OligoTRAFTACs: A generalizable method for transcription factor degradation

Abstract

Dysregulated transcription factors (TFs) that rewire gene expression circuitry are frequently identified as key players in disease. Although several TFs have been drugged with small molecules, the majority of oncogenic...

c-Myc-Targeting PROTAC Based on a TNA-DNA Bivalent Binder for Combination Therapy of Triple-Negative Breast Cancer

“…35 Most recently, Crews et al reported the development of the second-generation TRAFTAC (oligo-TRAFTAC) that induced degradation of two oncogenic TFs including c-Myc. 36 Additionally, DNA aptamer AS1411 has been used as a targeting ligand in PROTAC construction, which induced nucleolin degradation and inhibited breast cancer cell proliferation and migration. 37 While these natural DNA and RNA sequences either inherently possess or are evolved to exhibit binding affinities to target proteins, they could be easily degraded by ubiquitous nucleases and might not bind targets with sufficient affinities, thus affecting PROTAC efficacy and limiting the utility.…”

Current Status of Oligonucleotide-Based Protein Degraders

“…To generate double-stranded warheads, a cMYC binding consensus sequence 5′-CACGTGGTTGCCACGTG-3′ and a brachyury binding DNA sequence 5′-AATTTCACACCTAGGTGTGAAATT-3′ were referenced. With its significantly improved handiness, the author group considered oligoTRAFTAC as a generalizable platform for other TFs, although washout experiments showed that the withdrawal of oligoTRAFTAC did not prolong degradation responses [ 17 ]. Again, the authors used zebrafish as an animal model in the in vivo studies, finding that microinjection of oligoTRAFTAC OT17 induced tail deformation in 70% of the injected zebrafish embryos [ 17 ].…”

“…With its significantly improved handiness, the author group considered oligoTRAFTAC as a generalizable platform for other TFs, although washout experiments showed that the withdrawal of oligoTRAFTAC did not prolong degradation responses [ 17 ]. Again, the authors used zebrafish as an animal model in the in vivo studies, finding that microinjection of oligoTRAFTAC OT17 induced tail deformation in 70% of the injected zebrafish embryos [ 17 ]. Notably, the in vivo studies confirmed that phosphodiester bonds in the oligoTRAFTAC molecules are vulnerable in living animals due to nucleases including exonucleases and endonucleases, whereas phosphorothioate backbones in the oligoTRAFTAC molecules largely avoided nuclease attacks, showing nuclease stability.…”

“…It has been reported that one TF is able to recognize several similar oligonucleotide sequences, and one oligonucleotide sequence could be shared among several TFs [ 27 ]. For example, TCF3 recognizes an E-box consensus sequence similar to that of c-Myc [ 17 ]. This strongly indicates that avoiding off-target effects requires a well-designed oligonucleotide sequence for one TF.…”

Enriching Proteolysis Targeting Chimeras with a Second Modality: When Two Are Better Than One

“…The oligonucleotide competes with native RNA for binding the RBP, and the simultaneous recruitment of E3 ligase allows target ubiquitination and degradation. By using a structure-based approach, a set of oligonucleotide analogues that selectively binds Lin28A, a stem cell factor and oncoprotein involved in Starting from a chimeric DNA:CRISPR-RNA molecule, i.e., Transcription Factor TArgeting Chimera (TRAFTAC), that binds a dCas9-HaloTag7 fusion adaptor, 135 Crews and coworkers 136 described the development of the second-generation TRAFTACs, so-called "oligoTRAFTACs". OligoTRAFTACs are constituted of a TF-binding oligonucleotide and an E3 ligase binder.…”