_Kim.png)
Pharmacophore-Model-Based Virtual-Screening Approaches Identified Novel Natural Molecular Candidates for Treating Human Neuroblastoma
, Ghadeer I. Alrefaei 4, Mohammad Habibur Rahman Molla 1, Nouf H. Alsubhi 5, Faisal Alzahrani 2,3 and Foysal Ahammad 1,6,*
Round 1
Reviewer 1 Report
All the suggestions are written in the review report PDF file, I advice to use a translator service because I found really difficult to follow the main idea of the paper and the syntax of the writing. Also you have to rewrite the introduction because of the order of generalities and specificities of the main idea, the order of the complexes along the paper should be the same so we don't get lost. My final conclusion and advice is to rethink the writing strategy of the paper in order to help readers understanding.
Comments for author File: 
Comments.pdf
Author Response
Pharmacophore-model-based virtual screening approaches identified novel natural molecular candidates for treating human neuroblastoma.
Dear F A Dain:
I’m pleased for reading this original article and I have to congratulate for your effort and vision that you have shown in this paper. Nevertheless, there are some changes and recommendation I suggest before your article could be published.
Response: Thank you professor for your appreciation. Your evaluation of my manuscript made it more convenient and suitable for the reader.
General Review
Question 1: I strongly recommend rewriting the introduction section; it was really difficult to follow the main idea of it, the order of the ideas in my opinion it´s not the better, remember, you have to start with the general idea and then focusing in the specifics ideas of the paper in this case the virtual screening and the complexes you find out. Also, I suggest using a certified translator if your English writing its not full dominated.
Response: Thank you for your valuable suggestions. We added a more generalized idea in the first paragraph of the introduction part which has been marked as yellow. We arranged the step-wise direction for arranging the introduction part (General idea, BET protein, mechanism of cancer development, BET role in neuroblastoma, current treatment side effects, computer-aided drug design, and aim of this study). Based on the acceptance we would be able to send the manuscript for language edition.
Question 2: In order to improve the understanding of the figures and tables, I suggest to have information in the caption that will help understanding the abbreviations and values, also in the results section would be grateful if you describe better the results of the methodology you are using to discover new potential complexes, for people not involved in the virtual-screening could be thankful if you described.
Response: Thank you for your time to evaluate my manuscript. We added the full form for most abbreviations provided in the whole manuscript. The abbreviations have also been attached below the table relying on your suggestions. We arranged the results section in an easier format for the reader. The provided graphical abstract will facilitate easier understanding among the reader of the overall methodology in a manuscript generation.
Question 3: As your work is focused in gene expression and proteins activity, I recommend having extremely careful writing correctly the gene name and the protein name, as you would know, gene are written in capital letter and protein names in lowercase. Also, clearly defining in the context of the writing which are you talking about?
Response: Thank you for your observation. We changed the gene name in capital and the protein name in lowercase according to your suggestions by focusing on your provided example (should be written MYCN : as gene; mycN or myc-N : as protein). The whole manuscript has been corrected.
Question 4: You used the discussion as a summary of the results section like you were telling us again what you have done and discovered instead of making a discuss between your results and previous studies.
Response: We added more important information in the discussion section and evaluated the manuscript scientifically. Please find the attached paragraph in the discussion part marked as yellow. We compared our studies to the previous research. Please find the attached paragraph
“Inhibition of the neuroblastoma by targeting BET protein overexpression is a new research finding, as the previous studies revealed that the several scientists attempted to find BET protein inhibitor using a combination of two drugs with some of them using recombinant protein”
Question 5: You must follow the same order presenting the complexes results so we don’t get lost along the paper finding out again which complex are we talking about
Response: Thank you for your comment. We re-ordered our presentation based on your observation. MM-GBSA analysis is now in the upper position in the materials and methods section to cope with the result section.
Point by point review
- In abstract, at line 22 and 23: MYCN / myc-N (because your are referring to the protein product, the letters should be in lowercase)
Response: Corrected
- In abstract, at line 25: You should establish if you are referring to MYCN as protein or as gene, should be written MYCN : as gene; mycN or myc-N : as protein
Response: Corrected
- In abstract, at line 31: Should be referred which proteins your are talking about.
Response: Corrected
- In abstract, at line 35: You have established the ADME definition but you didn´t have for ADMET
Response: Corrected
- In abstract, at line 37: You have to define the MM-GBSA methods for better understanding.
Response: Corrected
- In abstract, at line 40: In vitro and In vivo / In vitro and In vivo.
Response: Corrected
- In Introduction, at line 48: Must define BRD2, BRD3, BRD4 and BRDT, ¿Does any of it has the same importance?
Response: Thank you. We corrected the sentence. Please find attached sentence in the introduction part.
“BET series of proteins (Brd2, Brd3, Brd4, and Brdt) are chromatin reader protein which are well-known for regulating the transcription of genes’
- In introduction, at line 51: it is not clear which activity of MYCN ¿MYCN activity or MYCN expression?
Response: Corrected
- In introduction, at line 64: antagonists’ / antagonist´s
Response: Corrected
- In introduction, at line 79: treatment[15] / treatment [15]
Response: Corrected
- In introduction, at line 80: in vivo / in vivo
Response: Corrected
- In introduction, at line 80: to targeting / to target
Response: Corrected
- In introduction, at line 81: you should define AML for better understanding
Response: Corrected
- In introduction, at line 85: of the MYC / of MYC
Response: Corrected
- In introduction, at line 92: in silico / in silico
Response: Corrected
- In introduction, at line 100: in vitro and in vivo / in vitro and in vivo
Response: Corrected
- In introduction, at line 102: in vivo / i in vivo
Response: Corrected
- In introduction, at line 102: technique / techniques
Response: Corrected
- In introduction, at line 102: indicate / indicating
Response: Corrected
- In materials and methods, at line 118: It would be better if you could define the PD database
Response: Corrected
- In materials and methods, at line 135: you mentioned “a known active inhibitor” but is not clear which
Response: Corrected. Please find the attached sentence below.
“Validation was essential when evaluating the quality of our model through protein-ligand interactions; several known active inhibitors (Table S1) were used to distinguish between the selected active and inactive compounds”
- In materials and methods, at line 149: it is not well understood why does ZINC databases are used, you must establish this at the introduction section
Response: Corrected. Please find the attached sentence below.
“…. can generate hit to lead compounds more rapidly compared to the conventional drug design process from the ZINC database through virtual screening as it contains several libraries [21][22][23]”
- In materials and methods, at line 151: [37], [38] / [37][38]
Response: Corrected
- In materials and methods, at line 160: protein / Protein
Response: Corrected.
- In materials and methods, at line 180: [19],[35] / [19][35]
Response: Corrected
- In materials and methods, at line 193: [39],[40] / [39][40]
Response: Corrected
- In materials and methods, at line 208: You Mentioned “our study determined” but you need to write the reference so we can follow previous experiments easier
Response: Corrected. We also modified the sentence and mentioned the toxicity studies.
- In materials and methods, at line 234: It is not well understood “with which to calculate”
Response: Corrected. The sentence made easier to the reader and marked as yellow.
- In results, at line 242: IC50 / IC50
Response: Corrected.
- In results, at Figure 1: structure (B) pharmacophore / structure, (B) pharmacophore
Response: Corrected. Thank you for your observation. Slightly modified the sentence.
- In results, at line 282: ready-to-dock and / ready-to-dock and
Response: The sentence has modified scientifically and marked as yellow
- In results, at line 302: Figure 3A / Figure 3.A
Response: Corrected
- In results, at Figure 4: The order of the proteins are in different order along the paper, keep a pattern so we don’t get lost
Response: Thank you for your observation. We changed the order of antagonists and also figure 4, figure 5, table 3, table 4, Figure 7, figure 8, figure 9, and figure 10. As the order has been changed based on the binding affinity score.
- In results, at line 364: energy[19][25] / [19] [25]
Response: Corrected
- In results, at table 2 and 3: abbreviations must be defined at the bottom of the table
Response: Corrected
- In results, at table 2: You have 6 complex names, it seems that you repeated the complex name: ZINC4104882, but the real problem is that you have different values for the same complex calling your results into question
Response: Thank you for your concern. We apologized for the mistake. We corrected the figure. Please see the attached table 2.
- In results, at Figure 6: representing (A) / representing, (A)
Response: Corrected
- In results, at Figure 8: in the figure caption you said “ indicates the numbers of ligands and their patterns of expression” but it is not indicated in the result section how does this figure has to be with expression pattern or exactly which expression pattern do you refer?
Response: Thank you for your comment. The sentence has been rearranged based on your evaluation. We made more clear and acceptable for the reader. Please find it marked as yellow.
- In results, at line 473: (black) ZINC2509501 / (black) ZINC2509501
Response: Made it new graph and removed the black colour. Now it showed by gray colour.
- In discussion, at line 485 and 486: nuroblastoma / Neuroblastoma
Response: Corrected
- In discussion, at line 487: are also been / has also been
Response: Corrected
- In discussion, at line 489 and 490: It is not clear along the paper why do you use in some cases Brd4 and in other BRD4, you have to establish if your are talking about a protein, you must write it in lowercase and y capital letter if you are referring to a gene.
Response: Corrected
- In discussion, at line 495: MYCN / MYCN
Response: Corrected
- In discussion, at line 505: you wrote “based on further”, you can’t based results or used it as a fact if this information don’t even exist
Response: Corrected
- In conclusion, at line 533: “can be potentially block” , this line with all the 534 doesn’t has meaning at all the way you wrote it, has to be rewritten
Response: Corrected. Please find the attached sentence.
“…which can attach to the Brd4 protein and have the possibility to block the activity of this protein overexpression subsequently suppress the MYCN overexpression expression”
- In supplementary materials, at line 548: IC50s / IC50
Response: Corrected
Author Response File: Author Response.pdf
Reviewer 2 Report
The paper focuses on an interesting topic, the search and development of new molecules for the treatment of neuroblastoma.
However, most of the design includes only database search/comparison/verification and in silico processing of information, without a strong experimental design.
The introduction and discussion do not give to the reader an adeguate amount of information to understand the experiment or to process the results for possible future applications.
English requires extensive review, especially the introduction and discussion chapters, where grammar and syntax mistakes are present.
Author Response
The paper focuses on an interesting topic, the search and development of new molecules for the treatment of neuroblastoma.
Response: Thank you for your appreciation. Your kind words make me more enthusiastic to perform future research.
Question 1: However, most of the design includes only database search/comparison/verification and in silico processing of information, without a strong experimental design.
Response: Thank you for your comment. Our study revealed the possibility of further lab-based research to discover lead compounds against neuroblastoma. We performed in-silico drug design and found four potential lead candidates to treat neuroblastoma. Other researchers may become take benefit from cancer drug development through in-vitro and in-vivo analysis from this manuscript.
We also added two more analyses (Radius of gyration and Intramolecular hydrogen bond) from the generated simulation trajectory file. Please see the attached figure 11.
Question 2: The introduction and discussion do not give to the reader an adeguate amount of information to understand the experiment or to process the results for possible future applications.
Response: Thank you for your time and evaluation of our manuscript. We changed the introduction and discussion part by adding more important information for the readers. Please find the attached paragraph marked as yellow. A summary of the experimental methodology was mentioned in the provided graphical abstract. The development of anti-cancer agents would be the future prospect of our computer-aided drug design (CADD). Please refer to the yellow-marked in the discussion section.
Question 3: English requires extensive review, especially in the introduction and discussion chapters, where grammar and syntax mistakes are present.
Response: Thank you for your comment. All authors evaluated the manuscript again and also used Grammarly software to evaluate the grammar as well as other mistakes. Although based on your suggestion we would be able to perform English language edition of the required pages.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
It has been a joy to see you again with this magnificent paper you are trying to publish, in general the idea seems to be great in this new review your paper is better understood, I congratulate you for your effort doing the changes I remarked. It would be nice if you could do a grammar check again, at least for the MYCN form, because I found at line 67 MYCN instead of the italic form. Also the order of the ZINC complexes are not the same in different parts of the results like in the figure 10 for mention one, if you started in the table 2 in one order I hardly suggest to keep that order in every table or every figure. It is only spell checks and minor changes you need to do, there I wish you my best for you and your team.
Author Response
Question 1: It has been a joy to see you again with this magnificent paper you are trying to publish, in general the idea seems to be great in this new review your paper is better understood, I congratulate you for your effort doing the changes I remarked. It would be nice if you could do a grammar check again, at least for the MYCN form, because I found at line 67 MYCN instead of the italic form.
Response: Thank you for reviewing my manuscript. MYCN has been corrected to italic form and marked as yellow.
Question 2: Also the order of the ZINC complexes are not the same in different parts of the results like in the figure 10 for mention one, if you started in the table 2 in one order I hardly suggest to keep that order in every table or every figure. It is only spell checks and minor changes you need to do, there I wish you my best for you and your team.
Response: Thank you for your comments. We have arranged the writing blow the figure 10 based on the serial provided in table 2.
Author Response File: Author Response.pdf
Reviewer 2 Report
Dear author,
I appreciate the changes and modification you made on your paper, I still find there are major language issues in the paper and unfortunately these make the paper itself hard to read and to be understood.
Some new grammar mistakes were introduced with the revised parts, and some of the statement regarding neuroblastoma in the introduction and discussion are not accurate and don't have reference.
The revision did not add to the paper any stronger experimental design. For example all the molecular and pharmacological features described for the natural compounds are not compared to the ones characterizing the molecules currently or previously used as BRD4 protein inhibitors against cancer in clinical trials.
Author Response
Question 1: I appreciate the changes and modification you made on your paper, I still find there are major language issues in the paper and unfortunately these make the paper itself hard to read and to be understood.
Response: We would be able to language edit of our manuscript from the expert panel of MDPI through getting acceptance.
Question 2: Some new grammar mistakes were introduced with the revised parts, and some of the statement regarding neuroblastoma in the introduction and discussion are not accurate and don't have reference.
Response: Thank you for your observations. We revised the introduction and discussion sections with the addition of new references and also modified the sentences through marking as yellow. We also modified grammatical errors by our expert and paid software. We will be able to recheck grammar again by the MDPI expert panel based on acceptance. Our expert panel also revised this manuscript and made the manuscript easier for understanding among the reader. We tried to change the edited sentences based on the round 1 revised parts.
Question 3: The revision did not add to the paper any stronger experimental design. For example all the molecular and pharmacological features described for the natural compounds are not compared to the ones characterizing the molecules currently or previously used as BRD4 protein inhibitors against cancer in clinical trials.
Response: I would like to express my gratitude for your effort. It is an in-silico drug design, so we want to publish computer-based work. Other researchers may start to perform lab-based work based on our results. Recently, several MDPI journals have also published in-silico work without lab-based data. So I hope you will consider our team’s time and efforts in your journal also.
Author Response File: Author Response.pdf
