The tem­per­ature-dependent conformational ensemble of SARS-CoV-2 main protease (M(pro))

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M(pro), is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M(pro) were obtained at cryogenic tem­per­ature or room tem­per­ature only. Here we report a series of high-resolution crystal structures of unliganded M(pro) across multiple tem­per­atures from cryogenic to physiological, and another at high humidity. We inter­rogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M(pro), including a mobile zinc ion inter­leaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intra­molecular network bridging the active site and dimer inter­face. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.