Overview of current state of targeted protein degradation and thoughts on where the field is heading with respect to clinical candidates, new degradation targets and different degradation strategies.

A brief look at the Arvinas platform and pipeline.

Our research focuses on leveraging our ubiquitin-mediated, small molecule-induced protein degradation technology (uSMITE) for the treatment of cancer and other diseases. I will present the discovery and evaluation of first-in-class potent and selective degraders of tropomyosin receptor kinases (TRK) that inhibited cell growth with low nanomolar IC50 values and demonstrated sustained tumor growth inhibition in xenografted tumor models using the oral administration route.

Eurofins Discovery is diversifying its novel E3scan™ ligand-binding platform with additional E3 ligase target assays. Here, we present assay validation data for E3scan, including for E3 ligases that have not been utilized in targeted protein degradation and for which no small molecule ligands have been previously reported. Our E3scan platform enables accelerated screening and SAR analysis, with rapid turnaround times and the largest assay panel available on a single technology platform.

We report covalent inhibitors of USP7 that unexpectedly promote a b-elimination reaction of the initial covalent adducts, thereby converting the active site cysteine residue to dehydroalanine. Unlike in conventional reversible-covalent inhibition, these compounds irreversibly destroy a catalytic residue whilst simultaneously converting the inhibitor to a non-electrophilic byproduct. This finding expands the scope of covalent inhibitor modalities and offers intriguing insights into enzyme-inhibitor dynamics in the ubiquitin-proteasome system and beyond.

Formation of ternary complexes between a ligase, a molecular glue, and a disease-modulating protein is the first step in a sequence of events leading to protein degradation. In this presentation, we present SPR methods for determining the affinities of the small molecule glue for the ligase and discuss methods for characterizing the affinities and kinetics of ternary complex formation involving the ligase, the molecular glue, and the recruited protein.

Molecular glue degraders are a novel therapeutic modality and induce destabilization of proteins that would otherwise be considered undruggable due to the lack of a ligandable pocket. Their discovery however has so far been serendipitous. The Proxygen glue degrader discovery platform enables rational screening for such molecules on an industrial scale. Here, we present a case study of the subsequent chemical optimization of the resulting hit molecules.

As targeted protein degradation strategies expand, understanding the impacts of compound permeability, the kinetics of ternary complex formation, and ubiquitination are critical.  NanoBRET assays measure cellular compound permeability, the kinetics of complex formation and ubiquitination.  Using dBET1 and dBET6 PROTACs, we demonstrate that dBET6 is more permeable than dBET1.  Furthermore, dBET6 induces more complex formation and ubiquitination.  These results provide insight into the difference in degradation between dBET6 and dBET1. 

Small molecules that induce protein degradation through ligase-mediated ubiquitination, have shown considerable promise as a new pharmacological modality. Thalidomide and related IMiDs provided the clinical proof of concept, while significant progress has recently been made towards chemically induced targeted protein degradation using heterobifunctional small molecule ligands. We will present recent work towards a better understanding of the molecular principles that govern neo-substrate recruitment, and other small molecule degraders.

This presentation will focus on the discovery and characterization of bifunctional molecules designed to leverage the ubiquitination pathway for degradation of a target protein. We will discuss strategies for the discovery of ligands for both the target protein and the ligase complex, determination of the kinetics of their interactions in binary and tertiary complexes, and the application of structural biology to design new ligands.

War against HIV was won by development of antiviral drugs. Successful HIV therapy involves combination of three drugs. Traditional mono-antiviral therapy has not been successful due to poor efficacy and emergence of resistance. Drugs that targeted viral protein for ubiquitin E3 ligase mediated degradation can eliminate the viral protein and prove to be highly efficacious. Progenra has targeted SARS-CoV-2 viral proteins with PROTAC drugs. Potent and selective PROTACs degrade viral proteins in cells and block viral growth. Discovery and development of PROTAC drugs that target SARS-CoV-2 will be discussed.

The discovery of covalent inhibitors of KRAS^G12C has reinvigorated the field of KRAS drug discovery. While these compounds have shown promising clinic results, we wanted to explore PROTAC-mediated degradation as a complementary strategy to modulate KRAS^G12C.  We report the development of LC-2, the first PROTAC capable of degrading endogenous KRAS^G12C.  LC-2 induces rapid, sustained KRAS^G12C degradation and suppresses MAPK signaling. LC-2 demonstrates that PROTAC-mediated degradation can attenuate oncogenic KRAS levels.

Targeted protein degradation is mediated by Chimeric Targeting Molecules (CTMs), which bind to a target protein and an E3 ligase, resulting in target protein ubiquitylation and proteasomal destruction. This presentation will describe Nurix’s DNA-encoded library (DEL) platform for the discovery of novel binders to enable CTM discovery. This presentation will also describe the discovery of orally bioavailable degraders of BTK, a clinically relevant target for oncology and immunology applications.

The application of DNA-encoded library (DEL) technology to the discovery of protein degraders is increasingly appreciated among researchers in the field. The nature of the DEL selection, the structure of libraries, and flexibility of the screening experiment, lend themselves to the degradation approach. In this presentation we will examine the current state of the art of DEL design and of selection methodologies, and their application to novel degrader discovery.