Targeted protein degradation (TPD) using heterobifunctional chimeras holds the potential to expand target space and grow the ‘druggable proteome.'  Most acutely, this provides an opportunity to target proteins that lack enzymatic activity or have otherwise proven intractable to small molecule inhibition. Bridging covalent ligand discovery with chimeric degrader design has emerged as a potential mechanism to advance both fields.  Here, the authors, employ a set of biochemical and cellular tools to deconvolute the role of covalent modification in TPD using Bruton’s tyrosine kinase.  Results reveals that covalent target modification is fundamentally compatible with the protein degrader mechanism of action.

Mass spectrometry-based targeted proteomics approaches have emerged as a promising technology to monitor absolute abundance of therapeutic target proteins that cannot be achieved via traditional protein detection technologies. We developed and applied these high-throughput strategies to address key MoA questions on PROTACs projects, including target protein and E3 abundance, protein turnover rates, and also for compound profiling. Case studies will be shown to demonstrate the technology and the impact on several PROTAC projects.

Using our proprietary chemoproteomics platform, we identified site-selective covalent ligands for the CRL4^DCAF2 E3 ligase. DCAF2 is a substrate receptor upregulated in specific cancers. A ligand was developed into hetero-bifunctional degraders that exhibited robust cellular DCAF2-dependent BRD2/4 degradation. Our work validates DCAF2 as a novel E3 ligase substrate receptor amenable to targeted protein degradation and demonstrates the utility of the Frontier Platform to discover novel ligands enabling proximity-inducing therapeutics.

Recent chemoproteomics advances have enabled covalent ligand discovery across a broad range of new targets. Here, we discuss the expanding role of chemical biology and chemoproteomics to support covalent lead discovery efforts, from early hit-finding to late lead optimization.

Once considered too dangerous to leverage as a drug modality, the field of covalent small molecule discovery is seeing a resurgence. It’s a resurgence boosted by the proven efficacy and safety of approved covalent kinase inhibitors and driven by advances in chemoproteomics and structural biology technologies that enable target discovery and more precision in therapeutic design than ever before. This talk will highlight key advances in these fields and how they are driving the development of new covalent therapeutics.

Cell-surface proteins present unique opportunities for diagnostic and therapeutic targeting. Despite major advances in proteomic methods, our understanding of surfaceome content and organization remains limited. Using photochemical proximity labeling, we are generating high-confidence protein interaction networks for cell surface proteins in diverse cell types and contexts. This data forms the centerpiece of an integrated Membrane Interactome knowledge-base (MInt), incorporating in-house generated data for target discovery and prioritization.

Chemical biology has broad influence on many drug discovery programs. For example, chemical biology tools and techniques can be used to understand target engagement, selectivity/off-target profiles and binding sites of lead matter, which can be critical to the progression of a project. This presentation will focus on the development of new and innovative chemistry to offer improved methods to access and use chemical probes in a variety of applications.

Targeted covalent inhibition of disease associated proteins has become a powerful methodology in drug discovery with the approval of commercial drugs for targets previously deemed undruggable. We will showcase examples of combining chemoproteomics approaches together with protein structure-function relation at residue level for identifying actionable targets and novel druggable pockets.

There are significant expanses of the potential druggable protein landscape that are relatively unexplored for small molecule drug discovery. In this talk, I will discuss the development and deployment of complementary in situ proximity barcoding chemoproteomic approaches to map protein activity states and/or interaction partners directly in native cellular environments. In particular, I will focus on the application of these platforms for functional ligand binding site discovery, high-throughput ligand profiling and mechanism-of-action interrogation for challenging protein classes.

Analysis of on and off-target effects during lead optimization, target validation, uncovering mechanisms of resistance and potential for rational  therapeutic combinations or sequencing, as well as drug target biochemistry and modulation are critical elements of the biopharmaceutical late stage preclinical pipeline. The reverse phase protein array technology is a powerful analytical platform that is able to quantitatively measure hundreds of protein drug targets and phosphorylated signaling architecture at once from microscopic quantities of cells and is especially well-suited for these efforts.

Ras isoform mutants play a major role in most aggressive and deadly cancers in humans (e.g., pancreas, lung, ovary). While the majority of drug discovery efforts target oncogenic Ras signaling inside the cell, only few a endeavors have been focused on the cell-surface. Using quantitative label-free membrane proteomics we were able to identify more than 500 cell surface proteins found unique or upregulated on the surface of KRasG12V -expressing cells.

Affinity purification-mass spectrometry (AP-MS) with aptamer libraries enriched directly on molecularly profiled cancer patient tissue was used for novel drug discovery. This method allows for unbiased detection of cancer-specific proteins that elude classical proteomic identification methods. Targets were validated with RNA expression data from our clinico-genomic database and IHC on patient tissue. Cell surface targets were validated on cell lines by mass spectrometry, flow cytometry, immunocytochemistry and with cytotoxicity assays.