An artificial intelligence system reveals liquiritin inhibits SARSCoV-2 by mimicking type I interferon

Abstract

The pandemic COVID-19 has spread to all over the world and greatly threatens safety and health of people. COVID-19 is highly infectious and with high mortality rate. As no effective antiviral treatment is currently available, new drugs are urgently needed. We employed transcriptional analysis to uncover potential antiviral drugs from natural products or FDA approved drugs. We found liquiritin significantly inhibit replication of SARS-CoV-2 in Vero E6 cells with EC50 = 2.39 μM. Mechanistically, we found liquiritin exerts anti-viral function by mimicking type I interferon. Upregulated genes induced by liquiritin are enriched in GO categories including type I interferon signaling pathway, negative regulation of viral genome replication and etc. In toxicity experiment, no death was observed when treated at dose of 300 mg/kg for a week in ICR mice. All the organ indexes but liver and serum biochemical indexes were normal after treatment. Liquiritin is abundant in licorice tablet (~0.2% by mass), a traditional Chinese medicine. Together, we recommend liquiritin as a competitive candidate for treating COVID-19. We also expect liquiritin to have a broad and potent antiviral function to other viral pathogens, like HBV, HIV and etc.

Introduction

Began at the end of year 2019, a novel coronavirus named SARS-CoV-2 caused outbreaks of pulmonary diseases (COVID-19) worldwide. It has greatly threatened the public health in global and killed tens-of-thousands of people1. By May 2nd, there are > 340,000 cumulative cases globally, with > 240,000 deaths. At present, some drugs are considered modestly effective in treating COVID-19, including chloroquine and remdesivir. However, the efficacy and safety of these drugs for SARS-CoV-2 pneumonia patients are not conclusive after several clinical trials. Current studies showed controversial effects in different trials2. As there is no specific treatment against COVID-19, identifying effective and safe antiviral agents to combat the disease is urgently needed.

Previous strategies for anti-viral drug development mainly focus on blocking receptors or inhibiting proteases. However, boosting the protective ability of the host was rarely considered. Herein, we consider a method to inhibit the gene expression of multiple factors that related to viral replication with one single compound. Previously, the chemical treated cell cultures were measured and analyzed by microarray or L1000 techniques3,4. The gene set enrichment analysis (GSEA) or Venn diagram were applied to connect the gene expression profile to up / down gene sets of certain diseases. Such technique, named connectivity map (CMAP) has been applied in screening drugs for obesity5,6. We proposed that similar strategy can be applied to inhibit host machinery proteins that supporting the viral replication and to induce genes that blocking the viral replication.

Liquiritin is one of the main flavonoids in Glycyrrhiza uralensis, which acts as an antioxidant and has antidepressant, neuroprotective, anti-inflammatory and therapeutic effects on heart system diseases7–11. Liquiritin plays a strong protective effect on vascular endothelial cells in myocardial ischemia-reperfusion injury model11. It can also protect smoking-induced lung epithelial cell injury12.

Type I interferon (INF) is important cytokines to protect host from viral infection. Almost all human cells can produce INFα/β, which are the best-defined type I INFs. INFs are able to induce the downstream IFN stimulated genes (ISGs) to inhibit the viral replication, including MX1, PKR, OAS, IFITM, APOBEC1, TRIM and etc13.

In present study, we first predicted the efficacy of compounds to inhibit the viral replication. Then, we tested them using Vero E6 cell lines. We found liquiritin is able to inhibit infection of SARS-CoV-2 efficiently with EC50 = 2.39 μM. Mechanistically, we found liquiritin mimicked type I INF to induce ISGs and thus protect cells from infection. We also evaluated the bioavailability, metabolism and safety of liquiritin.

Results

Prediction of efficacy against host genes related to viral replication

To perform GSEA against chemical induced transcriptomes, a gene set is required. In the case of SARS-CoV-2, a reasonable gene set that are enriched in viral processes by analyzing the ACE2-expressed AT2 cells were reported by Zhao et. al14. These genes include TRIM27, IFITM3, TMPRSS2, LAMP1 and etc. The full list is shown in Methods section. We chose the FDA approved drugs and natural products as the compound library (3682 in total). We employed InfinityPhenotype15, which is an artificial intelligence based platform, to predict efficacy of potential drugs (Figure 1a). InfinityPhenotype takes molecule formula as input and calculate the enrichment score, similar as in CMAP, but only one side is considered. All the scores were plotted in Figure 1b. The top scored compounds are shown in Supp. Table 1. In the natural product list, liquiritin (−0.32) and agnuside (−0.31) have emerged. In FDA approved drugs, we obtained procaterol (−0.23), pibrentasvir (−0.23) and carbocisteine (−0.21). Liquiritin ranks first among all the compounds.

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