More than 240,000 experimentally determined, atomic-level, three-dimensional structures of biomolecules housed in the Protein Data Bank (PDB) support basic and applied research and education across the sciences, impacting fundamental biology, biomedicine, biotechnology, and energy sciences. This talk will explore how open access to PDB data at RCSB.org facilitates small-molecule drug discovery/development in both academia and the biopharmaceutical industry, encompassing target validation, target druggability, fragment screening, and structure-guided drug discovery. The RCSB Protein Data Bank is jointly funded by the US National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Institutes of Health (R01GM157729).

Deubiquitinating enzymes (DUBs) play an important role in the cell cycle, cellular physiology and protein regulation, making them desirable as potential therapeutic targets. DUBs are responsible for cleaving the bond between a ubiquitin and its selective protein. We uncovered potent and selective inhibitors for a DUB protein by leveraging Valo’s DEL capabilities alongside an HTS campaign. Both HTS and DEL campaigns identified similar motifs in the chemical structure of the top hits, and conclusions from both strategies influenced lead molecule design.

At GSK, we improve decision-making from DNA Encoded Library (DEL) selections by leveraging extensive internal datasets from past experiments involving numerous target proteins. In this talk, we will demonstrate that calibrating results with historical background binders and evaluating chemical series with known "frequent hitters" enhances our ability to discern chemical series that interact with target proteins. Additionally, we can assess the historical productivity of individual DELs.

DEL screening has become an established hit identification strategy employed across the global small molecule portfolio at Pfizer. Our hit confirmation toolbox includes an on-DNA confirmation workflow which employs non-combinatorial resynthesis on-DNA and binder identification by Bead Assisted Ligand Isolation—Mass Spec (BALI-MS). We developed a cleavable linker platform that enables us to access off-DNA samples directly from the products of on-DNA resynthesis. This talk will describe how we utilize this Cleavable Linker Platform to deliver microgram quantities of DEL hits from on-DNA synthesized samples for further analysis.

Our objective is to generate protein-ligand-binding at scale.  To accomplish this, we will screen human proteins with two direct binding assays—enantioselective affinity-selection mass spectrometry and DNA-encoded library screening.  All the binding data (both positive and negative) will be placed into the public domain. I will speak about our technological approaches and some of the emerging data.

Protein X is a key regulator in the immune system and is associated with multiple autoimmune and inflammatory diseases. Despite its intriguing biological role, the development of small-molecule inhibitors has been challenging due to the target's difficult-to-drug nature. By adopting an integrated screening approach, several hits were identified through both high-throughput screening (HTS) and DNA-encoded library technology (DELT) screening. 

We present an optimized MS-based covalent screening platform designed to maximize throughput, streamline hit triaging and enable mechanistic characterization. Platform capabilities have been expanded to include photoaffinity library screening of reversible hits and the development of competition assays with covalent probes to accelerate early discovery efforts. We will also discuss leveraging integrated screening data to facilitate the identification of tractable, selective hits as actionable starting points.

MOMA Therapeutics was launched to understand ATPases, systematically target and define them as a target class. Our KNOMATIC platform successfully addresses these historically challenging targets through an integrated approach combining novel target-ID, structural prediction, covalent fragment screening and DEL technology. Within six months of target validation for a novel DDR ATPase, the platform delivered three chemical series with nanomolar biochemical potency, enabled structure-based design, and demonstrated cellular target engagement assays.

Acid-sensing ion channels (ASICs) are sensory receptors that are therapeutic targets for opioid-free pain management. I describe the discovery of first- and best-in-class orally bioavailable ASIC1 inhibitors. We screened a small molecule library using a calcium-based high-throughput FLIPR screen. We used functional selectivity assays via electrophysiology (manual and automated patch-clamp) for lead optimization using proprietary stable mammalian cell lines expressing human ASIC subtypes.

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 end-user accessible 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.