PONE-D-24-43186Discovery of Novel TACE Inhibitors Using Graph Convolutional Network, Molecular Docking, Molecular Dynamics Simulation, and Biological EvaluationPLOS ONE

Dear Dr. chun,

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Kind regards,

Cheorl-Ho Kim, Ph.D.

Academic Editor

PLOS ONE

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Kangwon National University 2024, a Korea Basic Science Institute (National Research Facilities and Equipment Center) grant funded by the Ministry of Education (grant no. 2022R1A6C101A739), and NIH grant numbers R01GM127701 and R01HG012117.] Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

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Additional Editor Comments:

Thank you for your kind submission of your work and I am very pleased to inform you that your submission would be considered for publication.

Please contact me when you have any problem in revision.

Thanks a lot

Cheorl-Ho Kim

Prof

SKKU Biological Science

Suwon Korea

[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

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

Reviewer #1: Yes

Reviewer #2: Yes

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

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Reviewer #1: Yes

Reviewer #2: Yes

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

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Reviewer #1: Yes

Reviewer #2: 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: The manuscript entitled “Discovery of Novel TACE Inhibitors Using Graph Convolutional Network, Molecular Docking, Molecular Dynamics Simulation, and Biological Evaluation” has many mistakes, authors need to rectify many portions.

• Line 97: The sentence "Therefore, its potential to identify novel TACE inhibitors with greater accuracy and efficiency was examined in this study" is unclear. The sentence does not specify what "its" refers to. It should be rewritten for clarity.

• Line 79: The phrase "TNF-α, is also produced by neurons and glia," includes an unnecessary comma after "TNF-α."

• Line 191: The sentence "TACE, Ligand, and Zn2+ ion was uploaded to the server for each complex and CHARMM36 force field [32] setup was performed using the solution builder protocol on the CHAR..." ends abruptly and seems incomplete.

• The author required to update recent references can be seen PMID: 37065061, 39065802, 35424125, 34297427, 35014595, 36936534.

• Check the sentence: "metrics such as the Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC) curve..."

• Confusing sentence please correct it: TPR of 1 usually indicates perfect performance at a specific threshold, but it doesn’t make sense in relation to the ROC curve unless further clarification is provided.

• It's unclear whether "perfect predictions" refers to all metrics being 1.0 or something else. A more precise explanation would enhance clarity.

• "2OI0 and co-crystallized ligand was utilized to figure out the interacting amino acid residues..."

• Check the sentence "Quinapril, Vorinostat, and Alvimopan with their exceptionally low CDocker energy, emerge as a promising candidate..."

Good Luck!

Reviewer #2: The authors work on Discovery of Novel TACE Inhibitors Using Graph Convolutional Network, Molecular Docking, Molecular Dynamics Simulation, and Biological Evaluation contributes to academic knowledge, but the discussion need to be improved upon. Further comments can be found on the annotated report

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Reviewer #1: Yes: Shahzaib Ahamad

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-24-43186.pdf

Discovery of Novel TACE Inhibitors Using Graph Convolutional Network, Molecular Docking, Molecular Dynamics Simulation, and Biological Evaluation

PONE-D-24-43186R1

Dear Dr. Chun,

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,

Cheorl-Ho Kim, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Dear Dr WJ Chun

Thank you for your submission of your study and revision.

I have checked and examined the revision and found that the revision is appropriately done.

As I have decided MINOR REVISION in a previous decision letter, I will accept your revision at this occasion.

Thank you

Sincerely

Cheorl-Ho Kim PhD Professor

SKKU

Biological Science Dept

Molecular Glycobiology

Reviewers' comments:

No more comments.