A New Plant Growth Regulator: An In Silico Evaluation

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The authors, in the article titled “A New Plant Growth Regulator: In-Silico Evaluation”, investigated Agavenin, a steroidal saponin from Agave species, as a potential plant growth regulator. They focused on its selective interaction with gibberellin and auxin receptors and evaluated its stability, binding affinity, and bioavailability using computational approaches.

Abstract: I advise you to add or rephrase sentences so that the purpose of the research is more clearly emphasized.

Materials and Methods: Everywhere, it is necessary to specify whether this is your own methodology, whether you developed it yourselves, or if you followed or adapted it from another source.

Results and Discussion: Throughout this chapter, you present the results but do not discuss them. Add information on what other studies have found, whether similar studies exist, and compare your findings with theirs. Highlight any unusual observations or noteworthy points—explain why they occur. This is the purpose of the discussion section.

Conclusion: The current conclusion is inappropriate—it reads as a summary rather than highlighting the main findings. Please correct this: The conclusion is too long; discuss details in the results and discussion sections. In the conclusion, write the main research conclusions, emphasize your contribution to science, and explain how your work impacts previous research.

References: The references are incorrectly cited. Please check the citation guidelines for the correct format and order.

Furthermore, throughout the text, in-text citations are inconsistent—this must be corrected! The manuscript is very hard to read; please fix paragraphs and spacing in the text to separate figure titles from the following paragraph, and also separate chapters from each other. Standardize the spelling of in silico. Standardize the wording “figure…” in the text. All other comments are attached and highlighted in the text.

Comments for author File: Comments.pdf

Author Response

Comments 1: Abstract: I advise you to add or rephrase sentences so that the purpose of the research is more clearly emphasized.

Response 1: I appreciate your comment. The abstract has been revised and the topic is addressed differently. The changes are found from lines 21 to 39 on page 1 of the manuscript.

Comments 2: Materials and Methods: Everywhere, it is necessary to specify whether this is your own methodology, whether you developed it yourselves, or if you followed or adapted it from another source.

Response 2: I appreciate your comment, and based on it, sources were added that address the methodologies for each of the techniques used. In molecular docking, for example, on line 121 of page 3, the methodology for this technique is addressed from the outset. And so it is with each methodology section.

Comments 3: Results and Discussion: Throughout this chapter, you present the results but do not discuss them. Add information on what other studies have found, whether similar studies exist, and compare your findings with theirs. Highlight any unusual observations or noteworthy points—explain why they occur. This is the purpose of the discussion section.

Response 3: Following their recommendations, comparisons were added and the results obtained in the study were discussed. Sources were also added to support each results section. The changes can be seen in the discussions from 3.1 to 3.4 of the manuscript.

Comments 4: Conclusion: The current conclusion is inappropriate—it reads as a summary rather than highlighting the main findings. Please correct this: The conclusion is too long; discuss details in the results and discussion sections. In the conclusion, write the main research conclusions, emphasize your contribution to science, and explain how your work impacts previous research.

Response 4: In response to the comments, the conclusions section was revised, and the most important points of this work were highlighted. The changes can be seen from lines 483 to 504 on page 15.

Comments 5: References: The references are incorrectly cited. Please check the citation guidelines for the correct format and order.

Response 5: Changes were made to the form of citations throughout the document.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

How do the results of this study contradict the present theory of plant growth regulation?

What are the possible implications of Agavenin's receptor specificity for sustainable agricultural practices?

How could the in silico findings of the research become relevant for real-world farming practice?

What are the research gaps in understanding Agavenin's effect on plant physiology beyond docking studies?

How do the molecular dynamics simulations inform our understanding of Agavenin's potential efficacy?

Author Response

Comments 1: How do the results of this study contradict the present theory of plant growth regulation?

Response 1: Naturally, growth regulators act through receptors like these. Agavenine shows low affinity/stability with the brassinosteroid receptor BRI1 but shows selective and stable binding with the gibberellin (GA3Ox2) and auxin (IAA7) receptors, which may make it a good growth regulator in culture media.

Comments 2: What are the possible implications of Agavenin's receptor specificity for sustainable agricultural practices?

Response 2: Selectivity for GA3Ox2 and IAA7 (and poor engagement of BRI1) implies fewer off-target effects, more predictable phenotypes, and potentially lower doses (all desirable for biostimulants in sustainable systems).

Comments 3: How could the in silico findings of the research become relevant for real-world farming practice?

Response 3: The Docking/MolecularDynamics/ADME properties can: (a) prioritize Agavenin for in vitro receptor activation and greenhouse assays; (b) inform formulation and delivery (ADME suggests good membrane permeability and the highest drug-likeness among tested ligands); and (c) guide trait targeting, paving a path toward seed treatments or foliar sprays if bioefficacy is confirmed.

Comments 4: What are the research gaps in understanding Agavenin's effect on plant physiology beyond docking studies?

Response 4: Results are computational only and calls for:
• In vitro receptor activation/competition assays; in vivo plant bioassays and phenotyping.
• Gene-expression profiling to map downstream signaling and pathway crosstalk.
• Pharmacokinetics in planta (uptake, translocation, metabolism), dose–response, and formulation/stability studies.
• Selectivity/off-target profiling across additional receptors and safety/environmental fate.

Comments 5: How do the molecular dynamics simulations inform our understanding of Agavenin's potential efficacy?

Response 5: Collectively, molecular dynamics simulations improve confidence that a compound not only binds to its target, but can do so in a stable, specific, and functional manner under biological conditions, increasing the likelihood of its true efficacy. In this case, MD shows stable complexes for AG–GA3Ox2 and AG–IAA7, consistent with sustained receptor engagement and thus higher likelihood of functional activity. Conversely, the AG–BRI1 complex exhibits larger fluctuations/instability, aligning with low predicted efficacy in the brassinosteroid pathway.

I really appreciate all your questions and I hope my answers have clarified your doubts about the work.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

• Please correct the citation format throughout the text.
• There are missing periods, and the spelling of words needs to be standardized.
• Please standardize the spacing and paragraphs throughout the entire text.
• Please review the citation guidelines again and make the necessary corrections.
• All other comments and mistakes have been highlighted within the text.

Comments for author File: Comments.pdf

Author Response

Comments 1:  Please correct the citation format throughout the text.

Response1: Thank you for your comment. The text was revised, and the citation errors in the manuscript were corrected.

Comments 2: There are missing periods, and the spelling of words needs to be standardized.

Response 2: Punctuation errors were corrected and some words were standardized throughout the text.

Comments 3: Please standardize the spacing and paragraphs throughout the entire text.

Response 3: The spacing was standardized and the paragraphs were separated on the indicated lines.

Comments 4: Please review the citation guidelines again and make the necessary corrections.

Response 4: We review the citation guidelines and we did the indicated corrections.

Comments 5: We appreciate your corrections and comments, and we've attached the file with these improvements. We hope you enjoy the new document.

Author Response File: Author Response.pdf