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

UNLABELLED: 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 3CLproT21I/E166A (SARS2-T21I/E166A) showed cross-resistance to simnotrelvir, nirmatrelvir, and ensitrelvir, but not significant resistance to bofutrelvir. Biochemical and cellular assays confirmed that 3CLproT21I/E166A was associated with the differential resistance to these protease inhibitors. Crystallographic structural analysis indicated that the alanine substitution disrupted hydrogen bonding interactions surrounding the γ-lactam rings (P1) of the inhibitors, which is similar to the model rebuilding observed with the previously reported E166V mutation. However, in contrast to the valine substitution, the alanine substitution resulted in a more spacious S2 subsite, thereby causing stronger interaction between the P1 and residues F140 and Ser1 of protomer B. Further computational simulations demonstrated that the covalent binding of bofutrelvir preserves strong binding affinity despite modifications in the S2 subsite caused by the E166A mutation, suggesting that inhibitors containing an aldehyde warhead may partially overcome resistance. Notably, both simnotrelvir and bofutrelvir exhibited therapeutic efficacy against the SARS2-T21I/E166A variant in K18-hACE2 mice. These findings advance our understanding of the resistance profiles and mechanistic underpinnings of SARS-CoV-2 3CLpro and underscore the necessity for diversified antiviral therapeutic strategies.

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.