Journal: Journal of Pharmaceutical Analysis

Article Title: DT-TRAP enables accurate target recognition via simplified dosing and low-temperature incubation

doi: 10.1016/j.jpha.2026.101605

Figure Lengend Snippet: Dose-responsive target-responsive accessibility profiling (TRAP) identifies TEPP-46 targets in complex proteomes. (A) Volcano plots showing lysine accessibility changes in HeLa cell lysates. Each treatment group contained 100 μg of HeLa lysate and was treated with TEPP-46 at multiple concentrations (1 nM, 10 nM, 50 nM, 100 nM, 500 nM, 1 μM, 5 μM, and 10 μM), followed by ligand incubation for 1 h and TRAP labeling for 30 min, both performed at 25 °C. Thresholds were defined as TRAP ratio <0.5 or >2 with statistical significance assessed by one-way analysis of variance (ANOVA); ∗∗∗P < 0.001. (B) Dose-responsive accessibility changes at lysine residues K305/K311 of pyruvate kinase M2 (PKM2) upon TEPP-46 treatment, fitted using a four-parameter logistic (4 PL) model ( R 2 = 0.9951; n = 3 independent biological replicates). (C) Quantitative TRAP analysis of lysine-containing peptides within PKM2. Blue indicates TRAP peptides exhibiting the strongest accessibility changes, while cyan denotes peptides showing weaker or inconsistent changes ( n = 3 independent biological replicates). (D) Crystal structure of PKM2 (PDB: 3U2Z ) showing TEPP-46 (yellow) bound near the K305/K311 region. The TRAP-identified peptide segment exhibiting altered accessibility (K305/K311) is highlighted in blue, whereas non-responsive peptides are shown in cyan. PDB: protein data bank.

Article Snippet: The small-molecule compounds TEPP-46, geldanamycin, staurosporine, and aspirin were purchased from MedChemExpress (Monmouth Junction, NJ, USA).

Techniques: Incubation, Labeling

Journal: Journal of Pharmaceutical Analysis

Article Title: DT-TRAP enables accurate target recognition via simplified dosing and low-temperature incubation

doi: 10.1016/j.jpha.2026.101605

Figure Lengend Snippet: Target identification of TEPP-46 using two- and three-dose target-responsive accessibility profiling (TRAP) analyses. (A) Quadrant plot showing proteins with consistent lysine accessibility changes in HeLa cell lysates. Each group contained 100 μg of HeLa cell lysate and was treated with TEPP-46 at 1 and 5 μM, followed by ligand incubation for 1 h at 25 °C and TRAP labeling for 30 min at the same temperature ( n = 3 independent biological replicates). Proteins with TRAP ratios (TEPP-46/control >2 or < 0.5) and statistical significance assessed by one-way analysis of variance (ANOVA; ∗∗∗ P < 0.001) were designated as potential targets. Accessibility decreases and increases are highlighted in blue and red, respectively. Each protein is represented by the peptide with the highest TRAP score. (B) Three-dimensional scatter plot showing shared targets across three doses of TEPP-46 (1, 5, and 10 μM). Drug incubation and TRAP labeling conditions were identical to those described in (A). Pyruvate kinase M2 (PKM2) was identified as the only consistent target (red) under statistical thresholds (TRAP ratio >2 or < 0.5; one-way ANOVA; ∗∗∗ P < 0.001). (C) Crystal structure of PKM2 (PDB: 3U2Z ) showing TEPP-46 (yellow) binding and corresponding lysine accessibility changes. The TRAP-identified peptide containing residues K305/K311 is highlighted in blue, whereas non-responsive peptides are shown in cyan, statistical significance assessed by one-way ANOVA (∗∗∗ P < 0.001, ∗∗∗∗ P < 0.0001). PDB: protein data bank.

Article Snippet: The small-molecule compounds TEPP-46, geldanamycin, staurosporine, and aspirin were purchased from MedChemExpress (Monmouth Junction, NJ, USA).

Techniques: Drug discovery, Incubation, Labeling, Control, Binding Assay

Journal: Science Advances

Article Title: A comprehensive map of missense trafficking variants in rhodopsin and their response to pharmacologic correction

doi: 10.1126/sciadv.aef3518

Figure Lengend Snippet: ( A ) Heatmaps showing surface trafficking for Method 2 at baseline with the DMSO vehicle (top; same as bottom) and with 30 μM YC-001 treatment (bottom) for all missense and nonsense variants. Heatmaps are normalized and colored as in . ( B to C ) RHO structure (PDB: 1F88) colored according to the average trafficking score at each position with (B) DMSO vehicle or (C) 30 μM YC-001 (red: greater average trafficking defect). Side chains are shown for residues with an average trafficking score <0.5. ( D ) RHO structure is colored according to the degree of correction, defined as the difference in average trafficking scores at each position between 30 μM YC-001 and DMSO vehicle (blue: greater correction). ( E ) Scatterplot comparing trafficking scores at baseline with the DMSO vehicle ( x -axis) versus with 30 μM YC-001 (y-axis). Variants with significant differences between treatment conditions (5% FDR) are shown in blue, with 550 variants above the y = x line (significantly increased trafficking with YC-001) and none below. ( F ) Rescue plots showing surface trafficking with vehicle (gray) and with 30 μM YC-001 (blue) for higher-frequency misfolding and mistrafficking variants identified in clinical cohorts, ordered by relative frequency, with mean and 95% confidence intervals. Thresholds for moderate confidence (<0.7) and high confidence (<0.5) trafficking defects are indicated as dotted and dashed lines, respectively. Variants that show no rescue have a white background. Variants that show significant rescue (5% FDR) to a level below 0.7 have a gray background. Variants that show significant rescue to a level above 0.7 have a green background.

Article Snippet: One day later, cells were treated with 1) 2 μM doxycycline hyclate (ApexBio, A4052) to induce rhodopsin variant expression and 2) either DMSO or the YC-001 corrector molecule (MedChemExpress, HY-124717).

Techniques: