SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential
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Abstract
Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between twenty and thirty proteins to carry out their viral replication cycle including infection, immune evasion, and replication. Among these, nonstructural protein 16 (Nsp16), a 2’-O-methyltransferase, plays an essential role in immune evasion. Nsp16 achieves this by mimicking its human homolog, CMTr1, which methylates mRNA to enhance translation efficiency and distinguish self from other. Unlike human CMTr1, Nsp16 requires a binding partner, Nsp10, to activate its enzymatic activity. The requirement of this binding partner presents two questions that we investigate in this manuscript. First, how does Nsp10 activate Nsp16? While experimentally-derived structures of the active Nsp16/Nsp10 complex exist, structures of inactive, monomeric Nsp16 have yet to be solved. Therefore, it is unclear how Nsp10 activates Nsp16. Using over one millisecond of molecular dynamics simulations of both Nsp16 and its complex with Nsp10, we investigate how the presence of Nsp10 shifts Nsp16’s conformational ensemble in order to activate it. Second, guided by this activation mechanism and Markov state models (MSMs), we investigate if Nsp16 adopts inactive structures with cryptic pockets that, if targeted with a small molecule, could inhibit Nsp16 by stabilizing its inactive state. After identifying such a pocket in SARS-CoV-2 Nsp16, we show that this cryptic pocket also opens in SARS-CoV-1 and MERS, but not in human CMTr1. Therefore, it may be possible to develop pan-coronavirus antivirals that target this cryptic pocket.
Statement of Significance
Coronaviruses are a major threat to human health. These viruses employ molecular machines, called proteins, to infect host cells and replicate. Characterizing the structure and dynamics of these proteins could provide a basis for designing small molecule antivirals. In this work, we use computer simulations to understand the moving parts of an essential SARS-CoV-2 protein, understand how a binding partner turns it on and off, and identify a novel pocket that antivirals could target to shut this protein off. The pocket is also present in other coronaviruses but not in the related human protein, so it could be a valuable target for pan-coronavirus antivirals.
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SciScore for 10.1101/2020.12.10.420109: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)This analysis was performed using the cluster centers and the equilibrium probabilities derived from the MSMs built on the residue level SASA described above. MSMssuggested: (MSMS, RRID:SCR_003532)Sequences alignment was performed on Clustal Omega server (56). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Sequence alignment was visualized, and the sequence conservation score was generated using Jalview 2 software (57). Jalviewsuggested: …SciScore for 10.1101/2020.12.10.420109: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)This analysis was performed using the cluster centers and the equilibrium probabilities derived from the MSMs built on the residue level SASA described above. MSMssuggested: (MSMS, RRID:SCR_003532)Sequences alignment was performed on Clustal Omega server (56). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Sequence alignment was visualized, and the sequence conservation score was generated using Jalview 2 software (57). Jalviewsuggested: (Jalview, RRID:SCR_006459)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.12.10.420109: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)Markov State Models A Markov State Model (MSM) is a statistical framework for analyzing molecular dynamics simulations that provides a network representation of a free energy landscape. ( 37, 48, 49) To quantify cryptic pocket opening across the homologs and changes between monomeric Nsp16 and the Nsp10/Nsp16 complex, we performed … SciScore for 10.1101/2020.12.10.420109: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Missing residues in the crystal structure of CMTr1 were modeled using the Modeller package (39). Modellersuggested: (MODELLER, RRID:SCR_008395)Markov State Models A Markov State Model (MSM) is a statistical framework for analyzing molecular dynamics simulations that provides a network representation of a free energy landscape. ( 37, 48, 49) To quantify cryptic pocket opening across the homologs and changes between monomeric Nsp16 and the Nsp10/Nsp16 complex, we performed several measurements that rely on MSMs built based on the simulation data. MSMssuggested: (MSMS, RRID:SCR_003532)Sequences alignment was performed on Clustal Omega server (56). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Sequence alignment was visualized, and the sequence conservation score was generated using Jalview 2 software (57). Jalviewsuggested: (Jalview, RRID:SCR_006459)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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