Affinity Selection-Mass Spectrometry (ASMS) identifies small molecule ligands for soluble and membrane proteins via a mass-encoded readout. Additionally, this binding assay approach enables compound competition binding assessments and binding site mapping with membrane proteins without purifying the target.   This presentation reviews several applications across diverse ASMS platforms at distinct service labs, including studies with poorly ligandable proteins.

Affinitey Selection Mass Spectrometry (ASMS) has been implemented at AbbVie for screening, hit confirmation, and direct-to-biology applications. Learnings based on our particular ASMS method will be discussed and best use cases will be presented.

Cellular metabolites control many biological processes through direct interactions with proteins, including allosterically regulating many classes of proteins. We have developed technology using LC/MS based metabolomics and an endogenous metabolite library to systematically discover functional allosteric pockets. These pockets enable an efficient drug discovery campaign using AI/ML-enabled structure-based drug design. This has been successfully accomplished several times, including for our oncology development candidate, which will be presented.

A diverse range of biophysical technologies plays a vital role in early-stage drug discovery, unraveling molecular interactions crucial for understanding drug-target interactions, thereby guiding rational drug development. High-throughput assays including SPR, AS/MS, and fluorescence spectroscopy (TdF/DSF) enable simultaneous evaluation of binding affinities, kinetics, thermodynamics, and potential mechanisms of action, expediting identification of potential drug candidates. This presentation focuses on collaborative efforts to develop, optimize, and utilize biophysical assays to screen and identify drug candidates from various modalities. Our team leveraged different capabilities to accelerate hit validation through evaluation of biophysical parameters, optimizing assay parameters based on modality for efficiency and throughput.

Class A GPCRs are small receptors that often lack an extracellular domain. GPCRs mediate physiological functions through ligand binding, and in orphan GPCRs these ligands are unidentified. GPCRs are attractive targets for indications from brain injury to obesity, but structural study has been hindered by their innate qualities. Here we present and compare novel structures of a class A orphan GPCR with bound ligand to inform mechanism and drug discovery.

Access to high resolution structural data on protein-ligand complexes is a prerequisite for structure-based drug design. For proteins refractory to X-ray crystallography, high throughput structure determination by electron cryo-microscopy (cryo-EM) has the potential to be transformational for medicinal chemistry. This talk will describe a workflow, from protein production through to high resolution structural data, applied to a biologically important ion channel target in complex with a chemically diverse range of ligands. The depth of structural data generated provides important insights into ligand functional structure-activity relationships and, moreover, demonstrates the potential of the workflow to support iterative compound design cycles.

Measuring direct binding and kinetics to membrane proteins has long been a challenge due to poor behavior of these targets when purified out of their native environments. Surface Plasmon Resonance Microscopy (SPRm), which combines optical microscopy with label-free SPR, allows for detection of binding in the whole cell environment. Using SPRm, we measured binding affinities on several targets that are in excellent agreement with radioligand binding and functional IC50 assays.

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. I will include some case studies against cancer targets.

Chemical probes offer a valuable way to interrogate the function and disease-relevance of proteins and can also serve as leads for drug development, yet most proteins in the human proteome lack small-molecule ligands that can serve as probes. More generally, the boundaries, if any, on the ligandability, and therefore potential druggability, across proteomes remains poorly understood. I will describe our efforts to develop powerful photoaffinity-based chemical proteomic strategies to broadly map ligandable sites on proteins directly in cells, and how this information can be advanced into useful chemical probes for targets that play critical roles in human health and disease.

Belharra Therapeutics applies a novel chemistry-enabled non-covalent probe library and quantitative mass spectrometry to identify chemical probes that selectively bind any pocket, on any protein, in live cells. This next-gen chemoproteomics discovery engine identifies chemical probes that selectively engage diverse protein classes including transcription factors, adaptors, ion channels, and transporters, dramatically increasing the scope of the druggable proteome.

The design of covalent drugs targeting residues other than Cys,  such as His, or Tyr, is gaining significant traction. I will discuss strategies and opportunities to design covalent ligands targeting those residues  using both ligand-first structure-based design or covalent-fragment screening. I will present our successful implementations of both approaches.

We introduce COOKIE-Pro (COvalent Occupancy KInetic Enrichment via Proteomics), a novel method for quantifying covalent inhibitor binding kinetics proteome-wide. The method accurately determines kinact and KI values using a desthiobiotin probe and mass spectrometry. By integrating direct-to-biology synthesis with COOKIE-Pro, we enabled rapid screening of covalent fragments without purification, generating high-confidence hits within days. This approach overcomes limitations of traditional methods and accelerates development of selective covalent therapeutics.