Yoshinori Taguchi,† Takuya Tomita,† Takuma Nishizawa, Dai Nakamura, Showmitra Saha, Takanori Oyoshi, Kohei Sato, Nobuyuki Mase, Yasushi Saeki, and Tetsuo Narumi (†: These authors contributed equally to this work)

Protein ubiquitination is a pivotal post-translational modification that regulates diverse biological processes depending on the type of ubiquitin chain linkage. Recently, ester-linked ubiquitin chains have been identified, yet their inherent hydrolytic instability has posed a significant challenge for biochemical investigations. In this study, we chemically synthesized a stable and isosteric amide analog of an ester-linked ubiquitin dimer, in which serine (Ser) at position 20 of the proximal ubiquitin was replaced with 2,3-diaminopropionic acid (Dap). The desired amide analog was synthesized using a convergent approach involving the sequential chemoselective ligation of three peptide fragments generated through Fmoc-based solid-phase peptide synthesis. Employing this chemically robust ubiquitin probe, we uncovered a previously unrecognized interaction between Ser20- linked ubiquitin chains and spliceosome-associated factors, notably ubiquitin-specific protease 39 (USP39). These findings highlight the potential of our ester-to-amide bioisosteric strategy to unlock mechanistic insights into atypical ubiquitin modifications. Our approach not only circumvents the intrinsic instability of ester-linked ubiquitin chains but also provides a broadly applicable framework for dissecting their biological roles, paving the way for future discoveries in ubiquitin signaling.