Synthesis at the Interface of Chemistry and Biology

Cross-Linking Profiling of Molecular Glue Degrader-Induced E3 Ligase Interactome to Expand Target Space

Molecular glue (MG) degraders, small molecules with significant therapeutic potential for targeting undruggable proteins, are emerging as new modality in drug discovery. Profiling the E3 ligase interactome induced by MG degraders provides insights into their mechanism of action and identifies clinically relevant neosubstrates for degradation, thereby offering new therapeutic opportunities. However, established methods face significant challenges in comprehensive and accurate profiling of MG degrader-induced E3 ligase interactome. Herein, we introduce the concept of globally cross-linking profiling of the MG degrader-induced E3 ligase interactome in living cells, achieved by integrating genetic code expansion technology with mass spectrometry-based proteomics. Our approach presents an efficient and robust strategy for identifying neosubstrates recruited to cereblon E3 ligase by the known degraders CC-885 and DKY709, offering valuable insights for clinical evaluation and significantly expanding their target space. Moreover, we developed two novel MG degraders with potent antiproliferative effects on cancer cells, and application of our method identified neosubstrates, revealing a previously unrecognized target landscape and advancing our understanding of E3 ligase-neosubstrate interactions. Overall, our study provides a powerful tool for neosubstrate identification and expanding target space of E3 ligase, opening new opportunities for developing next-generation MG degraders to address the clinical challenge of undruggable targets.

Noncanonical Amino Acids Dictate Peptide Assembly in Living Cells

ConspectusEmulating the structural features or functions of natural systems has been demonstrated as a state-of-the-art strategy to create artificial functional materials. Inspired by the assembly and bioactivity of proteins, the self-assembly of peptides into nanostructures represents a promising approach for creating biomaterials. Conventional assembled peptide biomaterials are typically formulated in solution and delivered to pathological sites for implementing theranostic objectives. However, this translocation entails a switch from formulation conditions to the physiological environment and raises concerns about material performance. In addition, the precise and efficient accumulation of administered biomaterials at target sites remains a significant challenge, leading to potential biosafety issues associated with off-target effects. These limitations significantly hinder the progress of advanced biomaterials. To address these concerns, the past few years have witnessed the development of in situ assembly of peptides in living systems as a new endeavor for optimizing biomaterial performance benefiting from the advances of stimuli-responsive reactions regulating noncovalent interactions. In situ assembly of peptides refers to the processes of regulating assembly via stimuli-responsive reactions at target sites. Due to the advantages of precisely forming well-defined nanostructures at pathological lesions, in situ-formed assemblies with integrated bioactivity are interesting for the development of next-generation biomedical agents.Despite the great potential of in situ assembly of peptides for developing biomedical agents, this research area still suffers from a limited toolkit for operating peptide assembly under complicated physiological conditions. Considering the advantages of amino acids in being incorporated into peptide backbones and modified with stimuli-responsive units, development of an amino acid toolkit is promising to address this concern. Therefore, our laboratory has been intensively engaged in designing and discovering stimuli-responsive noncanonical amino acids (ncAAs) to expand the toolkit for manipulating peptide assembly under various biological conditions. Thus far, we have synthesized peptides containing ncAAs 4-aminoproline, 2-nitroimidazole alanine, Se-methionine, sulfated tyrosine, and glycosylated serine, which allow us to develop acid-responsive, redox-responsive, and enzyme-responsive assembly systems. Based on these stimuli-responsive ncAAs, we have established complex self-sorting assembly, self-amplified assembly, and dissipative assembly systems in living cells to optimize the bioactivity of peptides. The resulting in situ assembly systems exhibit morphological adaptability to the biological microenvironment, which contributes to overcoming delivery barriers and improvement of targeting accumulation. Therefore, by utilizing the developed toolkit, we have further created supramolecular PROTACs, supramolecular antagonists, and supramolecular probes for cancer treatment and diagnosis to highlight the implications of ncAAs for biomedical usage. In this Account, we summarize our journey of in situ self-assembly of peptides in living cells utilizing stimuli-responsive ncAAs, with an emphasis on the mechanism for regulating peptide assembly and optimizing the bioactivity of peptides. Eventually, we also provide our forward conceiving prospects on the challenges for the further development of in situ assembly of peptides in living systems and the clinical translation of in situ-formulated biomaterials.