SARS-CoV-2 3CLpro mutations T21I and E166A confer differential resistance to simnotrelvir, bofutrelvir, and ensitrelvir.

Inhibiting the catalytic activity of 3CLpro is a mainstream strategy to block coronavirus replication. However, the appearance of SARS-CoV-2 3CLpro resistance to protease inhibitors raises concerns for effective therapies. In this work, we first investigated the resistance profile of simnotrelvir, an approved anti-SARS-CoV-2 drug that targets 3CLpro. We found that the T21I/E166A mutations in 3CLpro equally emerged when SARS-CoV-2 was passaged in the HEK293T-hACE2 cells with increasing concentrations of simnotrelvir. The SARS-CoV-2 isolate carrying 3CLpro IMPORTANCE: Considering that the nirmatrelvir-resistant SARS-CoV-2 has emerged in immunocompromised patients who received long-term Paxlovid therapy, it is essential to investigate the response of resistance 3CLpro mutants to various protease inhibitors. Simnotrelvir, a novel inhibitor targeting SARS-CoV-2 3CLpro, has been authorized for the treatment of mild-to-moderate COVID-19 in China and has treated over 1 million patients. However, the resistance profile of simnotrelvir to SARS-CoV-2 remains unknown. Here, we identified that 3CLpro with T21I/E166A mutations confers resistance to simnotrelvir and showed cross-resistance to nirmatrelvir and ensitrelvir, but not bofutrelvir. More importantly, we further revealed that E166A showed a novel resistance mechanism to both the covalent inhibitors consisting of a γ-lactam ring and non-covalent inhibitors like ensitrelvir, which is different from that of E166V previously reported. In contrast, bofutrelvir maintains high affinity to T21I/E166A, suggesting that inhibitors with aldehyde warhead can partly neutralize the resistance.