Semisynthesis of Ubiquitin and SUMO-Rhodamine 110-Glycine through Aminolysis of Boc-Protected Thioester Counterparts

Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases

Post-translational modifications with ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are regulated by isopeptidases termed deubiquitinases (DUBs) and Ubl proteases. Here, we describe a mild chemical method for the preparation of fluorescence polarization substrates for these enzymes that is based on the activation of C-terminal Ub/Ubl hydrazides to acyl azides and their subsequent functionalization to isopeptides. The procedure is complemented by native purification routes and thus circumvents the previous need for desulfurization and refolding. Its broad applicability was demonstrated by the generation of fully cleavable substrates for Ub, SUMO1, SUMO2, NEDD8, ISG15, and Fubi. We employed these reagents for the investigation of substrate specificities of human UCHL3, USPL1, USP2, USP7, USP16, USP18, and USP36. Pronounced selectivity of USPL1 for SUMO2/3 over SUMO1 was observed, which we rationalize with crystal structures and biochemical assays, revealing a SUMO paralogue specificity mechanism distinct from SENP family deSUMOylases. Moreover, we investigated the recently identified Fubi proteases USP16 and USP36 and found both to act as bona fide deFubiylases, harboring catalytic activity against isopeptide-linked Fubi. Surprisingly, we also noticed the activity of both enzymes toward ISG15, previously not identified in chemoproteomics, which makes USP16 and USP36 the first human DUBs with specific isopeptidase activity toward three distinct modifiers. The methods described here for the preparation of isopeptide-linked, fully folded substrates will aid in the characterization of further DUBs/Ubl proteases. More broadly, our findings highlight possible limitations associated with fluorogenic substrates and Ubl activity-based probes and stress the importance of isopeptide-containing reagents for validating isopeptidase activities and quantifying substrate specificities.

Functionalization of Rhodamine Platforms with 3-Hydroxy-4-pyridinone Chelating Units and Its Fluorescence Behavior towards Fe(III)

Functionalization of xanthene fluorophores with specific receptor units is an important topic of research aiming for the development of new analytical tools for biological sciences, clinical diagnosis, food and environmental monitoring. Herein, we report a new dihydrorosamine containing two active amino groups, which was functionalized with 3-benzyloxy-1-(3′-carboxypropyl)-2-methyl-4-pyridinone through an amide coupling strategy. Benzylated mono- and di-functionalized dihydrorosamine derivatives (H in position 9 of the xanthene) were obtained, but with modest reaction yields, requiring long and laborious purification procedures. Looking for a more efficient approach, rhodamine 110 was selected to react with the carboxypropyl pyridinone, enabling the isolation of the corresponding mono- and di-functionalized derivatives in amounts that depend on the excess of pyridinone added to the reaction. The structure of all compounds was established by ¹H and ¹³C NMR, MS (ESI) and their absorption and emission properties were evaluated in dichloromethane. The fluorescence behavior of the debenzylated mono-rhodamine 110 derivative in the presence of Fe(III) was studied, making it an interesting fluorogenic dye for future optical sensing applications.

N-benzylpiperidinol derivatives as novel USP7 inhibitors: Structure-activity relationships and X-ray crystallographic studies

USP7 as a deubiquitinase plays important roles in regulating the stability of some oncoproteins including MDM2 and DNMT1, and thus represents a potential anticancer target. Through comparative analysis of USP7 co-crystal structures in complex with the reported piperidinol inhibitors, we noticed that the USP7 Phe409 sub-site might have good adaptability to the ligands. Based on this observation, 55 N-aromatic and N-benzyl piperidinol derivatives were designed, synthesized and biologically evaluated, among which compound L55 was identified as a highly selective and potent USP7 inhibitor (IC₅₀ = 40.8 nM, K_D = 78.3 nM). X-ray crystallographic studies revealed that L55 bound to USP7 with a new pose that was very different from the previously reported inhibitors. The results of cellular assays showed that L55 had strong antitumor activity against LNCaP (IC₅₀ = 29.6 nM) and RS4; 11 (IC₅₀ = 41.6 nM) cells, probably through inducing cell death and restricting G0/G1 and S phases. Moreover, L55 dose-dependently reduced the protein levels of MDM2 and DNMT1 and increased the protein levels of p53 and p21. These findings could have valuable implications for designing novel structural classes of USP7 inhibitors.