Proteins are essential components of living matter – they function as building blocks for cells and tissues, as well as participate in signaling and practically all biochemical activities. However, each protein operates correctly only for a limited amount of time and is eliminated by molecular machinery after it has reached its “functional shelflife”. To maintain a healthy and functional proteome, cells tightly control protein turnover processes, ensuring that misfolded, damaged, and old proteins exit the game in a timely manner. This sophisticated mechanism of degradation was recently hijacked by the drug discovery industry to develop new small molecule therapies — protein degraders.
Image credit:Dilok Klaisataporn, iStock.
What is protein degradation?
According to Nello Mainolfi, CEO of Kymera Therapeutics (NASDAQ: KYMR), practically every big pharma player and medium-sized biotech business today has internal R&D research or external collaborations in the field of protein degraders. The boom sparked by these small molecule therapies is due to a number of causes, which we will cover in this article, together with notable companies in the field, and three case studies revealing innovative strategies to go about designing targeted protein degraders.
Small molecule inhibitors (SMIs), one of the most commonly used methods of treating illnesses, have essential limitations. SMIs can currently reach protein targets of only around 20% of the proteome. According to the medical journal EBioMedicine, over 75% of known proteins lack active sites for SMIs binding, which means that traditional therapeutics can't inhibit their function. To overcome the limitations, researchers took a fresh approach to small molecules, turning an old tool into a novel therapy.
The idea began to take shape in the 1990s, when Proteonix, a biotech company, submitted a patent for a bifunctional molecule that targets the ubiquitin-proteasome system (UPS). Despite the fact that Proteonix never developed a medication based on the patent, it kicked off two decades of active research in the field. The first Proteolysis targeting chimera (PROTAC) was introduced in 2001, and it consisted of two ligands connected by a flexible linker. The basic chemical architecture of modern PROTACs is the same: one ligand targets the E3 enzyme, which is a component that sends outdated proteins to the proteasome, and another ligand targets a protein of interest (POI) that has to be degraded. A PROTAC binds both E3 and POI, bringing them closer to form an induced proximity complex. In some cases, when the proteins align appropriately, the POI gets ubiquitinated, which marks it for degradation by the proteasome.
Advantageous therapeutic modality
PROTACs have an advantage over conventional small molecule inhibitors because of their unique mechanism of action. To maximize the therapeutic potential of SMIs, high and frequent doses are usually needed because one needs a stoichiometric ratio of the SMI and POI (i.e. occupancy-based pharmacology). However, one PROTAC molecule can trigger the breakdown of several POI molecules through the catalytic mechanism, thus PROTACs require substantially lower concentrations in the cell to achieve efficacy. This phenomenon has the potential benefit of lowering a drug's toxicity and improving its side effect profile. As such, the factor that defines the efficacy of a PROTAC is not the affinity but the kinetics of binding – a measure of how rapidly a PROTAC can bring both targets together to start the process. As a result, chimeras can function by binding to every nook or cranny on a protein, possibly extending the pool of druggable target options.
The race for better degraders
One of the first companies that started commercial development of PROTAC therapeutics is Arvinas (NASDAQ: ARVN). Dr. Craig Crews, a co-founder of the company and a scientist from Yale University, was the one who discovered PROTAC technology in the early 2000s. Almost two decades later, in 2019, Arvinas was also the first to announce that its protein degrader candidates got into clinical trials. Today, the company has a strong portfolio, with two medications, ARV-110 and ARV-471, in Phase 2 clinical trials. Both drugs address solid tumors, ARV-110 acts as a ligand for the Androgen Receptor (AR) in prostate cancer, and ARV-471 targets Estrogen Receptor (ER) in breast cancer. In 2018, the company priced a $120 million IPO. It has a number of notable collaborations, including Bayer, Certara and others.
Another known player in the protein degradation space, Kymera Therapeutics (NASDAQ: KYMR), which was founded in 2015. The company has programs that target IRAK4, IRAKIMiD, STAT3 and MDM2, each of which center on a critical signaling node within the IL-1R/TLR, JAK/STAT or p53 pathways.The most advanced program is the IRAK4 degrader, KT-474 which is in Phase I clinical trials for the treatment of immunology-inflammation diseases such as hidradenitis suppurativa and atopic dermatitis. The IRAKIMiD degrader, KT-413 is aiming to treat MYD88-mutated diffuse large B cell lymphoma. Kymera is also developing selective STAT3 degraders for the treatment of hematological malignancies and solid tumors, as well as autoimmune diseases and fibrosis. KT-333 is a first-in-class STAT3 protein degrader currently in Phase I clinical trials and was granted orphan drug designation for the treatment of Peripheral T-cell lymphoma (PTCL) by the U.S Food and Drug Administration (FDA). Finally, their MDM2 degrader program is aiming to treat hematological malignancies and solid tumors. KT-253, a highly potent MDM2 degrader, unlike small molecule inhibitors, has the ability to suppress the MDM2 feedback loop and can rapidly induce apoptosis with brief exposures.
Kymera Therapeutics debuted on IPO in 2020, raising more than $170 million. The company has a number of R&D collaborations, with a notable $150 million Sanofi deal in 2020, promising to bring additional $2 billion or more, should things work out as planned.
Another company in the protein degradation space is C4 Therapeutics, which focuses not only on target discovery and PROTAC development but also on potential protein degrader optimization strategies. C4’s small molecule degrader CFT7455, a treatment designed to target DNA-binding protein IKZF1/3 in multiple myeloma patients, received an orphan drug designation from the FDA in August 2021. CFT7455 Phase 1/2 Trial in Multiple Myeloma and Non-Hodgkin’s Lymphomas was Initiated in June 2021, with top-line clinical data results to be expected this later year. The biotech went on IPO in 2020, raising more than $200 million.
Roivant Discovery is the drug discovery engine for Roivant Sciences (NASDAQ: ROIV). The company is approaching discovery and design of novel small molecules and protein degraders using its QUAISAR computational platform, which combines physics-based simulations and machine learning to address biologically and genetically validated, but previously intractable protein targets. The company has an impressive technological stack, comprising quantum mechanics, thermodynamics, molecular simulation, artificial intelligence, and supercomputing infrastructure.
Roivant Sciences has a diversified business strategy and more than $2 billion in total funding via IPO and post-IPO rounds of financing.
Cedilla Therapeutics, located in Cambridge, is working on a new way to target protein degradation. Instead of bringing UPS components to a protein of interest, it looks for unrecognized allosteric binding sites for ligands that can destabilize protein structure. Destabilized proteins are degraded by inner cell mechanisms and no longer function in a cell.
The nature of the ubiquitin degradation process functions only inside cells and not in the intracellular matrix –is a restriction that PROTACs have yet to overcome. As a result, PROTAC molecules are unable to reach targets that are outside of cells. However, lysosome-targeting chimeras, or LYTACs, are a new option for targeted protein breakdown. PROTACs and LYTACs have similar structures and modes of action, however, the latter connect target proteins to the transmembrane receptor CI-M6PR at the cell surface. The creation of a trimeric complex between a POI, a receptor, and a LYTAC causes the protein to be degraded by protease enzymes in the lysosome.
Cedilla raised a total of $139 million from a group of investors, including Casdin Capital, Boxer Capital, RA Capital Management and others.
Another player in the LYTAC space is San Francisco-based Lycia Therapeutics, which is focusing on the applications of lysosomal targeting chimeras in three main areas: hardly-druggable membrane or circulating proteins, diseases that are driven by protein aggregation and diseases in which autoantibodies play a role. In 2021, Eli Lilly tapped Lycia’s LYTAC platform to develop therapeutics for immunology and pain in a $35 million pact, with up to $1.6 billion in promised biobucks.
Lycia Therapeutics raised a total of $120 million from a number of investors, including Eli Lilly. RTW Investments LLC, Versant Ventures, and others.
Finally, there is a new player rapidly building its presence in the protein degradation space -- Celeris Therapeutics, a biotech company founded in 2021 in Gras, Austria, and headquartered in Silicon Valley, California. In February 2022, Celeris Therapeutics entered a research collaboration with Merck KGaA, enabling the latter to use Celeris’s graph-based artificial intelligence (AI) platform for discovering and designing novel small molecule binders and bifunctional degraders. Just two months later, Celeris Tx also partnered with Boehringer Ingelheim to allow the pharma giant use AI-platform Celeris One to generate novel proximity-inducing compounds to degrade pathogenic proteins agreed upon with Boehringer.
The company has received $6 million to date from a number of venture capitalists, including R42, APEX Ventures, Pace Ventures Enigma, i&i biotech and longevitytech.fund.
Chemical matter matters in TPD space
Targeted protein degraders, one of the most intriguing therapeutic areas of modern day, is in dire need of new and reliable chemistry. Booming biological assays in this field of drug discovery require production of hundreds and thousands of new functional intermediates and bifunctional molecules. The time needed for production of new derivatives is crucial for any new project in this therapeutic area.
To facilitate further work on bifunctional molecules, Enamine scientists constantly update the company toolbox with newly synthesized intermediates and functionalized ligands. The actively developing area of Molecular Glues keeps the Enamine team highly motivated to synthesize new Building Blocks and intermediates.
Enamine offers distinct tools that you can mix-up to design molecules of your special interest. The following options are available for synthesis of new molecules or immediate delivery to your research site:
- Cereblon ligands and functionalized intermediates
- VHL ligands and ligands with linkers
- Active degraders & ubiquitin E3 ligases inhibitors
- Orthogonal PEG-linkers and their carba-analogs
- Halo- and Photo- Capture Tags
- SPLAMs (DCAF focused sulfonamides)
- Click Chemistry Intermediates
- Molecular Glues
Review Enamine Protein Degradation Toolbox for more details and examples of chemical structures.
Bright future ahead for targeted protein degradation
The continuation of intense scientific research on protein degraders broadens the scope of this modality's future prospects. Third-generation controllable PROTACs that can be regulated by visual and UV light are being developed, new targets appear – including RNA-binding proteins and DNA-binding proteins. While more than 600 E3 ligases have been discovered in human cells, only a few have been verified for PROTAC use. For instance, degraders with ligands for cancer-and tissue-specific E3 ligases will improve the selectivity of potential therapeutic candidates while lowering toxicity and side effects.
However, there is still much work to be done in this field, as some protein degrader characteristics have to be improved. Chimeras are larger than traditional small-molecule pharmaceuticals, which has an impact on cell permeability. This could pose difficulties in the case of oral delivery, as well as hamper migration across biological boundaries to treat central nervous system illnesses.