Cooperativity and Communication between the Active Sites of the Dimeric SARS-CoV-2 Main Protease

Zvornicanin, S. N.; Shaqra, A. M.; Flynn, J. M.; Intravaia, L. E.; Martinez, H. C.; Jia, W.; Gupta, D. K.; Moquin, S.; Dovala, D.; Bolon, D. N. A.; Kelch, B. A.; Schiffer, C. A.; Kurt Yilmaz, N.

doi:10.1101/2025.07.31.667456

bioRxiv · 10.1101/2025.07.31.667456

Cooperativity and Communication between the Active Sites of the Dimeric SARS-CoV-2 Main Protease

Zvornicanin, S. N.·Shaqra, A. M.·Flynn, J. M.·Intravaia, L. E.·Martinez, H. C.·Jia, W.·Gupta, D. K.·Moquin, S.·Dovala, D.·Bolon, D. N. A.·Kelch, B. A.·Schiffer, C. A.·Kurt Yilmaz, N.

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Abstract

The coronaviral main protease (Mpro) is essential for the replication of the virus, and has been the subject of various biochemical, structural and enzymatic studies, as well as a drug target against SARS-CoV-2 infections. SARS-CoV-2 Mpro is known to be active as a dimer, with the N terminus of one protomer completing a key active site pocket of the other protomer. Despite apparent cooperativity in catalytic activity, how the two distal active sites in the dimer communicate and might be modulating binding and/or catalysis at the other remain to be clarified. Here, we have investigated the interplay between cooperativity, dimerization, and substrate cleavage in SARS-CoV-2 Mpro through a combination of enzymatic assays, crystal structures, and protein characterization. To disentangle the contribution of each active site to the observed enzymatic activity, we developed a cleavage assay involving heterodimers of active and inactive (C145A or inhibitor-bound) monomers. Strikingly, we found that heterodimerization increased cleavage efficiency per active monomer. Additionally, we mapped a network of critical residues bridging the two active sites and probed this network through engineered mutations. By dissecting the cooperativity and communication between the active sites, we provide new insights into the Mpro reaction cycle and functional significance of its dimeric architecture.

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Zvornicanin, S. N., Shaqra, A. M., Flynn, J. M., Intravaia, L. E., Martinez, H. C., Jia, W., Gupta, D. K., Moquin, S., Dovala, D., Bolon, D. N. A., Kelch, B. A., Schiffer, C. A., Kurt Yilmaz, N.. 2025-07-31. Cooperativity and Communication between the Active Sites of the Dimeric SARS-CoV-2 Main Protease. https://doi.org/10.1101/2025.07.31.667456

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