PROTAC Targeting c-Myc

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As a leading CRO, BOC Sciences provides technical support for PROTAC research targeting various targets, such as kinases. Our drug discovery platform includes small molecule platform, cell technology platform, multi-omics technologies, as well as research animal and model platform, enabling us to fully support the c-Myc PROTAC development.

What is c-Myc?

c-Myc is a transcription factor that regulates the pre-oncogenic protein network and is highly expressed in over 50% of human cancers. It forms a heterodimeric complex c-Myc/Max with MAX, collectively recognizing DNA enhancer elements (E-box, CAC[G/A]TG) to regulate the transcription of downstream genes involved in important cellular processes such as proliferation, apoptosis, and angiogenesis. The c-Myc is a potential therapeutic target for triple-negative breast cancer (TNBC). However, c-Myc lacks a stable conformation and suitable small molecule binding sites. Its action is mediated through protein-protein interactions, making it a challenging druggable target. Directly targeting c-Myc is difficult, so in addition to directly targeting the Myc pathway by inhibiting the Myc-Max interaction and the interaction of the Myc-Max complex with DNA, indirectly regulating Myc downstream pathways is also an important approach for treating Myc-related diseases.

The development of direct and indirect c-Myc inhibitors is in the early stages. The discovered small molecule inhibitors have poor drug-like properties, and there is an urgent need to discover drugs with better pharmacological properties. Targeting Myc, a undruggable target, seems to be a plausible approach based on the development of targeted protein degraders using weak-binding inhibitors.

c-Myc PROTAC and Inhibitor

Proteolysis targeting chimeras (PROTAC) use the ubiquitin-proteasome system (UPS) to maintain cellular protein homeostasis. PROTAC catalytically induces the ubiquitination of the target and marks it with a poly-Ub chain, leading to recognition and degradation by the 26S proteasome. Therefore, a single dose of PROTAC can degrade multiple equivalents of the protein of interest (POI), making the dose, dosing frequency, and toxicity lower than small molecule inhibitors. As c-Myc lacks stable or druggable sites, PROTACs can use low-affinity small molecule ligands or oligonucleotides as protein ligands to disrupt the dependence on druggable pockets. Targeted therapies, such as small molecule inhibitors, may induce compensatory protein expression after administration, reducing efficacy and increasing side effects. PROTACs can effectively downregulate the level of the POI by accelerating UPS-mediated degradation, preventing compensatory protein expression.

c-Myc PROTAC Development

PROTAC molecules consist of three covalently linked parts: a ligand binding to the POI, a ligand recognizing the E3 ligase, and a connecting fragment linking these two ligands. PROTAC can recruit both E3 ligase and POI, forming an E3-PROTAC-POI ternary complex. c-Myc itself is a transcription factor suitable for nucleic acid aptamer binding. Developing nucleic acid aptamers that bind to c-Myc, combined with PROTAC technology, has great potential for targeted degradation of c-Myc protein and cancer treatment.

Fig. 1 Aptamer-based PROTAC targeting c-Myc/Max. (Li, 2023)

BOC Sciences provides comprehensive customization services for c-Myc PROTAC development.

• c-Myc PROTAC Design: Considering c-Myc as a transcription factor, oligonucleotides can be chosen as the target protein targeting ligands. Oligonucleotides can be conjugated to the E3 ligand through a linker to form a nucleic acid-based PROTAC.
• Nucleic Acid Aptamer Screening: 1) Establish a DNA template library containing random sequences of multiple nucleotides; 2) Using nucleoside triphosphates (NTPs) as substrates, generate the corresponding oligonucleotide library through DNA primer extension reactions; 3) Incubate the oligonucleotide sequences from the library with c-Myc/Max complex in vitro, isolate ligands, and use them as templates for reverse transcription to obtain the corresponding DNA templates for the next round of screening; 4) Through multiple rounds of screening and amplification, identify potential ligand sequences.
• c-Myc PROTAC Synthesis: Couple oligonucleotides with small molecule ligands to synthesize complex molecules, optimize the linker, and develop new conjugation methods.
• c-Myc PROTAC Validation: Analyze the targeting specificity, affinity, and effectiveness of PROTAC in vitro, such as validating the activity of PROTAC in degrading c-Myc through Western blot experiments. Furthermore, in mouse tumor models, verify the inhibitory effect of PROTAC on tumor growth.

Progress in c-Myc PROTAC Development

c-Myc is a potentially effective therapeutic target for various tumors, including TNBC. Some small molecules targeting MYC have been developed and entered clinical stages. For example, the cell-penetrating peptide OMO-103 has been proven safe and potentially effective in preliminary human trials. The small molecule inhibitor MYCi975 has been found to disrupt the Myc-Max dimer, promote Myc degradation, and kill cancer cells. PROTACs that bind to and degrade Myc are also under development. A PROTAC based on threose nucleic acid (TNA) and DNA has been reported, using the TNA aptamer and pomalidomide to construct a PROTAC that mediates intracellular c-Myc/Max degradation through the endogenous proteasome pathway. The combination of PROTAC and palbociclib showed enhanced cytotoxicity in human and mouse TNBC cell lines, providing a promising model for tumor research and therapeutic intervention based on targeted degraders. In addition to PROTACs, several new drug development companies are strategically positioning themselves to selectively target c-Myc with molecular glues.

Reference

1. Li, X., et al., c-Myc-Targeting PROTAC Based on a TNA-DNA Bivalent Binder for Combination Therapy of Triple-Negative Breast Cancer, J. Am. Chem. Soc., 2023, 145, 16, 9334-9342.

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