From the journal RSC Chemical Biology Peer review history

17-Aug-2020

Dear Dr Tepe:

Manuscript ID: CB-REV-06-2020-000111
TITLE: Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors

Thank you for your submission to RSC Chemical Biology, published by the Royal Society of Chemistry. I sent your manuscript to reviewers and I have now received their reports which are copied below.

After careful evaluation of your manuscript and the reviewers’ reports, I will be pleased to accept your manuscript for publication after revisions.

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Dr Cai-Guang Yang
Associate Editor
RSC Chemical Biology

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Reviewer 1

Author of this manuscript reviewed natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors. Overall, it is a well-written, clear and comprehensive review. However, there are rooms for improvement.

First, I suggest that Fig 1 includes a diagram for beta 1, 2 and 5 subunits for three proteasomal activities;
Also, the authors should indicate the clinical impact of this study in both Abstract and Conclusions sections.
There are some typos and formatting errors in the text that should be fixed.

Reviewer 2

This is an interesting and well-written work that addresses a relevant topic to the readers of RSC Chemical Biology.
The authors present a well-balanced work that deals with the biological properties of proteasome inhibitors, their synthesis and structure-activity relationships.
Being mostly dedicated to the specific chemical space of natural products, I find it lacking in some references dedicated to this topic, such as Nat. Prod. Rep., 2015, 32, 705-722.


However, the manuscript is mostly descriptive in its nature, which although relevant for its aim, leaves out other aspects that are important. Specifically, I believe the authors should dedicate some space in their manuscript to reflect on the current challenges of the field, its technical limitations and future paths to the future.

Minor comments:

Earlier in the manuscript, the authors refer to IKBα as the “sequestered form of transcription factor NF-ĸB)”. This is not accurate, as IKBa is an inhibitor of NF-kB.

“In subsequent in vitro studies, TP-110 also repressed the chymotrypsin-like activity of the proteasome in human

prostate cancer PC-3 cells, inhibiting the proteasome activity by 56% with 0.1 μg/mL.” For the sake of comparability, I suggest the authors express all results in micro or nanomolar, so that the different molecules can be compared.



For all this, I believe this work can be accepted after these minor changes

Reviewer 3

Overall, a nice collection and worth reading. Just needs a few minor corrections.

-A separate section after introduction about general mechanism of inhibition ( with a figure) might be a valuable addition. Only a line or two has been written about the same in the article.
-Pg 2-4. A general introduction has been provided about natural products targeting the proteasome and its mechanisms; however, including a brief timeline/chronology of the discovery and mechanism of action would be great.
For instance, many implicit references have been made like “At that time, the crystal structure”, but a timeline/ year hasn’t been mentioned. The reader might find it difficult to skim through the references to understand the timeline.

-Since most of the natural products are covalent inhibitors, have any of these been screened to rule out PAINS?

This text has been copied from the PDF response to reviewers and does not include any figures, images or special characters.

Dear Editor,
We thank you and the reviewers for their kind responses to our review article. The article has been revised to incorporate all of the reviewers comments. On our revised version we have highlighted all changes from our original article. We hope you will find the current revised article suitable for publication.
Best regards,
Jetze Tepe

Author Response: We thank the reviewers for their kind and positive evaluation of this review. We have addressed all of the comments the reviewers suggested in our revised manuscript and the specific corrections are listed below and highlighted in our revised version.

Referee: 1
• Comment 1: First, I suggest that Fig 1 includes a diagram for beta 1, 2 and 5 subunits for three proteasomal activities; Figure 1 has been altered to include the labeled beta 1, 2, and 5 substrates and a key including their proteolytic activities
• Comment 2: Also, the authors should indicate the clinical impact of this study in both Abstract and Conclusions sections. The review covers natural products as proteasome inhibitors and no natural products have thus far been used clinically. However, in response to the reviewer’s comments we have added in the conclusion: Thus far, the clinical impact of proteasome inhibitors has been significant with several agents currently clinically used to treat several hematological cancers, including multiple myeloma.
• Comment 3: There are some typos and formatting errors in the text that should be fixed. The typos and formatting errors have been fixed.

Referee 2:
• Comment 1: Being mostly dedicated to the specific chemical space of natural products, I find it lacking in some references dedicated to this topic, such as Nat. Prod. Rep., 2015, 32, 705-722. Thank you for your suggestion; agosterol C has been added to the discussion in the terpenoid section of the review. Furthermore, the association between proteasome inhibition and ER stress/apoptosis has also been included in the introduction (pg 2, paragraph 1).
• Comment 2: Specifically, I believe the authors should dedicate some space in their manuscript to reflect on the current challenges of the field, its technical limitations and future paths to the future. The current limitations of the use of natural products as scaffolds in drug design have now been acknowledged in the conclusion of the review: “ Inherent challenges associated with the use of natural product-based inhibitors include product isolation from crude mixtures and subsequent synthesis of the complex substrates, as exemplified in the case of some natural product-based inhibitors.” RSC Chemical Biology Page 2 of 30
• Comment 3: Earlier in the manuscript, the authors refer to IKBα as the “sequestered form of transcription factor NF-ĸB)”. This is not accurate, as IKBa is an inhibitor of NF-kB. This comment has been resolved, the review now states “Ubiquitin-proteasome-mediated degradation has been implicated in the regulation of many signalling proteins including cyclins (involved in cell-cycle progression), p53 (tumor suppressor),2 and IKBα (inhibitor of transcription factor NF-ĸB).3”
• Comment 4: “In subsequent in vitro studies, TP-110 also repressed the chymotrypsin-like activity of the proteasome in human prostate cancer PC-3 cells, inhibiting the proteasome activity by 56% with 0.1 μg/mL.” For the sake of comparability, I suggest the authors express all results in micro or nanomolar, so that the different molecules can be compared. All values which were previously given in µg/mL or ng/mL are now represented as µM or nM.

Referee 3:
• Comment 1: A separate section after introduction about general mechanism of inhibition (with a figure) might be a valuable addition. Only a line or two has been written about the same in the article. This comment has been resolved through a brief description of inhibition using bortezomib as an example. Figure 1B (illustrating the covalent interaction between Thr1 and bortezomib) has also been included in the review.
• Comment 2: Pg 2-4. A general introduction has been provided about natural products targeting the proteasome and its mechanisms; however, including a brief timeline/chronology of the discovery and mechanism of action would be great. For instance, many implicit references have been made like “At that time, the crystal structure”, but a timeline/ year hasn’t been mentioned. The reader might find it difficult to skim through the references to understand the timeline. Thank you for your suggestion. A chronology has been included throughout the introduction to illustrate the key discoveries in association with the ubiquitin-proteasome pathway and discovery of crystal structures has been included.
• Comment 3: Since most of the natural products are covalent inhibitors, have any of these been screened to rule out PAINS? This is an excellent point made by the reviewers but it would be difficult to systematically comment on each of the natural products. For clear examples of PAINS, such as curcumin, the text already identifies them as such. For example: “The promiscuous active agent curcumin (151)…” However, in the absence of a specific statement or data on that in the literature, we are hesitant to label suspected PAINS as such, in this review without supporting data.

01-Sep-2020

Dear Dr Tepe:

Manuscript ID: CB-REV-06-2020-000111.R1
TITLE: Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors

Thank you for submitting your revised manuscript to RSC Chemical Biology. After considering the changes you have made, I am pleased to accept your manuscript for publication in its current form. I have copied any final comments from the reviewer(s) below.

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With best wishes,

Dr Cai-Guang Yang
Associate Editor
RSC Chemical Biology

Reviewer 3

Comments were addressed.