A large-scale screen to target SARS-CoV-2: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is initially expressed as two large polyproteins. Its main protease, M ^pro , is essential to yield functional viral proteins, making it a key drug target. Günther et al. used x-ray crystallography to screen more than 5000 compounds that are either approved drugs or drugs in clinical trials. The screen identified 37 compounds that bind to M ^pro . High-resolution structures showed that most compounds bind at the active site but also revealed two allosteric sites where binding of a drug causes conformational changes that affect the active site. In cell-based assays, seven compounds had antiviral activity without toxicity. The most potent, calpeptin, binds covalently in the active site, whereas the second most potent, pelitinib, binds at an allosteric site. Science , this issue p. 642

The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host’s innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.

Nearly identical Pd nanocubes yield an x-ray powder diffraction pattern with interference fringes affording access to unprecedented structural details of nanocrystal size, shape, and complex atomic displacement for a billion-sized population. The excellent agreement between diffraction data and molecular dynamics (MD) provides strong experimental validation of MD simulations and the proposed data-interpretation paradigm. These results show that individual atomic displacements within the nanocubes are not only a function of disrupted bonds and the crystallographic plane of the adjacent surface, but are complex strain gradients extending across all surfaces of the particle strongly influenced by atomic displacements. This observation of nonuniform surface strain and the manner in which it is affected by different sizes, shapes, and locations within each facet could be the key to understanding many surface related properties of shaped nanocrystals including those associated with important catalysis applications.

Using coherent X-ray diffraction imaging (CXDI) as an in situ tool, we determined the shape and strain state of a platinum nanoparticle with ≈160 nm diameter supported by a strontium titanate substrate. The experiment was performed at a temperature of 400 K under continuous gas flow conditions of pure Ar and Ar/CO mixtures. The nanoparticle was preselected by scanning electron microscopy (SEM) and postanalyzed by atomic force microscopy (AFM). We obtain a very good agreement between the overall nanoparticle size, shape, and defect structure as determined by CXDI and AFM. In addition, we compare the strain state in the nanoparticle near surface region and its bulk: For pure Ar flow, we find a slight compressive strain in the nanoparticle bulk compared to an expansion in the near surface region. We ascribe the latter to the presence of high index vicinal surfaces. Our analysis suggests that under mixed Ar/CO flow at 400 K reshaping of the nanoparticle occurred. New high index facets developed, leading to a stronger lattice expansion, also propagating into the nanoparticle bulk. Our high-resolution experiments pave the way for future CXDI experiments under operando catalytic reaction conditions.

Bimetallic catalysts can undergo segregation or redistribution of the metals driven by oxidizing and reducing environments. Bragg coherent diffraction imaging (BCDI) was used to relate displacement fields to compositional distributions in crystalline Pt-Rh alloy nanoparticles. Three-dimensional images of internal composition showed that the radial distribution of compositions reverses partially between the surface shell and the core when gas flow changes between ${\mathrm{O}}_2$ and ${\mathrm{H}}_2$. Our observation suggests that the elemental segregation of nanoparticle catalysts should be highly active during heterogeneous catalysis and can be a controlling factor in synthesis of electrocatalysts. In addition, our study exemplifies applications of BCDI for in situ 3D imaging of internal equilibrium compositions in other bimetallic alloy nanoparticles.