compounds can ameliorate obesity must be proved experimentally.

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Reviewer #1: Yes: Dicky John Davis G

Reviewer #2: No

Reviewer #3: Yes: Subhadip Banerjee

Reviewer #4: No

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Unveiling the Anti-Obesity Potential of Kemuning (Murraya paniculata): A Network Pharmacology Approach

PONE-D-23-41424R1

Dear Dr. Kusuma,

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. Please note that the comments from Reviewer 2 are irrelevant to this article and do not need to be addressed by the authors. Additionally, the manuscript does not mention the source of the plant leaves used in the experiments (line 158 onwards). Therefore, the authors are advised to include the source of the plant leaves to aid in the reproducibility of the methodology.

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

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Kind regards,

Md. Ashraful Hasan, Ph.D.

Academic Editor

PLOS ONE

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: (No Response)

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 #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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 #1: Yes

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 #1: Yes

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 #1: Murraya paniculata leaves water and ethanol extracts, active compounds were identified and protein targets for obesity, wherein molecular docking and dynamics simulation where done for PPARG and EP300 protein in the study and complimented with in-vitro studies.

Authors have adequately addressed the comments raised in a previous round of review such as

1) LC-MS chromatogram has been provided

2) Molecular dynamics study was also done.

3) In-vitro studies using 3T3-L1 cells have been conducted.

Revised manuscript has shown that M.paniculata extract can decrease PPARG and EP300 gene expression.

Reviewer #2: The manuscript attempts to identify the risk factors associated with the nutritional status of 0-59 years children in Ethiopia.

The manuscript presents data required for the analysis and have cited the source. I have reviewed the manuscript with the help of colleagues from Community Medicine and Biostatistics and have the following suggestions to make.

1. The key-words may be arranged alphabetically.

2. In the background, the burden of undernutrition documented by previous studies needs to be added.

Any nutritional programme, if ongoing or carried out in the past should also be detailed for better understanding.

3. In Methods, a brief description of study area and settings is desired since this information is necessary for better understanding by readers outside of the region and it is often cumbersome to go through the reports.

4. Since the study design is cross-sectional, it is preferable to use the prevalence ratio (PP) as the effect estimate rather than the odds ratio. How can the authors justify this choice? (Line 182).

5. Results. The manuscript displays inconsistency in the number of digits after decimal points. Some sections feature only one digit, while others have two. Authors may like to use uniform decimal places across all sections.

6. There are some errors, perhaps typographical in the manuscript e.g Page 15, Line 365, 'to'?

7. References: The manuscript should be checked for uniformity of citation. Some references does not show month and some citation dates missing (eg Ref 15, 16, 19,20).

Reviewer #3: (No Response)

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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 #1: Yes: Dicky John Davis G

Reviewer #2: No

Reviewer #3: Yes: Subhadip banerjee

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