An author’s perspective: Shuanglin Qin on advancing oligonucleotide-based PROTACs for undruggable therapeutic targets

Author: Shuanglin Qin, Professor and Doctoral Supervisor, Hunan University of Chinese Medicine (Changsha, China)

Shuanglin Qin is a Professor and Doctoral Supervisor, currently serving as Executive Director of the Center for Precision Medicine in Traditional Chinese Medicine at Hunan University of Chinese Medicine. He has received the Hunan Provincial Distinguished Young Scholars Fund and was selected for the “Chutian Scholars Program” in Hubei province. His research focuses on identifying active ingredients in traditional Chinese medicine and natural products, studying their molecular targets, and improving their potential as drugs. He was the first to introduce the concept of the PROTAC probe technique for identifying key pharmacological targets and has successfully applied it to discover key targets of several anti-cancer compounds. In 2023, he was awarded the Best Researcher Award by the International Research Awards on Oncology and Cancer Research. In addition, he has published more than 30 papers as first or corresponding author (including co-authorship) in leading journals such as Organic Letters, Organic Chemistry Frontiers, and the European Journal of Medicinal Chemistry. Professor Shuanglin Qin has also led several research projects funded by the National Natural Science Foundation of China and the China Postdoctoral Science Foundation (both Beijing, China). In addition, he serves on the editorial board of Life Research and is a youth editorial board member for Traditional Medicine Research and Medical Data Mining. He is also a reviewer for over ten SCI journals, including the International Journal of Biological Macromolecules, European Journal of Medicinal Chemistry, and Digital Discovery.

1. Please could you provide a brief summary of your paper?

Undruggable targets account for approximately 85% of human disease-related targets and represent a therapeutic category that is challenging to address with traditional methods despite their significant clinical relevance. These targets typically feature planar functional interfaces and lack efficient ligand-binding pockets, making conventional pharmaceutical approaches ineffective. However, the emergence of oligonucleotide-based proteolysis-targeting chimeras (PROTACs) has revitalized therapeutic optimism by facilitating proteasome-dependent targeted degradation of previously undruggable proteins. These PROTACs specifically target transcription factors (TFs) and RNA-binding proteins, presenting novel therapeutic strategies for diseases associated with these elusive targets.

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2. What was the initial inspiration or problem that sparked the idea for this paper?

During our systematic review and analysis of PROTAC technology, we became particularly intrigued by the unique capabilities of oligonucleotide-based PROTACs in targeting previously undruggable proteins. Equipped with programmable oligonucleotide ligands, these PROTACs can specifically bind DNA-binding domains of TFs or RNA-binding domains of RNA-binding proteins, facilitating targeted protein degradation. For example, oligonucleotide-based PROTACs, such as TF-PROTACs, have already successfully degraded clinically relevant proteins including p65 and E2F1.

3. Delivery and stability are key hurdles for oligonucleotide therapeutics. What are the most promising solutions you see emerging for these issues?

Although oligonucleotide therapeutics possess substantial potential in disease treatment, addressing their delivery and stability remains essential. Currently, promising solutions include chemical modifications (e.g., phosphodiester bonds, 2′-O-methyl modifications, base modifications), nanocarrier systems (lipid nanoparticles, polymer nanoparticles, inorganic nanoparticles), ligand conjugation strategies (receptor-targeting ligands, cell-penetrating peptides), exosome-based delivery platforms, and emerging technologies such as DNA nanotechnology and the CRISPR-Cas9 system. These approaches enhance oligonucleotide stability, nuclease resistance, binding affinity, cellular uptake, and targeted delivery efficacy.

4. Specificity is often a concern with targeted degradation. How do these hybrid PROTACs mitigate off-target effects?

To mitigate off-target risks associated with oligonucleotide-based PROTACs, meticulous design of oligonucleotide sequences serving as ligands for proteins of interest and E3 ligases is crucial. Bioinformatic databases, such as the Eukaryotic Promoter Database, facilitate the screening and optimization of specific oligonucleotide sequences, ensuring precise ligand selection for PROTAC synthesis. Furthermore, selecting appropriate E3 ubiquitin ligases, considering their distinct tissue and cell-type-specific expression profiles, allows targeted degradation of proteins within specific cellular contexts. In addition, employing optimized drug delivery systems further reduces off-target interactions. For instance, researchers have recently developed a hydrophobic cell penetrating peptide (CPP) and mixed duplex oligonucleotide (HDO) conjugate PROTAC, known as CPP/HDO-PROTAC. This innovation remarkably enhances intracellular delivery and degradation efficacy.

5. How does the mechanism of action of these oligonucleotide-based PROTACs differ from traditional small-molecule PROTACs?

Traditional small-molecule PROTACs primarily rely on small molecules as ligands, which interact directly with active ligand-binding pockets of target proteins, leading to their proteasomal degradation. In contrast, oligonucleotide-based PROTACs utilize oligonucleotide sequences as ligands, capable of specifically recognizing and binding DNA- or RNA-binding proteins, which frequently lack suitable small-molecule binding pockets. Thus, oligonucleotide-based PROTACs uniquely enable targeted degradation of these otherwise undruggable transcription factors and RNA-binding proteins.

6. What are the main barriers that still stand between these technologies and clinical translation? How could these be overcome?

Beyond previously mentioned challenges concerning delivery systems, stability and off-target effects, clinical translation of oligonucleotide-based PROTACs faces additional hurdles, notably the hook effect and immunogenicity. To address these, drug structures and dosing regimens can be optimized by carefully refining linker designs to enhance metabolic stability and minimize hook effects. Additionally, comprehensive assessment of immunogenicity, including thorough evaluation of immune responses during preclinical stages, is critical. Overcoming these barriers could accelerate the clinical advancement of oligonucleotide-based PROTAC therapies.

7. If resources were no limitation, what would your dream experiment or next big project in this field look like?

If resources were unlimited, my ideal experiment or next major research project would involve several key aspects:

• Conducting large-scale, high-throughput screening to evaluate combinations of PROTACs with diverse oligonucleotide sequences and E3 ligase ligands for undruggable targets.
• Integrating multi-omics technologies like proteomics, transcriptomics and metabolomics to study mechanisms aiding in PROTAC optimization.
• Developing innovative, targeted delivery systems for oligonucleotide-based PROTACs to enhance therapeutic efficacy and reduce toxicity.
• Establishing a comprehensive program to explore the synergistic potential of combining oligonucleotide-based PROTACs with other therapies.
• Analyzing clinical samples to formulate personalized treatment plans, leveraging molecular biology and bioinformatics to understand individual variations in undruggable targets and customize PROTAC-based treatments for better clinical outcomes.

Disclaimer: the opinions expressed are solely those of the author and do not express the views or opinions of Bioanalysis Zone or Taylor & Francis Group.