Download MendeleyStructural and Proteomic Analysis of the Mouse Cathepsin B-DARPin 4m3 Complex Reveals Species-Specific Binding Determinants.
Zaric, M., Tusar, L., Kramer, L., Vasiljeva, O., Novak, M., Impens, F., Usenik, A., Gevaert, K., Turk, D., Turk, B.(2025) Int J Mol Sci 26
- PubMed: 41465336 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.3390/ijms262411910
- Primary Citation Related Structures:
9S60 - PubMed Abstract:
Cathepsin B (CatB) is a lysosomal cysteine protease that plays a major role in various pathologies and is therefore considered a valuable therapeutic target. To address species-specific inhibitor challenges, we characterized the selective binding of designed ankyrin repeat protein (DARPin) 4m3 toward mouse cathepsin B (mCatB) over human CatB (hCatB). The mCatB-DARPin 4m3 complex was validated by size-exclusion chromatography (SEC), nano-differential scanning fluorimetry (nano-DSF), and surface plasmon resonance (SPR), revealing high affinity binding (K D = 65.7 nM) and potent inhibition (Ki = 26.7 nM; mixed competitive/noncompetitive). DARPin 4m3 showed no binding/inhibition toward hCatB. The 1.67 Å crystal structure of the complex-the first for mCatB-identified key interaction residues (e.g., I65/Q66 in mCatB vs. S65/M66 in hCatB) conferring selectivity. Proteomic analysis of endogenous substrates using a support vector machine (SVM) revealed greater similarity between mCatB and hCatB cleavages (Area Under the Curve (AUC) = 0.733) than between mCatB and other human cathepsins (AUC = 0.939-0.965). Clustering and SVM methods offer broadly applicable tools for protease specificity profiling in drug discovery. This study demonstrates the utility of DARPins for species-selective targeting and highlights the importance of integrated structural and proteomic approaches for dissecting protein-protein interactions.
- Molecular and Structural Biology, Department of Biochemistry, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia.
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