The novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 2.3 million people, killed over 160,000, and caused worldwide social and economic disruption 1,2 . There are currently no antiviral drugs with proven clinical efficacy, nor are there vaccines for its prevention, and these efforts are hampered by limited knowledge of the molecular details of SARS-CoV-2 infection. To address this, we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), identifying 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (29 FDA-approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds). Screening a subset of these in multiple viral assays identified two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the Sigma1 and Sigma2 receptors. Further studies of these host factor targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.

Highlights d Phosphoproteomics analysis of SARS-CoV-2-infected cells uncovers signaling rewiring d Infection promotes host p38 MAPK cascade activity and shutdown of mitotic kinases d Infection stimulates CK2-containing filopodial protrusions with budding virus d Kinase activity analysis identifies potent antiviral drugs and compounds

ABSTRACTAn outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.

Millimeter-size single-crystal monolayer graphene is synthesized on polycrystalline Cu foil by a method that involves suppressing loss by evaporation of the Cu at high temperature under low pressure. This significantly diminishes the number of graphene domains, and large single crystal domains up to ∼2 mm in size are grown.

The growth of bilayer and multilayer graphene on copper foils was studied by isotopic labeling of the methane precursor. Isotope-labeled graphene films were characterized by micro-Raman mapping and time-of-flight secondary ion mass spectrometry. Our investigation shows that during growth at high temperature, the adlayers formed simultaneously and beneath the top, continuous layer of graphene and the Cu substrate. Additionally, the adlayers share the same nucleation center and all adlayers nucleating in one place have the same edge termination. These results suggest that adlayer growth proceeds by catalytic decomposition of methane (or CH(x), x < 4) trapped in a "nano-chemical vapor deposition" chamber between the first layer and the substrate. On the basis of these results, submillimeter bilayer graphene was synthesized by applying a much lower growth rate.

Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.

Improving electrochemical activity of graphene is crucial for its various applications, which requires delicate control over its geometric and electronic structures. We demonstrate that precise control of the density of vacancy defects, introduced by Ar(+) irradiation, can improve and finely tune the heterogeneous electron transfer (HET) rate of graphene. For reliable comparisons, we made patterns with different defect densities on a same single layer graphene sheet, which allows us to correlate defect density (via Raman spectroscopy) with HET rate (via scanning electrochemical microscopy) of graphene quantitatively, under exactly the same experimental conditions. By balancing the defect induced increase of density of states (DOS) and decrease of conductivity, the optimal HET rate is attained at a moderate defect density, which is in a critical state; that is, the whole graphene sheet becomes electronically activated and, meanwhile, maintains structural integrity. The improved electrochemical activity can be understood by a high DOS near the Fermi level of defective graphene, as revealed by ab initio simulation, which enlarges the overlap between the electronic states of graphene and the redox couple. The results are valuable to promote the performance of graphene-based electrochemical devices. Furthermore, our findings may serve as a guide to tailor the structure and properties of graphene and other ultrathin two-dimensional materials through defect density engineering.

The thermal conductivity (κ) of suspended graphene membranes made by chemical vapor deposition (CVD) was measured by micro-Raman mapping. Cracks and wrinkles present in these suspended graphene membranes were identified by micro-Raman mapping, and κ values and their statistics were obtained on membranes free of such imperfections in a single mapping. Based on this new technique, an average κ value of 1875 ± 220 W m(-1) K(-1) at 420 K was measured on 26 suspended graphene membranes that were free of wrinkles, ~27% higher than the average value measured from 12 graphene membranes with wrinkles. These results suggest that the variation in published thermal conductivity values for suspended graphene samples could, at least in part, be due to the presence or absence of wrinkles.