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We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property-free knowledge base for future anticoronavirus drug discovery.

Cell-free protein synthesis (CFPS) platforms, once primarily a research tool to produce difficult to express proteins, are increasingly being pursued by the synthetic biology community for applications including biomanufacturing, rapid screening systems, and field-ready sensors. While consistency within individual studies is apparent in the literature, challenges with reproducing results between laboratories, or even between individuals within a laboratory, are discussed openly by practitioners. As the field continues to grow and move toward applications, a quantitative understanding of expected variability for CFPS and the relative contribution of underlying sources will become increasingly important. Here we offer the first quantitative assessment of interlaboratory variability in CFPS. Three laboratories implemented a single CFPS protocol and performed a series of exchanges, both of material and personnel, designed to quantify relative contributions to variability associated with the site, operator, cell extract preparation, and supplemental reagent preparation. We found that materials prepared at each laboratory, exchanged pairwise, and tested at each site resulted in 40.3% coefficient of variation compared to 7.64% for a single operator across days using a single set of materials. Reagent preparations contributed significantly to observed variability; extract preparations, however, surprisingly did not explain any of the observed variability, even when prepared in different laboratories by different operators. Subsequent exchanges showed that both the site and the operator each contributed to observed interlaboratory variability. In addition to providing the first quantitative assessment of interlaboratory variability in CFPS, these results establish a baseline for individual operator variability across days that can be used as an initial benchmark for community-driven standardization efforts. We anticipate that our results will narrow future avenues of investigation to develop best practices that will ultimately drive down interlaboratory variability, accelerating research progress and informing the suitability of CFPS for real-world applications.

A fundamental understanding of chemical interactions and transport mechanisms that result from introducing multiple chemical species into a polymer plays a key role in the development and optimization of membranes, coatings, and decontamination formulations. In this study, we explore the solvent-assisted desorption of a penetrant (2,5-lutidine) in polyurethane with aprotic (acetonitrile) and protic (methanol) solvents. Chemical interactions between solvent, penetrant, and polymer functional groups are characterized via time-resolved Fourier transform infrared spectroscopy (FTIR) during single and multicomponent exposures. For both solvents, an increase in the extraction rate of the penetrant is observed when the solvent is applied during desorption. Inspection of the FTIR spectra reveals two potential mechanisms that facilitate the enhanced desorption rate: (1) penetrant/solvent competition for hydrogen donor groups on the polymer backbone and (2) disruption of the self-interaction (cohesive forces) between neighboring polymer chains. Finally, the aprotic solvent is found to generate an order of magnitude greater desorption rate of the penetrant, which is attributed to a greater disruption of the self-interaction during penetrant desorption compared to the protic solvent and the inability of an aprotic solvent to form larger and potentially slower penetrant-solvent complexes.

Chemical warfare agents (CWA) can be absorbed by variety of materials including polymeric coatings like paints through bulk liquid contact, thus presenting touch and vapor hazards to interacting personnel. In order for accurate hazard assessments and subsequent decontamination approaches to be designed, it is necessary to characterize the absorption and distribution of highly toxic species, as well as their chemical simulant analogs, in the subsurface of engineered, heterogeneous materials. Using a combination of judicious sample preparation in concert with scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS), it should be possible to directly measure the uptake and distribution of CWA simulants in the subsurface of complex multilayer coatings. Polyurethane and alkyd coatings were applied to aluminum and silicon substrates and contaminated with 2-chloroethyl ethyl sulfide (CEES) and dimethyl methylphosphonate (DMMP). The surfaces and cross-sectional interfaces of the contaminated coatings were probed with SEM-EDS to provide imaging, spectral, and elemental mapping data of the contaminant-material systems. This work demonstrated SEM-EDS capability to detect and spatially resolve unique elemental signatures of CWA simulants within military coatings. The visual and quantitative results provided by these direct measurements illustrate contaminant spatial distributions, provide order-of-magnitude approximations for diffusion coefficients, and reveal material characteristics that may impact contaminant transport into complex coating materials. It was found that contaminant uptake was significantly different between the topcoat and primer layers.

For several decades, the Fersht laboratory has been a world leader in research on protein structure and mechanism. There are pressing medical and financial needs for new medicines. Here, I use examples to illustrate how drug discovery could be more successful if it increased utilisation of approaches from the Fersht laboratory.