Evaluating the structure-based virtual screening performance of SARS-CoV-2 main protease: A benchmarking approach and a multistage screening example against the wild-type and Omicron variants

Noha Galal; Botros Y. Beshay; Omar Soliman; Muhammad I. Ismail; Mohamed Abdelfadil; Mohamed El-Hadidi; Reem K. Arafa; Tamer M. Ibrahim

doi:10.1371/journal.pone.0318712

Peer Review History

Original SubmissionNovember 27, 2024
27 Nov 2024 Author Response https://doi.org/10.1371/journal.pone.0318712.r001
16 Dec 2024 Decision Letter - Ahmed A. Al-Karmalawy, Editor PONE-D-24-54776Evaluating the Structure-Based Virtual Screening Performance of SARS-CoV-2 Main Protease: A Benchmarking Approach and a Multistage Screening Example Against the Wild-type and Omicron VariantsPLOS ONE Dear Dr. Ibrahim, 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. Please submit your revised manuscript by Jan 30 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 . When you're 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. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. 3. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://www.mdpi.com/1420-3049/28/3/1296 https://www.sciencedirect.com/science/article/pii/S0010482521002626?via%3Dihub https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0284301 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. 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: Partly 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: 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: The work is quite interesting and the findings are well put together. The only concern here is the time scale of the MD simulation. I was wondering if there were any replicates carried out to validate the MD simulations, mostly for sanity check? If not, then 100 ns of MD with CHARMM is inadequate sampling in my opinion. This is also reflected in certain structural analysis, where the system stability is seen towards the end of the simulations. Longer simulation times might provide greater insight into such situations. Along with the analysis performed, looking into non-covalent interaction energies to look into important residues that take part in binding and are important for stability might be useful. Using energy decomposition analysis for such is a good benchmark. Reviewer #2: The manuscript is well structured and relevant to its field and can be proceeded to publication. Authors cold just consider provide descriptions for both the bond angles and distances of their depicted ligand-target interaction patterns. Specially for Hydrogen bonding, this type of compound-protein polar interaction should be presented within hydrogen bond distances as well as bond angles since hydrogen bond depend on both. Authors should mention the Hydrogen bond angles as well as their distances, since the strength of hydrogen bonding is based on both parameters in a way to ensure the adequacy of optimum hydrogen bonding. ****** 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: Yes ******** [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. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0318712.r002
Revision 1
24 Dec 2024 Author Response 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 https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Response: We revised the PLOS ONE’s style requirements and addressed all of them. 2. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. Response: All findings are based on already published codes/methodologies. We cited them appropriately. 3. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: https://www.mdpi.com/1420-3049/28/3/1296 https://www.sciencedirect.com/science/article/pii/S0010482521002626?via%3Dihub https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0284301 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. Response: We addressed them and cited the references mentioned. Reviewers’ comments: Reviewer #1: The work is quite interesting and the findings are well put together. The only concern here is the time scale of the MD simulation. I was wondering if there were any replicates carried out to validate the MD simulations, mostly for sanity check? If not, then 100 ns of MD with CHARMM is inadequate sampling in my opinion. This is also reflected in certain structural analysis, where the system stability is seen towards the end of the simulations. Longer simulation times might provide greater insight into such situations. Along with the analysis performed, looking into non-covalent interaction energies to look into important residues that take part in binding and are important for stability might be useful. Using energy decomposition analysis for such is a good benchmark. Response: We thank the reviewer for raising this point. Indeed, the main focus of our study is to provide the community with an evaluation/assessment of the virtual screening performance via in-depth benchmarking analysis against the highly represented protein target in literature for COVID-19, the Mpro. The molecular dynamics protocol is an auxiliary approach and example of how to in-silico confirm the binding event of the proposed hits in the binding site of both WTMpro and OMpro. Furthermore, Mpro is extensively studied in literature and employing MD simulation for a 100 ns is a standard performance in many studies especially in the context of assessing ligand-protein stability, e.g., PLOS ONE. 2023;18(4):e0284301. doi: 10.1371/journal.pone.0284301; and https://www.tandfonline.com/doi/full/10.1080/07391102.2022.2148000 Nonetheless, we already performed a pilot MD simulation for 200 ns during our experimental setup for the co-crystal ligand (WT – PDB ID: 7L14), as shown in Figure R (please, see the "Response-to-reviewers" document). The RMSD fluctuations (blue line) did not differ greatly after 100 ns of simulation time. Based on all the previous, we decided to set the MD simulation time for 100 ns, and therefore, we kindly appreciate the reviewer’s understanding in this matter. We also provided extensive analyses of the MD trajectories including, MMGBSA free energy calculations, per-residue energy contribution, minimum distance analysis and providing different screenshots at different time points. Reviewer #2: The manuscript is well structured and relevant to its field and can be proceeded to publication. Authors cold just consider provide descriptions for both the bond angles and distances of their depicted ligand-target interaction patterns. Specially for Hydrogen bonding, this type of compound-protein polar interaction should be presented within hydrogen bond distances as well as bond angles since hydrogen bond depend on both. Authors should mention the Hydrogen bond angles as well as their distances, since the strength of hydrogen bonding is based on both parameters in a way to ensure the adequacy of optimum hydrogen bonding. Response: We thank the reviewer for his comment. The H-bonding is depicted already in Figure 9 and 10 in the manuscript (H-bonding count). The native function of gromacs for H-bonding count considering both the distance and angle (please, see gromacs documentation). We quote the following from gromacs documentation: “A) Distance Criterion: The distance between the donor atom (typically a hydrogen bond donor such as an OH or NH group) and the acceptor atom must be less than or equal to rHB=0.35 nm. B) Angle Criterion: The angle formed by the hydrogen atom, the donor atom, and the acceptor atom must be less than or equal to αHB=30∘.” Furthermore, based on the binding free energy (ΔG), in “Binding free energy (ΔG) via MM/GBSA calculation“ in the manuscript, the van der Waals energy was found to be the major contribution to the calculated ΔG for both WTMpro and OMpro complex systems. This minimizes the importance of providing more insights into some details for the H-bonding interactions. Nonetheless, we already provided detailed distance analysis of the key H-bonding interactions for the WTMpro in the section “ Minimum Distance analysis”. Thank you, Attachments Attachment Submitted filename: Response-to-reviewers.docx https://doi.org/10.1371/journal.pone.0318712.r003
21 Jan 2025 Decision Letter - Ahmed A. Al-Karmalawy, Editor Evaluating the structure-based virtual screening performance of SARS-CoV-2 main protease: A benchmarking approach and a multistage screening example against the wild-type and Omicron variants PONE-D-24-54776R1 Dear Dr. Ibrahim, 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, Ahmed A. Al-Karmalawy, PhD Academic Editor PLOS ONE 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 #1: All comments have been addressed Reviewer #2: (No Response) ******** 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 #1: Yes Reviewer #2: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: (No Response) ****** 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 #1: Yes Reviewer #2: (No Response) ****** 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 #1: Yes Reviewer #2: (No Response) ****** 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 #1: The reviewer's comments are addressed. This paper is now suitable for publication and can be accepted. Reviewer #2: (No Response) ****** 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 #1: No Reviewer #2: Yes ******** https://doi.org/10.1371/journal.pone.0318712.r004
Formally Accepted
Acceptance Letter - Ahmed A. Al-Karmalawy, Editor PONE-D-24-54776R1 PLOS ONE Dear Dr. Ibrahim, 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 If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks 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 Associate Professor Ahmed A. Al-Karmalawy Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0318712.r005

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