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Schematic representation of the integrated computational and experimental workflow. The study design comprises two complementary branches. The computational branch (left) includes protein preparation, ligand parameterization, 100 ns MD simulation, trajectory analysis (RMSD, RMSF, Rg, H-bonds, contact frequency), and MM/GBSA binding free energy calculation. The experimental branch (right) comprises cell culture, MTT cytotoxicity assays for single drugs, combination ratio testing (SN: HQ = 1:1, 1:2, 2:1), CI/DRI analysis, and mechanistic validation via <t>apoptosis</t> and cell cycle assays. The integration of both approaches provides a comprehensive understanding of the synergistic mechanism
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Schematic representation of the integrated computational and experimental workflow. The study design comprises two complementary branches. The computational branch (left) includes protein preparation, ligand parameterization, 100 ns MD simulation, trajectory analysis (RMSD, RMSF, Rg, H-bonds, contact frequency), and MM/GBSA binding free energy calculation. The experimental branch (right) comprises cell culture, MTT cytotoxicity assays for single drugs, combination ratio testing (SN: HQ = 1:1, 1:2, 2:1), CI/DRI analysis, and mechanistic validation via apoptosis and cell cycle assays. The integration of both approaches provides a comprehensive understanding of the synergistic mechanism

Journal: BMC Pharmacology & Toxicology

Article Title: Computational-experimental repurposing reveals synergistic sorafenib/hydroxychloroquine response in KRAS-mutant breast cancer

doi: 10.1186/s40360-026-01122-2

Figure Lengend Snippet: Schematic representation of the integrated computational and experimental workflow. The study design comprises two complementary branches. The computational branch (left) includes protein preparation, ligand parameterization, 100 ns MD simulation, trajectory analysis (RMSD, RMSF, Rg, H-bonds, contact frequency), and MM/GBSA binding free energy calculation. The experimental branch (right) comprises cell culture, MTT cytotoxicity assays for single drugs, combination ratio testing (SN: HQ = 1:1, 1:2, 2:1), CI/DRI analysis, and mechanistic validation via apoptosis and cell cycle assays. The integration of both approaches provides a comprehensive understanding of the synergistic mechanism

Article Snippet: The Annexin V-FITC apoptosis recognition kit (Miltenyi Biotec) was conducted to assess apoptosis.

Techniques: Binding Assay, Cell Culture, Biomarker Discovery

Apoptosis investigation via flow cytometry. Cells were stained with Annexin V-FITC and propidium iodide (PI) to distinguish viable (lower left), early apoptotic (lower right), late apoptotic (upper right), and necrotic (upper left) populations. Representative dot plots are shown for: ( a ) untreated control; ( b ) hydroxychloroquine (23.6 µM); ( c ) sorafenib (9.4 µM); and ( d ) their combination (5 µM HCQ + 1 µM Sorafenib). ( e ) Quantitative summary of cell populations across treatment groups. Hydroxychloroquine treatment significantly reduced viable cells (from 88.09% to 8.52%, **** p < 0.000001) and significantly increased early apoptosis (2.43% to 5.54%, **** p < 0.000001), late apoptosis (1.75% to 34.87%, **** p < 0.000001), and necrosis (2.23% to 49.40%, **** p < 0.000001) compared to control

Journal: BMC Pharmacology & Toxicology

Article Title: Computational-experimental repurposing reveals synergistic sorafenib/hydroxychloroquine response in KRAS-mutant breast cancer

doi: 10.1186/s40360-026-01122-2

Figure Lengend Snippet: Apoptosis investigation via flow cytometry. Cells were stained with Annexin V-FITC and propidium iodide (PI) to distinguish viable (lower left), early apoptotic (lower right), late apoptotic (upper right), and necrotic (upper left) populations. Representative dot plots are shown for: ( a ) untreated control; ( b ) hydroxychloroquine (23.6 µM); ( c ) sorafenib (9.4 µM); and ( d ) their combination (5 µM HCQ + 1 µM Sorafenib). ( e ) Quantitative summary of cell populations across treatment groups. Hydroxychloroquine treatment significantly reduced viable cells (from 88.09% to 8.52%, **** p < 0.000001) and significantly increased early apoptosis (2.43% to 5.54%, **** p < 0.000001), late apoptosis (1.75% to 34.87%, **** p < 0.000001), and necrosis (2.23% to 49.40%, **** p < 0.000001) compared to control

Article Snippet: The Annexin V-FITC apoptosis recognition kit (Miltenyi Biotec) was conducted to assess apoptosis.

Techniques: Flow Cytometry, Staining, Control