Review Reports - Epigenetic Dysregulation in Neurodegeneration: The Role of Histone Deacetylases and Emerging Inhibitor Strategies

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

It is an interesting work, I have some suggestions

1.- I suggest to update references

2.- Describe and add Figures which support the mechanism (HDAC inhibition/activation) under precise targets supported with references.

3.- I suggest to draw molecules with their enantiomer active structure or mention the racemic uses.

4.- Include those molecules in clinical trials as well as those located at public patents

Author Response

Thank you sir/ mam for your comments and suggestions on our manuscript entitled “Epigenetic Modulation of Histone Deacetylases in Neurological Disorders: Nitrogen-Heterocyclic Inhibitors and Therapeutic Strategies”. We have carefully responded to each of the comments and suggestions made by the reviewer and have marked the revised areas in the revised manuscript.

Reviewer 1

I suggest to update references.

Response: We appreciate the reviewer’s suggestion. The reference has been updated and highlighted.

Describe and add figures which support the mechanism (HDAC inhibition/activation) under precise targets supported with references.

Response: We appreciate the reviewer’s suggestion. The (Fig.1.) mentioned in the manuscript supports the mechanism of hdac inhibition and description is provided.

I suggest to draw molecules with their enantiomer active structure or mention the racemic uses.

Response: We appreciate the reviewer’s suggestion. However, most of the referenced studies do not provide detailed information on enantiomerically active structures and report the compounds as racemic mixtures.

Include those molecules in clinical trials as well as those located at public patents.

Response: We appreciate the reviewer’s suggestion. They are added and highlighted.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript provides a comprehensive and well-structured overview of HDAC biology and inhibition in neurodegenerative disorders. Overall, the literature covered is impressive and reflects the authors’ strong command of the field and the article’s topic is timely and can be accepted for publication after addressing some issues.

“The review is logically structured and well-written, bringing the reader from basic epigenetic concepts to sophisticated therapeutic approaches. Adding some recent articles of HDACs would increase the overall review. PMID: 39598445; https://doi.org/10.3389/fphar.2024.1488585
“The discussion of HDAC isoforms and their disease-specific roles can be improved by clarifying complex mechanistic differences across AD, PD, and HD.”
“Figures and tables are informative, well-designed, and significantly enhance the clarity of the presented concepts, especially for readers less familiar with epigenetic regulation. The quality of Figures can be improved. To help readers better understand the topic, the authors should think about including a brief graphic that summarizes the involvement of HDAC isoforms in various neurodegenerative diseases.
The authors must address the reasons why promising preclinical HDAC inhibitors have failed in late-stage clinical trials. This could enhance the conversation about clinical translation.
The authors can add a brief comparative table highlighting pan-HDAC inhibitors versus isoform-selective inhibitors (including advantages, limitations, and BBB penetration).
A brief subsection on new biomarkers or epigenetic readouts that might be utilized to track HDAC-target interaction in vivo might be included by the authors.
The authors must include multi-target-directed ligands and emerging strategies such as PROTACs as this would add novelty and forward-looking value to the review.
“Overall, this review represents a valuable contribution to the neuroepigenetics literature and will serve as a useful reference for researchers developing HDAC-based therapeutic strategies.

Author Response

Reviewer 2

The review is logically structured and well written, guiding the reader from basic epigenetic concepts to sophisticated therapeutic approaches. Adding some recent articles on HDACs would further enhance the overall review.
PMID: 39588445
https://doi.org/10.3389/fphar.2024.1488585

Response: We thank the reviewer for this positive assessment. In response, we have updated the manuscript by incorporating several recent and relevant studies on HDAC biology and inhibition, including the suggested reference (PMID: 39588445).

The discussion of HDAC isoforms and their disease-specific roles can be improved by clarifying complex mechanistic differences across AD, PD, and HD.

Response: We appreciate this suggestion. The manuscript has been revised to improve clarity regarding isoform-specific and disease-dependent roles of HDACs in Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease.

Figures and tables are informative, but the quality of figures can be improved. Consider including a brief graphic summarizing HDAC isoform involvement in neurodegenerative diseases.

Response: The quality of the images has been improved.

The authors must address the reasons why promising preclinical HDAC inhibitors have failed in late-stage clinical trials.

Response: We appreciate this insightful recommendation and added the following data’

Add a comparative table highlighting pan-HDAC inhibitors versus isoform-selective inhibitors.

Response: We thank the reviewer for this valuable suggestion. A new comparative table has been added summarizing pan-HDAC inhibitors versus isoform-selective inhibitors, highlighting their advantages, limitations, and BBB penetration characteristics.

Include a brief subsection on biomarkers or epigenetic readouts to track HDAC–target interaction in vivo.

Response: We appreciate this insightful recommendation. We have added the following data in future perspective section in article.

Include multi-target-directed ligands and emerging strategies such as PROTACs.

Response: We appreciate this insightful recommendation and added.

Overall assessment of the manuscript.

Response: We sincerely thank the reviewer for the positive overall evaluation and for recognizing the value of this review as a resource for researchers developing HDAC-based therapeutic strategies.

Reviewer 3 Report

Comments and Suggestions for Authors

The review is extremely long and requires substantial restructuring and revision. It is very difficult to follow the biological relevance amid the extensive chemical details. In its current form, the manuscript appears more suitable for publication in a chemistry-focused journal or book rather than Biomolecules. Alternatively, the review could be divided into disease-specific topics or revised in another manner; nonetheless, significant revision is necessary.

The title does not fully correspond to the review content.
The Introduction is excessively long and should be shortened and divided into clearly structured paragraphs according to content. At present, the text is written in a narrative style, which makes it difficult to identify the main messages. The goal of a review article should not be to maximize length, but to concisely summarize the most important findings for readers.
This comment applies to the entire manuscript.
Additionally, the Introduction, as well as other sections, contains inconsistent font styles that should be unified. If emphasis is required, the use of bold font is sufficient.
Section 2 – Histone Deacetylases: Functional Roles and Therapeutic Potential
This section also requires division into paragraphs based on thematic content to improve readability and clarity. This comment applies to other sections as well.
The review is overloaded with excessively detailed compound chemical analyses and reads more like a chemistry article than a biological review. The key biological information related to the compounds shown in Figures 3, 4, and others could be summarized in tables. The remaining detailed chemical analyses would be more appropriate for a separate, chemistry-focused review. The abundance of chemical details obscures the biological significance.
Data from human studies, mouse models, and cell-based models are all mixed together, which obscures the central message of the review. Focusing primarily on human-related data would be sufficient and would improve the coherence of the manuscript.
The cell types and their origins are not adequately described. Providing only brief cell line names or titles is insufficient; more detailed explanations are required.
It is unclear where the scaffolds shown in Figure 4 originate from and why they were selected. The text does not adequately explain or emphasize this point.
All abbreviations used in the figures should be fully explained in the figure legends.
The Conclusions section is superficial and lacks a concrete summary of the main findings. Font inconsistencies are also present in this section and should be corrected.

Author Response

Reviewer 3:

The title does not fully correspond to the review content.

Response: We appreciate this observation. The title has been carefully revised.

The Introduction is excessively long and should be shortened and divided into clearly structured paragraphs according to content. At present, the text is written in a narrative style, which makes it difficult to identify the main messages. The goal of a review article should not be to maximize length, but to concisely summarize the most important findings for readers. This comment applies to the entire manuscript. Additionally, the Introduction, as well as other sections, contains inconsistent font styles that should be unified. Emphasis is required; the use of bold font is sufficient.

Response: We thank the reviewer for this valuable suggestion. The Introduction has been shortened, reorganized into clearly structured paragraphs, and revised to highlight key messages more concisely.

Section 2 – Histone Deacetylases: Functional Roles and Therapeutic Potential. This section also requires division into paragraphs based on thematic content to improve readability and clarity. This comment applies to other sections as well.

Response: We thank the reviewer for this valuable suggestion. Division into paragraphs has been done.

The review is overloaded with excessively detailed compound chemical analyses and reads more like a chemistry article than a biological review. The key biological information related to the compounds shown in Figures 3, 4, and others could be summarized in tables. The remaining detailed chemical analyses would be more appropriate for a separate chemistry-focused review. The abundance of chemical detail obscures the biological significance.

Response: we would emphasize the particular value of our chemical perspective, which makes our review special and more informative for chemists and biologists.

Data from human studies, mouse models, and cell-based models are all mixed together, which obscures the central message of the review. Focusing primarily on human-related data would be sufficient and would improve the coherence of the manuscript.

Response: We have grouped cell-based and human- related data on the one or other subject under discussion.

The cell types and their origins are not adequately described. Providing only brief cell line names or titles is insufficient; more detailed explanations are required.

Response: We thank the reviewer for this point. Cell types and experimental systems used in the cited studies are identified at first mention throughout the manuscript (e.g., SH-SY5Y neuroblastoma cells, HEK293/HEK293T cells, primary neurons, transgenic mouse-derived neurons). As this is a review article, extended methodological descriptions were not given, consistent with standard practice, while maintaining sufficient information to contextualize biological relevance.

It is unclear how the scaffolds shown in Figure 4 originate from and why they were selected. The text does not adequately explain or emphasize this point.

Response: We thank the reviewer for this point. The origin and rationale for scaffold selection are described in the corresponding text and figure legend. We believe this information adequately explains their relevance.

All abbreviations used in the figures should be fully explained in the figure legends.

Response: We thank the reviewer for this helpful suggestion. All abbreviations used have now been fully defined in the corresponding figure legends to improve clarity and readability.

Conclusions are superficial and contain font inconsistencies

Response: We thank the reviewer for this comment. The Conclusions section has been revised. Font formatting has been carefully checked and is consistent throughout the section.

Reviewer 4 Report

Comments and Suggestions for Authors

The manuscript with ID: biomolecules-4038915 titled “Epigenetic modulation by Nitrogen Heterocyclic Histone Deacetylase Inhibitors in Neurological Disorders” by Pawar, Y.; et al. is a Review work where the authors outlined the most recent advances in the field of treatments against neurodegenerative malignancies and the promising histone deacetylase biomarker to tailor selective and efficient strategies for patients. This is a topic of growing interest and the manuscript is generally well-written.

However, it exists some points that need to be addressed (please, see them below detailed point-by-point) to improve the scientific quality of the submitted manuscript paper before this article will be consider for its publication in Biomolecules.

1) Introduction. “Neurological disorders represent (…) Alzheimer’s disease is the leading casue (…) Parkinsons’s disease (PD) is expected to affect approximately 25.2 million people worldwide by 2050 (…) neurological burden of the future” (lines 41-63). Could the authors provide quantitative data insights according to the disability-adjusted life years (DALYs) related to neurodegenerative diseases? This will significantly aid the potential readers to better understand the significance of this devoted Review work.

2) “Early diagnosis and intervention (…) mitigate symptoms and enhance overall well-being” (lines 74-77). Here, it should be also discussed about the emerging nanoscale imaging tools [1] or positron emission tomography (PET) [2] to find biomarkers of neurodegenerative diseases for the early prognosis. This will strengthen the importance to gain insights of the biomolecular biomarkers that could act as trigger factors for the disease progression.

[1] https://doi.org/10.1002/smsc.202500351

[2] https://doi.org/10.1038/s41380-025-03081-2

3) “Functioning in concert with histone acetyltransferases (HATs) (…) Neurodegenerative disorders such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and Huntington’s disease (HD), (…)” (lines 111-121). Here, it should not be neglected amyotrophic lateral sclerosis as neurodegenerative disease. Some insights should be furnished in this regard.

4) Histone deacetylases: Functional roles and therapeutic potential. A schematic representation highlighting the interplay of the histone deacetylase classes with their triggers and inhibitors will also benefit the potential readers.

5) HDAC Inhibitors in the Treatment of Neurodegenerative Disorders. Figure 4 (line 448). The lettering is slightly blurry. The font size should be enlarged to overcome this issue.

6) HDAC inhibitors in the treatment of neuro-oncological disease (lines 1155-1389). Did the authors taken into account the potential biased related to the sex, race and age of the patients to the different HDAC inhibitor treatments? Some insights should be furnished in this regard.

7) “5. Conclusion” (lines 1390-1447). This section perfectly remark the most relevant outcomes found by the authors in this field and the promising future prospectives. It may be remarkable to also briefly discuss about the potential future action lines to pursue the topic covered in this work.

8) Finally, some statements are in lower case lettering in the Conclusion section as “has established its position” (line 1410) or “Within this context” (line 1430), among others. The authors should fix this issue.

Author Response

Reviewer 4:

“Neurological disorders represent (…) Alzheimer’s disease is the leading cause (…) Parkinson’s disease (PD) is expected to affect approximately 25.2 million people worldwide by 2050 (…) neurological burden of the future” (lines 41–83). Could the authors provide quantitative data insights according to the disability-adjusted life years (DALYs) related to neurodegenerative diseases? This will significantly aid the potential readers to better understand the significance of this devoted Review work.

Response: We appreciate this important suggestion. The Introduction section has been revised to include quantitative data on disability-adjusted life years (DALYs) associated with major neurodegenerative diseases.

“Early diagnosis and intervention (…) mitigate symptoms and enhance overall well-being” (lines 74–77). Here, it should also be discussed about the emerging nanoscale imaging tools [1] or positron emission tomography (PET) [2] to find biomarkers of neurodegenerative diseases for the early prognosis. This will strengthen the importance to gain insights of the biomolecular biomarkers that could act as trigger factors for the disease progression.

[1]https://doi.org/10.1002/smc.202500351
[2] https://doi.org/10.1038/s41380-025-03081-2

Response: The relevant section has been expanded to include discussion on emerging diagnostic approaches, including nanoscale imaging tools and positron emission tomography (PET), for the identification of biomarkers in neurodegenerative diseases and references are also updated.

“Functioning in concert with histone acetyltransferases (HATs) (…) Neurodegenerative disorders such as Parkinson’s disease (PD), Alzheimer’s disease (AD), and Huntington’s disease (HD) (…)” (lines 111–121). Here, it should not be neglected amyotrophic lateral sclerosis as neurodegenerative disease. Some insights should be furnished in this regard.

Response: We appreciate this insightful comment. The manuscript has been revised to include amyotrophic lateral sclerosis (ALS) in the discussion of neurodegenerative disorders influenced by histone acetylation–deacetylation balance.

Histone deacetylases: Functional roles and therapeutic potential. A schematic representation highlighting the interplay of histone deacetylase classes with their triggers and inhibitors will also benefit the potential readers.

Response: We thank the reviewer for this constructive suggestion. The functional roles of histone deacetylases and their therapeutic potential, including the interplay between HDAC classes, their triggers, and inhibitors, are already comprehensively presented in a tabulated format in the manuscript. We believe that this table effectively conveys the requested schematic-style overview in a clear and reader-friendly manner; therefore, no additional schematic figure was added.

HDAC inhibitors in the Treatment of Neurodegenerative Disorders. Figure 4 (line 448). The lettering is slightly blurry. The font size should be enlarged to overcome this issue.

Response: Figure 4 has been revised to improve resolution and font size, ensuring better readability and visual clarity.

HDAC inhibitors in the treatment of neuro-oncological disease (lines 1155–1389). Did the authors take into account the potential biased related to the sex, race and age of the patients to the different HDAC inhibitor treatments? Some insights should be furnished in this regard.

Response: The section on HDAC inhibitors in neuro-oncological diseases has been revised to include discussion on potential biological variables such as sex, age, and demographic factors that may influence therapeutic response.

“5. Conclusion” (lines 1390–1447). This section perfectly remark the most relevant outcomes found by the authors in this field and the promising future prospects. It may be remarkable to also briefly discuss about the potential future action lines to pursue the topic covered in this work.

Response: We thank the reviewer for pointing out this issue. The identified typographical and formatting errors in the Conclusion section have been corrected.

Finally, some statements are in lower case lettering in the Conclusion section as “has established its position” (line 1410) or “Within this context” (line 1430), among others. The authors should fix this issue.

Response: We thank the reviewer for pointing out this issue. The identified typographical and formatting errors in the Conclusion section have been corrected.

Reviewer 5 Report

Comments and Suggestions for Authors

Yogesh Pawar and colleagues present a quite comprehensive review article on the action and potential of histone deacetylase inhibitors in the treatment of neurological disorders, such as Alzheimer's, Huntington's and Parkinson's diseases. In general, the article is easy to follow, however, in my opinion, it would benefit from some shortening, especially in the introductory parts of each section. A large part of the information contained therein could easily be accommodated in the relevant figure legends.

Several parts of the text have a different font size and/or appear in bold. Please check for consistency and correct all these issues. Besides highlighting compound numbers in bold, I don’t see a reason to highlight IC50 values or publication years, or other information.

Authors may also consider to combine the relevant compound structure figures for each disorder.

Author Response

Reviewer 5:

In general, the article is easy to follow; however, in my opinion, it would benefit from some shortening, especially in the introductory parts of each section. A large part of the information contained therein could easily be accommodated in the relevant figure legends.

Response: We thank the reviewer for this valuable suggestion. The introductory sections of each chapter have been carefully revised and streamlined to improve conciseness and readability. Redundant descriptions were reduced, and where appropriate, supporting information has been shifted to the corresponding figure legends to enhance clarity without compromising scientific content.

Several parts of the text have a different font size and/or appear in bold. Please check for consistency and correct all these issues. Besides highlighting compound numbers in bold, I don’t see a reason to highlight IC50 values or publication years, or other information.

Response: We appreciate the reviewer for pointing out these formatting inconsistencies. The entire manuscript has been thoroughly checked, and font size and style have now been standardized throughout. Bold formatting has been removed for compound number, IC50 values, publication years, and other information have been reformatted to normal text for consistency and improved presentation.