A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
1 May, 2020The 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. 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, these scientifics 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, they 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.
So far, no clinically available antiviral drugs have been developed for SARS-CoV, SARS-CoV-2 or MERS-CoV. Clinical trials are ongoing for treatment of COVID-19 with the nucleoside analog RNA-dependent RNA Polymerase (RdRP) inhibitor Remdesivir, and recent data suggests a new nucleoside analog may be effective against SARS-CoV-2 infection in laboratory animals. Clinical trials on several vaccine candidates are also underway, as are trials of repurposed compounds inhibiting the human protease TMPRSS2. Thus, there is great potential in systematically exploring the host dependencies of the SARS-CoV-2 virus to identify other host proteins already targeted by existing drugs. Therapies targeting the host-virus interface, where the emergence of mutational resistance is arguably less likely, could potentially pre- sent durable, broad-spectrum treatment modalities. Unfortunately, limited knowledge of the molecular details of SARS-CoV-2 infection precludes a comprehensive evaluation of small molecule candidates for host-directed therapies. We sought to address this gap by systemati- cally mapping the interaction landscape between SARS-CoV-2 proteins and human proteins.
In this study, 332 high-confidence SARS-CoV-2-human PPIs connected to multiple biological processes, including protein trafficking, translation, transcription and ubiquitination regulation have been identified. Against these targets they found 69 ligands, including FDA approved drugs, compounds in clinical trials, and preclinical compounds. Antiviral tests in two different laboratories reveal two broad sets of active drugs and compounds; those impinging on translation, and those modulating Sigma1 and Sigma2 receptors. Within these sets are at least five targets and over ten different chemotypes, suggesting a rich landscape for optimization.
The chemo-proteomic analysis that emerges from this study not only highlights clinically actionable drugs that target human proteins in the interactome, it provides a context for interpreting their mechanism of action. The potent efficacy of the translation inhibitors on viral infectivity—in the 10 to 100 nM range—makes these molecules attractive as candidate antivirals, and also highlights this pathway as a point of intervention. While the mechanism of action of the drugs targeting the Sigma1 and Sigma2 receptors remains less defined, their activity as both anti- and pro-viral agents is mechanistically suggestive. The relatively strong efficacy of PB28, at 280 nM IC90 in the viral titer assay, and its high selectivity against off-targets, suggests that molecules of this class may be optimized towards therapeutics. Whereas it is unclear that approved drugs like clemastine and cloperastine, which are used as antihistamines and antitussives, have pharmacokinetics suitable for antiviral therapy, nor are they free of binding to side-effect targets, they have been used for decades. We do caution against their use outside of controlled studies, due to their side-effect liabilities. By the same standard, we find that the widely used antitussive dextromethorphan harbors proviral activity and therefore its use should merit caution and further study in the context of COVID-19. More positively, there are dozens of approved drugs that are active against Sigma receptors that remain untested, some of which, intriguingly, have begun to appear in other studies, although not recognized as Sigma ligands. Therefore, this area of pharmacology has great promise for repurposing and for the optimization of new agents in the fight against COVID-19.
