Nɛ-acetyl lysine derivatives with zinc binding groups as novel HDAC inhibitors

HDAC inhibitors have been developed very rapidly in clinical trials and even in approvals for treating several cancers. However, there are few reported HDAC inhibitors designed from Nɛ-acetyl lysine. In the current study, we raised a novel design, which concerns Nɛ-acetyl lysine derivatives containing amide acetyl groups with the hybridization of ZBG groups as novel HDAC inhibitors.

16b-c" with "the treatment of intermediates 16b-c with hydroxyl amine". 7. Page 3, left column, line 5, the sentence "which was under the ester……give compounds 16a-c" need to be rewritten. 8. Page 2, left column, line 48, "Followed by…." is incorrect. 9. "lysine analogs" is incorrect and should be "lysine derivatives". 10. Move some of the conclusions into the introduction to make the conclusions clear and concise.
Decision letter (RSOS-190338.R0) 29-Mar-2019 Dear Professor Bin: Title: Nε-acetyl-lysine analogues with Zinc binding groups as novel HDAC inhibitors Manuscript ID: RSOS-190338 Thank you for your submission to Royal Society Open Science. The chemistry content of Royal Society Open Science is published in collaboration with the Royal Society of Chemistry.
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RSC Subject Editor:
Comments to the Author: (There are no comments.) ********************************************** Reviewers' Comments to Author: Reviewer: 1 Comments to the Author(s) HDAC is an important epigenetic target in drug discovery and development. The authors developed Nε-acetyl-lysine analogues with Zinc binding groups as HDAC inhibitors. The best compound 18c had an IC50 value of 500 nM for HDACs. Besides, WB and MTS assay were used to evaluate the antitumor activity of all synthetic compounds. This manuscript has provided an effective strategy for developing novel HDAC inhibitors. Minor comments: 1) the values of the anti-proliferative assay in Fig. 4 should be provided based on dose-dependent curve-fitting. 2) in order to evaluate 18c toxicity, the authors need to determine the IC50s of 18c and SAHA against both tumor cells and normal cells, then calculate and compare their selective index.

Reviewer: 2
Comments to the Author(s) This manuscript described the design and synthesis of HDAC inhibitors by hybridizing acetyllysine and zinc binding group. Their enzymatic and cellular activities were also characterized. The most promising compound 18c had reasonable inhibition against HDACs. Interestingly, 18c demonstrate the comparable antiproliferative activities against several cancer cell lines but the less toxicity for normal cells than that of SAHA. Therefore, it is worthy of eventual publication in Royal Society Open Science if the authors can address the following concerns: 1. Should add some discussion about whether the synthesized compounds intend to be pan-or specific-HDAC inhibitors.
2. The cellular data is just described for the acetylation level of tubulin which is only relevant for HDAC6. HDAC1-3 are involved in acetylation of H3, which is strongly suggested to be present in the figure. 3. The authors should give dose-dependent curves in Fig. 4. 4. The authors should check English and careless typos in the text, and the format of the structural formula in SI.

Reviewer: 3
Comments to the Author(s) Nε-Acetyl-lysine analogs with Zinc binding groups as novel HDAC inhibitors Fang Wang, et al The manuscript describes the design, synthesis, and evaluation of a series of novel L-lysine derivatives hybridized a zinc binding group as HDAC inhibitors. No matter their weaker potency compared to that of SAHA against HDAC and cancer cell lines, the study is interesting and of novelty, the inhibitory effect of compound 18 on HDAC and cancer cell lines also confirmed the rationality of the design. However, a few issues still should be addressed before the manuscript can be accepted for publication. 1. The expected proton and carbon number of most compounds differ greatly from those found in the 1H-and 13C-NMR spectra. In addition, there are some unreasonable peaks such as 12.85 ppm of compound 11 and 7.89 ppm of compound 18b carbon peak. 2. What is the purity of the test compound? 3. The structures of 14b, 14c, and 14n on Pages S4, S5, and S8 need to be redrawn. 4. The SD values of the IC50 of 11, 18b, 18c, and SAHA should be added to Data in Table 2. 5. Page 2, left column, lines 47, 52, and 54, change "treating trifluoroacetic acid with compound 7", "the treatment of hydroxyl amine with compound 9", "Treatment of hydroxyl amine with compound 10" to "treating compound 7 with trifluoroacetic acid", "the treatment of compound 9 with hydroxyl amine", "Treatment of compound 10 with hydroxyl amine". 6. On Page 3, left column, line 8, replace "the treatment of hydroxyl amine with intermediates 16b-c" with "the treatment of intermediates 16b-c with hydroxyl amine". 7. Page 3, left column, line 5, the sentence "which was under the ester……give compounds 16a-c" need to be rewritten. 8. Page 2, left column, line 48, "Followed by…." is incorrect. 9. "lysine analogs" is incorrect and should be "lysine derivatives". Thank you for submitting the above manuscript to Royal Society Open Science. On behalf of the Editors and the Royal Society of Chemistry, I am pleased to inform you that your manuscript will be accepted for publication in Royal Society Open Science subject to minor revision in accordance with the referee suggestions. Please find the reviewers' comments at the end of this email.
The reviewers and handling editors have recommended publication, but also suggest some minor revisions to your manuscript. Therefore, I invite you to respond to the comments and revise your manuscript.
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Supplementary files will be published alongside the paper on the journal website and posted on the online figshare repository (https://figshare.com). The heading and legend provided for each supplementary file during the submission process will be used to create the figshare page, so please ensure these are accurate and informative so that your files can be found in searches. Files on figshare will be made available approximately one week before the accompanying article so that the supplementary material can be attributed a unique DOI. ************************************* RSC Associate Editor Comments to the Author: The authors have done a good job responding to the comments and concerns raised by the previous review. However, there are still a few relatively minor items that need to be addressed before I am comfortable recommending final acceptance.
(1) Overall the grammar of the manuscript could still be improved. The authors are strongly encouraged to seek assistance in this area to that their message is not lost during final editing. In particular, the paragraph at the top right of Page 2 needs to be edited for clarity and message.
(2) Please include copies of 1H and 13C NMR spectra in the supporting information. Title: Nε-acetyl-lysine analogues with Zinc binding groups as novel HDAC inhibitors Manuscript ID: RSOS-190338.R2 It is a pleasure to accept your manuscript in its current form for publication in Royal Society Open Science. The chemistry content of Royal Society Open Science is published in collaboration with the Royal Society of Chemistry.
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