An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition
G.D. Noske, Yun Song, R.S. Fernandes, R. Chalk, Haitem Elmassoudi, L. Koekemoer, David Owen, Tarick J. El‐Baba, Carol V. Robinson, Glaucius Oliva, André S. Godoy
Abstract
Abstract The main protease from SARS-CoV-2 (M pro ) is responsible for cleavage of the viral polyprotein. M pro self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S M pro to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of M pro N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the M pro dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.