An engineered stable mini-protein to plug SARS-Cov-2 Spikes
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Abstract
The novel betacoronavirus SARS-CoV-2 is the etiological agent of the current pandemic COVID-19. Like other coronaviruses, this novel virus relies on the surface Spike glycoprotein to access the host cells, mainly through the interaction of its Receptor Binding Domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with binding of the SARS-CoV-2 Spike protein to ACE2 have a great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 Spike protein and the host ACE2 receptor, we here engineered a mini-protein with the aim of creating a soluble and stable Spike interactor. This mini-protein, which was recombinantly produced in high yields, possesses a stable α helical conformation and is able to interact with the RBD of glycosylated Spike protein from SARS-CoV-2 with nanomolar affinity, as measured by microscale thermophoresis. By plugging the Spike protein, our mini-protein constitutes a valid tool for the development of treatments against different types of coronavirus.
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SciScore for 10.1101/2020.04.29.067728: (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 To complete missing regions in the cryo EM structure, we computed the homology model of SARS-CoV-2 S protein using MODELLER [14], and the structure 2ajf as a template. MODELLERsuggested: (MODELLER, RRID:SCR_008395)Mutations in the basic scaffold were generated using the software Coot [15]. Cootsuggested: (Coot, RRID:SCR_014222)Models were energy minimised using the GROMACS package [12]. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Figures were generated with Pymol [16]. Pymolsuggested: (PyMOL, RRID:SCR_000305)Protein expression and purification: The gene encoding Spikeplug was synthesised and … SciScore for 10.1101/2020.04.29.067728: (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 To complete missing regions in the cryo EM structure, we computed the homology model of SARS-CoV-2 S protein using MODELLER [14], and the structure 2ajf as a template. MODELLERsuggested: (MODELLER, RRID:SCR_008395)Mutations in the basic scaffold were generated using the software Coot [15]. Cootsuggested: (Coot, RRID:SCR_014222)Models were energy minimised using the GROMACS package [12]. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Figures were generated with Pymol [16]. Pymolsuggested: (PyMOL, RRID:SCR_000305)Protein expression and purification: The gene encoding Spikeplug was synthesised and codon-optimised for E. coli expression by GeneArt® Gene Synthesis company (Invitrogen) and subsequently sub-cloned into pETM-13 vector (EMBL, Germany) between the NcoI and XhoI restriction sites. EMBLsuggested: (ChEMBL, RRID:SCR_014042)Results from OddPub: Thank you for sharing your data.
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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