COVID-19

Validation of activity and specificity of chemical inhibitors of; ATM, ATR, and DNAPK. H460 cells were treated with 1 uM camptothecin (CPT) or 20 ug/ml bleomycin for 1 h in the presence of the indicated inhibitors: DNAPK-i1—NU7026, DNAPK-i2—NU7441. MSH6,

Primary myeloma cells were treated with DMSO or ritonavir for 72 hours before annexin V/DAPI staining. Values are normalized to DMSO-treated samples (n=1 for each patient sample).

HCV replicon genotype 1b cells were passaged in the presence of G418 alone (medium 694 control) or G418 with miravirsen, SPC4729 (oligonucleotide negative control) or telaprevir for 28 days in fixed concentrations at a multiple (X) of the EC₅₀ of miravirsen or telaprevir. Colony formation was assessed by staining surviving cells with crystal violet.

Low-micromolar amounts of chloroquine, chlorpromazine, loperamide, and lopinavir inhibit MERS-CoV-induced cytopathology. Huh7 cells in 96-well plates were infected with MERS-CoV isolate EMC/2012 (MOI, 0.005) in the presence of 0 to 20 uM LPV. Cells were incubated for 2 days, and cell viability was monitored using an MTS assay. In addition, the potential toxicity of compound treatment only was monitored in parallel mock-infected Huh7 cell cultures. Graphs show the results (averages and standard deviations [SD]) of a representative experiment that was performed in quadruplicate. All experiments were repeated at least twice. For each compound, the calculated EC50, CC50, and SI values are given.

Dexamethasone and largazole cooperate to suppress invasion and to restore E-cadherin localization to the cell peripher y. ( a) Phase contrast micrographs showing morphological changes in MDA-MB-231 cells induced by E-cadherin expression combined with 100 nM dexamethasone and 10 nM largazole treatments. Insets show the cells at higher magnification. (b ) Fluorescence (E-Cad-GFP) or immunofluorescence microscopy (g -catenin (g-Cat.)) of 231/E-Cad-GFP cells treated for 72 h with vehicle (Control), 100 n M dexamethasone, 10 nM largazole or 100 nM dexamethasone + 10 nM largazole (Dex. + Larg.). (c ) Invasion assays were per formed with the indicated cell lines treated for 72 h with or without 100 nM dexamethasone + 10 nM largazole using modified Boyden chambers impregnated with matrigel. The results are presented as the average number of cells that invaded through the membrane per field s.d. of five randomly chosen fields, and are representative of three independently per formed experiments.

MDA-MB-231 cells were treated with simvastatin (SIM) or rosuvastatin (ROSU) in combination with ZOL for 48 h. Vitality and apoptosis were measured by using the cell titer blue and the caspase 3/7 Glo assay. Data are shown as mean ± SD of at least three individual experiments (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001).

Western blot analysis of HCV NS3 protease cleavage of MAVS. The catalytic efficiency of four proteases (H, H-A156T, 41 and 41-A156T) from individuals H and 41 were tested in the absence or presence of an NS3 protease inhibitor (danoprevir). Expression of the HCV NS3 proteases resulted in cleavage of the lambda cI repressor with MAVS cleavage site. Expression of the protease was induced with IPTG for 3 h. The lambda cI repressor with MAVS cleavage site was not cleaved by an NS3 protease that included a substitution in catalytic residue S139A. Similarly, different catalytic efficiencies were observed with different proteases.

bDNA analysis showing that the JAK1/2 inhibitors CYT387, AZD1480 and Baricitinib positively regulate UCP1 expression in PSC-WA. Values are mean ± s.d. of n = three biological replicates and differences from DMSO are significant for * P < 0.005. P values were calculated using the two-tailed paired Student's t-test.

Immunohistochemistry and quantification of cleaved caspase 3 expression in DU145-DR tumor xenografts from (D). Scale bar, 100 mm. Data represent the mean ± SD. *p < 0.05.

Western blotting showed that in U87 cells treated with pitavastatin, the LC3-II isoform dramatically increased after statin treatment and showed at day 2, 3 and 4.

The Nucleotide analog reverse-transcriptase inhibitor Tenofovir disoproxil fumarate was added to TZM-bl cells. Cells were inoculated with 0.05 ng mock-exposed and semen-exposed HIV, and 0.5 ng HIV as infectivity-matched control. Infection rates were measured 3 days post infection by measuring β-galactosidase or or 4 days post infection by measuring luciferase activities. The left panels show the mean enzyme activities ± standard deviation derived from triplicate infections. RLU/s: relative light units per second. Middle panels show normalized infection rates in which reporter enzyme activities obtained from infected cells in the absence of inhibitor were set at 100%. The right panels depict the calculated IC50 values. The number above the bar represents the fold-change in the IC50 derived from 0.05 ng semen-exposed relative to 0.05 or 0.5 ng mock-exposed virus infection. Ns, no statistically significant difference; **** p<0.0001; *** p<0.001 (unpaired t-test).

(A) NPCs were treated with 3µM of the GSK3 inhibitor (tideglusib) for 24 hours. Representative images of untreated SPG11-NPCs (SPG11‐NT) and tideglusib-treated SPG11-NPCs (SPG11-Tide) on day 3. Cell proliferation was analyzed using colabeling of PCNA in Nestin/Sox2-positive NPCs. Nuclei were visualized with DAPI. Scale bar = 50µm. (B) Increased numbers of Nestin/Sox2‐positive cells colabeled with PCNA in CHIR99021-treated SPG11-NPCs. (C) Tideglusib-treated SPG11-NPCs, compared to untreated NPCs, revealed restoration of cell proliferation similar to the CTRL‐NPCs.

A) MV411 or B) Kasumi 1 cells were incubated with YM155 (0.25 x IC50) in the presence or absence of i) 0.5 x IC50 or ii) 1 x IC50 of Daunorubicin or iii) 0.5 x IC50 or iv) 1 x IC50 of Cytarabine for 72h. Following 72h treatment, cells were subject to a resazurin reduction assay. Percentages were normalised to DMSO controls. Column, mean of 3 independent experiments; Bars, SEM. *p<0.05, **p<0.01, ***p<0.005. Students t-test. Similar trends were observed with 0.5 x and 1 x IC50 of YM155 in combination with Daunorubicin or Cytarabine (data not shown).

Immunofluorescence of NF-κB/p65 in HCT 116 and SW 1116 cells exposed to TNFα (25 ng/ml) with or without nafamostat mesilate(FLU) (100 μM). Scale bars: 20 μm.

The effect of drugs on sperm movement. Purified human sperm were incubated under capacitating conditions for 0, 15, 30, 60 or 120 min, and motility was measured in the presence of disulfirum. The standard deviation is shown as bars. Statistical differences by Student's t-test compared with control are annotated as “*” for p<0.05 or “**” for p<0.01.

The indicated liver cancer cell lines—Hep-3B, Huh-7 and PLC were treated with or without 5 types anti-hepatitis B virus drugs (C) with the concentration of 100 μM, and M1 virus (MOI = 10) for 72 hours. Following 72 hours, cell viabilities were determined by MTT assay (mean ± SD). N.S. Not significant.

HIV PIs variably alter intracellular HIV epitope stability. (A) HLA-A02–restricted SL9 epitope (SLYNTVATL, aa 77–85 in HIV-1 Gag p17) was degraded in PBMC extracts pretreated with DMSO (control, circles), 5 µM of Nelfinavir (triangles) or 5 µM of Saquinavir (squares). Remaining peptide was quantified by RP-HPLC analysis after 0, 10, 30 and 60 minutes. 100% represents the amount of peptide at time 0 calculated as the surface under the peptide peak detected by RP-HPLC (815.986, 821.569, and 813.118 for DMSO, Saquinavir, and Nelfinavir, respectively). Times at which 50% of the SL9 peptide remained correspond to peptide half-lives (37 min, 52 min and 24 min for Control, Saquinavir and Nelfinavir respectively). (B–F) HLA-A02–SL9, HLA-B57-KF11, HLAB57-ISW9, HLA-B57-TW10 and HLA-A11-ATK9 epitopes (from B to F respectively) were degraded in PBMC extracts pretreated with DMSO, 2 µM or 5 µM PI (Saquinavir, Ritonavir, Nelfinavir, Atazanavir or Darunavir). The cytosolic half-lives in control condition were 33.87, 25.66, 14.83, 119.4 and 37.21 minutes for SL9, KF11, ISW9, TW10 and ATK9 respectively. Fold differences of each epitope half-life upon treatment compared to control are presented in each panel. All data represent the average of 4 different experiments using 4 different PBMC extracts. *P < 0.05, **P < 0.01, ***P < 0.001, 1-way ANOVA with Dunnett’s post-test.
 

NCI-H929 EV and miR-137 OE cells were treated with ATM activator Chloroquine Phosphate (CQ), specific ATM inhibitor KU-55933, and ATR inhibitor AZ20 for 12 hr. Immunoblotting showed the expression of p-ATM, p-Chk2, p-BRCA1, p-ATR and p-Chk1.

(d) BT549 cells were treated and analyzed by immunofluorescence microscopy as in Figure b. (e) BT549 cells were treated as described in Figure b and analyzed for invasion as in Figure 3c. (f) Quantitation of junctional E-cadherin staining of the indicated cell lines treated with DMSO vehicle or Dex.+ Larg. as described in Figure b. Results are presented as the mean of analyses of three different fields of cells for each sample±s.d. Statistical significance was assessed using Student’s t -test.

Dexamethasone and largazole cooperate to suppress invasion and to restore E-cadherin localization to the cell peripher y. ( a) Phase contrast micrographs showing morphological changes in MDA-MB-231 cells induced by E-cadherin expression combined with 100 nM dexamethasone and 10 nM largazole treatments. Insets show the cells at higher magnification. (b ) Fluorescence (E-Cad-GFP) or immunofluorescence microscopy (g -catenin (g-Cat.)) of 231/E-Cad-GFP cells treated for 72 h with vehicle (Control), 100 n M dexamethasone, 10 nM largazole or 100 nM dexamethasone + 10 nM largazole (Dex. + Larg.). (c ) Invasion assays were per formed with the indicated cell lines treated for 72 h with or without 100 nM dexamethasone + 10 nM largazole using modified Boyden chambers impregnated with matrigel. The results are presented as the average number of cells that invaded through the membrane per field s.d. of five randomly chosen fields, and are representative of three independently per formed experiments.

Schistosomicidal effects of PZQ, ART and OXA on 14-day-schistosomula. Magnification of the in vitro-cultured schistosomula treated with PZQ, ART, and OXA at 10 μM. Drugs were added at day 14 and schistosomula were analyzed at day 21 (late treatment). 0.1% DMSO in medium (solvent of the drugs; used as negative control) had no effect on schistosomula development.

The impact of GSK3β inhibitor TDZD-8 (10 μM) on the GSK3β phosphorylation (A), the protein expression (B) and mRNA level (C) of α-SMA and collagen I in acetaldehyde-induced HSCs activation. The data were representative of at least three independent experiments. All values were expressed as mean ± SD. *P < 0.01, ***P < 0.01 vs. the control group, #P < 0.05, ##P < 0.01, ###P < 0.01 vs. the acetaldehyde group.

(A) BoDV-1 infection was measured by IFA. BoDV-1 P40 was detected with a primary monoclonal antibody (red), nuclei were stained with DAPI (blue), merged image (scale bars: 50 μm). Favipiravir: T-705

C, SA-beta gal staining results of A549-LKB1 cells treated by trametinib (30 nmol/L), radiotherapy (2 Gy), and HCQ (50 μmol/L). Cells were treated by HCQ and/or trametinib 4 hours prior to radiotherapy. Drugs were washed out 24 hours after radiotherapy. Cells were incubated for additional 48 hours before staining. D, Clonogenic survival assay of A549-LKB1 cells treated with trametinib (30 nmol/L) and HCQ (50 μmol/L).

(C) Impact of HCV clearance by DAA treatment on the Nrf2 nuclear translocation. HCV infected Huh-7.5 cells day 12 were given two rounds of antiviral treatment with IFN-α, sofosbuvir, ledipasvir or combination of sofosbuvir plus ledipasvir. After 72 hours, cells were split, and then treated again with the same antiviral agent. After two rounds of antiviral treatment, the expressions of HCV core and pNrf2 were measured by immunostaining.

Validation of activity and specificity of chemical inhibitors of; ATM, ATR, and DNAPK. H460 cells were treated with 1 uM camptothecin (CPT) or 20 ug/ml bleomycin for 1 h in the presence of the indicated inhibitors: DNAPK-i1—NU7026, DNAPK-i2—NU7441. MSH6,

Primary myeloma cells were treated with DMSO or ritonavir for 72 hours before annexin V/DAPI staining. Values are normalized to DMSO-treated samples (n=1 for each patient sample).

HCV replicon genotype 1b cells were passaged in the presence of G418 alone (medium 694 control) or G418 with miravirsen, SPC4729 (oligonucleotide negative control) or telaprevir for 28 days in fixed concentrations at a multiple (X) of the EC₅₀ of miravirsen or telaprevir. Colony formation was assessed by staining surviving cells with crystal violet.

Low-micromolar amounts of chloroquine, chlorpromazine, loperamide, and lopinavir inhibit MERS-CoV-induced cytopathology. Huh7 cells in 96-well plates were infected with MERS-CoV isolate EMC/2012 (MOI, 0.005) in the presence of 0 to 20 uM LPV. Cells were incubated for 2 days, and cell viability was monitored using an MTS assay. In addition, the potential toxicity of compound treatment only was monitored in parallel mock-infected Huh7 cell cultures. Graphs show the results (averages and standard deviations [SD]) of a representative experiment that was performed in quadruplicate. All experiments were repeated at least twice. For each compound, the calculated EC50, CC50, and SI values are given.

Dexamethasone and largazole cooperate to suppress invasion and to restore E-cadherin localization to the cell peripher y. ( a) Phase contrast micrographs showing morphological changes in MDA-MB-231 cells induced by E-cadherin expression combined with 100 nM dexamethasone and 10 nM largazole treatments. Insets show the cells at higher magnification. (b ) Fluorescence (E-Cad-GFP) or immunofluorescence microscopy (g -catenin (g-Cat.)) of 231/E-Cad-GFP cells treated for 72 h with vehicle (Control), 100 n M dexamethasone, 10 nM largazole or 100 nM dexamethasone + 10 nM largazole (Dex. + Larg.). (c ) Invasion assays were per formed with the indicated cell lines treated for 72 h with or without 100 nM dexamethasone + 10 nM largazole using modified Boyden chambers impregnated with matrigel. The results are presented as the average number of cells that invaded through the membrane per field s.d. of five randomly chosen fields, and are representative of three independently per formed experiments.

MDA-MB-231 cells were treated with simvastatin (SIM) or rosuvastatin (ROSU) in combination with ZOL for 48 h. Vitality and apoptosis were measured by using the cell titer blue and the caspase 3/7 Glo assay. Data are shown as mean ± SD of at least three individual experiments (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001).

Western blot analysis of HCV NS3 protease cleavage of MAVS. The catalytic efficiency of four proteases (H, H-A156T, 41 and 41-A156T) from individuals H and 41 were tested in the absence or presence of an NS3 protease inhibitor (danoprevir). Expression of the HCV NS3 proteases resulted in cleavage of the lambda cI repressor with MAVS cleavage site. Expression of the protease was induced with IPTG for 3 h. The lambda cI repressor with MAVS cleavage site was not cleaved by an NS3 protease that included a substitution in catalytic residue S139A. Similarly, different catalytic efficiencies were observed with different proteases.

bDNA analysis showing that the JAK1/2 inhibitors CYT387, AZD1480 and Baricitinib positively regulate UCP1 expression in PSC-WA. Values are mean ± s.d. of n = three biological replicates and differences from DMSO are significant for * P < 0.005. P values were calculated using the two-tailed paired Student's t-test.

Immunohistochemistry and quantification of cleaved caspase 3 expression in DU145-DR tumor xenografts from (D). Scale bar, 100 mm. Data represent the mean ± SD. *p < 0.05.

Western blotting showed that in U87 cells treated with pitavastatin, the LC3-II isoform dramatically increased after statin treatment and showed at day 2, 3 and 4.

The Nucleotide analog reverse-transcriptase inhibitor Tenofovir disoproxil fumarate was added to TZM-bl cells. Cells were inoculated with 0.05 ng mock-exposed and semen-exposed HIV, and 0.5 ng HIV as infectivity-matched control. Infection rates were measured 3 days post infection by measuring β-galactosidase or or 4 days post infection by measuring luciferase activities. The left panels show the mean enzyme activities ± standard deviation derived from triplicate infections. RLU/s: relative light units per second. Middle panels show normalized infection rates in which reporter enzyme activities obtained from infected cells in the absence of inhibitor were set at 100%. The right panels depict the calculated IC50 values. The number above the bar represents the fold-change in the IC50 derived from 0.05 ng semen-exposed relative to 0.05 or 0.5 ng mock-exposed virus infection. Ns, no statistically significant difference; **** p<0.0001; *** p<0.001 (unpaired t-test).

(A) NPCs were treated with 3µM of the GSK3 inhibitor (tideglusib) for 24 hours. Representative images of untreated SPG11-NPCs (SPG11‐NT) and tideglusib-treated SPG11-NPCs (SPG11-Tide) on day 3. Cell proliferation was analyzed using colabeling of PCNA in Nestin/Sox2-positive NPCs. Nuclei were visualized with DAPI. Scale bar = 50µm. (B) Increased numbers of Nestin/Sox2‐positive cells colabeled with PCNA in CHIR99021-treated SPG11-NPCs. (C) Tideglusib-treated SPG11-NPCs, compared to untreated NPCs, revealed restoration of cell proliferation similar to the CTRL‐NPCs.

A) MV411 or B) Kasumi 1 cells were incubated with YM155 (0.25 x IC50) in the presence or absence of i) 0.5 x IC50 or ii) 1 x IC50 of Daunorubicin or iii) 0.5 x IC50 or iv) 1 x IC50 of Cytarabine for 72h. Following 72h treatment, cells were subject to a resazurin reduction assay. Percentages were normalised to DMSO controls. Column, mean of 3 independent experiments; Bars, SEM. *p<0.05, **p<0.01, ***p<0.005. Students t-test. Similar trends were observed with 0.5 x and 1 x IC50 of YM155 in combination with Daunorubicin or Cytarabine (data not shown).

Immunofluorescence of NF-κB/p65 in HCT 116 and SW 1116 cells exposed to TNFα (25 ng/ml) with or without nafamostat mesilate(FLU) (100 μM). Scale bars: 20 μm.

The effect of drugs on sperm movement. Purified human sperm were incubated under capacitating conditions for 0, 15, 30, 60 or 120 min, and motility was measured in the presence of disulfirum. The standard deviation is shown as bars. Statistical differences by Student's t-test compared with control are annotated as “*” for p<0.05 or “**” for p<0.01.

The indicated liver cancer cell lines—Hep-3B, Huh-7 and PLC were treated with or without 5 types anti-hepatitis B virus drugs (C) with the concentration of 100 μM, and M1 virus (MOI = 10) for 72 hours. Following 72 hours, cell viabilities were determined by MTT assay (mean ± SD). N.S. Not significant.

HIV PIs variably alter intracellular HIV epitope stability. (A) HLA-A02–restricted SL9 epitope (SLYNTVATL, aa 77–85 in HIV-1 Gag p17) was degraded in PBMC extracts pretreated with DMSO (control, circles), 5 µM of Nelfinavir (triangles) or 5 µM of Saquinavir (squares). Remaining peptide was quantified by RP-HPLC analysis after 0, 10, 30 and 60 minutes. 100% represents the amount of peptide at time 0 calculated as the surface under the peptide peak detected by RP-HPLC (815.986, 821.569, and 813.118 for DMSO, Saquinavir, and Nelfinavir, respectively). Times at which 50% of the SL9 peptide remained correspond to peptide half-lives (37 min, 52 min and 24 min for Control, Saquinavir and Nelfinavir respectively). (B–F) HLA-A02–SL9, HLA-B57-KF11, HLAB57-ISW9, HLA-B57-TW10 and HLA-A11-ATK9 epitopes (from B to F respectively) were degraded in PBMC extracts pretreated with DMSO, 2 µM or 5 µM PI (Saquinavir, Ritonavir, Nelfinavir, Atazanavir or Darunavir). The cytosolic half-lives in control condition were 33.87, 25.66, 14.83, 119.4 and 37.21 minutes for SL9, KF11, ISW9, TW10 and ATK9 respectively. Fold differences of each epitope half-life upon treatment compared to control are presented in each panel. All data represent the average of 4 different experiments using 4 different PBMC extracts. *P < 0.05, **P < 0.01, ***P < 0.001, 1-way ANOVA with Dunnett’s post-test.
 

NCI-H929 EV and miR-137 OE cells were treated with ATM activator Chloroquine Phosphate (CQ), specific ATM inhibitor KU-55933, and ATR inhibitor AZ20 for 12 hr. Immunoblotting showed the expression of p-ATM, p-Chk2, p-BRCA1, p-ATR and p-Chk1.

(d) BT549 cells were treated and analyzed by immunofluorescence microscopy as in Figure b. (e) BT549 cells were treated as described in Figure b and analyzed for invasion as in Figure 3c. (f) Quantitation of junctional E-cadherin staining of the indicated cell lines treated with DMSO vehicle or Dex.+ Larg. as described in Figure b. Results are presented as the mean of analyses of three different fields of cells for each sample±s.d. Statistical significance was assessed using Student’s t -test.

Dexamethasone and largazole cooperate to suppress invasion and to restore E-cadherin localization to the cell peripher y. ( a) Phase contrast micrographs showing morphological changes in MDA-MB-231 cells induced by E-cadherin expression combined with 100 nM dexamethasone and 10 nM largazole treatments. Insets show the cells at higher magnification. (b ) Fluorescence (E-Cad-GFP) or immunofluorescence microscopy (g -catenin (g-Cat.)) of 231/E-Cad-GFP cells treated for 72 h with vehicle (Control), 100 n M dexamethasone, 10 nM largazole or 100 nM dexamethasone + 10 nM largazole (Dex. + Larg.). (c ) Invasion assays were per formed with the indicated cell lines treated for 72 h with or without 100 nM dexamethasone + 10 nM largazole using modified Boyden chambers impregnated with matrigel. The results are presented as the average number of cells that invaded through the membrane per field s.d. of five randomly chosen fields, and are representative of three independently per formed experiments.

Schistosomicidal effects of PZQ, ART and OXA on 14-day-schistosomula. Magnification of the in vitro-cultured schistosomula treated with PZQ, ART, and OXA at 10 μM. Drugs were added at day 14 and schistosomula were analyzed at day 21 (late treatment). 0.1% DMSO in medium (solvent of the drugs; used as negative control) had no effect on schistosomula development.

The impact of GSK3β inhibitor TDZD-8 (10 μM) on the GSK3β phosphorylation (A), the protein expression (B) and mRNA level (C) of α-SMA and collagen I in acetaldehyde-induced HSCs activation. The data were representative of at least three independent experiments. All values were expressed as mean ± SD. *P < 0.01, ***P < 0.01 vs. the control group, #P < 0.05, ##P < 0.01, ###P < 0.01 vs. the acetaldehyde group.

(A) BoDV-1 infection was measured by IFA. BoDV-1 P40 was detected with a primary monoclonal antibody (red), nuclei were stained with DAPI (blue), merged image (scale bars: 50 μm). Favipiravir: T-705

C, SA-beta gal staining results of A549-LKB1 cells treated by trametinib (30 nmol/L), radiotherapy (2 Gy), and HCQ (50 μmol/L). Cells were treated by HCQ and/or trametinib 4 hours prior to radiotherapy. Drugs were washed out 24 hours after radiotherapy. Cells were incubated for additional 48 hours before staining. D, Clonogenic survival assay of A549-LKB1 cells treated with trametinib (30 nmol/L) and HCQ (50 μmol/L).

(C) Impact of HCV clearance by DAA treatment on the Nrf2 nuclear translocation. HCV infected Huh-7.5 cells day 12 were given two rounds of antiviral treatment with IFN-α, sofosbuvir, ledipasvir or combination of sofosbuvir plus ledipasvir. After 72 hours, cells were split, and then treated again with the same antiviral agent. After two rounds of antiviral treatment, the expressions of HCV core and pNrf2 were measured by immunostaining.