Biology subjects

Ferguson, F.

Publications and source records attributed to Ferguson, F..

4 recordsLinked to original sources

bioRxiv2026

A reversible GNAS-PKA-RUNX2 checkpoint governs skeletal stem cell fate in fibrous dysplasia

Fibrous dysplasia (FD) arises from activating GNAS mutations that increase cAMP signaling in skeletal stem/progenitor cells (SSPCs), but the underlying mechanisms and whether the resulting fate imbalance can be reversed remain unclear. Using controlled GNAS induction with transcriptomic, pharmacologic, and cell-fate analyses, we identify a PKA-dependent checkpoint governing SSPC lineage commitment. GNASR201C redirects SSPCs toward osteoclastogenesis while suppressing osteoblast maturation; genetic or pharmacologic PKA inhibition reverses both effects, revealing this fate decision is dynamically reversible. Mechanistically, PKA phosphorylates RUNX2, the master regulator of osteogenesis, enforcing its cytoplasmic retention and blocking osteogenic transcription; a non-phosphorylatable RUNX2 mutant restores nuclear localization and osteoblast differentiation, defining RUNX2 phosphorylation as a disease-initiating molecular switch. Critically, PKA inhibition in vivo reduces fibrosis and osteoclast burden in established bone lesions, demonstrating reversibility even in advanced FD. These findings define a druggable GNAS-PKA-RUNX2 checkpoint and identify PKA inhibition as a strategy to reverse existing disease in FD.

cell biology↗

bioRxiv2026

TubercuProbe: A Cross-Attention Graph-Sequence Model for Cross-Species Chemoproteomic Discovery in Mycobacterium tuberculosis

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 ({Delta}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{approx}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.

biochemistry↗

bioRxiv2025

A Lipid Prodrug Strategy Enhances Targeted Protein Degrader CNS Pharmacokinetics

Targeted protein degraders that recruit the von-hippel Lindau E3-ligase complex often have poor physicochemical properties, requiring extensive medicinal chemistry optimization prior to use in hypothesis-testing experiments in vivo, and with few blood-brain-barrier permeable examples disclosed. In this study, we systematically examine a panel of fatty acid promoieties as agents to enhance degrader pharmacokinetics and BBB-exposure. We characterize effects on cellular E3-ligase engagement, cellular BRD4 degradation kinetics, murine plasma stability, and murine blood plasma and brain pharmacokinetics and pharmacodynamics. We identify degrader prodrugs with significantly improved CNS exposure relative to the parent degrader. This led to successful BRD4. degradation in perfused brain samples, demonstrating that fatty acid promoieties can accelerate progress towards proof of principle in vivo experiments for CNS degrader projects.

pharmacology and toxicology↗

bioRxiv2024

A Kinetic Scout Approach Accelerates Targeted Protein Degrader Development

Bifunctional molecules such as targeted protein degraders induce proximity to promote gain-of-function pharmacology. These powerful approaches have gained broad traction across academia and the pharmaceutical industry, leading to an intensive focus on strategies that can accelerate their identification and optimization. We and others have previously used chemical proteomics to map degradable target space, and these datasets have been used to develop and train multiparameter models to extend degradability predictions across the proteome. In this study, we now turn our attention to develop generalizable chemistry strategies to accelerate the development of new bifunctional degraders. We implement lysine-targeted reversible-covalent chemistry to rationally tune the binding kinetics at the protein-of-interest across a set of 25 targets. We define an unbiased workflow consisting of global proteomics analysis, IP/MS of ternary complexes and the E-STUB assay, to mechanistically characterize the effects of ligand residence time on targeted protein degradation and formulate hypotheses about the rate-limiting step of degradation for each target. Our key finding is that target residence time is a major determinant of degrader activity, and this can be rapidly and rationally tuned through the synthesis of a minimal number of analogues to accelerate early degrader discovery and optimization efforts.

pharmacology and toxicology↗