An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

The global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires an urgent need to find effective therapeutics for the treatment of coronavirus disease 2019 (COVID-19). In this study, we developed an integrative drug repositioning framework, which fully takes advantage of machine learning and statistical analysis approaches to systematically integrate and mine large-scale knowledge graph, literature and transcriptome data to discover the potential drug candidates against SARS-CoV-2. Our in silico screening followed by wet-lab validation indicated that a poly-ADP-ribose polymerase 1 (PARP1) inhibitor, CVL218, currently in Phase I clinical trial, may be repurposed to treat COVID-19. Our in vitro assays revealed that CVL218 can exhibit effective inhibitory activity against SARS-CoV-2 replication without obvious cytopathic effect. In addition, we showed that CVL218 can interact with the nucleocapsid (N) protein of SARS-CoV-2 and is able to suppress the LPS-induced production of several inflammatory cytokines that are highly relevant to the prevention of immunopathology induced by SARS-CoV-2 infection.


Supplementary Text
The good pharmacokinetic and toxicokinetic characteristics of CVL218 in animals 1. CVL218 has the highest tissue distribution in the lung tissue of rats.
We further performed in vivo pharmacokinetic and toxicokinetic evaluation of CVL218 in animals (Methods). We first examined the concentrations of CVL218 over different tissues in rats at different time points post oral administration at different doses (supplementary Fig S4 and supplementary Table S4), which was also previously reported in [1]. Among seven tissues (i.e., lung, spleen, liver, kidney, stomach, heart and brain), we observed that lung had the highest CVL218 concentration, which was 188-fold higher compared to that of plasma (supplementary Table S5). The observation that lung had the highest concentration of CVL218 was in line with the fact that the SARS-CoV-2 virus has the most pathological impact in lung with high viral loads, which suggested that CVL218 has the great potential to be used for the indications of the lung lesions caused by SARS-CoV-2 infection, if its antiviral profile can be established in animal models and clinical trials.
Furthermore, we compared the pharmacokinetic data between CVL218 and arbidol, a broadspectrum antiviral drug had been recommended to treat the SARS-CoV-2-infected patients [2].
We found that the pharmacokinetic parameters of CVL218 and arbidol were comparable, with similar plasma concentrations and drug exposures (supplementary Table S6). Arbidol was mostly distributed in stomach and plasma post administration in rats (supplementary Table S5). In contrast, higher distributions of CVL218 in tissues especially in lung rather than plasma compared to those of arbidol indicated a superior pharmacokinetic profile of CVL218, which may render it as a better potential antiviral treatment of SARS-CoV-2 infection in lung.

The toxicity study demonstrated a safety profile of CVL218 in rats.
In rats after being orally administrated 20/60/160 mg/kg of CVL218 for 28 consecutive days and followed by 28 more days without drug administration (Methods), we observed no significant difference in body weight of rats among different dosage and the control groups (supplementary Fig S5a).
We next conducted a toxicokinetic analysis of CVL218 in rats (Methods). In particular, rats were given CVL218 20/60/160 mg/kg by oral gavage once a day for consecutive 28 days, followed by 28 more days without CVL218 administration, to investigate the reversibility of the toxic effects of the compound and examine whether there is any potential delayed-onset toxicity of this drug in rats. The results showed that, the maximum tolerable dose (MTD) and the no-observed adverse effect level (NOAEL) were 160 mg/kg and 20 mg/kg, respectively. The exposure of female rats to CVL218 (AUC0−24) was 7605 h· ng/mL in day 1 and 6657 h· ng/mL in day 28, while that of male rats (AUC0−24) was 9102 h· ng/mL in day 1 and 10253 h· ng/mL in day 28 (supplementary Table   S7). Based on the toxicokinetic results from the repeated dose studies, all rats survived after a 28day treatment period and showed no apparent sign of toxicity.

CVL218 exhibits a favorable safety profile in monkeys.
Monkeys were administered CVL218 (5, 20 or 80 mg/kg) by nasogastric feeding tubes with a consecutive daily dosing schedule for 28 days, followed by a 28-day recovery period (Methods).
Only a slight decrease of body weight was observed in the high-dose (80 mg/kg) group, and all changes were reversed after a 28-day recovery period (supplementary Fig S5b), demonstrating a favorable safety profile for CVL218 in monkeys. Further examination of the toxicokinetic data of CVL218 in monkeys showed that the increase of the exposure of CVL218 (AUC0−24) was approximately dose proportional, and after consecutive 28 days of drug administration, the accumulation was not apparent. The exposure of female monkeys to CVL218 (AUC0−24) was 19466 h· ng/ml in day 1 and 18774 h· ng/ml in day 28 (supplementary Table S8), while that of male monkeys (AUC0−24) was 16924 h· ng/ml in day 1 and 22912 h· ng/ml in day 28. The maximum tolerable dose (MTD) of CVL218 in monkeys was 80 mg/kg, and the dose of 5 mg/kg was considered as the no-observed adverse effect level (NOAEL).
Overall, the above in vivo data showed that CVL218 possesses good pharmacokinetic and toxicokinetic characteristics in rats and monkeys, and its high-level distribution in the therapeutically targeted tissue (i.e., lung) may greatly favor the treatment of SARS-CoV-2 infection.

Figure. S5.
Effects of CVL218 on body weight in rats (a) and monkeys (b). Rats and monkeys were orally administered 20/60/160 mg/kg and 5/20/80 mg/kg of CVL218, respectively, for 28 consecutive days and then followed by 28 more days without drug administration. No significant difference was observed between the control group and drug administrated groups at different drug dosages according to two-tailed t-test under the FDR of 0.05. Table S1. The top list of drug candidates identified by CoV-DTI followed by the large-scale relation extraction method BERE and a minimum of manual checking. The drug candidates with both significant prediction scores (p-values < 0.05) and associated with viruses according to text mining results are listed below. Those trivial non-drug candidates (minerals, endogenous substances, chemical reagents and antiseptics) were also excluded from the list. Table S2. The remaining drug candidates in the top list identified by the connectivity map analysis using the gene expression profiles of the peripheral blood mononuclear cell (PBMC) samples of three SARS-CoV-2 infected patients and the bronchoalveolar lavage fluid (BALF) samples of two SARS-CoV-2 infected patients [4]. Table S3.
Comparison of CoV-DTI on the original knowledge graph and the updated knowledge graph after incorporating the human protein-virus protein interactions derived from [5]. Shown are the mean±SD values over ten replicates of 10-fold cross-validation.
a. The concentrations of arbidol in different tissues of rats at 5/15/360 min time points with 54 mg/kg oral administration were obtained from [6]. Table S4.
Comparison of the tissue distributions of CVL218 and arbidol in rats, following 20 mg/kg and 54 mg/kg oral administrations, respectively. Table S5.
Comparison of the tissue to plasma concentration ratios between CVL218 and arbidol in rats. The concentrations of CVL218 over different tissues of rats were measured at the 180 min time point following 20 mg/kg oral administration. The concentrations of arbidol over different tissues of rats at the 15 min time point following 54 mg/kg oral administration were obtained from the literature [6,7]. Means and standard deviations are shown.
a. The pharmacokinetic data of arbidol were obtained from [7]. Table S6.
Comparisons of the pharmacokinetic parameters in rats between CVL218 and arbidol following 20/40 mg/kg and 18/54 mg/kg oral administrations, respectively. Table S7. Toxicokinetic parameters of CVL218 in rats in a four-week toxicity study. Table S8. Toxicokinetic parameters of CVL218 in monkeys in a four-week toxicity study.