Biology subjects

Machata, S.

Publications and source records attributed to Machata, S..

4 recordsLinked to original sources

bioRxiv2026

Discovery of CDK4-selective molecular glue degraders by high-throughput proteomics

Molecular glue degraders (MGDs) are proximity-inducing molecules that promote the destruction of disease-causing proteins by stabilizing novel interfaces between E3 ubiquitin ligases and target proteins. The rational design of MGDs remains exceptionally challenging, historically relying on serendipitous discoveries. Here, we deployed a high-throughput, mass spectrometry (MS)-based screen evaluating thousands of cereblon (CRBN)-directed compounds to expedite the identification of novel neosubstrates. This workflow led to the discovery of NE26394, a first-in-class MGD that selectively eliminates cyclin-dependent kinase 4 (CDK4), a critical oncogenic driver of cell cycle progression. Mechanistically, NE26394-induced CDK4 recognition by CRBN depends on the co-recruitment of endogenous INK4 family proteins. In CDK4-dependent cancer models, NE26394 effectively mimics the anti-proliferative RB-E2F pathway perturbations induced by clinical CDK4 inhibitors, rendering it an attractive candidate for further preclinical development.

biochemistry↗

bioRxiv2026

Integrated proteomic screening reveals design principles of CRBN molecular glue degraders

Cereblon (CRBN)-based molecular glue degraders (MGDs) induce the degradation of diverse disease-relevant proteins, underscoring their broad therapeutic potential. Here we systematically expand the CRBN neosubstrate landscape using a target-agnostic discovery approach. By integrating deep proteomic and ubiquitinomic profiling of a 960-compound library, we identify compound-induced ubiquitination and depletion of over 230 endogenous proteins. Among these, 124 represent previously unreported CRBN neosubstrates, with over half lacking a predicted G-loop degron. We provide this dataset via an interactive resource, NeosubstratesDB. Complementary cellular and biochemical assays mechanistically define the interaction domain of IRAK1 and establish G-loop-dependent degradation for BCL6. Interpretable machine learning (iML) integrating proteomic profiles with chemical structures highlights key molecular fingerprints driving neosubstrate selectivity for targets such as CSNK1A1, ZFP91 and WEE1. Together, these findings significantly expand the repertoire of CRBN neosubstrates and provide a framework for rational design of next-generation MGDs.

biochemistry↗

bioRxiv2024

Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics

Molecular glue degraders (MGDs) are small molecules that harness the ubiquitin-proteasome system to induce degradation of target proteins, including those lacking conventional druggable pockets. Given the challenges in their rational design, MGD discovery predominantly relies on screening-based approaches, such as cell viability assays. However, one potential limitation of such screening methods is the risk of overlooking non-essential neosubstrates of potential therapeutic value. To address this concern, we present a high-throughput proteome-wide MGD screening platform utilizing label-free, data-independent acquisition mass spectrometry (DIA-MS) for integrated proteomics and ubiquitinomics analysis. Processing a diverse set of 100 CRBN-ligands across two cancer cell lines reveals a broad array of neosubstrates, including 50 novel candidates validated by MS-based ubiquitinomics. These findings considerably expand the current landscape of CRBN-mediated neosubstrates. Comprehensive hit validation and structure-degradation relationship analyses guided by global proteomics, identifies highly selective and potent phenyl glutarimide-based degraders of novel neosubstrates, including KDM4B, G3BP2 and VCL, none of which contain the classical CRBN degron motif. This study demonstrates that comprehensive, high-throughput proteomic screening offers new opportunities in MGD drug discovery.

biochemistry↗

bioRxiv2024

Identification of a fungal antibacterial endopeptidase that modulates immune responses

Aspergillus fumigatus is a saprophytic fungus dwelling in soil and on decaying plant material, but also an opportunistic pathogen in immunocompromised patients. In its environmental niche, A. fumigatus faces competition from other microorganisms including bacteria. Here, we describe the discovery of the first secreted antibacterial protein in A. fumigatus. We identified a secreted fungal endopeptidase, designated CwhA, that cleaves peptidoglycan of Gram-positive bacteria at specific residues within the peptidoglycan stem peptide. Cleavage leads to bacterial lysis and the release of peptidoglycan cleavage products. Expression of cwhA is induced by the presence of bacteria. Furthermore, CwhA is highly abundant in murine lungs during invasive pulmonary aspergillosis and peptidoglycan cleavage products generated by CwhA stimulate cytokine production of human immune cells. Although CwhA does not affect human cells directly, this novel player in fungal-bacterial interactions could affect A. fumigatus infections by inhibiting Gram-positive bacteria in its vicinity, and modulating the immune system.

microbiology↗