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Pepstatin-Based Probes for Photoaffinity Labeling of Aspartic Proteases and Application to Target Identification. 2023

Suyuan Chen, and Chunguang Liang, and Hongli Li, and Weimeng Yu, and Michaela Prothiwa, and Dominik Kopczynski, and Stefan Loroch, and Marc Fransen, and Steven H L Verhelst
Leibniz Institut für Analytische Wissenschaften - ISAS, e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.

Aspartic proteases are a small class of proteases implicated in a wide variety of human diseases. Covalent chemical probes for photoaffinity labeling (PAL) of these proteases are underdeveloped. We here report a full on-resin synthesis of clickable PAL probes based on the natural product inhibitor pepstatin incorporating a minimal diazirine reactive group. The position of this group in the inhibitor determines the labeling efficiency. The most effective probes sensitively detect cathepsin D, a biomarker for breast cancer, in cell lysates. Moreover, through chemical proteomics experiments and deep learning algorithms, we identified sequestosome-1, an important player in autophagy, as a direct interaction partner and substrate of cathepsin D.

UI MeSH Term Description Entries
D010436 Pepstatins N-acylated oligopeptides isolated from culture filtrates of Actinomycetes, which act specifically to inhibit acid proteases such as pepsin and renin.
D002402 Cathepsin D An intracellular proteinase found in a variety of tissue. It has specificity similar to but narrower than that of pepsin A. The enzyme is involved in catabolism of cartilage and connective tissue. EC 3.4.23.5. (Formerly EC 3.4.4.23).
D003978 Diazomethane A diazonium compound with the formula CH2N2. Diazirine
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000071456 Sequestosome-1 Protein A multidomain protein that is highly conserved among multicellular organisms. It contains a ZZ-type ZINC FINGER domain, C-terminal UBIQUITIN - associated (UBA) domain, and interacts with many other signaling proteins and enzymes including, atypical PROTEIN KINASE C; TNF RECEPTOR-ASSOCIATED FACTOR 6; subunits of the mTORC1 complex, and CASPASE-8. It functions in AUTOPHAGY as a receptor for the degradation of ubiquitinated substrates, and to co-ordinate signaling in response to OXIDATIVE STRESS. EBI3-Associated Protein of 60 KDa,EBIAP Protein,Phosphotyrosine-Independent Ligand For The Lck SH2 Domain Of 62 Kda,Ubiquitin-Binding Protein p62,EBI3 Associated Protein of 60 KDa,Phosphotyrosine Independent Ligand For The Lck SH2 Domain Of 62 Kda,Sequestosome 1 Protein,Ubiquitin Binding Protein p62
D016282 Aspartic Acid Endopeptidases A sub-subclass of endopeptidases that depend on an ASPARTIC ACID residue for their activity. Aspartic Endopeptidases,Aspartyl Endopeptidases,Acid Endopeptidases, Aspartic,Endopeptidases, Aspartic Acid,Endopeptidases, Aspartyl
D019920 Photoaffinity Labels Biologically active molecules which are covalently bound to the enzymes or binding proteins normally acting on them. Binding occurs due to activation of the label by ultraviolet light. These labels are used primarily to identify binding sites on proteins. Labels, Photoaffinity

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