Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors

Geraldo Rodrigues Sartori; Andrei Leitão; Carlos A. Montanari; Charles A. Laughton

doi:10.1371/journal.pone.0222055

Peer Review History

Original SubmissionAugust 15, 2019
11 Sep 2019 Decision Letter - Freddie Salsbury , Jr, Editor PONE-D-19-23070 Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors PLOS ONE Dear Dr. Laughton, Thank you for submitting your manuscript to PLOS ONE. 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. ============================== This manuscript is on the border of a minor vs major revision. Reviewer #2's points are fairly minor and should be addressed readily. Reviewer #1 has three questions about the methodology used and one about the strength of a conclusion. These need to be addressed. It is possible they may be addressable without additional calculations, but additional calculations might be needed. ============================== We would appreciate receiving your revised manuscript by Oct 26 2019 11:59PM. When you are ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. 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PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. [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: Yes Reviewer #2: Yes ****** 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: No ****** 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: Dear Editor, dear authors, the submitted manuscript “Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors“ describes a method to identify potent inhibitors for a cysteine protease and to predict the selectivity of the respective inhibitor. Rodrigues Sartori and colleagues nicely show that potent nitril inhibitors typically bind to their target protease via conformational selection. Overall the study is conclusive, but some minor issues need to be addressed before publication: (1) The authors mention that ICK is a weak cathepsin L inhibitor because it shows a high ligand RMSD during their simulations. High RMSD means the ligand tends to leave the active site more easily. Can this RMSD also be used to access / categorize the potency of cysteine protease inhibitors? Why is it not included in the current decision tree? To me this would seem to be a straight forward approach. (2) Nitrile inhibitors are covalent-reversible inhibitors. I would assume that potency of such an inhibitor correlates with the stability of the covalent complex. The stability of the covalent complex is not only defined by the energy of the cross-link formation, but also by the enzyme – inhibitor environment. Can the authors comment on that? How is this included in the calculations? (3) Using the method described in the manuscript, is it possible to compare different classes of inhibitors? The energy of covalent bond formation might be different. How can this be included in the calculations? (4) On page 11, lines 410 – 417 the authors conclude that inhibitors binding to cysteine proteases via conformational selection are in general stronger inhibitors as compared to those binding via induced fit. This conclusion is based on the observation that ICL is a weak cathepsin K inhibitor. In my opinion this is not enough evidence to draw such a general conclusion. It could as well be just a coincidence. Overall the manuscript and the figures are clear and well-made and I believe that this report will be read with great interest by the scientific community. Reviewer #2: This manuscript combines MD simulation, PCA analysis and decision tree to identify the activity of different compounds agsinst at papain-family proteins. The topic and protocol is interesting. Just a few issues the author need to address: 1. The author needs to put the unit of the distance and RMSD into table 2's legend. 2. In line 317, it showed "Results are presented in Error! Reference source not found., and in more detail in S9-S12 Figs 318 in the supporting information.". Author needs to fix this error. 3. In order to compare, the rangle of X and Y axisis should be added in figure 2. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). 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Revision 1
1 Nov 2019 Author Response PONE-D-19-23070 Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors PLOS ONE Dear Dr. Salsbury, We thank you and the reviewers for your guidance. Below we detail our responses to each of the issues raised, and hope that you find this satisfactory. Regards, Charlie Laughton Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Response: We have gone through the manuscript carefully, and hope now it fully matches up to PLOSOne’s style requirements. 2. We noted that several of your references did not auto populate and instead the manuscript contains the following "Error! Reference source not found", please replace this with the appropriate reference during your next revision. Response: We have corrected some references; in our local version of the manuscript these format correctly (we use Mendeley) but will double-check this during the resubmission upload process. 3. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. Response: Datasets (molecular dynamics trajectory files) necessary to reproduce our study findings have been deposited in Zenodo. Here are the URLs and DOIs: https://zenodo.org/record/3518308 10.5281/zenodo.3518308 https://zenodo.org/record/3522090 10.5281/zenodo.3522090 https://zenodo.org/record/3523307 10.5281/zenodo.3523307 https://zenodo.org/record/3523367 10.5281/zenodo.3523367 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 Response: no response required 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Response: no response required 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: No Response: see above – datasets are now deposited at Zenodo 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 Response: no response required 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: Dear Editor, dear authors, the submitted manuscript “Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors“ describes a method to identify potent inhibitors for a cysteine protease and to predict the selectivity of the respective inhibitor. Rodrigues Sartori and colleagues nicely show that potent nitril inhibitors typically bind to their target protease via conformational selection. Overall the study is conclusive, but some minor issues need to be addressed before publication: (1) The authors mention that ICK is a weak cathepsin L inhibitor because it shows a high ligand RMSD during their simulations. High RMSD means the ligand tends to leave the active site more easily. Can this RMSD also be used to access / categorize the potency of cysteine protease inhibitors? Why is it not included in the current decision tree? To me this would seem to be a straight forward approach. Response: We address this on page 13 of the manuscript in the section “Structural Analysis of Molecular Dynamics Simulations”. We show that while it is true that in some cases (e.g. ICK) high ligand RMSD and low affinity/potency correlate, they do not always do so. This is why we did not use this in the decision tree. We have added a sentence at the end of this section to clarify this. (2) Nitrile inhibitors are covalent-reversible inhibitors. I would assume that potency of such an inhibitor correlates with the stability of the covalent complex. The stability of the covalent complex is not only defined by the energy of the cross-link formation, but also by the enzyme – inhibitor environment. Can the authors comment on that? How is this included in the calculations? Response: This is a good point, we had not fully explained our approach. We have re-written part of the section “Binding Free Energy Calculations using the MMGBSA Method” to answer this question. (3) Using the method described in the manuscript, is it possible to compare different classes of inhibitors? The energy of covalent bond formation might be different. How can this be included in the calculations? Response: A good point, we have added a short discussion of this to the conclusions section; we suggest that a QM-derived term measuring the strength of the cross-link bond would be sufficient. (4) On page 11, lines 410 – 417 the authors conclude that inhibitors binding to cysteine proteases via conformational selection are in general stronger inhibitors as compared to those binding via induced fit. This conclusion is based on the observation that ICL is a weak cathepsin K inhibitor. In my opinion this is not enough evidence to draw such a general conclusion. It could as well be just a coincidence. Response: in fairness we only claimed the result “strengthened the hypothesis” rather than proved it, but we have altered the final part of this section to qualify our analysis further, in line with the referee’s comments. Overall the manuscript and the figures are clear and well-made and I believe that this report will be read with great interest by the scientific community. Reviewer #2: This manuscript combines MD simulation, PCA analysis and decision tree to identify the activity of different compounds agsinst at papain-family proteins. The topic and protocol is interesting. Just a few issues the author need to address: 1. The author needs to put the unit of the distance and RMSD into table 2's legend. Response: this has been done. 2. In line 317, it showed "Results are presented in Error! Reference source not found., and in more detail in S9-S12 Figs 318 in the supporting information.". Author needs to fix this error. Response: this has been done. 3. In order to compare, the rangle of X and Y axisis should be added in figure 2. Response: We have amended the legend to this figure to say that all panels are at the same magnification (range of X and Y values), and what this is (40 Angstoms x 40 Angstroms). Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0222055.r002
20 Nov 2019 Decision Letter - Freddie Salsbury , Jr, Editor Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors PONE-D-19-23070R1 Dear Dr. Laughton, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. If you have any billing related questions, 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, Freddie Salsbury , Jr, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0222055.r003
Formally Accepted
6 Dec 2019 Acceptance Letter - Freddie Salsbury , Jr, Editor PONE-D-19-23070R1 Ligand-induced Conformational Selection Predicts the Selectivity of Cysteine Protease Inhibitors Dear Dr. Laughton: I am pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Freddie Salsbury , Jr Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0222055.r004

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