Let’s Talk about Sex Hormone Receptors and Their Physical Interaction with Sonic Hedgehog Protein: A Computational Study with Emphasis on Progesterone Receptor

Round 1

Reviewer 1 Report

In this manuscript, the authors build upon prior research concerning the Hedgehog-GLI (HH-GLI) signaling pathway's involvement in breast and prostate cancers. The primary focus of this study is to investigate the potential binding of SHH-N with the progesterone receptor (PR), which belongs to the nuclear sex hormone receptor (SHR) subfamily. Utilizing molecular docking, robust molecular dynamic (MD) simulations, and free energy calculations, the research anticipates stable binding interactions between SHH-N-cholesterol and all three SHRs: ERα, AR, and PR. Of particular interest is the observation that the C-terminally cholesteroylated N-terminal domain of SHH demonstrates the strongest binding affinity with ERα followed by AR and PR. This finding suggests a non-canonical interaction with potential biological significance. The manuscript is well-structured and easily comprehensible, making it suitable for publication with the following considerations:

1.     Rearrange the residue annotations in Figure 7 to avoid overlap with the protein model. Consider summarizing these residues in a table format.

2.     Incorporate a calibration bar in Figure 7 to indicate the B-factor. Adjust the color of the small molecule ligand (e.g., change it from blue) to ensure it is distinguishable from the B-factor.

3.     Consider revising the title to be more scientifically rigorous while maintaining a descriptive tone consistent with scientific publication standards.

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

The authors demonstrated that the mature form of the sonic hedgehog protein (SHH-N), thought its cholesterol moiety, interacts not only with the estrogen receptor alpha (ERα) and androgen receptor (AR), but also with progesterone receptor (PR).

 1.     The overall structure of this paper is very long, especially in the Introduction section. I found very difficult to follow the logical links between the different parts. The decision is your, but you may consider reducing some parts if you want to catch the reader’s attention. The discussion, instead, which is usually long, is here very short…

 2.     The abstract starts by describing your previous works, which are certainly very interesting and well-documented. However, it is not common to begin an abstract describing previous publications.

3.     In the abstract, the main methods used are cited, but they can be expressed more clearly. The following analyses/procedures were conducted…

 4.     Abstract conclusion seems to underline the importance of ERalpha (“a more favorable enthalpy of binding with SHH-N-cholesterol than with estradiol”), while I understood that the most original part of the paper was described to be on PR.

5.     Line 548 (end of Dicussion): “ targeting interaction between SHH-N and SHRs 548 might be a valuable strategy for the treatment of such tumors”: which tumors?

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Thank you for your modifications. I think that the abstract is now more understandable and easy to follow.