PMC:7321036 / 44382-50179 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7321036","sourcedb":"PMC","sourceid":"7321036","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7321036","text":"Mapping Kinase Activities to Pharmacological Modulators Identifies SARS-CoV-2 Therapies\nTo identify effective therapies for SARS-CoV-2 infection, kinase inhibitors were mapped to the most differentially regulated kinase activities (Figure 7 A) and to specific phosphorylation sites (Table S8; STAR Methods). This resulted in a list of 87 drugs and compounds: 10 FDA-approved, 53 undergoing clinical testing, and 24 pre-clinical. Many of the drugs and compounds identified were reported to target several host kinases in cell-free assays at a minimum, but many have been observed to hit targets in cellular assays as well (Figure 7A). We reasoned that testing molecules with both overlapping and unique targets would help specify the molecular targets of greatest importance for SARS-CoV-2. Here, 68 total drugs and compounds were tested for antiviral efficacy (via qRT-PCR, anti-NP antibody, plaque assay, and/or TCID50) and cellular toxicity at two different institutions (in New York [Mount Sinai, 25 drugs/compounds] and Paris [Institut Pasteur, 62]) and in two cell lines (Vero E6 [68] and A549-ACE2 [61]). All pharmacological profiling results can be found in Figure S5 and Table S8.\nFigure 7 Mapping Regulated Kinases to Kinase Inhibitors Identifies SARS-CoV-2 Therapies\n(A) Kinase inhibitors (left) mapped to kinases (right) whose activity was regulated by SARS-CoV-2 infection. Lines connecting them indicate known kinase targets for each drug/compound.\n(B) Vero E6 cells pre-treated with remdesivir at the indicated doses, followed by SARS-CoV-2 infection for 48 h. Percent viral titer compared with mock drug treatment (anti-NP antibody; red line, dots, and text) and cell viability (black) is depicted. Error bars represent SD.\n(C) As in (B). Vero E6 cells were treated with the CK2 inhibitor silmitasertib. Physical interactions between N protein and the CSNK2A2 and CSNK2B CK2 subunits were observed in a prior study (Gordon et al., 2020).\n(D) Predicted increased kinase activity for the p38 signaling pathway and drugs/compounds targeting pathway members (ralimetinib, MAPK13-IN-1, and ARRY-797) and upstream drivers (gilteritinib).\n(E–G) As in (B). Vero E6 cells treated with the AXL inhibitor gilteritinib (E), the MAPK11/14 inhibitor ralimetinib (F), or the MAPK13 inhibitor MAPK13-IN-1 (G) prior to SARS-CoV-2 infection.\n(H) A549-ACE2 lung epithelial cells were treated with the MAPK14 inhibitor ARRY-797 prior to SARS-CoV-2 infection.\n(I) Small interfering RNA (siRNA) knockdown of p38 pathway genes in A549-ACE2 leads to a significant decrease in SARS-CoV-2 viral replication (red), as assessed by qRT-PCR in the absence of effects on cell viability (black). ACE2 and non-targeting siRNAs are included as positive and negative controls, respectively.\n(J and K) Vero E6 or A549-ACE2 cells were treated with PIKFYVE inhibitor apilimod (J) or the CDK inhibitor dinaciclib (K) prior to SARS-CoV-2 infection.\nSee also Figure S6.\nWe found pharmacological inhibitors of CK2, p38 MAPK signaling, PIKFYVE, and CDKs to possess strong antiviral efficacy. Cells were pre-treated with inhibitor molecules, followed by SARS-CoV-2 infection (STAR Methods), and virus quantity (anti-NP antibody against SARS-CoV-2) and cell viability were quantified 48 h after infection. As a positive control and for comparison, remdesivir was tested, and the expected favorable antiviral activity was observed (half maximal inhibitory concentration [IC50 ] = 1.28 μM; Figure 7B). Silmitasertib, an inhibitor of CSNK2A1 and CSNK2A2, was found to possess antiviral activity (IC50 = 2.34 μM; Figures 7C and S5). In conjunction with data supporting physical interaction (Gordon et al., 2020) and co-localization with N protein (Figure 5F), as well as a potential role in remodeling extracellular matrix upon infection (Figures 5 and S3), CK2 signaling appears to be an important pathway hijacked by SARS-CoV-2. Furthermore, silmitasertib is currently being considered for human testing as a potential treatment for COVID-19.\nTo probe SARS-CoV-2 dependence on MAPK signaling, SARS-CoV-2 replication was measured in response to pharmacological and genetic perturbation of MAPK components that were upregulated during infection (Figure 7D). Potent antiviral activity was observed for gilteritinib (Figure 7E; IC50 = 0.807 μM), an inhibitor of AXL kinase, upstream of p38; ralimetinib (Figure 7F; IC50 = 0.873 μM), an inhibitor of MAPK11 (p38ɑ) and MAPK14 (p38β); MAPK13-IN-1 (Figure 7G; IC50 = 4.63 μM), an inhibitor of MAPK13 (p38-δ); and ARRY-797 (Figure 7H; IC50 = 0.913 μM) in A549-ACE2 cells, a MAPK14 inhibitor. To further probe the dependence of SARS-CoV-2 on p38 pathway members, small interfering RNA (siRNA)-mediated knockdown of MAP2K3, p38-δ (MAPK13), and p38-ɣ (MAPK12) was performed in A549-ACE2 cells, and a significant decrease in SARS-CoV-2 replication was observed for all three, with little to no effect on cell viability (Figure 7I).\nIn addition, we noted marked regulation of phosphatidylinositol enzyme activities for PIK3CA, PLCB3, and PIKFYVE, suggesting a potential role for the appropriate balance of phosphatidylinositol species. To target this process, apilimod, a small-molecule inhibitor of PIKFYVE, was tested and found to possess strong antiviral activity in two cell lines (Vero E6, IC50 \u003c 0.08 μM; A549-ACE2, IC50 = 0.007 μM), corroborated by a recent study (Ou et al., 2020; Figure 7J). Lastly, we noted pronounced regulation of CDK signaling pathways (Figure 4B) and cell cycle stage (Figure 6I) during viral infection, suggesting that the virus may regulate the cell cycle to enhance viral replication. Accordingly, strong antiviral activity for the CDK inhibitor dinaciclib was observed across two cell lines (Vero E6, IC50 = 0.127 μM; A549-ACE2, IC50 = 0.032 μM) 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