This presentation will discuss the areas of greatest opportunity for next-generation TPD approaches and how Amphista’s new degrading mechanisms are addressing these. In particular, we will discuss strategies to design orally active bifunctional degraders, as well as other key data from the Amphista Eclipsys platform which enable the rapid generation of potent degraders using new mechanisms and new chemical warheads.

Being a transcription factor, MYC inherently lacks catalytic activity and deep small molecule pockets and instead contains extensive regions of predicted disorder that have evolved to mediate macromolecular interactions. In the recent years, we systematically identified MYC partner proteins by mass spectrometry and analyzed their potential as cancer targets by genetic screens. We have recently developed degrading compounds for the most promising targets and are currently testing them in preclinical cancer models.

Small molecule degraders such as PROTACs (PROtein Targeting Chimeras) have emerged as new promising pharmacological modalities but currently their development is limited by the small number of ligands targeting E3 ligases. We developed a workflow developing PROTACs interacting with new E3 ligases and established assay systems for their validation as highly selective degrader chemical tools.

Several cyclin-dependent kinase inhibitors are successful drugs on the market. However, inhibition of the kinase activity is leading to drug resistance and moreover other scaffolding functions of CDKs cannot be inhibited traditionally, thus providing an escape mechanism. While previous CDK PROTACs focus on CDK 4 and 6 we developed a very potent CDK 4/6/9 triple PROTAC with pM degradation and superior cellular activity. 

This talk will discuss structure-guided and data-driven approaches to the design of PROTACs and molecular glues. Alternative cereblon warheads and their application in the development of JAK- and LCK- PROTACs with in vivo anti-tumor activity in pediatric ALL models will be described. Development of a large Molecular Glue Library and discovery of GSPT and CK1a degraders with in vivo anti-tumor efficacy will also be disclosed.

By employing the AdPROM system, the Sapkota lab has demonstrated that highly selective targeted protein post-translational modifications can be achieved through proximity-induction. This talk will focus on the application of the AdPROM system to uncover KLHDC2 as an efficient new degrader of K-RAS, beta-catenin, FoxP3 and STK33 through proximity-induction. The talk will also introduce the newly developed AdPhosphatase system, through which intracellular phospho-proteins can be targeted for dephosphorylation through proximity-induction to rewire cell signalling.

Histone Deacetylase enzymes (HDACs) are viable drug targets in hematologic cancers and offer promise in neurodegenerative disorders and cardiovascular diseases. Of the eleven zinc-dependent HDAC enzymes, HDAC 1, 2 & 3 are localised in the nucleus and exist in several multiprotein corepressor complexes regulating gene transcription. In this presentation, I will describe our efforts towards the targeted degradation of these enzymes within corepressor complexes using heterobifunctional molecules.

Whilst the degrader modality has great therapeutic promise, ligands have only been developed for E3s with a broad expression/activity profile. We have developed a proteome-scale activity-based profiling platform for HECT/RBR/RCR/RZ and single subunit RING E3 ligases. We demonstrate its potential to access undruggable targets by facilitating the development of tissue-specific degraders.

Chromosomal translocation-encoded proteins are important cancer therapy targets because of tumour-specificity. However, they are among hard-to-drug proteins because they are often transcription factors. Intracellular antibodies are starting points as inhibitors as fusion with E3 ligases creates intracellular antibody biodegraders to eliminate such target proteins in a binary interaction. Biodegraders, and chemical surrogates, will be discussed that target the transcription factor LMO2 originating from the t(11;13) chromosomal translocation in T-ALL.

Classical molecular glue degraders have been identified serendipitously, but rational screening strategies are emerging rapidly. Here, I will highlight the recent advances in molecular glues for targeted protein degradation, discuss the challenges in discovery strategies, and will present several screening workflows to identify novel molecular glues.

The successful development of degraders relies on good characterization and understanding of the mechanism of action and the drug properties that govern pharmacology. This talk explores the properties related to drug metabolism, pharmacokinetics, and pharmacodynamics (DMPK-PD) of degraders. Gathering reliable ADME and PKPD information and insights is crucial to allow the selection of a degrader dose that is both safe and efficacious in patients.

PROTAC is attracting more and more attention since many compounds have reached the clinic over the last few years. While the safety profile of the clinical candidates appears well tolerated, it is still too early to draw a general conclusion on the safety of this new modality. I will discuss ways to evaluate PROTAC safety both in vitro and in vivo, which I hope will be of interest to the people joining this conference.

Extracellular Targeted Protein Degradation is an emerging new modality that allows the removal of soluble and plasma membrane targets using the scavenger asialoglycoprotein receptor (ASGPR) present in high abundance in the liver. We describe the synthesis and characterization of heterobifunctional molecules that drive the clearance and degradation of the disease-causative plasma protein PCSK9 in mice through hijacking of the endogenous endolysosomal pathway. This proof-of-concept study offers the potential for exploring this modality for many additional difficult-to-drug disease targets.

Integral membrane/secreted protein integrity and abundance is overseen by ERAD; a specialised UPS branch that recognises and retrotranslocates misfolded forms across the endoplasmic reticulum’s lipid bilayer, ubiquitylating the polypeptides to target them for degradation. With more than 25 different E3s embedded in the ER membrane, defining the complexes they form and responsibilities they undertake is required to appreciate the ubiquitylation and degradation capacity at this organelle. This talk will cover ER-E3 complexes as novel targets for degraders and glues, pre-emptive degradation of surface and secreted proteins, and strategies to identify small molecules targeting novel ER-E3s.

Although using DNA-encoded libraries (DELs) to find small molecule binders of target proteins is well-established, identifying DEL hits for functions other than binding remains challenging. We have developed a technique where DNA-linked small molecules can be selected based on their ability to catalyze the transfer of ubiquitin to target proteins. Our work provides the framework for applying DEL technology to the de novo discovery of molecular glues.

Targeted protein degradation approaches have so far been limited to eukaryotic systems, due to considerable differences between prokaryotic and eukaryotic protein degradation pathways. In our study, we developed bacterial PROTACs (BacPROTACs), reprogramming a major proteolytic complex of Gram-positives and mycobacteria, ClpCP, towards selected neo-substrates. BacPROTAC technology represents a versatile research tool enabling the inducible degradation of bacterial proteins and paves the way to a novel antibiotic development strategy.

We have seen a recent blast of machine learning algorithms applied to drug design. While these techniques most likely will dominate in long term, are they ready to surpass traditional physics-based molecular modeling (MM)? We advocate that an integration of both techniques is the best option for the coming years, allowing broad applicability and high success rates. Applications and examples of small molecules and TPD will be provided.

UM171 is currently exploited as a supporting molecule for developing cell therapy products but the molecular mechanism remained elusive. We discovered the protein degradation properties of UM171 and identified epigenetic modulator CoREST complex as the primary target. Subsequently we unraveled the critical elements required for substrate recognition by the UM171 modulated Cul3KBTBD4 ubiquitin ligase. Overall, our study provides molecular mechanism for UM171 and point towards new therapeutic applications for UM171.