A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein–protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 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.

In this study, scientists successfully expressed 26 of its 29 proteins based on the genome of the new coronavirus, and tagged these proteins for subsequent screening. Using affinity purification mass spectrometry (AP-MS), scientists found 332 SARS-CoV-2 protein-human protein interactions with high confidence.

Figure1. SARS-CoV-2 protein–protein interaction network.

Note:332 high-confidence interactions between 26 SARS-CoV-2 proteins (red diamonds) and human proteins (circles; drug targets: orange; protein complexes: yellow; proteins in the same biological process: blue). Edge color proportional to MiST score; edge thickness proportional to spectral counts. Physical interactions among host proteins (thin black lines) were curated from CORUM, IntAct, and Reactome. An interactive protein–protein interaction map can be found at kroganlab.ucsf.edu/network-maps. ECM, extracellular matrix; ER, endoplasmic reticulum; snRNP, small nuclear ribonucleoprotein. n = 3 biologically independent samples.

Based on the data of these protein interactions, researchers have found different biological processes involved in different SARS-CoV-2 proteins, including DNA replication, epigenetics and gene expression regulation, vesicle transport, lipid modification, etc. Among them, the role of the SARS-CoV-2 and multiple innate immune system pathways has attracted attention-research has found that the SARS-CoV-2 protein can affect the interferon pathway and the NF-κB pathway. In addition, two human proteins that regulate antiviral innate immune signaling pathways will also be targeted and targeted by SARS-CoV-2 proteins.

Finding the interaction of these proteins will also find the potential "fate" of the SARS-CoV-2. In response to the information discovered in the research, scientists are looking for molecules that can selectively interfere with the interaction between viral proteins and human proteins among approved drugs, drugs in clinical trials, and compounds that have not yet entered clinical trials. This work has found 69 so-called "old drugs" that can target 63 different protein interactions.

So, do these found molecules really have antiviral activity? In order to answer this question, the researchers conducted two experiments in the United States and France respectively-at Mount Sinai Hospital in New York, a group of scientists used immunofluorescence in cell lines to evaluate 37 drugs; in France In the Pasteur Institute, another group of scientists tested the antiviral effects of 44 drugs and tested them by qRT-PCR.

Figure 2. Drug–human target network.

Note: Protein–protein interactions of SARS-CoV-2 baits with approved drugs (green), clinical candidates (orange) and preclinical candidates (purple) with experimental activities against the host proteins (white background) or previously known host factors (grey background) are shown.

These two experiments found that two types of molecules can effectively reduce the infectivity of viruses. One type is protein biogenesis inhibitors, which can inhibit the translation of mRNA; The other is the corresponding ligands of Sigma1 and Sigma2 receptors, which can regulate the function of these receptors. Subsequent studies have shown that these molecules can act to block virus infection before the virus invades cells.
     The researchers pointed out in the discussion session that these two types of drugs can target at least 5 different targets and have more than 10 different chemical types, so there is huge room for optimization. These findings indicate that we can target the host protein to develop corresponding antiviral therapies, which is expected to overcome the problem of virus resistance and ultimately lead to a broad-spectrum antiviral therapy to better respond to the next pandemic.