PONE-D-25-11337Pharmacophore-based virtual screening, Docking, and MD simulation studies: An in-silico perspective for the identification of potential MBL inhibitorsPLOS ONE

Dear Dr. Snoussi,

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: In some sections of the manuscript including the title, the author mentioned "Pharmacophore-based virtual screening", what does this mean? Given that in the main texts of the objectives, methodology, results and discussion, nothing can be referenced to pharmacophore based screening or virtual screening by pharmacophore model, I recommend that this is expunged from the submission to avoid confusion. In addition, how was the docking study validated? All concerns raised by the reviewers need to be adequately addressed, after then, the manuscript can be reconsidered. 

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Yusuf Oloruntoyin Ayipo, Ph.D

Academic Editor

PLOS ONE

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Additional Editor Comments:

In some sections of the manuscript including the title, the author mentioned "Pharmacophore-based virtual screening", what does this mean? Given that in the main texts of objectives, methodology, results and discussion, nothing can be referenced to pharmacophore based screening, I recommend that this is expunged from the submission to avoid confusion. In addition, how was the docking study validated? All concerns raised by the reviewers need to be adequately addressed, after that, the manuscript can be reconsidered.

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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: Yes

Reviewer #4: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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: 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: 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: SECTION 1: PLOS ONE REVIEWER GUIDELINES

• What are the main claims of the paper and how significant are they for the discipline?

I think they are moderately significant.

• Are the claims properly placed in the context of the previous literature? Have the authors treated the literature fairly?

Yes, fairly well.

• Do the data and analyses fully support the claims? If not, what other evidence is required?

Yes, data supports claim.

• PLOS ONE encourages authors to publish detailed protocols and algorithms as supporting information online. Do any particular methods used in the manuscript warrant such treatment? If a protocol is already provided, for example for a randomized controlled trial, are there any important deviations from it? If so, have the authors explained adequately why the deviations occurred?

Adequately, but more information / request is provided in notes below.

• If the paper is considered unsuitable for publication in its present form, does the study itself show sufficient potential that the authors should be encouraged to resubmit a revised version?

Yes, the paper is good for publication upon minor revision detailed below.

• Are original data deposited in appropriate repositories and accession/version numbers provided for genes, proteins, mutants, diseases, etc.?

Original data are cited. More requests in notes below.

• Does the study conform to any relevant guidelines such as CONSORT, MIAME, QUORUM, STROBE, and the Fort Lauderdale agreement?

Does not seem applicable here.

• Are details of the methodology sufficient to allow the experiments to be reproduced?

Nearly so; suggestions for improvement provided in notes below.

• Is any software created by the authors freely available?

Does not seem applicable here.

• Is the manuscript well organized and written clearly enough to be accessible to non-specialists?

Nearly so; suggestions for improvement provided in notes below.

• Is it your opinion that this manuscript contains an NIH-defined experiment of Dual Use concern?

Not at this time.

SECTION 2: MY COMMENTS / RECOMMENDATIONS / REQUESTS

• For the sake of readability, I ask that the Authors rephrase the first sentence of the abstract to clarify that antibiotic resistance is what is being proliferated (if that is the intent of the Authors), and not that the very identification of NDM-1 causes a proliferation of antibiotic resistance. Also, I ask that all abbreviations are defined throughout the manuscript, including in the abstract (examples include ML, CHARMM36, CGneFF, LINCS, NVT, NPT, PC, and PCA).

• As with all abbreviations, I recommend writing techniques like “quantitative structure-activity relationship” (QSAR) and “molecular dynamics” (MD) in lower case.

• Line 67 – “Expanding upon this basis, a recent work employed a multi-step virtual screening method for the identification of non-β-lactam inhibitors against NDM-1.” Lacking citation to the “recent work”.

• Line 76-81 – “The objective of this investigation was to employ computational methods to comprehensively investigate and identify natural product compounds that exhibit inhibitory activity against NDM-1.” I recommend rewording as “identify and investigate”, in consistence with the flow of the story. Also, I recommend caution on the use of past tense to describe the objective of the study. Finally, there seem to be a duplicate statement of objective, I therefore recommend making that section more succinct and thus avoid potential confusion.

• Line 83 – I recommend Authors should not make the claim of “strong interactions” until the results have been presented (and discussed).

• Line 84 – For clarity and readability, and to avoid bogus claims, I recommend the language of “identified ‘an inhibitor’”, not ‘the inhibitor’

• Line 141 – I recommend that Authors should refrain from hyphenating or abbreviating molecular dynamics simulations; it is not conventional to do so. Same issue in line 169 with free energy landscape.

• Line 149 – For readability, Authors should consider rewording “for the neutralization its charge”

• Line 152 – The “raised to” statement did not initially clarify a reference temperature. I strongly recommend that Authors make clear and simple the procedural steps involved in all analyses.

• Line 152 – “In addition, the entire system was raised to a temperature of 310 K using a timestep of 2 fs for a simulation time of 100 ps in the NVT ensemble and pressure (NPT) for a duration of 1 ns each at 310 K and 1 atmosphere.”

The statement seem to lack clarity and contains too many contradictory contents; some thoughts: what is the reference temperature of the post-minimization simulation, was there an annealing step, how long were the isothermal or annealing steps (what is the distinction between the 100 ps and 1 ns mentioned), what was the timestep for each? These were not immediately clear upon first-time reading, hence the need to detail all procedures in plain language as much as possible.

• Line 155 – Authors should use conventional language; “production” rather than “manufacturing” for the data collection phase of the molecular dynamics simulations

• Line 156 – To enhance clarity and readability, Authors should consider rewording “Velocity scaling employed to ensure a constant environment of simulation”. The statement should also be clarified to be pertaining to system temperature and not merely ‘environment of simulation’.

• Line 159 – “The hydrogen bonding patterns within the protein-ligand complex were examined utilizing GROMACS' internal tools in order to gain a more comprehensive understanding of the dynamic interactions” – Authors should mention the specific GROMACS tool being used here, and describe its implementation. Also, Authors should stay consistent in representing the GROMACS software in uppercase—no need to provide full meaning (line 142).

• Line 176 – To enhance readability, Authors should consider placing a comma after “kB”

• Line 197 – To enhance readability, Authors should consider replacing “The that” with “The”

• Line 210 – Authors should consider supplying the appropriate citation to PyMol (and to every software being utilized for the study—as was done for GROMACS)

• Authors should consider including the unit of the distance column in Table 2.

• Section 3.4: RMSD – To strengthen claim, I recommend that the Authors make a short, informational comment (with citation(s)) on the potential effects of the protein instability that has been induced by ligand interactions, thus placing that protein stability information in proper context.

• I recommend that the Authors include the molecular structures of all four ligands (the control as well as the three identified) somewhere appropriate in the manuscript main. Also, was the control molecule the same for all analysis performed?

• Line 409 – Could the Authors make comments or provide citations to justify that “1-2 hydrogen bonds” is sufficient for S904-0022 to be deemed relevant for further analyses including in-vitro.

Reviewer #2: The manuscript presents a comprehensive computational study aimed at identifying potential inhibitors of New Delhi Metallo-beta-lactamase-1 (NDM-1) using pharmacophore-based virtual screening, molecular docking, and molecular dynamics (MD) simulations. The study is technically sound, with robust methodologies and data supporting the conclusions. Below is a summary of the review comments and recommendations:

STRENGHTS:

Methodology: The study employs a well-structured, multi-step computational approach, including machine learning-based QSAR modeling, molecular docking, and MD simulations.

Data-Driven Conclusions: The conclusions are supported by extensive data analysis, including binding free energy calculations and interaction analysis.

Validation and Controls: The use of a control molecule (ORV) and cross-validation for the QSAR model enhances the validity of the findings.

Clarity and Structure: The manuscript is well-organized and generally well-written, with clear sections and effective use of figures and tables.

AREAS OF IMPROVEMENTS:

Statistical Analysis:

Provide additional validation metrics for the QSAR model (e.g., RMSE, MAE).

Include confidence intervals or error estimates for key metrics.

Consider performing statistical tests to compare binding affinities and stability.

Data Availability:

Ensure all raw data (e.g., docking scores, MD trajectories, QSAR model data) are included in the supplementary materials or deposited in a public repository.

Clearly state any restrictions on data sharing in the Data Availability Statement.

Language and Clarity:

Correct minor grammatical errors and improve sentence structure.

Simplify overly complex sentences and avoid repetition.

Ensure consistency in terminology (e.g., use "beta" or "β" consistently).

Figures and Tables:

Improve clarity of labels and legends in some figures (e.g., Figure 3).

Future Directions:

Briefly discuss potential limitations of the computational approach and how these will be addressed in future work.

Reviewer #3: The topic is highly relevant given the global public health threat posed by antibiotic resistance, particularly from NDM-1-producing bacteria. The study's use of advanced computational tools to address this challenge is commendable. However, there are several areas where clarity, scientific rigor, and presentation can be improved. These include methodological details, justification of certain choices, and deeper discussion of results in the context of prior literature. Additionally, minor language and formatting issues detract from readability and should be addressed.

For an instance, the authors need to provide justifications for some of the parameters and methods used in the analysis. e.g docking parameters, MACCS keys, k=3 in k-means clustering, etc.

Reviewer #4: The manuscript presents a computational approach for identifying potential NDM-1 inhibitors, leveraging machine learning-based QSAR modeling, molecular docking, and MD simulations. The study is well-structured and relevant, but certain areas need improvement. The QSAR model should provide more details on feature selection, data preprocessing, and validation metrics such as RMSE or MAE to enhance reproducibility.

Additionally, molecular docking parameters, including ligand flexibility, scoring functions, and docking poses, should be clearly specified. While the results suggest strong binding affinities, binding free energy calculations would be more robust if confidence intervals or standard deviations were included.

Furthermore, benchmarking against known NDM-1 inhibitors is necessary to assess the novelty and effectiveness of the proposed compounds. Some figures, such as RMSD and FEL plots, need clearer axis labeling and statistical annotations for better interpretation.

The manuscript is generally well-written, though minor grammatical issues and abstract restructuring could improve readability. It has strong potential but requires major revisions to enhance computational clarity, statistical validation, and data presentation before publication.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

Reviewer #4: Yes:  Abdulquadir Aderinto

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Submitted filename: Manuscript.docx

Structure-Based Virtual Screening, Molecular Docking, and MD Simulation Studies: An In-Silico Approach for Identifying Potential MBL Inhibitors

PONE-D-25-11337R1

Dear Dr. Snoussi,

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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Kind regards,

Yusuf Oloruntoyin Ayipo, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The submission has scientific relevance as a potential starting point in search for new antibiotics to combat the MBL-inclined antibiotic resistance. The manuscript is well-prepared and the authors have responded positively to all concerns initially raised by the editor and respective reviewers. The quality has improved significantly up to the standard for publication in this title. I hereby recommend its acceptance for publication in the current form provided it passes other editorial checks.

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 #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 #3: Yes

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

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 #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 #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 #3: The authors have addressed my concerns in the first review and I believe it should be accepted for a 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 #3: No

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