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.

We evolved muscarinic receptors in yeast to generate a family of G protein-coupled receptors (GPCRs) that are activated solely by a pharmacologically inert drug-like and bioavailable compound (clozapine-N-oxide). Subsequent screening in human cell lines facilitated the creation of a family of muscarinic acetylcholine GPCRs suitable for in vitro and in situ studies. We subsequently created lines of telomerase-immortalized human pulmonary artery smooth muscle cells stably expressing all five family members and found that each one faithfully recapitulated the signaling phenotype of the parent receptor. We also expressed a G i-coupled designer receptor in hippocampal neurons (hM 4D) and demonstrated its ability to induce membrane hyperpolarization and neuronal silencing. We have thus devised a facile approach for designing families of GPCRs with engineered ligand specificities. Such reverse-engineered GPCRs will prove to be powerful tools for selectively modulating signal-transduction pathways in vitro and in vivo.cell engineering ͉ molecular evolution ͉ receptorome B ecause of the assorted cellular responses directed by them, their number, and the ease of which they are pharmacologically screened, the superfamily of G protein-coupled receptors (GPCRs) is one of the most therapeutically important targets in the proteome (1). However, the potential of this family is restricted by our ability to assess their function, which currently involves transgenic, knockout, and/or in vivo studies with selective drugs. Genetic studies are frequently limited to loss-of-function phenotypes, whereas nonselectiveness of a drug often interferes with interpretation of pharmacological studies. Knowledge of the roles of the individual family members is being bolstered by the ongoing creation of knockout mice for many GPCRs. Selective activation of individual GPCR subtypes in a defined tissue, in either a knockout or wild-type animal, is currently problematic but, if possible, would serve to complement present findings by providing novel insights into disease states resulting from overstimulation of certain signaling pathways.One approach to this problem has been to rationally modify receptors to favor synthetic over natural substrate/ligand recognition, and subsequently, these mutant proteins have been used as bio-tools to study protein function in complex biological environments (2, 3). At the forefront of such modified GPCRs is Ro1, a G i/o -coupled opioid receptor activated by a synthetic but not a native ligand, which has been conditionally expressed in transgenic mice to study cardiac function after its selective activation (4). Such mutant receptors, like Ro1, have been classified as receptors activated solely by synthetic ligands (RASSLs), because they are activated by synthetic ligands but not by their endogenous ligands (5). RASSLs, as in the case of Ro1, have been demonstrated to be valuable tools (4, 6); however, because the synthetic ligand frequently has high affinity and/or potency at the native receptor (5,7,8), this pote...

The identification of protein function based on biological information is an area of intense research. Here we consider a complementary technique that quantitatively groups and relates proteins based on the chemical similarity of their ligands. We began with 65,000 ligands annotated into sets for hundreds of drug targets. The similarity score between each set was calculated using ligand topology. A statistical model was developed to rank the significance of the resulting similarity scores, which are expressed as a minimum spanning tree to map the sets together. Although these maps are connected solely by chemical similarity, biologically sensible clusters nevertheless emerged. Links among unexpected targets also emerged, among them that methadone, emetine and loperamide (Imodium) may antagonize muscarinic M3, alpha2 adrenergic and neurokinin NK2 receptors, respectively. These predictions were subsequently confirmed experimentally. Relating receptors by ligand chemistry organizes biology to reveal unexpected relationships that may be assayed using the ligands themselves.