The activity of the reference compound, remdesivir (IC50 = 0.76 µM) was confirmed in this study. Remdesivir targets the viral nsp12 RNA-dependent RNA polymerase(8) and is currently under evaluation in an adaptive, randomized, double-blind, placebo-controlled phase III clinical trial(9). Nafamostat (IC50 = 0.04 µM) is thought to target processing of virus spike proteins, inhibiting membrane fusion(9).
Tioguanine (IC50 = 1.71 µM) has been reported as an inhibitor of the viral protease PL-Pro in MERS and SARS-CoV(10). One possibility is that tioguanine is phosphorylated leading to a failure of faithful RNA copying. Camostat was also reported to inhibit the entry of SARS-CoV-2 in CaCo-2 cells by targeting the serine protease TMPRSS2(11). These results indicate that the assay procedure is able to confirm the activity of clinically relevant compounds suggested to be active against both viral entry and replication mechanisms. Of the HIV aspartyl protease inhibitors currently being evaluated in clinical trials for SARS- CoV-2, lopinavir was active only at the highest concentration in the dose response (Figure S4), and ritonavir and darunavir were inactive at the primary screening stage (Table S1), suggesting this class of enzyme may not play a role in viral processing. Several of the more active compounds (Table 1) showed a relatively small difference between the cytotoxic and antiviral IC50 values with CI values < 3 (eg., thioguanosine, amuvatinib, cetylpyridinium and sorafenib). Many of these compounds have detailed data available on their pharmacokinetics and safety in human subjects and patients. It will be important to use this information to establish whether a sufficiently high concentration can be safely achieved at the site of action, presumably the lung epithelium, before proposing follow on clinical studies.
The antimalarials chloroquine and its close relative hydroxychloroquine are reported to show antiviral activity against SARS-CoV(9). These are now being tested either as monotherapy or combination therapy in clinical trials (clinicaltrials.gov updated 30.03.2020). With the Caco-2 cell line, chloroquine diphosphate was inactive as a reference (Figure S2). The analogue mefloquine, (IC50 = 14.1 µM), showed inhibition in dose response, while tafenoquine and amodiaquine were inactive (Figure S4). Similarly, lumefantrine and primaquine, both commonly used anti-malarials, were inactive (Table S1). This discrepancy with chloroquine may be due to the differences in the origin of the cell lines used in the different in-vitro measurements. Additional in-vitro studies using relevant human cell lines or, ideally, primary tissue explant models are needed to clarify chloroquine’s anti SARS-Cov-2 properties in-vitro.
Several antifungal compounds were identified, with chlormidazole, ravuconazole, posaconazole and ketoconazole having IC50’s in the range of 2µM. In addition, cloconazole, and oxiconazole gave IC50 values at 20µM or less (Table 1 and Figure S4), although results showed some cytotoxicity in the same range. Reports of antiviral activity for this class of compounds are uncommon, but exceptions include posaconazole against parechovirus A3(12). The effective concentrations are an order of magnitude higher than those reported for the antifungal activity in-vitro. Similar membrane interacting molecules have been reported to interfere with virus-host membrane fusion mechanisms(13) and this may be a potential mechanism of action for this compound class.
Dapivirine (IC50 = 0.73 µM) is a non-nucleoside reverse transcriptase inhibitor developed as an anti-HIV agent. It has been recently shown to have broad antiviral activity with in vitro micromolar IC50 values against influenza A and B(14). Almitrine (IC50 = 1.42 µM) was authorized for COPD later withdrawn after risk benefit balance reassessment(15). This compound was selected, among others, after a virtual screening analysis against the SARS-CoV-2 viral protease Mpro(16) and, following additional confirmatory in-vitro and in-vivo studies, may be a viable candidate for further development. The orally available farnesyl transferase inhibitor ionafarnib (IC50 = 5.68 µM) has been studied in renal carcinoma(17) and has anti-viral activity in hepatitis D(18).
The crystallization of SARS-CoV-2 spike protein complexed to Angiotensin-Converting Enzyme-2 (ACE2) [PDB code = 6M18](19), has shed new light on possible SARS-CoV-2 virus entry mechanisms modulating virus-host interactions. ACE2 is expressed in Caco-2, Calu-3 and Vero-6 cells on the apical membrane domains(20). A recent report pointed to the potential for elevated ACE-2 expression levels caused by modulation of the ACE/ACE2/AT1R/TMPRSS2 system by “sartans” class compounds (e.g., candesartan, telmisartan,) or ACE inhibitors (e.g. captopril, or the pro-drug enalapril). Such inhibitors might, paradoxically, be either beneficial or deleterious for Covid-19 patients(21). AT1R inhibitors may induce ACE2 beneficially but at the expense of facilitating viral entry. In our study, we were unable to identify either classical ACE inhibitors such as Captopril or classical AT1R inhibitor “sartans” as inhibitors in the primary screen (Table S1).
Comparison of the recently proposed interactome compounds(3), with the set screened in this study showed 40 identical and 12 similar compounds (Table S2). The 5 profiled compounds from the 7 hits were: loratadine (IC50 = 15.13 µM); nafamostat (IC50 = 0.04 µM), pevonedistat (IC50 = 0.63µM); camostat (IC50 = 0.64 µM); and idarubicin (IC50 > 20 µM). The corresponding identified biochemical targets were: Serine proteases (nafamostat and camostat); Histamine 1 receptor (loratadine); Topoisomerases (idarubicin/daunorubicin); and the NEDD-8 activating enzyme (pevonedistat). The lack of activity of the predicted compound ligands, for the majority of the originally identified pathways, may be due to target expression levels, compound solubility or chemical/metabolic stabilities.
The relatively potent pre-clinical compound, NSC319276 (IC50 < 0.02 µM) has been reported to elevate intracellular Zn2+, leading to modulation of p53 folding(22). The compound also interferes with transition metal metabolism, inducing oxidative stress and depletion of nucleotide reserves, suggesting a possible mechanism for inhibiting viral replication. LY2228820, (IC50 = 0.87 µM) also known as ralimetinib, is a potent and selective inhibitor of α and β isoforms of p38 MAPK in vitro(23). Ralimetinib, was involved in a stopped phase 2 clinical trial for tamoxifen-resistant ovarian cancer(24). Papaverine (IC50 = 1.1. µM) is a non-narcotic alkaloid for heart disease, impotency, and psychosis. It was recently found to be an effective inhibitor of multiple strains of influenza virus. Papaverine is a phosphodiesterase (PDE) inhibitor(25), like ethaverine (IC50 = 0.64 µM) and drotaverine (IC50 = 6.07 µM) which both inhibit PDE-4(26).
Hematoporphyrin (IC50 = 1.85 µM) is a photodynamic activated DNA intercalator and single strand breaker with anticancer activity(27), which also shows antiviral effects via DNA polymerase inactivation(28). SB- 612111 (IC50 = 0.77 µM) has been developed as a potent and selective NOP antagonist(29) and binds the Opiate and Adenosine receptor proteins(29). Amuvatinib was one of the most potent compounds identified (IC50 = 0.02 µM) but was unsuccessful in trials for solid tumors and small cell lung carcinoma, but was well tolerated(30). Amuvatinib is a multi-targeted tyrosine kinase inhibitor (c-MET, c-RET and the mutant forms of c-KIT, PDGFR and FLT3). Additional tyrosine kinase inhibitors identified were sorafenib (IC50 = 1.55 µM), regorafenib (IC50 = 1.67 µM), pexidartinib (5.43) and vatalanib (IC50 = 18.27 µM) suggesting a role for kinase signaling in the receptor mediated host response to SARS-Cov-2.