Oligonucleotide-base PROTAC Technology Development
Oligonucleotide-based proteolysis targeting chimeras (PROTAC) is an innovative drug development strategy. It utilizes the ubiquitin-proteasome system (UPS) or proteases to degrade specific target proteins. Traditional PROTACs are usually small molecules, However, oligonucleotide-based PROTACs use DNA or RNA fragments to target proteins such as transcription factors (TFs) and RNA-binding proteins (RBPs) that would otherwise be difficult to interfere with with small molecule drugs. BOC Sciences offers a comprehensive range of oligonucleotide-based PROTAC development services designed to help customers leverage this emerging technology for breakthrough therapeutic applications.
What is oligonucleotide-based PROTAC?
Oligonucleotide-binding proteins, such as TFs, RBPs and DNA-binding proteins, can induce a variety of diseases and are potential therapeutic targets. However, these proteins are generally considered untargeted because they lack enzyme catalytic sites or ligand-binding pockets. In general, TFs exhibit shallow, flat protein surfaces that do not promote strong intermolecular interactions and have no ligand binding sites. In addition, TF naturally interacts with downstream promoter sequences with dissociation constants in the low nanomolar range. These obstacles mean that small molecule binders do not bind effectively to TF. While antibody drugs can exhibit strong interactions with TF and RBP in the nanomolar range if properly designed, it has long been known that they are not suitable for targeting, mainly because their structures are too large and complex to pass through cell membranes using existing techniques. Therefore, utilizing oligonucleotides is considered a promising solution to target these difficult proteins, as they can be efficiently delivered into cells by means such as transfection or transduction, thus displaying strong intermolecular interactions in the nanomolar range.
Oligonucleotide-based PROTACs consist of oligonucleotide chains (short DNA or RNA sequences) and E3 ubiquitin ligase ligands that target the degradation of TF and other oligonucleotide-binding proteins. Oligonucleotides, as ligands to target proteins, can be designed to specifically recognize and bind unique nucleic acid sequences associated with target proteins.
Using the inherent TF DNA-binding ability, Li et al. developed chimeric oligonucleotides containing TF-specific DNA sequences and E3 ligase recruitment fragments, called transcription factor targeting chimeras (TRAFTACs). TRAFTAC can recruit TF of interest (TOI) and VHL E3 ligases of interest via the intermediate protein dCas9HT7, and induce the degradation of disease-associated TF NF-κB and brachyury in the additional presence of haloPROTAC. Subsequently, Liu et al. reported similar TF-PROTACs that conjugate DNA oligonucleotides to a VHL ligand via an in situ click reaction, which selectively degrades the TF of interest. Two VHL-based TF-PROTAC families, NF-κB-PROTAC and E2F-PROTAC, were developed, which induce cellular endogenous p65 and E2F1 protein degradation, respectively. At the same time, an oligonucleotide-based PROTAC (O'PROTACs) was designed to directly incorporate TF-recognizing double-stranded oligonucleotides into the E3 ligand and induce in vitro degradation of lymphocyte enhancer binding factor 1 (LEF1) and ETS-associated gene (ERG), two transcription factors highly associated with cancer. Recently, the second generation of TRAFTACs (oligoTRAFTACs) was successfully synthesized by directly attaching TF-binding oligonucleotides to the E3 ligand recruiting and demonstrated their ability to induce the degradation of two carcinogenic TFS (c-Myc and brachyury). Taken together, these results suggest that oligonucleotide-based TF-targeting PROTACs provide a generable platform for achieving selective degradation of many TFS and have potential for anticancer drug development that targets most "undruggable" proteins.
Oligonucleotide-based PROTACs targeting TFs. (A) TRAFTAC recruits E3 ligase complex through dCas9-HT7 in the presence of haloPROTAC. (B) TF-PROTAC formed in-situ via a copper-free strain-promoted azide–alkyne cycloaddition (SPAAC) reaction to recruit E3 ligase complex. (C) O'PROTAC or oligoTRAFTAC with E3 ligand and oligonucleotide directly attached. (Li, K., 2022)
Advantages of oligonucleotide-based PROTACs
Since oligonucleotide DNA is a natural ligand for transcription factors, oligonucleotide-based PROTACs are universal and flexible, and can be easily adapted to target other transcription factors by replacing parts of the DNA of chimeric oligonucleotides, paving the way for targeting traditionally untreatable transcription factors.
The natural nature of the oligonucleotide sequence gives oligonucleotide-based PROTACs a high affinity with specific DNA or RNA sequences, which ensures that oligonucleotide-based PROTACs can accurately identify and efficiently degrade the target protein, significantly reducing the occurrence of off-target events, and thereby reducing the risk of potential side effects.
Oligonucleotide-based PROTACs' oligonucleotide composition is like a custom code lock, which can be precisely designed according to the DNA binding characteristics of the target protein. This coding plasticity enables oligonucleotide-based PROTACs to have a wide range of targeting capabilities against a diverse range of protein targets, demonstrating a high degree of adaptability and flexibility in drug design.
In addition, given the stability and tissue permeability of oligonucleotides, and the low immunogenicity and toxicity, the oligonucleotide-based PROTAC platform offers a promising strategy for the clinical development of therapeutic PROTACs for the treatment of various diseases caused by transcription factor dysfunction.
Our oligonucleotide-base PROTAC development services
Custom oligonucleotide synthesis: Using cutting-edge synthesis technology, we can quickly and accurately generate custom oligonucleotides that match the gene sequence of your specified protein. Services cover a wide range of modification and coupling options designed to enhance the stability, affinity and biopotency of oligonucleotides.
Target protein selection and validation: A team of experienced researchers will work closely to help you identify the ideal target for oligonucleotide PROTAC development. A combination of cutting-edge bioinformatics and molecular biology tools to rigorously validate targets to ensure maximum project success.
PROTAC design and optimization: With the help of advanced algorithms and molecular simulation techniques, bifunctional molecules are carefully constructed to ensure efficient binding of oligonucleotides to target E3 ubiquitin ligand. Through multiple rounds of in vivo and in vitro tests, the degradation efficiency and specificity of PROTAC were continuously optimized.
Comprehensive analysis support: A comprehensive analysis platform including mass spectrometry, high performance liquid chromatography (HPLC) and next generation sequencing (NGS) to evaluate the structural integrity and biological activity of synthesized oligonucleotides PROTAC.
Pre-clinical evaluation system: Provides a comprehensive pre-clinical evaluation protocol involving cellular level assays and in vivo model studies to measure the pharmacokinetics, pharmacodynamics and therapeutic potential of PROTAC. The research environment follows strict regulations to ensure the accuracy and reproducibility of the data.
Why choose BOC Sciences?
- Years of experience in oligonucleotide synthesis and TPD research and development.
- Extensive expertise in the development of oligonucleotide-based PROTAC.
- From target protein target identification, oligonucleotide synthesis, PROTAC design to preclinical evaluation, we provide one-stop service.
- Simplified synthesis route of PROTAC molecule with complex structure.
- Artificial intelligence (AI) is used to predict the performance and optimal design of oligonucleotide-based PROTACs.
FAQ
1. What is oligonucleotide-based PROTAC?
Oligonucleotide-based PROTAC is a drug molecule that uses an oligonucleotide (such as a fragment of DNA or RNA) as a ligand to recognize and bind to a target protein, while the other end is linked to a ligand of an E3 ubiquitin ligase via a linker, thereby inducing ubiquitization of the target protein and subsequent proteasome degradation.
2. Why are oligonucleotides selected as part of PROTAC?
Oligonucleotides can recognize specific regions of proteins because of their high specificity, and binding sites can be found even on proteins that lack traditional small molecule drug targets. This is particularly useful for transcription factors and RNA-binding proteins that are difficult to medicate.
3. What are the advantages of oligonucleotide-based PROTACs?
The main advantage of oligonucleotide-based PROTACs is their ability to target "undruggable" proteins that are difficult to reach with traditional small molecules. Their high specificity means fewer off-target effects, while their programmability allows different ligands to be designed for different proteins.
4. How to design oligonucleotide-based PROTACs?
Designing oligonucleotide-based PROTACs involves selecting the appropriate oligonucleotide sequence to ensure specific binding to the target protein, selecting the appropriate E3 ubiquitin ligand, and designing the linkers that connect the two. This usually requires bioinformatics analysis and experimental validation.
5. How can the safety and effectiveness of oligonucleotide-based PROTACs be guaranteed?
Safety and efficacy need to be evaluated in vitro and in vivo, including cytotoxicity, off-target effects, pharmacokinetics and pharmacodynamics studies.
References:
- Li, K., Crews, C. M. PROTACs: past, present and future. Chemical Society Reviews. 2022, 51(12): 5214-5236.
- Shih, P. C., et al. Current status of oligonucleotide-based protein degraders. Pharmaceutics. 2023, 15(3): 765.
* PROTAC® is a registered trademark of Arvinas Operations, Inc., and is used under license.
