Fleur M. Ferguson

The atypical cyclin-dependent kinase subfamily (CDK14–18) encompasses five related proteins with unclear function, and for which individual depletion has not demonstrated sustained therapeutic relevance. We report here that CDK16 and CDK18 compensate each other and liver cancer cells are sensitive to the concomitant inactivation of both kinases, resulting in persistent defects in DNA repair and subsequent cell death. These effects are linked to a role of CDK16/18 in regulating nucleocytoplasmatic transport through phosphorylation of nuclear pore complex components, including NUP35. Genetic ablation of Cdk16 and Cdk18 in established liver tumors driven by MYC and beta-catenin oncogenes triggers DNA damage in cancer cells without affecting adjacent normal tissue, ultimately leading to tumor regression. Collectively, these findings provide a rationale for the development of CDK16–18 inhibitors—likely targeting multiple subfamily members due to their structural similarity—as a strategy against aggressive cancers, such as hepatocellular carcinoma, where effective treatment options remain limited.

Silva MC, Ferguson FM, Cai Q, Donovan KA, Nandi G, Patnaik D, Zhang T, Huang H-T, Lucente DE, Dickerson BC, Mitchison TJ, Fischer ES, Gray NS, Haggarty SJ. 2019. Targeted degradation of aberrant tau in frontotemporal dementia patient-derived neuronal cell models. eLife 8:e45457. doi: 10.7554/eLife.45457.

JWJ-01-378 recruits cereblon (CRBN) to induce potent and selective degradation of oncogenic TRK fusions, leading to a collapse in signaling and loss of cancer cell viability. Graphic was created using https://biorender.com.

Pathological seeding of protein misfolding is a hallmark of proteinopathies. However therapeutic strategies to clear these aggregates are lacking, impairing both study of their biological importance in disease etiology and progression as well as development of therapeutics. This is due in part to the need to selectively clear oligomerized proteins whilst leaving functional monomers intact, as well as the challenge of developing molecules that act on the full complement of ‘misfolds’ the protein can adopt throughout the course of disease. In this work, we describe a dopant system consisting of an engineered alpha-synuclein protein construct that rapidly co-aggregates into existing WT alpha-synuclein oligomers, enabling rapid degradation of the entire assembly in the presence of a small molecule trigger. This work provides proof-of-principle for an approach that transforms pathological seeding from a disease-driver into a therapeutic vulnerability, and is potentially applicable to any proteinopathy without requiring a small molecule binder of the pathologic species.

Activity-based protein profiling (ABPP) and residue-specific chemoproteomics have transformed human chemical biology, yet applying these approaches to pathogens remains limited by biosafety constraints, low throughput, and the absence of reusable atlases. We present TubercuProbe, a cross-species machine learning framework that leverages large-scale human chemoproteomic knowledge to prioritize compound-protein interactions in Mycobacterium tuberculosis (Mtb) and other pathogens. Our model integrates a graph isomorphism network (GINE) for ligand encoding with frozen ESM-C (600M) protein embeddings via bidirectional cross-attention. Trained on >2M ChEMBL compound-protein pairs (predominantly human targets), TubercuProbe achieves R2=0.77 (MSE=0.45) for continuous affinity prediction and transfers effectively to binary cysteine reactivity prediction (CysDB AUPRC=0.63). Ablation studies reveal that pretrained features are highly transferable across freezing strategies (∆AUPRC<0.03), suggesting the model captures fundamental protein-molecule interaction patterns. As a case study, we prioritize cysteine-reactive electrophiles and molecular glues for three Mtb virulence proteins (PtpB, SapM, Rv3671c), providing candidate probes for prospective ABPP validation. Orthogonal comparison with Boltz-2 structure predictions shows moderate correlation (Pearson r≈0.69). TubercuProbe provides a lightweight, sequence-driven first-pass ranker that enables pre-experimental prioritization - reducing the time, cost, and experimental burden of chemoproteomic discovery in biosafety-restricted systems. We discuss extensions toward multitask learning that jointly predicts non-covalent binding and covalent reactivity, recognizing that effective covalent probes must both reach their target and react once there.

Unbiased identification of drug‐targets in live cells is essential for understanding the mechanism‐of‐action and potential off‐target effects of drugs. The BioTAC system to measure these effects is previously developed. However, BioTAC has limitations, including lysine‐directed biotinylation chemistry, and relatively long biotin labeling times. Herein, the development of the APEXTAC system, a small molecule guided proximity labeling platform based on the APEX2 peroxidase proximity labeling enzyme, is described as a complementary tool. A head‐to‐head comparison is performed between the APEXTAC system and the BioTAC system for (+)‐JQ1 target‐ID and demonstrated that APEXTAC can label E3‐ligases via their ligands without requiring a proteasome inhibitor which can significantly perturb cell state. The APEXTAC system supports live cell target‐ID across numerous molecules and targets, including components of the protein homeostasis machinery, without degradation of the labeling system, highlighting its potential application to the targeted protein degradation field.

The discovery of immune checkpoint blockade as a therapeutic strategy to induce immunogenic cancer cell elimination has shown great success in the treatment of various cancers. However, limited response rates highlight the need for further development in this field. Promising new preclinical developments include the discoveries of proteolysis-targeting chimeras (PROTACs) to interfere with tumor immune escape signaling. Pharmacological induction of targeted protein degradation by these chimeras has shown advantages in inhibiting non-enzymatic protein functions and difficult to target protein–protein interactions. Furthermore, the induced degradation was shown to promote changes in the major histocompatibility complex I ligandome, which can be leveraged for an immune stimulus, increasing the cancer immune response. In this minireview, we highlight the research efforts ongoing towards employing PROTACs in immunotherapy for cancer treatment. Specifically, we outline how the unique mechanism of action can be leveraged to enhance the immune response or inhibit immune suppression.