Structure-Based Drug Design Targeting Topoisomerase II Alpha: Discovery of Potential Antitumor Xanthone Derivatives

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This study employed CADD methods to screen 3,000 xanthone derivatives and identified two potential TOP2A inhibitors. The compounds were systematically evaluated using molecular docking, molecular dynamics simulations, steered molecular dynamics simulations, and pharmacophore modeling. The workflow is clear, the combination of methods is reasonable, and the data analysis is relatively detailed, giving the study scientific value and potential significance for drug discovery. However, the manuscript currently has notable shortcomings in the following aspects, and major revisions are recommended before publication.

 

1. Provide at least one piece of preliminary in vitro validation data.
2. Standardize the writing; check whether spaces are required between numbers and units (e.g., “200 ps” instead of “200ps”).
3. The font size in Figure 9 is too small.
4. The pH condition is not specified.The pH value used in the MD and SMD simulations is not stated.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript presents a well-structured computational study combining molecular docking, molecular dynamics, steered molecular dynamics, clustering, and pharmacophore modeling to identify potential TOP2A inhibitors. The workflow is coherent and the results are scientifically relevant. However, the manuscript requires minor revisions related to language quality, terminology, clarity of methodology, and cautious interpretation of results.

Point 1. Abstract, page 1
The statement regarding cancer statistics is inaccurate. The manuscript states that cancer contributes to 19 million deaths annually, which is incorrect. This value refers to new cases rather than deaths. This should be corrected to reflect accurate epidemiological data.

Point 2. Introduction, page 1
The phrase “In addition to the development of social life” is stylistically incorrect and unclear. It should be reformulated to reflect scientific English, for example “With the development of modern society”.

Point 3. Introduction, page 2
The use of the phrase “countries of the second and third world” is outdated and inappropriate in scientific writing. It should be replaced with “low- and middle-income countries”.

Point 4. Introduction, page 2
The expression “acceptable and low price of anti-cancer drugs” is not precise. It should be replaced with “affordable and accessible anticancer drugs”.

Point 5. Introduction, page 1
The manuscript incorrectly refers to TOP2A as “a crucial DNA gyrase”. This is scientifically incorrect because DNA gyrase is a bacterial enzyme. The correct term is “DNA topoisomerase”.

Point 6. Methods description, page 3
The phrase “atomistic simulations combined with structural analysis methods” lacks precision. It should explicitly state that molecular dynamics and steered molecular dynamics simulations were used.

Point 7. Results, Table 1, page 4
There is inconsistency in unit formatting, for example “kcal. mol-1”. Units should be consistently written throughout the manuscript.

Point 8. Results, page 5
Long and complex sentences reduce readability, particularly in the description of ligand–protein interactions. Some sentences should be divided into shorter statements to improve clarity.

Point 9. Methods and Results, page 6
The description of the fast pulling ligand method is not fully precise. The correct terminology is “fast pulling of ligand (FPL)”.

Point 10. Results, page 7
The regression equation is presented without clear explanation of variable units. The authors should specify the units of all parameters and ensure consistency with the rest of the manuscript.

Point 11. Results, page 9
The phrase “this molecule was considered a HIT compound” should be revised to a more precise formulation such as “this molecule was identified as a HIT compound”.

Point 12. Results, page 10
There is a grammatical error in the phrase “To analysis structure-activity relationship”. It should be corrected to “To analyze the structure–activity relationship”.

Point 13. Results, page 11
Unit formatting remains inconsistent in expressions such as “kcal.mol-1”. This issue appears repeatedly and should be corrected globally.

Point 14. Discussion, page 13
The phrase “through pilot study” should be corrected to “through a pilot study”.

Point 15. Discussion, page 13
The manuscript lacks sufficient emphasis on the limitations of computational methods. The authors should explicitly acknowledge that docking and MD predictions may not directly translate into biological activity.

Point 16. Discussion, page 13–14
Some conclusions are overstated, particularly regarding binding affinity and potential biological activity. The authors should moderate these claims and clearly distinguish between computational prediction and experimental validation.

Point 17. ADMET analysis, page 13
The statement “no risk of cytochrome P450 inhibition” is too absolute. It should be reformulated to indicate that no significant inhibition was predicted, rather than definitively excluded.

Point 18. Materials and Methods, page 14
The ligand preparation section does not specify whether energy minimization or geometry optimization was performed. This should be clarified to improve reproducibility.

Point 19. General language issues
The manuscript contains numerous minor grammatical errors, awkward phrasing, and stylistic inconsistencies. A thorough language revision by a native English speaker or professional editing service is recommended.

Point 20. General formatting issues
There are inconsistencies in notation, spacing, and formatting of units and symbols throughout the manuscript. These should be standardized according to journal guidelines.

Final recommendation
The manuscript is scientifically sound and presents valuable results. However, minor revisions are required to improve clarity, language quality, and precision. After addressing the comments listed above, the manuscript will be suitable for publication.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

I've reviewed the manuscript submitted by Thi Thuy Huong Le et al., and here are some points that should be addressed before publication.

1.- It would be beneficial for the authors to conduct a docking consensus rather than choosing a single program for docking, after evaluating four of them. In addition, why was MOE not used to docking analysis?

2.- The authors should appropriately describe which residues are DC8, DG13, DG7, among others.

3.- The RMSD values ​​are not included in the validation of the 12 experimental inhibitors. Typically, these values ​​are used to discuss validation.

4.- Authors mention “The results showed that all complexes reached equilibrium after approximately 50 ns”. Hence, MDs at 100 ns are too short to discuss stability. MDs should be performed at least 200 ns. In addition, plots from process equilibrium of system should be included as supporting information.

5.- RMSF, Radius of gyration calculations should be included as part of the MDs assessment.

6.- In the workflow, authors filter ligands by Ro5 after docking simulations. Why? Why not before?. This should be explained in discussion section.

7.- It would be interesting if the authors provided more details about the characteristics of the clustered ligands. For example, in cluster 3, what were the characteristics/descriptors of the ligands? Were they similar? Please briefly describe this in the manuscript.

8.- ADMET section is poorly discussed. Any improvement? Results are similar or not to reference inhibitors.

9.- Any in vitro experiment to validate?

10.- The conclusions need to be rewritten. Please be more concise.

Minor:

Access date to PubChem database

Open Babel version.

Access date to SwissADME websever

Access date to ChemAxon webserver

Access date to The pkCSM

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

I think it can be accepted in its current form.

Reviewer 3 Report

Comments and Suggestions for Authors

Authors have addressed most of the points.