Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Hameedi, M. A.; Teixeira Prates, E.; Garvin, M. R.; Mathews, I.; Amos, B. K.; Demerdash, O.; Bechthold, M.; Iyer, M.; Rahighi, S.; Kneller, D. W.; Kovalevsky, A.; Irle, S.; Vuong, V.-Q.; Mitchell, J. C.; Labbe, A.; Galanie, S.; Wakatsuki, S.; Jacobson, D.

doi:10.1101/2021.11.11.468228

bioRxiv · 10.1101/2021.11.11.468228

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Hameedi, M. A.·Teixeira Prates, E.·Garvin, M. R.·Mathews, I.·Amos, B. K.·Demerdash, O.·Bechthold, M.·Iyer, M.·Rahighi, S.·Kneller, D. W.·Kovalevsky, A.·Irle, S.·Vuong, V.-Q.·Mitchell, J. C.·Labbe, A.·Galanie, S.·Wakatsuki, S.·Jacobson, D.

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Abstract

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like (3CLpro) protease can cleave human immune signaling proteins, like NF-{kappa}B Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.14 [A] resolution crystal structure of 3CLpro C145S bound to NEMO226-235 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro- NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for in the pathology of COVID-19.

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Hameedi, M. A., Teixeira Prates, E., Garvin, M. R., Mathews, I., Amos, B. K., Demerdash, O., Bechthold, M., Iyer, M., Rahighi, S., Kneller, D. W., Kovalevsky, A., Irle, S., Vuong, V.-Q., Mitchell, J. C., Labbe, A., Galanie, S., Wakatsuki, S., Jacobson, D.. 2021-11-15. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. https://doi.org/10.1101/2021.11.11.468228

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