An instructive attempt on developing aptamer-constructed PROTAC for breast cancer treatment

Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that consist of a protein of interest (POI) ligand, an E3 ubiquitin ligase (E3) ligand, and an optimized linker to attach both ligands.1Li L. Mi D. Pei H. Duan Q. Wang X. Zhou W. Jin J. Li D. Liu M. Chen Y. In vivo target protein degradation induced by PROTACs based on E3 ligase DCAF15.Signal Transduct. Targeted Ther. 2020; 5: 129https://doi.org/10.1038/s41392-020-00245-0Crossref PubMed Scopus (43) Google Scholar Upon binding to a POI, PROTACs induce proximity of the POI and E3 and then result in the formation of a productive “POI-PROTACs-E3” ternary complex, which facilitates the ubiquitination and subsequent degradation of the POI via the ubiquitin-proteasome system. In the past two decades, PROTACs have advanced dramatically and evolved from peptide-based PROTACs and small-molecule PROTACs to orally efficacious clinical candidates that degrade pathogenic proteins in patients.2Li K. Crews C.M. PROTACs: past, present and future.Chem. Soc. Rev. 2022; 51: 5214-5236https://doi.org/10.1039/d2cs00193dCrossref PubMed Scopus (95) Google Scholar In this issue of Molecular Therapy – Nucleic Acids, Zhang et al. successfully developed a novel PROTAC that employed a nucleic acid aptamer instead of a peptide or small molecule as the POI ligand.3Zhang L. Li L. Wang X. Liu H. Zhang Y. Xie T. Zhang H. Li X. Peng T. Sun X. et al.Development of a novel PROTAC using the nucleic acid aptamer as a targeting ligand for tumor selective degradation of nucleolin.Mol. Ther. Nucleic Acids. 2022; 30: 66-79https://doi.org/10.1016/j.omtn.2022.09.008Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar According to this design principle, they reported the first nucleolin-targeting aptamer-constructed PROTAC ZL216, which selectively degraded nucleolin in vitro and in vivo. They also showed that ZL216 could inhibit the proliferation and migration of hormone receptor (HR)-positive breast cancer cells.3Zhang L. Li L. Wang X. Liu H. Zhang Y. Xie T. Zhang H. Li X. Peng T. Sun X. et al.Development of a novel PROTAC using the nucleic acid aptamer as a targeting ligand for tumor selective degradation of nucleolin.Mol. Ther. Nucleic Acids. 2022; 30: 66-79https://doi.org/10.1016/j.omtn.2022.09.008Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar The authors presented the proof of concept of aptamer-constructed PROTACs, and their results expanded construction tools for PROTAC design (Figure 1). Aptamers are single-stranded nucleic acids with excellent affinities and selectivity for their targets. At present, aptamers have been extensively utilized in tumor therapy and targeted drug delivery due to their exclusive advantages, including low immunogenicity, high tissue permeability, favorable stability, and ease of preparation.4Zhou J. Rossi J. Aptamers as targeted therapeutics: current potential and challenges.Nat. Rev. Drug Discov. 2017; 16: 181-202https://doi.org/10.1038/nrd.2016.199Crossref PubMed Scopus (1138) Google Scholar AS1411 is a short, single-stranded DNA oligonucleotide that specifically binds to nucleolin, which is overexpressed on several cancer cells as well as tumor-associated blood vessels and has been implicated in various processes of tumorigenesis and angiogenesis. A previous publication reported that AS1411 exerted promising antiproliferative activities against tumor cells, and relevant clinical trials are currently being investigated.5He J. Peng T. Peng Y. Ai L. Deng Z. Wang X.Q. Tan W. Molecularly engineering triptolide with aptamers for high specificity and cytotoxicity for triple-negative breast cancer.J. Am. Chem. Soc. 2020; 142: 2699-2703https://doi.org/10.1021/jacs.9b10510Crossref PubMed Scopus (74) Google Scholar Inspired by these characteristics of aptamer, the authors employed AS1411 as nucleolin ligand to design the first aptamer-constructed PROTAC ZL216 in this study. Moreover, they demonstrated that the introduction of the aptamer AS1411 into the PROTAC design provided excellent serum stability and improved water solubility compared with free VHL E3 ligase-binding ligand (S, R, S)-AHPC-PEG3-azide (AHPC).3Zhang L. Li L. Wang X. Liu H. Zhang Y. Xie T. Zhang H. Li X. Peng T. Sun X. et al.Development of a novel PROTAC using the nucleic acid aptamer as a targeting ligand for tumor selective degradation of nucleolin.Mol. Ther. Nucleic Acids. 2022; 30: 66-79https://doi.org/10.1016/j.omtn.2022.09.008Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar These results suggested that aptamer-constructed PROTACs could circumvent the inherent poor membrane permeability or pharmacokinetic properties of conventional PROTACs. Compared with inhibitors, PROTACs often exert more profound influence on targets due to their event-driven pharmacological paradigm as well as their catalytic nature, thus producing more powerful therapeutic benefits. However, the lack of tissue specificity of conventional PROTACs between cancer cells and normal ones may lead to potential off-target effects and toxicity.6Moreau K. Coen M. Zhang A.X. Pachl F. Castaldi M.P. Dahl G. Boyd H. Scott C. Newham P. Proteolysis-targeting chimeras in drug development: a safety perspective.Br. J. Pharmacol. 2020; 177: 1709-1718https://doi.org/10.1111/bph.15014Crossref PubMed Scopus (84) Google Scholar The authors observed selective nucleolin degradation in breast cancer cells (MCF-7 and BT474) after aptamer-constructed PROTAC ZL216 treatment via the mechanism of PROTAC, but no significant influence on normal breast cells (MCF-10A), which was responsible for tumor-specific targeting ability of ZL216 to inhibit the proliferation and migration of breast cancer cells.3Zhang L. Li L. Wang X. Liu H. Zhang Y. Xie T. Zhang H. Li X. Peng T. Sun X. et al.Development of a novel PROTAC using the nucleic acid aptamer as a targeting ligand for tumor selective degradation of nucleolin.Mol. Ther. Nucleic Acids. 2022; 30: 66-79https://doi.org/10.1016/j.omtn.2022.09.008Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar Consistent with the recent emergence of photoPROTACs, antibody-PROTAC conjugates, aptamer-PROTAC conjugates, and Folate-caged PROTACs,7He M. Cao C. Ni Z. Liu Y. Song P. Hao S. He Y. Sun X. Rao Y. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021).Signal Transduct. Targeted Ther. 2022; 7: 181https://doi.org/10.1038/s41392-022-00999-9Crossref PubMed Scopus (46) Google Scholar the authors designed an aptamer-constructed PROTAC to realize targeted degradation of nucleolin in cancer cells, thereby providing a viable strategy to minimize potential toxicity and optimize treatment window of PROTACs. While considerable efforts from academia and industry have been undertaken to develop PROTACs targeting various pharmacological targets, the design of degraders of a subset of proteins (especially for undruggable targets, such as transcriptional factors) remains challenging since there are no available small-molecule inhibitors or binders. Furthermore, considering that lack of well-defined druggable pockets on these targets, the discovery of high-affinity ligands for these proteins is still intractable and time consuming.8Pei H. Guo W. Peng Y. Xiong H. Chen Y. Targeting key proteins involved in transcriptional regulation for cancer therapy: current strategies and future prospective.Med. Res. Rev. 2022; 42: 1607-1660https://doi.org/10.1002/med.21886Crossref PubMed Scopus (15) Google Scholar In the current study, the authors validated the feasibility of an aptamer-constructed PROTAC in degrading nucleolin.3Zhang L. Li L. Wang X. Liu H. Zhang Y. Xie T. Zhang H. Li X. Peng T. Sun X. et al.Development of a novel PROTAC using the nucleic acid aptamer as a targeting ligand for tumor selective degradation of nucleolin.Mol. Ther. Nucleic Acids. 2022; 30: 66-79https://doi.org/10.1016/j.omtn.2022.09.008Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar Other researchers have developed a generalizable platform termed TF-PROTACs in 2021, which utilized corresponding DNA oligonucleotides as POI ligands to selectively degrade endogenous transcription factors p65 and E2F1.9Liu J. Chen H. Kaniskan H.Ü. Xie L. Chen X. Jin J. Wei W. TF-PROTACs enable targeted degradation of transcription factors.J. Am. Chem. Soc. 2021; 143: 8902-8910https://doi.org/10.1021/jacs.1c03852Crossref PubMed Scopus (88) Google Scholar We speculate that these innovations will further accelerate the development of PROTACs and offer an alternative strategy for degradation of various therapeutic targets, especially for undruggable targets. One reasonable consideration is the generalizability of aptamers for designing PROTACs, and more PROTACs using aptamer as POI ligand or E3 ligand need to be prepared to investigate the therapeutic potential in the future. In addition, the factors that affect the degradation efficacy of aptamer-constructed PROTACs must be further clarified. Another consideration that includes pharmacokinetic properties and therapeutic benefits of aptamer-constructed PROTACs has not been examined in the existent study. In addition, the in vivo antitumor efficacy of aptamer-constructed PROTAC should be evaluated in the future. Toward clinical situation, triple-negative breast cancer (TNBC) is regarded as a more aggressive type of breast cancer, which was associated with poor prognosis and limited treatment options.10Bianchini G. De Angelis C. Licata L. Gianni L. Treatment landscape of triple-negative breast cancer - expanded options, evolving needs.Nat. Rev. Clin. Oncol. 2022; 19: 91-113https://doi.org/10.1038/s41571-021-00565-2Crossref PubMed Scopus (252) Google Scholar We expect more research on TNBC by using this novel aptamer-constructed PROTAC. Taken together, this work clearly suggested aptamer could be applied to the PROTAC design, thereby potentially broadening the degradable target spectrum and providing an additional chance to selectively degrade POIs in cancer cells. This work was supported by grants from the National Natural Science Foundation of China (81973160 and 81904206) and the Science and Technology Commission of Shanghai Municipality (21S11907800). Y.Z. and D.M. wrote the manuscript, Y.C. revised and arranged the manuscript. The authors declare no competing financial interest.