So far, more than 10 nucleic acid drugs have been approved for marketing worldwide, and many nucleic acid drugs are in the stage of clinical trials. Nucleic acid drugs are expected to become the third type of drugs after small molecule drugs and antibody drugs.

1. Biopharma PEG https://www.biochempeg.com
Several Types of PROTACs Based On Nucleic
Acids
In recent years, nucleic acid drugs have been developing vigorously with increasing
market demand and rapid marketing approval, covering many fields such as
cardiovascular and metabolic diseases, liver diseases and tumors. So far, more than 10
nucleic acid drugs have been approved for marketing worldwide, and many nucleic acid
drugs are in the stage of clinical trials. Nucleic acid drugs are expected to become the
third type of drugs after small molecule drugs and antibody drugs (Figure 1).
Figure 1. Marketed nucleic acid drugs (data source: pharmSnap Global Competitive
Intelligence Database for New Drugs)
A growing number of approved nucleic acid therapeutics demonstrate the potential to
treat disease by targeting disease-causing genes in vivo. Usually, conventional
treatments only produce short-term therapeutic effects because they target proteins rather
than the root cause of disease, while nucleic acid drugs directly act on disease-causing
target genes or target mRNAs, and play a role in treating diseases at the gene level.

2. Biopharma PEG https://www.biochempeg.com
Nucleic acid drugs include ASO, siRNA, Aptamer, miRNA, mRNA, saRNA, sgRNA, U1
snRNA, etc. Nucleic acid drugs have the advantages of high therapeutic efficiency, low
toxicity, strong specificity and wide application fields, showing their important value in
medicine, biological science and other fields.
PROTACs (proteolysis-targeting chimeras) is a drug development technology that
utilizes the ubiquitin-proteasome system (UPS) to degrade target proteins.
Structurally, PROTACs consist of three parts: an E3 ubiquitin ligase ligand and a target
protein ligand, and two active ligands are linked together by a specially designed "Linker"
structure to form a ternary complex. The target protein ligand of PROTAC binds to the
target protein, and the E3 ubiquitin ligase ligand binds to the substrate-binding region of
the intracellular E3 ubiquitin ligase, thereby "pulling" the target protein to the E3 ubiquitin
ligase by ubiquitinating the target protein, enabling the UPS system to degrade the target
protein (Figure 2).
​
Figure 2. Protein degradation mechanism mediated by PROTACs

3. Biopharma PEG https://www.biochempeg.com
Over the past 20 years, researchers have designed various forms of PROTACs based on
peptides and small molecules. However, peptide-based PROTACs have problems such
as low activity and immunogenicity, which greatly limit their clinical medical applications.
Compared with polypeptide PROTACs, small-molecule PROTACs are smaller, more
easily absorbed by the body, and have better druggability, so small-molecule PROTACs
are still the mainstream. With the development and progress of science and technology,
some new types of PROTACs continue to emerge, and nucleic acid-based PROTACs
emerge as the times require.
RNA-PROTACs
Functional defects in RNA binding proteins (RBPs) are at the root of many diseases, and
targeting RBPs with conventional drugs has proved difficult. RBPs bind to RNA in a
dynamic, coordinated, and sequence-selective manner to form ribonucleoprotein (RNP)
complexes that play a key role in RNA dependence. Certain diseases are caused by
genetic changes in RBP that affect their binding to RNA. In 2021, Jonathan Hall's
research group first proposed the design concept of RNA-based PROTACs, and the
author successfully constructed RNA-PROTACs targeting RBPs (RNA binding proteins).
Using small RNA mimics as targeting groups, they can specifically bind to RBPs RNA
binding sites. PROTACs ubiquitinated RBPs and then degraded them by ubiquitin
proteasome system. The authors performed a proof-of-concept demonstration of
degradation of two RBPs (stem cell factor LIN28 and splicing factor RBFOX1) and
demonstrated their use in cancer cell lines.
Oligonucleotide PROTACs
Transcription factors (TFs) represent an important class of therapeutic targets for the
treatment of diseases including cancer. Since TFS lack the active or allosteric sites
commonly found in kinases or other enzymes, it is difficult for traditional small-molecule

4. Biopharma PEG https://www.biochempeg.com
inhibitors to bind to them. Therefore, transcription factors were once considered as
"undruggable" targets, presenting an unsurmountable technical bottleneck. Professor
Wenyi Wei, Harvard University, and Professor Jian Jin, Icahn School of Medicine, Mount
Sinai, reported an oligonucleotide chain-based "TF-PROTAC", which is composed of
DNA oligonucleotides and E3 ligand linked by click reaction (Figure 3), and can selectively
degradate pathogenic TFs. The selectivity of TF-PROTAC depends on the DNA
oligonucleotides used.
Figure 3. Design strategy of TF-PROTAC
The authors successfully developed two series of VHL-based TF-PROTACs:
NF-κB-PROTAC (dNF-κB) and E2F-PROTAC (dE2F), which efficiently degrade
endogenous p65 and E2F1 proteins in cells, respectively, and showed excellent anti-cell
proliferation effect (Figure 4).

5. Biopharma PEG https://www.biochempeg.com
Figure 4. TF-PROTACs structure and protein degradation experiments
In 2021, Crews' group also reported oligonucleotide PROTACs targeting transcription
factors (TFs): oligoTRAFTACs (Figure 5). OligoTRAFTACs consist of oligonucleotide
chains that bind to TFs and E3 ubiquitin ligase ligands.
Figure 5. Design ideas of oligoTRAFTACs
Western blot experiments showed that oligoTRAFTACs successfully degraded two
oncogenic transcription factors: c-Myc and brachyury. In addition, the authors found that
oligoTRAFTACs could successfully degrade the brachyury of chordoma cell lines, and
also showed good degradation activity in the subsequent in vivo zebrafish model
experiments (Figure 6).

6. Biopharma PEG https://www.biochempeg.com
Figure 6. Degradation experiments of oligoTRAFTACs in a zebrafish model
PROTACs based on Aptamer
An Aptamer is a sequence of oligonucleotides (DNA or RNA). Oligonucleotide fragments
are usually obtained from nucleic acid libraries using Systematic evolutionof ligands by
exponential enrichment (SELEX) in vitro screening. Nucleic acid adaptors are widely
used because they can combine with a variety of target substances with high specificity
and selectivity. In 2021, Tan Weihong's research group first designed a PROTAC based
on the nucleic acid aptamer AS1411: ZL216 (Figure 7).

7. Biopharma PEG https://www.biochempeg.com
Figure 7. Design and synthesis of ZL216
AS1411 can specifically target nucleolin receptors that are highly expressed in tumor cells,
and the nucleolin receptors are internalized after binding to their ligands. The authors
proved that the PROTAC has high water solubility and serum stability through in vitro
experiments. Furthermore, the authors found that ZL216 promoted the formation of the
nucleolin receptor-ZL216-VHL ternary complex in breast cancer cells and efficiently
induced nucleolin receptor degradation in vitro and in vivo. Subsequent cell proliferation
and migration experiments showed that ZL216 also inhibited the proliferation and
migration of breast cancer cells (Figure 8).
Figure 8. Results of IP experiments, cell proliferation and migration experiments
Aptamer-PROTAC Conjugates (APCs)
PROTAC is a promising targeted protein degradation strategy. As an effective method
for targeted protein degradation, PROTACs significantly outperform traditional
small-molecule drugs in terms of catalytic properties, high selectivity, overcoming drug
resistance, and effective blocking of non-druggable targets. But PROTACs generally have
high molecular weight and high hydrophobicity, and their physicochemical properties

8. Biopharma PEG https://www.biochempeg.com
largely exceed the "rule of five" (RO5). Therefore, the development of conventional
PROTACs into drugs is often limited by their poor cell membrane permeability, poor
pharmacokinetic (PK) properties, and lack of tumor-specific targeting.
To this end, Chunquan Sheng's research group proposed the design concept
of Aptamer-PROTAC Conjugates (APCs). APC is obtained by coupling the PROTAC
targeting BET protein with the Aptamer AS1411 (AS) by a cleavable linker chain ( Figure
9). Among them, the nucleic acid aptamer AS1411 can selectively target the highly
expressed nucleolin receptor on the surface of tumor cells. AS itself has good inhibitory
activity against nucleolin receptor-overexpressing tumors and is currently being evaluated
in a phase II clinical trial. Glutathione is abundant in tumor cells, so the linker chain selects
a disulfide bond that can be cleaved by glutathione (GSH), which can selectively respond
to the tumor microenvironment and release the active BET degrader after cleavage of the
linker chain.

9. Biopharma PEG https://www.biochempeg.com
Figure 9. Design strategy for APC
Compared with unmodified BET PROTAC (PRO), the APC conjugate (APR) showed
improved tumor-targeting ability in a mouse xenograft model of McF-7 cells, thereby
enhancing BET protein degradation in vivo and antitumor potency. Therefore, the APC
strategy provides a new design idea for the development of tumor-specific targeting
PROTACs.

10. Biopharma PEG https://www.biochempeg.com
Figure 10. Protein degradation experiments and in vivo imaging, anti-tumor experiments
The development of Aptamer PROTACs Conjugates (APCs) can be described as
"earth-shaking" since it was proposed. Compared with traditional PROTACs, nucleic
acid-based PROTACs improve the targeting of traditional small molecule PROTACs, and
play an important role in improving water solubility, membrane permeability, and tumor
targeting. Since nucleic acid drugs are easily hydrolyzed by nucleases in vivo, the half-life
is short, which greatly limits their application in biomedicine. Future research directions
should focus on improving the stability of nucleic acid drugs, prolonging half-life,
improving pharmacokinetic properties, and solving nucleic acid drug delivery problems.
As a professional PEG derivatives supplier, Biopharma PEG offers our clients with high
purity PEG linkers for PROTAC development. We have over 3000 high purity PEG linkers
in stock to empower your PEGylation, bioconjugation, crosslinking, ADC drug
development, biolabeling for pharmaceutical and biotech R&D.

11. Biopharma PEG https://www.biochempeg.com
References:
[1]. Non-small molecule PROTACs (NSM-PROTACs): Protein degradation kaleidoscope
[2]. Aptamer-PROTAC Conjugates (APCs) for Tumor-specific Targeting in Breast
Cancer.
[3]. Development of a Novel PROTAC using the Nucleic Acid Aptamer as a Targeting
Ligand for Tumor Selective Degradation of Nucleolin.
[4]. OligoTRAFTACs: A Generalizable Method for Transcription Factor Degradation.
[5]. RNA-PROTACs: Degraders of RNA-Binding Proteins.
[6]. TF-PROTACs Enable Targeted Degradation of Transcription Factors.
Related articles:
[1]. Future Perspective of PROTAC Combined With CRISPR In Anti-ancer Area
[2]. Four Major Trends In The Development of PROTAC
[3]. PROTAC And Other Protein Degradation Technology
[4]. PROTACs VS. Tranditional Small Molecule Inhibitors
[5]. Focus On PROTAC: Summary Of Targets From 2001 To 2019