DCAF1 is a substrate receptor of two distinct E3 ligases (CRL4DCAF1 and EDVP) and plays an important role in protein degradation and many cellular processes. We have identified binders to DCAF1 and will describe the optimization of these compounds and their use in the degradation of a protein of interest using a PROTAC approach.

In the last few years, the PROTAC technology has gained a major momentum for the discovery and development of new therapeutics for the treatment of human diseases, particularly cancer.  Our laboratory has been carrying out research in pushing the boundary in three different areas using the PROTAC technology. (1). Targeting those traditionally undruggable proteins; (2). Developing highly selective degraders to overcome on-target toxicities issues; (3) developing orally bioavailable degraders to overcome drug-resistances of traditional small-molecule drugs. I will present our latest progresses we have made in these three areas.

I will present our recent progress in the discovery of molecular glue degraders for intracellular proteins; it involves the sequence of rapid synthesis, phenotypic screening, proteomic profiling, and validation of hits and targets. I will also present our progress on the development of cancer-selective degraders for extracellular proteins involving novel antibody conjugates.

PROTACs have emerged as an innovative drug development platform. However, most PROTACs have been generated empirically because many determinants of PROTAC specificity and activity remain elusive. Through computational modelling and mutagenesis studies, we found that lysine accessibility for ubiquitination by the VHL E3 ligase plays an important role in determining the degradability of BCL-XL and BCL-2 by DT2216, a VHL-recruiting BCL-XL-specific PROTAC. Based on this information, we rationally designed and generated a BCL-XL and BCL-2 dual degrader, 753b, that can potently degrade both BCL-XL and BCL-2. Importantly, 753b exhibits an improved antileukemic activity compared to DT2216.

While the PROTAC approach to targeted protein degradation greatly benefits from rational design, the discovery of molecular glue degraders currently relies mostly on screening strategies. This paper will discuss the design of a cereblon-focused molecular glue library, and its screening in multiple assay modalities, including high-throughput proteomics. Discovery and characterization of monofunctional degraders of non-canonical cereblon neosubstrates will also be disclosed.

SyntheX created intracellular selection-based drug discovery platforms to identify protein interaction modulators. The ToRNeDO platform can empirically discover molecular glues that can achieve productive protein degradation of a prespecified neosubstrate using a particular E3 ubiquitin ligase. Using genetically engineered circuits, the platforms rely on intracellular drug selection, bypassing bottlenecks of in vitro and in sillico screening approaches. This presents a novel approach to discover functional molecular glues from a first pass screen.

We identified a range of cooperative, noncooperative, and uncooperative compounds in a single DNA-encoded library screen with bromodomain-containing protein (BRD)9 and the VHL–elongin C–elongin B (VCB) complex. Our most cooperative hit compound, 13-7, exhibits micromolar binding affinity to BRD9 but nanomolar affinity for the ternary complex with BRD9 and VCB, with cooperativity comparable to classical molecular glues.

Parkin ligase plays a critical role in mitophagy and mitobiogenesis. Mutations in parkin ligase lead to early onset of Parkinson’s disease. The dysfunction of parkin ligase is also attributed to late onset of PD. Progenra has discovered molecular glues that bind to parkin, activate parkin function in vitro, and restore mitochondrial damage by inducing mitophagy in neuronal cells. Role of parkin in PD, muscle function, and dementia will be described.

Targeted protein degradation technologies including the degradation tag (dTAG) system are powerful approaches to rapidly control protein abundance. This talk will describe our recent advances with the dTAG technology platform and our development of small molecule degraders with applications in refractory cancers.

BPTF is an essential member of the nucleosome remodeling factor, NURF, and has increasingly become identified as a pro-tumorigenic factor, prompting investigations into cancer-associated mechanisms involving BPTF, including MYC and MYCN regulation. Our lab has developed the first inhibitors of the BPTF bromodomain and PHD. Building on these results I will present our efforts at developing the first BPTF degraders to study the role of this protein in pediatric cancers.

Targeted protein degradation is an emerging modality that is increasingly used to tackle challenging drug targets. In this talk, I will present the targeted proteomics platforms we have developed and their impacts on mechanistic understanding and profiling of protein degraders. I will also share a unique protein degradation mechanism that we recently discovered for degraders of an epigenetic target.

We have developed novel TR-FRET-based high-throughput assay approaches based on our CoraFluor TR-FRET technology to facilitate the characterization of PROTACs and molecular glue degraders, including (a) the facile measurements of endogenous protein levels, (b) the kinetic and thermodynamic measurement of ligand binding affinities with endogenous and recombinant proteins, and (c) the quantitative determination of ternary complex cooperativity.

The diverse possibilities associated with PROTAC design and discovery supports strategic approaches built around synthetic novelty and efficiency. We are pursuing solid phase methods as a means to efficiently cover degrader chemical space, and applying it to the opportunities in anti-viral PROTAC discovery.