Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer

Abstract

As the area of small molecules interacting with RNA advances, general routes to provide bioactive compounds are needed as ligands can bind RNA avidly to sites that will not affect function. Small-molecule targeted RNA degradation will thus provide a general route to affect RNA biology. A non–oligonucleotide-containing compound was designed from sequence to target the precursor to oncogenic microRNA-21 (pre–miR-21) for enzymatic destruction with selectivity that can exceed that for protein-targeted medicines. The compound specifically binds the target and contains a heterocycle that recruits and activates a ribonuclease to pre–miR-21 to substoichiometrically effect its cleavage and subsequently impede metastasis of breast cancer to lung in a mouse model. Transcriptomic and proteomic analyses demonstrate that the compound is potent and selective, specifically modulating oncogenic pathways. Thus, small molecules can be designed from sequence to have all of the functional repertoire of oligonucleotides, including inducing enzymatic degradation, and to selectively and potently modulate RNA function in vivo.

Small molecule recognition of disease-relevant RNA structures

“…A RIBOTAC targeting pre-miR-21, dubbed TGP-21 RIBOTAC, was recently reported that is based on the dimeric binding compound TGP-21 (Table S1, ESI †). 190 TGP-21 was first validated in MDA-MB-231 TNBC cells, reducing levels of mature miR-21 and increasing levels of pre-miR-21, in accordance with its mechanism of inhibiting Dicer processing (Table S1, ESI †). 190 The binding dimer also increased expression of programmed cell death protein 4 (PDCD4) and phosphatase and tension homolog (PTEN), two proteins that are translationally repressed by miR-21.…”

“…190 TGP-21 was first validated in MDA-MB-231 TNBC cells, reducing levels of mature miR-21 and increasing levels of pre-miR-21, in accordance with its mechanism of inhibiting Dicer processing (Table S1, ESI †). 190 The binding dimer also increased expression of programmed cell death protein 4 (PDCD4) and phosphatase and tension homolog (PTEN), two proteins that are translationally repressed by miR-21. 190 Additionally, invasion assays confirmed TGP-21's ability to inhibit the invasive phenotype of MDA-MB-231 cells.…”

“…190 The binding dimer also increased expression of programmed cell death protein 4 (PDCD4) and phosphatase and tension homolog (PTEN), two proteins that are translationally repressed by miR-21. 190 Additionally, invasion assays confirmed TGP-21's ability to inhibit the invasive phenotype of MDA-MB-231 cells. 190 TGP-21 was optimized by appending a heterocyclic small molecule recruiter of RNase L to create TGP-21 RIBOTAC (Fig.…”

RNA-Targeted Therapies and High-Throughput Screening Methods

“…However, further research needs to be undertaken to evaluate their efficacy, bioavailability and safety before entering the clinical studies. Beyond these three examples, therapies targeting viral RNAs [187,188], RNA cleavage through RNase recruitment [189,190], mRNA translation by inhibiting eukaryotic translation initiation factors [191], as well as premature translational termination caused by nonsense mutations [192], are being developed. With respect to the huge number of RNA-targeted therapies in preclinical studies and clinical trials, it is apparent that these therapies will form a key part of personalised, precision medicine in the future.…”

Small molecules exploiting structural differences within microRNA-200 precursors family members reverse a type 2 diabetes phenotype

“…Three approaches have been used to develop miR inhibitors: (i) oligonucleotidebased antagomirs to bind to the mature miRs via base pairing (8); (ii) small molecules that target pri-or pre-miR structures found at functional Dicer or Drosha processing sites, thereby inhibiting biogenesis (9)(10)(11); and (iii) small molecules that target miR precursor structures to trigger cleavage of the RNA target (12)(13)(14). One of the challenges with targeting some miRs specifically with oligonucleotides is that family members can have the same or similar sequences (15,16).…”