A New Proteomics-Based Tool to Advance Targeted Protein Degradation Precision Medicine

Targeted protein degradation (TPD) has quickly become one of the most promising emerging therapeutic modalities, in large part for its ability to address targets outside the reach of conventional approaches – targets long considered undruggable. TPD works by harnessing the body’s innate protein recycling machinery to target and eradicate disease-causing proteins.

However, some of these proteins have remained undruggable due to undesirable side effects in healthy tissues, which limit their clinical application. TPD is uniquely positioned to develop safer therapeutics for these clinically validated targets through the use of tissue restricted E3 ligases (enzymes which tag these disease-causing proteins for recycling). Tissue restricted degradation overcomes the hurdle by eliminating unwanted toxicity, thereby enhancing the therapeutic window. ?Kymera is taking a unique approach towards accessing undruggable targets by utilizing our proprietary E3 Ligase Whole Body Atlas.

To systematically advance our E3 toolbox for this approach, we needed to expand our understanding of known and novel E3 ligases, and especially their expression profiles and localization. The human genome encodes at least 600 E3 ligases with diverse tissue expression patterns. To date, however, only a handful of well-established liganded E3 ligases have been identified, and these are for the most part widely expressed in the human body.

?At Kymera, we have developed an unbiased quantitative proteomics-based approach, building novel algorithms to rationally design next generation protein degrader medicines using our proprietary platform – the engine driving Kymera’s drug discovery efforts – to provide the tools and insights needed for success. One facet of the platform – known as the E3 Ligase Whole Body Atlas (or E3 Atlas) – is focused on characterizing the expression profiles in healthy and disease tissues of the almost 600 remaining, unliganded E3 ligases to identify those with differential expression profiles that could be exploited to generate protein degraders with tissue restricted or selective degradation profiles. Importantly, unlike antibody or transcript-based approaches, our workflows provide a direct measure of absolute abundances of E3 ligases unlocking not only relative expression patterns across whole body, but also cellular stoichiometry with target proteins. We do leverage publicly available RNA and antibody-based resources for cross referencing tissue expression profiles, especially to gain deeper patterns at the cell type resolution.

?The E3 Ligase Whole-Body Atlas builds on foundational proteomics work conducted in the lab of Professor Matthias Mann, a recognized leader in mass spectrometry-based proteomics, ?at the Max Planck Institute, during my days as a project leader in his group. My team at Kymera and I have leveraged and further advanced these analytical and computational methods to build the E3 Ligase Whole Body Atlas, which has been instrumental in advancing Kymera’s drug discovery platform.

The scope of the E3 Atlas illuminates a clear need to adopt a scalable and rapid workflow that would allow us to reliably create deep, precise and accurate global expression maps for all human E3 ligases. We collaborated with Professor Juergen Cox, a leading expert in Computational Proteomics at the Max Planck Institute, to develop a novel algorithm, called MaxQuantAtlas, to build large scale human protein concentration map in health and disease.

We shared our exciting findings, built upon our novel algorithm, MaxQuantAtlas, for the first time this week at the American Society for Biochemistry and Molecular Biology (ASBMB) meeting. Results reveal that the algorithm can sift through very heterogenous, quantitative proteomics data in a reliable and scalable manner, which has not been possible with other methods developed to date. It successfully captured the underlying biology of more than 4,000 proteomes at high resolution, scale, budget, and speed compared to conventional approaches. We also developed new quality control processes and parameters that help us make more informed decisions, as insights gleaned inform our drug development pipeline. MaxQuantAtlas enabled assembly of a first-in-class human E3 Ligase Whole Body Atlas over cell lines, primary cells, organoids, healthy and disease tissues.

The TPD field today leverages very few E3 ligases that are ubiquitously expressed, which leaves a huge opportunity to identify and explore a wealth of restrictive E3 ligases that are tissue-specific in their expression. Our proprietary E3 Ligase Whole Body Atlas allows us to learn critical lessons as we mine for viable E3 ligase candidates that exhibit the “sweet spot” of demonstrating clinical benefit with higher therapeutic benefit across as many tissues as possible. Kymera is actively building a portfolio of potent and safe protein degraders with this desired balance top of mind. For example, there is a clinically validated oncology target which has dose-limiting toxicity driven by on-target pharmacology in a type of blood cell. Through our work with the E3 Ligase Whole Body Atlas, we have characterized an E3 ligase?that is expressed broadly in all but that one blood cell type, and we have been able to create a degrader that spares this blood cell while killing the targeted cancer cells in preclinical studies. This work represents our first in vivo proof of concept with a tissue restricted E3 ligase, leading to tissue sparing biology.

Since its inception, Kymera has focused on the discovery of transformative therapeutics while continuing to make strategic investments that will enable us to advance TPD science – a mindset that has enabled us to build a comprehensive platform that holistically supports our rational approach to drug development. We are harnessing the power of quantitative proteomics by developing groundbreaking new computational proteomics solutions like MaxQuantAtlas, applying machine learning in mass spectrometry to generate accurate expression profiles, and answering more sophisticated questions. This combined approach has collectively led us to real insights about E3 ligase biology as well as how to harness it for a new class of drug targets – enabling us to expand the druggable proteome accessing potentially all target classes in human cells.?