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Three EWSR1::FLI1 fusion protein isoforms were expressed in the Ewing sarcoma cell lines with the same breakpoints, and their MDS analyses were performed with seven selected drugs (A) Normalized binding affinity scores of the seven chosen drugs. A/D depicts the normalized binding affinity fold change between the fusion protein and wild-type protein. (B) Cancer cell line expressed three EWSR1::FLI1 fusion protein isoforms. (C) Molecular dynamics simulation results between three EWSR1::FLI1 fusion protein isoforms and seven chosen drugs. (D) Small molecule-fusion protein complex in 3D.

Journal: iScience

Article Title: FusionTarget: Computational framework for drug repurposing against modeled fusion protein structures from genomic breakpoints

doi: 10.1016/j.isci.2026.116076

Figure Lengend Snippet: Three EWSR1::FLI1 fusion protein isoforms were expressed in the Ewing sarcoma cell lines with the same breakpoints, and their MDS analyses were performed with seven selected drugs (A) Normalized binding affinity scores of the seven chosen drugs. A/D depicts the normalized binding affinity fold change between the fusion protein and wild-type protein. (B) Cancer cell line expressed three EWSR1::FLI1 fusion protein isoforms. (C) Molecular dynamics simulation results between three EWSR1::FLI1 fusion protein isoforms and seven chosen drugs. (D) Small molecule-fusion protein complex in 3D.

Article Snippet: The Ewing sarcoma cell lines (RD-ES and SK-ES-1) containing the EWS-FLI1 fusion protein employed in this project so far were purchased from the American Tissue Culture Collection (ATCC).

Techniques: Binding Assay

Ewing sarcoma cell line sensitivity validation of the predicted EWSR1::FLI1 inhibitors (A) Previous studies of seven drugs in sarcoma. (B) IC 50 values for each cell line/drug combination. (C) Percent viability graphs depicting the IC 50 for each cell line drug combination at a log 10 [concentration]. Error bars have been removed for clarity. (D) Cell proliferation assay to assess the sensitivity of Ewing sarcoma cells to EWSR1::FLI1-predicted inhibitors over a 96-h time course, compared with rhabdomyosarcoma cells treated at the highest Ewing sarcoma IC 50 concentration. (E) Significant differential binding scores between normalized ones targeting fusion proteins and normalized ones targeting the wild-type FLI1 across six EWSR1::FLI1 fusions. (F) 200 nsec period MDS comparison of trifluridin, valruvicin, and the most studied small molecule TK-216 between EWSR1::FLI1 (587AA) fusion protein and FLI1 WT protein. (G) Top: mRNA level of NROB1 was examined in EWSR1::FLI1 positive and negative fusion cells. Bottom: mRNA level of TGFBR2 was examined in EWSR1::FLI1 positive and negative fusion cells. For all bar graphs, results are shown for statistical analyses done in three replicates; ∗, p < 0.05; ∗∗, p < 0.01; and ∗∗∗, p < 0.001.

Journal: iScience

Article Title: FusionTarget: Computational framework for drug repurposing against modeled fusion protein structures from genomic breakpoints

doi: 10.1016/j.isci.2026.116076

Figure Lengend Snippet: Ewing sarcoma cell line sensitivity validation of the predicted EWSR1::FLI1 inhibitors (A) Previous studies of seven drugs in sarcoma. (B) IC 50 values for each cell line/drug combination. (C) Percent viability graphs depicting the IC 50 for each cell line drug combination at a log 10 [concentration]. Error bars have been removed for clarity. (D) Cell proliferation assay to assess the sensitivity of Ewing sarcoma cells to EWSR1::FLI1-predicted inhibitors over a 96-h time course, compared with rhabdomyosarcoma cells treated at the highest Ewing sarcoma IC 50 concentration. (E) Significant differential binding scores between normalized ones targeting fusion proteins and normalized ones targeting the wild-type FLI1 across six EWSR1::FLI1 fusions. (F) 200 nsec period MDS comparison of trifluridin, valruvicin, and the most studied small molecule TK-216 between EWSR1::FLI1 (587AA) fusion protein and FLI1 WT protein. (G) Top: mRNA level of NROB1 was examined in EWSR1::FLI1 positive and negative fusion cells. Bottom: mRNA level of TGFBR2 was examined in EWSR1::FLI1 positive and negative fusion cells. For all bar graphs, results are shown for statistical analyses done in three replicates; ∗, p < 0.05; ∗∗, p < 0.01; and ∗∗∗, p < 0.001.

Article Snippet: The Ewing sarcoma cell lines (RD-ES and SK-ES-1) containing the EWS-FLI1 fusion protein employed in this project so far were purchased from the American Tissue Culture Collection (ATCC).

Techniques: Biomarker Discovery, Concentration Assay, Proliferation Assay, Binding Assay, Comparison