key: cord-1015517-8msh8cmd
authors: Dai, Yifei; Qiang, Weijie; Gui, Yu; Tan, Xue; Pei, Tianli; Lin, Kequan; Cai, Siwei; Sun, Liang; Ning, Guochen; Wang, Jianxun; Guo, Hongyan; Sun, Yimin; Cheng, Jing; Xie, Lan; Lan, Xun; Wang, Dong
title: A large-scale transcriptional study reveals inhibition of COVID-19 related cytokine storm by traditional chinese medicines
date: 2021-01-12
journal: Sci Bull (Beijing)
DOI: 10.1016/j.scib.2021.01.005
sha: 75a79a5865245560f32d8eddce2f55762e01209a
doc_id: 1015517
cord_uid: 8msh8cmd

Coronavirus disease-2019 (COVID-19) has become a major global epidemic. Facilitated by HTS(2) technology, we evaluated the effects of 578 herbs and all 338 reported anti-COVID-19 TCM formulae on cytokine storm-related signaling pathways, and identified the key targets of the relevant pathways and potential active ingredients in these herbs. This large-scale transcriptional study innovatively combines HTS(2) technology with bioinformatics methods and computer-aided drug design. For the first time, it systematically explores the molecular mechanism of TCM in regulating the COVID-19-related cytokine storm, providing an important scientific basis for elucidating the mechanism of action of TCM in treating COVID-19. [Figure: see text]

(TCM) has made great contributions to the fight against this epidemic. It is reported that more than 90% of COVID-19 patients in China had received TCM treatment, with the effective rate exceeding 90%

(http://www.satcm.gov.cn/xinxifabu/meitibaodao/2020-03-24/14213.html). Despite the remarkable therapeutic effects of TCM, the molecular mechanisms of TCM formulae inhibiting COVID-19 are still not fully understood. Here, we combined the automated high throughput sequencing-based high throughput screening (HTS 2 ) assay with bioinformatics and computer-aided drug design (CADD) to investigate the molecular mechanisms of TCM-mediated therapeutic effects on COVID-19-related cytokine storm (Fig. 1a) .

Evidence from a wide range of sources suggests that cytokine storm is an important indicator of the deterioration of COVID-19 [1] . Thereinto, the IL-6 and TNF-α pathways are likely to be the most important signaling pathways causing cytokine storm [2] . Interestingly, some TCMs might have immunosuppressive features to prevent and treat cytokine storm [3] . Moreover, in view of the characteristics of multiple targets and multiple pathways, TCM is suitable for the treatment of complex signal networks of the immune response.

HTS 2 is a high-throughput screening platform based on the gene expression signature that quantitatively analyzes cell transcriptional profiles at a large scale [4, 5] .

Therefore, we carried out the HTS 2 assay to detect the regulation of 578 herbal extracts on the IL-6 and TNF-α signaling pathways in immune cells (Table S1 online A total of 16 herbs was identified to have a significant inhibitory effect on the IL-6 pathway (Fig. 1b, Fig. S2a online), while 37 herbs suppress the TNF-α pathway significantly (Fig. 1c, Fig. S2b online) . In the heatmap of gene expression induced by these herbs, more than half of the genes are down-regulated, suggesting that these herbs have a significant inhibitory effect on the expression of cytokine storm-related genes (Fig. S2c , e online, Table S2 , S3 online). Notably, some of these herbs have been previously reported to reduce the production of IL-6 in inflammatory cells, such as Mufurongye [6] , Xuanfuhua [7] , and Guizhi [8] . And some herbs have been reported to decrease the level of TNF-α or down-regulate the gene expression of TNF-α, such as Cheqianzi [9] , Dangshen [10] , and Guanhuangbo [11] . Interestingly, the correlation heatmap showed a similarity of 16 herbs in suppressing the IL-6 pathway ( Fig (Table S4) .

Consistent with our findings, some previous studies reported that Lizhong Decoction could reduce the yield of inflammatory cytokines [12] , Liujunzi Decoction can regulate immunity and release of inflammatory factors [13] , and Huanglian Jiedu

Decoction exhibits a therapeutic effect on inflammation [14] . Notably, Qingfei Paidu Decoction, one of the most well-known anti-COVID-19 formulae, ranks fourth, and this prescription has been widely used and played a crucial role in the fight against COVID-19 in Wuhan, China. A recent study has shown that the main components of Qingfei Paidu Decoction are polysaccharide, and one of its most remarkable characteristics is an immunomodulatory activity [15] . Nonetheless, the mechanism of action (MOA) of Qingfei Paidu Decoction in inhibiting cytokine storm is still unclear.

Thus, we conducted further in-depth research on it.

By combining the HTS 2 assay and herb scoring results, we constructed a formula-herb-gene-pathway network diagram of Qingfei Paidu Decoction (Fig. 1d) .

In this formula, we identified 4 herbs with an inhibitory effect on the IL-6 or TNF-α pathways, including Guizhi, which significantly inhibits the IL-6 pathway, and Shegan, Baizhu, and Zexie, which significantly inhibit the TNF-α pathway. In To explore the key targets of herbs suppressing the IL-6 and TNF-α pathway, we built the protein-protein interaction (PPI) network (Fig. S5a, c online) . It was established based on the genes that represent components of these two pathways.

Subsequently, three centrality algorithms were used to calculate the whole network, and the top 10 targets were identified according to the results of topological analysis ( Fig. S5b, d online) . Thereinto, STAT3 and TNF-α were selected as the key target of the IL-6 and TNF-α pathway, respectively. Studies have shown that STAT3 is a potential molecular target for clinical syndromes characterized by systemic inflammation [16] , and the TNF-α inhibitors could show high therapeutic efficacy in treating chronic inflammatory diseases via the promotion of a rapidly decreased number of cells [17] .

In order to predict active ingredients with the binding potential to STAT3 and (Table S5 online) . Further, molecular docking was applied to predict the active ingredients that could bind to STAT3 or TNF-α, the two key proteins in the IL-6 and TNF-α signaling pathways. With the lowest Glide gscore, the compounds with the highest binding stability towards STAT3 and TNF-α are quercetagetin and 4-(3-Phenylacryloyloxymethyl)-6,7-dimethoxycoumarin, respectively (Table S6 online).

To interrogate the binding potential of the optimal active ingredient towards STAT3 and TNF-α, we next conducted molecular dynamics (MD) analysis (Fig. S6 online, Table S7 

The author declares that they have no conflict of interest. 

Coronavirus disease-2019 (COVID-19) has become a major global epidemic. Facilitated by HTS 2 technology, we evaluated the effects of 578 herbs and all 338 reported anti-COVID-19 TCM formulae on cytokine storm-related signaling pathways, and identified the key targets of the relevant pathways and potential active ingredients in these herbs. This large-scale transcriptional study innovatively combines HTS 2 technology with bioinformatics methods and computer-aided drug design. For the first time, it systematically explores the molecular mechanism of TCM in regulating the COVID-19-related cytokine storm, providing an important scientific basis for elucidating the mechanism of action of TCM in treating COVID-19.

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This work was supported by grants from the National Natural Science