Pan-Coronavirus Protease Engagement and Differentiated Pharmacology of Antiviral Candidate CMX990

Elshan, N. G. R. D.; Wolff, K. C.; Riva, L.; Bakowski, M. A.; Babarinde, S.; Chaudhary, A.; Zeller, M.; Woods, A. K.; Grabovyi, G.; Wilson, K. B.; Leonard, R. A.; McGovern, B. L.; Benjamin, J.; Suazo, I.; Gordon, M.; Weiss, F. O.; Ghorai, S.; Pedroarena, J. R.; Marquardt, K. L.; Bimal, M.; Weston, S.; Dillen, C.; Jadhav, A. M.; Kirkpatrick, M. G.; Gebara-Lamb, A.; Farhat, N.; Nguyen-Tran, V. T. B.; Chi, V.; Lee, K.-J.; McNamara, C. W.; Gupta, A. K.; Rahimi, A.; Teijaro, J. R.; Chen, J. J.; Joseph, S. B.; Frieman, M.; Heaton, N. S.; White, K.; Wilson, I. A.; Schultz, P. G.; Chanda, S. K.; Chatt

doi:10.64898/2026.09.29.755428

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bioRxiv · 10.64898/2026.09.29.755428

Pan-Coronavirus Protease Engagement and Differentiated Pharmacology of Antiviral Candidate CMX990

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Abstract

COVID-19 highlighted the need for antivirals that can be rapidly deployed against both current and future coronavirus threats. CMX990 is a clinical stage coronavirus main protease (Mpro) inhibitor bearing a unique trifluoromethoxymethyl ketone warhead. Here, we broadly evaluate its pan-coronavirus target engagement, antiviral breadth, and pharmacologic differentiation. Across a reporter panel of 24 Mpro enzymes spanning alpha-, beta-, delta-, and gamma-coronaviruses, CMX990 retained robust potent activity, including against nirmatrelvir-resistant SARS-CoV-2 variants. In direct comparison, nirmatrelvir and ensitrelvir showed diminished potency against non-SARS-CoV-2 coronaviruses. Live-virus assays corroborated this breadth, with potent, selective activity against SARS-CoV-2, SARS-CoV-1, MERS-CoV, and additional human coronaviruses. Structural studies revealed a conserved covalent binding mode centered on the catalytic Cys of coronavirus Mpro. In serial-passage studies, resistance emerged only after approximately twice as many serial passages under CMX990 selection as under nirmatrelvir selection, without selecting for the canonical nirmatrelvir-resistance substitution E166V. Extracellular washout experiments revealed superior persistence of antiviral activity relative to nirmatrelvir, consistent with durable target engagement. In a murine SARS-CoV-2 infection model, once-daily CMX990 protected against weight loss and reduced lung viral titers to near baseline levels. Collectively, these findings identify CMX990 as a structurally and functionally validated pan-coronavirus protease inhibitor supporting its potential as a pandemic-ready antiviral candidate.

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Elshan, N. G. R. D., Wolff, K. C., Riva, L., Bakowski, M. A., Babarinde, S., Chaudhary, A., Zeller, M., Woods, A. K., Grabovyi, G., Wilson, K. B., Leonard, R. A., McGovern, B. L., Benjamin, J., Suazo, I., Gordon, M., Weiss, F. O., Ghorai, S., Pedroarena, J. R., Marquardt, K. L., Bimal, M., Weston, S., Dillen, C., Jadhav, A. M., Kirkpatrick, M. G., Gebara-Lamb, A., Farhat, N., Nguyen-Tran, V. T. B., Chi, V., Lee, K.-J., McNamara, C. W., Gupta, A. K., Rahimi, A., Teijaro, J. R., Chen, J. J., Joseph, S. B., Frieman, M., Heaton, N. S., White, K., Wilson, I. A., Schultz, P. G., Chanda, S. K., Chatt. 2026-10-01. Pan-Coronavirus Protease Engagement and Differentiated Pharmacology of Antiviral Candidate CMX990. https://doi.org/10.64898/2026.09.29.755428

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