Discovery of repurposable drugs for HCoV
To further validate the 135 repurposable drugs against HCoVs, we first performed gene set enrichment analysis (GSEA) using transcriptome data of MERS-CoV and SARS-CoV infected host cells (see Methods). These transcriptome data were used as gene signatures for HCoVs. Additionally, we downloaded the gene expression data of drug-treated human cell lines from the Connectivity Map (CMAP) database36 to obtain drug–gene signatures. We calculated a GSEA score (see Methods) for each drug and used this score as an indication of bioinformatics validation of the 135 drugs. Specifically, an enrichment score (ES) was calculated for each HCoV data set, and ES > 0 and P < 0.05 (permutation test) was used as cut-off for a significant association of gene signatures between a drug and a specific HCoV data set. The GSEA score, ranging from 0 to 3, is the number of data sets that met these criteria for a specific drug. Mesalazine (an approved drug for inflammatory bowel disease), sirolimus (an approved immunosuppressive drug), and equilin (an approved agonist of the estrogen receptor for menopausal symptoms) achieved the highest GSEA scores of 3, followed by paroxetine and melatonin with GSEA scores of 2. We next selected 16 high-confidence repurposable drugs (Fig. 5a and Table 1) against HCoVs using subject matter expertise based on a combination of factors: (i) strength of the network-predicted associations (a smaller network proximity score in Supplementary Table S4); (ii) validation by GSEA analyses; (iii) literature-reported antiviral evidence, and (iv) fewer clinically reported side effects. Specifically, we showcased several selected repurposable drugs with literature-reported antiviral evidence as below.
Fig. 5 A discovered drug-protein-HCoV network for 16 candidate repurposable drugs.
a Network-predicted evidence and gene set enrichment analysis (GSEA) scores for 16 potential repurposable drugs for HCoVs. The overall connectivity of the top drug candidates to the HCoV-associated proteins was examined. Most of these drugs indirectly target HCoV-associated proteins via the human protein–protein interaction networks. All the drug–target-HCoV-associated protein connections were examined, and those proteins with at least five connections are shown. The box heights for the proteins indicate the number of connections. GSEA scores for eight drugs were not available (NA) due to the lack of transcriptome profiles for the drugs. b–e Inferred mechanism-of-action networks for four selected drugs: b toremifene (first-generation nonsteroidal-selective estrogen receptor modulator), c irbesartan (an angiotensin receptor blocker), d mercaptopurine (an antimetabolite antineoplastic agent with immunosuppressant properties), and e melatonin (a biogenic amine for treating circadian rhythm sleep disorders).
Table 1 Top 16 network-predicted repurposable drugs with literature-derived antiviral evidence.
HBV hepatitis B virus, HCV hepatitis C virus, HDV hepatitis delta virus, EBOV Ebola viruses, ZEBOV-GP Zaire Ebola virus glycoprotein, HIV human immunodeficiency virus, EBV Epstein-Barr virus, ANDV Andes orthohantavirus, EMCV encephalomyocarditis virus, FECV feline enteric coronavirus, RSV respiratory syncytial virus, EV71 enterovirus 71, HSV-1 and -2 herpes simplex viruses, CVB4 Coxsackievirus B4.

Selective estrogen receptor modulators
An overexpression of estrogen receptor has been shown to play a crucial role in inhibiting viral replication37. Selective estrogen receptor modulators (SERMs) have been reported to play a broader role in inhibiting viral replication through the non-classical pathways associated with estrogen receptor37. SERMs interfere at the post viral entry step and affect the triggering of fusion, as the SERMs’ antiviral activity still can be observed in the absence of detectable estrogen receptor expression18. Toremifene (Z = –3.23, Fig. 5a), the first generation of nonsteroidal SERM, exhibits potential effects in blocking various viral infections, including MERS-CoV, SARS-CoV, and Ebola virus in established cell lines17,38. Compared to the classical ESR1-related antiviral pathway, toremifene prevents fusion between the viral and endosomal membrane by interacting with and destabilizing the virus membrane glycoprotein, and eventually inhibiting viral replication39. As shown in Fig. 5b, toremifene potentially affects several key host proteins associated with HCoV, such as RPL19, HNRNPA1, NPM1, EIF3I, EIF3F, and EIF3E40,41. Equilin (Z = –2.52 and GSEA score = 3), an estrogenic steroid produced by horses, also has been proven to have moderate activity in inhibiting the entry of Zaire Ebola virus glycoprotein and human immunodeficiency virus (ZEBOV-GP/HIV)18. Altogether, network-predicted SERMs (such as toremifene and equilin) offer candidate repurposable drugs for 2019-nCoV/SARS-CoV-2.

Angiotensin receptor blockers
Angiotensin receptor blockers (ARBs) have been reported to associate with viral infection, including HCoVs42–44. Irbesartan (Z = –5.98), a typical ARB, was approved by the FDA for treatment of hypertension and diabetic nephropathy. Here, network proximity analysis shows a significant association between irbesartan’s targets and HCoV-associated host proteins in the human interactome. As shown in Fig. 5c, irbesartan targets SLC10A1, encoding the sodium/bile acid cotransporter (NTCP) protein that has been identified as a functional preS1-specific receptor for the hepatitis B virus (HBV) and the hepatitis delta virus (HDV). Irbesartan can inhibit NTCP, thus inhibiting viral entry45,46. SLC10A1 interacts with C11orf74, a potential transcriptional repressor that interacts with nsp-10 of SARS-CoV47. There are several other ARBs (such as eletriptan, frovatriptan, and zolmitriptan) in which their targets are potentially associated with HCoV-associated host proteins in the human interactome.

Immunosuppressant or antineoplastic agents
Previous studies have confirmed the mammalian target of rapamycin complex 1 (mTORC1) as the key factor in regulating various viruses’ replications, including Andes orthohantavirus and coronavirus48,49. Sirolimus (Z = –2.35 and GSEA score = 3), an inhibitor of mammalian target of rapamycin (mTOR), was reported to effectively block viral protein expression and virion release effectively50. Indeed, the latest study revealed the clinical application: sirolimus reduced MERS-CoV infection by over 60%51. Moreover, sirolimus usage in managing patients with severe H1N1 pneumonia and acute respiratory failure can improve those patients’ prognosis significantly50. Mercaptopurine (Z = –2.44 and GSEA score = 1), an antineoplastic agent with immunosuppressant property, has been used to treat cancer since the 1950s and expanded its application to several auto-immune diseases, including rheumatoid arthritis, systemic lupus erythematosus, and Crohn’s disease52. Mercaptopurine has been reported as a selective inhibitor of both SARS-CoV and MERS-CoV by targeting papain-like protease which plays key roles in viral maturation and antagonism to interferon stimulation53,54. Mechanistically, mercaptopurine potentially target several host proteins in HCoVs, such as JUN, PABPC1, NPM1, and NCL40,55 (Fig. 5d).

Anti-inflammatory agents
Inflammatory pathways play essential roles in viral infections56,57. As a biogenic amine, melatonin (N-acetyl-5-methoxytryptamine) (Z = –1.72 and GSEA score = 2) plays a key role in various biological processes, and offers a potential strategy in the management of viral infections58,59. Viral infections are often associated with immune-inflammatory injury, in which the level of oxidative stress increases significantly and leaves negative effects on the function of multiple organs60. The antioxidant effect of melatonin makes it a putative candidate drug to relieve patients’ clinical symptoms in antiviral treatment, even though melatonin cannot eradicate or even curb the viral replication or transcription61,62. In addition, the application of melatonin may prolong patients’ survival time, which may provide a chance for patients’ immune systems to recover and eventually eradicate the virus. As shown in Fig. 5e, melatonin indirectly targets several HCoV cellular targets, including ACE2, BCL2L1, JUN, and IKBKB. Eplerenone (Z = –1.59), an aldosterone receptor antagonist, is reported to have a similar anti-inflammatory effect as melatonin. By inhibiting mast-cell-derived proteinases and suppressing fibrosis, eplerenone can improve survival of mice infected with encephalomyocarditis virus63.
In summary, our network proximity analyses offer multiple candidate repurposable drugs that target diverse cellular pathways for potential prevention and treatment of 2019-nCoV/SARS-CoV-2. However, further preclinical experiments64 and clinical trials are required to verify the clinical benefits of these network-predicted candidates before clinical use.