All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
This manuscript now can be considered for publication, as the authors have adequately addressed all the concerns raised by the reviewers.
[# PeerJ Staff Note - this decision was reviewed and approved by Vladimir Uversky, a PeerJ Section Editor covering this Section #]
perfect
excellent
almost valid
no further comments
The authors have carefully revised the original manuscript. Moreover, they have performed lab experiments in order to support their findings. I have no other comments.
no comment
no comment
Reviewers have raised some serious concerns which requires substantial and thorough revision to appreciate the quality for publication in PeerJ. MAJOR revision is suggested. Therefore, authors are requested to revise their manuscript in light of reviewers comments and resubmit accordingly.
Furthermore, thorough English editing is required. Please revise the manuscript taking help from a colleague who is proficient in English and familiar with the subject matter, who can review your manuscript, or contact a professional editing service to review your manuscript.
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
[# PeerJ Staff Note: The Academic Editor has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at copyediting@peerj.com for pricing (be sure to provide your manuscript number and title) #]
Few figures need to be improved. Such as Figure 2 and 4.
1. If possible, the figure 4 could be edited for better view with clear content of labels.
2. In line no. 133, the authors have mentioned “A binding free energy less than zero indicates that the ligand binds to the receptor spontaneously”. Do the ligands bind repeatedly with the receptor or any spontaneous process of the thermodynamics occurs? Revise the statement accordingly. Please refer the below article for detailed information
a. Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods. International journal of molecular sciences, 17(2), 144. (2016) https://doi.org/10.3390/ijms17020144
4. The authors have selected only five best complex for molecular dynamics studies based on their binding energies. If possible display the remaining other targets with ligands not included in further analysis with binding energies in supplementary. It could be helpful for the follow-up studies
3. In line 174, “After the duplicates were removed, one thousand two hundred and twenty-three targets were obtained”, the authors could mention the same in numbers/integers and maintain uniformity.
.
.
.
The manuscript is novel, well written and the results are interesting, however, the major point that I have a concern regard are;
1- Experimental in vitro enzyme assay for the best selected target such as Hsp90 , PI3K , ....
one enzyme assay for one or two representative component of the plant will validate the in silico results.
2- Cell line inhibition measurement of the most representative component of the plant.
3- correlation of enzyme assay inhibition with cell line inhibition for both pure compounds and herbal extract will validate the finding more.
4- it is not clear if the anti-tumor effect of the herb extract is due to a principal compound or due to cumulative effect of the herb components, so I think it is required from the authors to clarify this point.
5- Statistical validation of the method used, use a reference or standard to compare with is essential.
6- I think addition of the scheme or flowchart for the sequence of the work will help understanding the logic of the manuscript, specially the idea seems novel.
7-Validation of the docking process by redocking of cocrystallized ligand and find RMSD values.
This paper addresses an interesting topic: to shed some light on the mechanisms of action of the herb Taraxacum mongolicum. The authors use the principal databases and software for data analysis and predictions to their scope and they find two possible active ingredients (Austricin and Quercetin) that probably interact with the protein encoded by the gene HSP90AA1 (Heat shock protein HSP 90-alpha).
The paper is well organized, includes sufficient introduction and background and the methods are described precisely.
The research question is well-defined and meaningful.
The investigation is all in silico, but it is well performed.
The methods are described precisely.
All the data have been provided.
The results are quite well presented, however they could be better described and discussed. In particular, it should be shown or described where the molecules interact with HSP60 with respect i.e. to ATP binding site in order also to speculate on possible consequences of the binding. Moreover, at least in the discussion section, the gene symbols should not be used to identify the proteins. Since there are no lab experiments confirming the in silico results, It is also necessary to maintain doubt sentences.
The figures need captions and some of them do not appear of sufficient resolution.
The English language should be improved. Some examples where the language could be improved are included in the PDF revised file.
I have some minor suggestions to make, therefore, please, check the PDF file.
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.