A research group led by Conor Caffrey at the University of California San Diego has revisited a set of older experimental compounds and found several that may offer a new direction in antiviral development for emerging COVID-19 variants. The team, working with collaborators in Brazil and Europe, has been studying how the SARS-CoV-2 virus continues to evolve resistance to current treatments and whether legacy chemical libraries could still hold value for modern drug discovery.
Sá Magalhães Serafim, M., Kronenberger, T., Francisco, K. R., de Sousa Reis, E. V., Gonçalves de Oliveira, E., Marcelino e Oliveira, F. K., Serraglio Fortes, I., Maciel Fernandes, T. H., Barbosa da Silva, E., Fajtova, P., Skinner, D. E., Syed, R. O., Lage de Siqueira-Neto, J., Poso, A., Fernandes Mota, B. E., Alves Coelho-dos-Reis, J. G., Santos Abrahão, J., Gonçalves Maltarollo, V., O’Donoghue, A. J., & Caffrey, C. R. (2025). Discovery of benzyl carbamate inhibitors of coronavirus M pro enzymes from a legacy collection of cysteine protease inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 40(1). https://doi.org/10.1080/14756366.2025.2585619
The project focused on a group of 141 compounds originally synthesised between the late 1990s and early 2010s. These molecules were designed to inhibit cruzain, an enzyme used by the parasite responsible for Chagas disease. Although Chagas and COVID-19 are unrelated conditions, cruzain and the coronavirus main protease, known as Mpro, have similar active-site features. That similarity has been noted in earlier structural studies, but this work represents one of the first systematic efforts to screen older anti-cruzain compounds specifically for antiviral potential against coronaviruses.
Initial screening highlighted five molecules with meaningful activity against Mpro. Two of these, labelled 1a and 5a, inhibited the enzyme strongly enough to justify further analysis. Because the compounds had been stored for more than a decade, the group reproduced them in the lab to confirm the original results. They also prepared a stereoisomer of 5a, called 5b, to test whether a mirror-image version could interact more effectively with the protease. Medicinal chemists often explore stereochemistry in this way, since small changes can influence binding strength and drug behaviour.
In laboratory assays, 5b showed the highest potency, suppressing Mpro activity even at low concentrations. It also demonstrated activity against the closely related proteases of SARS-CoV and MERS-CoV, suggesting some degree of breadth across the coronavirus family. Both 5a and 5b showed minimal interaction with human proteases, an important point when evaluating early-stage drug candidates to avoid side effects linked to off-target inhibition.
The group complemented these experimental tests with computational modelling. The simulations suggested that 5a and 5b bind tightly to Mpro but do not form irreversible complexes. This reversible binding pattern is considered favourable in many antiviral designs, offering strong inhibition without permanently altering cellular proteins. Toxicity testing in mammalian cells showed low cytotoxicity for both compounds, supporting their potential as leads for further development.
Their findings reflect a broader trend in antiviral research. As COVID-19 variants continue to emerge, some have shown reduced sensitivity to approved treatments such as Paxlovid, prompting increased interest in alternative protease inhibitors and in strategies that draw from existing chemical collections. Several research groups worldwide have highlighted that older libraries may contain structures unavailable in modern high-throughput screens, offering new options at a time when resistance can outpace drug-design cycles.
This study also contributes to a wider discussion about preparedness for future coronavirus outbreaks. Cross-reactive Mpro inhibitors, such as 5a and 5b appear to be, could help establish a foundation for rapid-response therapeutics that do not need to be built from scratch each time a new variant or related virus emerges.
Adrian graduated with a Masters Degree (1st Class Honours) in Chemical Engineering from Chester University along with Harris. His master’s research aimed to develop a standardadised clean water oxygenation transfer procedure to test bubble diffusers that are currently used in the wastewater industry commercial market. He has also undergone placments in both US and China primarely focused within the R&D department and is an associate member of the Institute of Chemical Engineers (IChemE).
