Metal coordination and enzymatic reaction of the glioma-target R132H isocitrate dehydrogenase 1: Insights by molecular simulations

Bharath Raghavan; Marco De Vivo; Paolo Carloni

doi:10.1371/journal.pone.0326425

Peer Review History

Original SubmissionOctober 23, 2024
23 Oct 2024 Author Response Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. https://doi.org/10.1371/journal.pone.0326425.r001
29 Mar 2025 Decision Letter - Michael Klymkowsky, Editor PONE-D-24-47203Metal Coordination and Enzymatic Reaction of the Glioma-Target R132H Isocitrate Dehydrogenase 1: Insights by Molecular SimulationsPLOS ONE Dear Dr. Carloni, Thank you for submitting your manuscript to PLOS ONE and sorry for the delays. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. No new experiments are required, but please address reviewer #2's class to consider other "donors". Please submit your revised manuscript by May 13 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. 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The preprint of the manuscript was submitted:https://doi.org/10.26434/chemrxiv-2024-jxd73 Parts of the results were also published as Chapter 7 of the thesis by Bharath Raghavan (first author): https://doi.org/10.18154/rwth-2024-07554. Please clarify whether this [conference proceeding or publication] was peer-reviewed and formally published. If this work was previously peer-reviewed and published, in the cover letter please provide the reason that this work does not constitute dual publication and should be included in the current manuscript. 7. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 8. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: N/A ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Here the Carloni team addresses a highly relevant and acute problem: the R132H mutation in Isocitrate Dehydrogenase 1 (IDH1) is a vital target in multiple brain cancers. IDH1 links metabolism to epigenetics, and as such plays a crucial role in these cancers, causing widespread changes in the epigenetic landscape of these tumors, through histone and DNA demethylases. IDH1/2 mutations can lead to hypermethylated histones and DNA which changes gene expression, commonly by overexpression. Despite the recognition of their critical tumorigenic role, still no drug leads and radiotracers which selectively bind only to the mutant over the wild type are so far lacking. Here, through comprehensive computational analysis, the authors predicted the structural determinants of the Michaelis complex of this mutant using QM/MM MD. They observe important differences from the X-ray structure, ranging from metal coordination to the positioning of key residues at the active site. Especially, the K212 mutation appears as the likely proton donor in the key proton-transfer step of the R132H IDH1 catalytic reaction. The authors then discover that the same residue in its deprotonated state appears involved in the reaction catalyzed by the wild-type enzyme, albeit via different mechanisms. The rigor of the work, its implications to drug discovery, and the new protocol that they employ, make me suggest accepting the manuscript as is. This is reenforced by the clarity of the presentation, text and figures. Reviewer #2: This manuscript presents a QM/MM-based molecular simulation study of the active-site architecture and mechanistic features of the R132H mutant of human isocitrate dehydrogenase 1 (IDH1). By comparing their simulated structure to both the wild-type and the inactive crystal structure of the mutant, the authors make a case that the proton donor in the mutant’s reaction is most likely Lys212'—a result with potential implications for selective drug design. Overall this is a well-designed and executed study with a number of strengths including the biological and therapeutic relevance and along with the open availability of all the QM/MM input files and trajectories is commendable. The one minor concern of this reviewer is that the was little exploration of alternative proton donors: While the simulations suggest Lys212’ is a key proton donor, it might be helpful for readers if the authors at least mentioned the other potential donors (e.g., Tyr139, Asp275) under different solvent or pH conditions could be critical. While presenting additional free energy or reaction-path calculations could further solidify the argument that Lys 212 is critical, this is not necessary for publication. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. 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Revision 1
26 Apr 2025 Author Response Reply to the reviewers. Reviewer #1: Here the Carloni team addresses a highly relevant and acute problem: the R132H mutation in Isocitrate Dehydrogenase 1 (IDH1) is a vital target in multiple brain cancers. IDH1 links metabolism to epigenetics, and as such plays a crucial role in these cancers, causing widespread changes in the epigenetic landscape of these tumors, through histone and DNA demethylases. IDH1/2 mutations can lead to hypermethylated histones and DNA which changes gene expression, commonly by overexpression. Despite the recognition of their critical tumorigenic role, still no drug leads and radiotracers which selectively bind only to the mutant over the wild type are so far lacking. Here, through comprehensive computational analysis, the authors predicted the structural determinants of the Michaelis complex of this mutant using QM/MM MD. They observe important differences from the X-ray structure, ranging from metal coordination to the positioning of key residues at the active site. Especially, the K212 mutation appears as the likely proton donor in the key proton-transfer step of the R132H IDH1 catalytic reaction. The authors then discover that the same residue in its deprotonated state appears involved in the reaction catalyzed by the wild-type enzyme, albeit via different mechanisms. The rigor of the work, its implications to drug discovery, and the new protocol that they employ, make me suggest accepting the manuscript as is. This is reenforced by the clarity of the presentation, text and figures. We thank the reviewer for highly praising our manuscript. Reviewer #2: This manuscript presents a QM/MM-based molecular simulation study of the active-site architecture and mechanistic features of the R132H mutant of human isocitrate dehydrogenase 1 (IDH1). By comparing their simulated structure to both the wild-type and the inactive crystal structure of the mutant, the authors make a case that the proton donor in the mutant’s reaction is most likely Lys212'—a result with potential implications for selective drug design. Overall this is a well-designed and executed study with a number of strengths including the biological and therapeutic relevance and along with the open availability of all the QM/MM input files and trajectories is commendable. We are grateful for the reviewers' careful consideration of our work and their constructive feedback. The one minor concern of this reviewer is that the was little exploration of alternative proton donors: While the simulations suggest Lys212’ is a key proton donor, it might be helpful for readers if the authors at least mentioned the other potential donors (e.g., Tyr139, Asp275) under different solvent or pH conditions could be critical. While presenting additional free energy or reaction-path calculations could further solidify the argument that Lys 212 is critical, this is not necessary for publication. We now add the following sentence (in quotes) to the last sentence in the discussion: Thus, the same residue appears to be well positioned to perform proton transfers in both wt- and mut-IDH1 isoforms (compare the position of Lys212' vis a vis the substrate in Figs 5A and D). This information is not provided by previous quantum chemical studies of the reaction. [10] "However, while the simulations do suggest a key role for Lys212’, our calculations do not rule out that other residues (such as, for instance, Tyr139), under different solvent and/or pH conditions, could act as proton donors in the enzymatic reaction" Attachments Attachment Submitted filename: Response to reviewers.pdf https://doi.org/10.1371/journal.pone.0326425.r003
30 May 2025 Decision Letter - Michael Klymkowsky, Editor Metal Coordination and Enzymatic Reaction of the Glioma-Target R132H Isocitrate Dehydrogenase 1: Insights by Molecular Simulations PONE-D-24-47203R1 Dear Dr. Carloni, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Michael Klymkowsky, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #3: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #3: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #3: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #3: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #3: 1. There is a mismatch between Fig 1(B) legend and the text in the Fig 1(B). Please correct the word ‘αKG and NADPH’ to ‘ICT and NADP+’ in the figure legend in order to match the labels. 2. There are some typographical errors in the manuscripts that should be corrected. Fig 2(A) legend: Lys212' as the bse initiator > Lys212' as the base initiator Page 3, line 54: anddressed > addressed Page 5, line 152: pre > per Page 6, line 189: X-structure > X-ray structure Page 7, line 204: the the > the ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #3: No ******** https://doi.org/10.1371/journal.pone.0326425.r004
Formally Accepted
Acceptance Letter - Michael Klymkowsky, Editor PONE-D-24-47203R1 PLOS ONE Dear Dr. Carloni, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Michael Klymkowsky Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0326425.r005

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