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

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.

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Design of a small molecule against an oncogenic noncoding RNA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1523975113 ◽

2016 ◽

Vol 113 (21) ◽

pp. 5898-5903 ◽

Cited By ~ 99

Author(s):

Sai Pradeep Velagapudi ◽

Michael D. Cameron ◽

Christopher L. Haga ◽

Laura H. Rosenberg ◽

Marie Lafitte ◽

...

Keyword(s):

Breast Cancer ◽

Small Molecules ◽

Cancer Cells ◽

Small Molecule ◽

Noncoding Rna ◽

Breast Cancer Cells ◽

Rational Design ◽

Pharmacokinetic Profile ◽

Tumor Burden

The design of precision, preclinical therapeutics from sequence is difficult, but advances in this area, particularly those focused on rational design, could quickly transform the sequence of disease-causing gene products into lead modalities. Herein, we describe the use of Inforna, a computational approach that enables the rational design of small molecules targeting RNA to quickly provide a potent modulator of oncogenic microRNA-96 (miR-96). We mined the secondary structure of primary microRNA-96 (pri-miR-96) hairpin precursor against a database of RNA motif–small molecule interactions, which identified modules that bound RNA motifs nearby and in the Drosha processing site. Precise linking of these modules together provided Targaprimir-96 (3), which selectively modulates miR-96 production in cancer cells and triggers apoptosis. Importantly, the compound is ineffective on healthy breast cells, and exogenous overexpression of pri-miR-96 reduced compound potency in breast cancer cells. Chemical Cross-Linking and Isolation by Pull-Down (Chem-CLIP), a small-molecule RNA target validation approach, shows that 3 directly engages pri-miR-96 in breast cancer cells. In vivo, 3 has a favorable pharmacokinetic profile and decreases tumor burden in a mouse model of triple-negative breast cancer. Thus, rational design can quickly produce precision, in vivo bioactive lead small molecules against hard-to-treat cancers by targeting oncogenic noncoding RNAs, advancing a disease-to-gene-to-drug paradigm.

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Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1901484116 ◽

2019 ◽

Vol 116 (16) ◽

pp. 7799-7804 ◽

Cited By ~ 36

Author(s):

Alicia J. Angelbello ◽

Suzanne G. Rzuczek ◽

Kendra K. Mckee ◽

Jonathan L. Chen ◽

Hailey Olafson ◽

...

Keyword(s):

Mouse Model ◽

Small Molecules ◽

Myotonic Dystrophy ◽

Small Molecule ◽

Neuromuscular Disorder ◽

Repeat Expansion ◽

Rna Structures ◽

Target Disease ◽

Preclinical Animal Models

Myotonic dystrophy type 1 (DM1) is an incurable neuromuscular disorder caused by an expanded CTG repeat that is transcribed into r(CUG)exp. The RNA repeat expansion sequesters regulatory proteins such as Muscleblind-like protein 1 (MBNL1), which causes pre-mRNA splicing defects. The disease-causing r(CUG)exp has been targeted by antisense oligonucleotides, CRISPR-based approaches, and RNA-targeting small molecules. Herein, we describe a designer small molecule, Cugamycin, that recognizes the structure of r(CUG)exp and cleaves it in both DM1 patient-derived myotubes and a DM1 mouse model, leaving short repeats of r(CUG) untouched. In contrast, oligonucleotides that recognize r(CUG) sequence rather than structure cleave both long and short r(CUG)-containing transcripts. Transcriptomic, histological, and phenotypic studies demonstrate that Cugamycin broadly and specifically relieves DM1-associated defects in vivo without detectable off-targets. Thus, small molecules that bind and cleave RNA have utility as lead chemical probes and medicines and can selectively target disease-causing RNA structures to broadly improve defects in preclinical animal models.

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A Mouse Model for in Vivo Detection and Disruption of TGF-Beta Signaling in Breast Cancer Metastasis

10.21236/ada512330 ◽

2009 ◽

Author(s):

Manav Korpal

Keyword(s):

Breast Cancer ◽

Mouse Model ◽

Cancer Metastasis ◽

Breast Cancer Metastasis ◽

Tgf Beta ◽

In Vivo Detection

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Identification of a small molecule as inducer of ferroptosis and apoptosis through ubiquitination of GPX4 in triple negative breast cancer cells

Journal of Hematology & Oncology ◽

10.1186/s13045-020-01016-8 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Yahui Ding ◽

Xiaoping Chen ◽

Can Liu ◽

Weizhi Ge ◽

Qin Wang ◽

...

Keyword(s):

Breast Cancer ◽

Cell Death ◽

Small Molecule ◽

Mode Of Action ◽

Rna Silencing ◽

Breast Cancer Cells ◽

Triple Negative ◽

Parent Compound ◽

Aggressive Breast Cancer

Abstract Background TNBC is the most aggressive breast cancer with higher recurrence and mortality rate than other types of breast cancer. There is an urgent need for identification of therapeutic agents with unique mode of action for overcoming current challenges in TNBC treatment. Methods Different inhibitors were used to study the cell death manner of DMOCPTL. RNA silencing was used to evaluate the functions of GPX4 in ferroptosis and apoptosis of TNBC cells and functions of EGR1 in apoptosis. Immunohistochemical assay of tissue microarray were used for investigating correlation of GPX4 and EGR1 with TNBC. Computer-aided docking and small molecule probe were used for study the binding of DMOCPTL with GPX4. Results DMOCPTL, a derivative of natural product parthenolide, exhibited about 15-fold improvement comparing to that of the parent compound PTL for TNBC cells. The cell death manner assay showed that the anti-TNBC effect of DMOCPTL mainly by inducing ferroptosis and apoptosis through ubiquitination of GPX4. The probe of DMOCPTL assay indicated that DMOCPTL induced GPX4 ubiquitination by directly binding to GPX4 protein. To the best of our knowledge, this is the first report of inducing ferroptosis through ubiquitination of GPX4. Moreover, the mechanism of GPX4 regulation of apoptosis is still obscure. Here, we firstly reveal that GPX4 regulated mitochondria-mediated apoptosis through regulation of EGR1 in TNBC cells. Compound 13, the prodrug of DMOCPTL, effectively inhibited the growth of breast tumor and prolonged the lifespan of mice in vivo, and no obvious toxicity was observed. Conclusions These findings firstly revealed novel manner to induce ferroptosis through ubiquitination of GPX4 and provided mechanism for GPX4 inducing mitochondria-mediated apoptosis through up-regulation of EGR1 in TNBC cells. Moreover, compound 13 deserves further studies as a lead compound with novel mode of action for ultimate discovery of effective anti-TNBC drug.

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Targeting RECQL5 Functions, by a Small Molecule, Selectively Kills Breast Cancer in Vitro and in Vivo

Journal of Medicinal Chemistry ◽

10.1021/acs.jmedchem.0c01692 ◽

2021 ◽

Vol 64 (3) ◽

pp. 1524-1544

Author(s):

Saikat Chakraborty ◽

Kartik Dutta ◽

Pooja Gupta ◽

Anubrata Das ◽

Amit Das ◽

...

Keyword(s):

Breast Cancer ◽

Small Molecule

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Feasibility of Harmonic Motion Imaging Using A Single Transducer: In Vivo Imaging of Breast Cancer in A Mouse Model and Human Subjects

IEEE Transactions on Medical Imaging ◽

10.1109/tmi.2021.3055779 ◽

2021 ◽

pp. 1-1 ◽

Cited By ~ 1

Author(s):

Md Murad Hossain ◽

Niloufar Saharkhiz ◽

Elisa E. Konofagou

Keyword(s):

Breast Cancer ◽

Mouse Model ◽

In Vivo Imaging ◽

Human Subjects ◽

Harmonic Motion ◽

Harmonic Motion Imaging ◽

Motion Imaging

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Small Molecule Antagonists of the Wnt/Beta-Catenin Signaling Pathway Target Breast Tumor-Initiating Cells in a Her2/Neu Mouse Model of Breast Cancer

PLoS ONE ◽

10.1371/journal.pone.0033976 ◽

2012 ◽

Vol 7 (3) ◽

pp. e33976 ◽

Cited By ~ 58

Author(s):

Robin M. Hallett ◽

Maria K. Kondratyev ◽

Andrew O. Giacomelli ◽

Allison M. L. Nixon ◽

Adele Girgis-Gabardo ◽

...

Keyword(s):

Breast Cancer ◽

Mouse Model ◽

Signaling Pathway ◽

Small Molecule ◽

Breast Tumor ◽

Beta Catenin ◽

Tumor Initiating Cells

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Screening antiproliferative drug for breast cancer from bisbenzylisoquinoline alkaloid tetrandrine and fangchinoline derivatives by targeting BLM helicase

BMC Cancer ◽

10.1186/s12885-019-6146-7 ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Wangming Zhang ◽

Shuang Yang ◽

Jinhe Liu ◽

Linchun Bao ◽

He Lu ◽

...

Keyword(s):

Breast Cancer ◽

Dna Binding ◽

Small Molecules ◽

Cancer Cells ◽

Small Molecule ◽

Breast Cancer Cells ◽

Dna Unwinding ◽

Protein Levels ◽

Blm Helicase ◽

Bisbenzylisoquinoline Alkaloids

Abstract Background The high expression of BLM (Bloom syndrome) helicase in tumors involves its strong association with cell expansion. Bisbenzylisoquinoline alkaloids own an antitumor property and have developed as candidates for anticancer drugs. This paper aimed to screen potential antiproliferative small molecules from 12 small molecules (the derivatives of bisbenzylisoquinoline alkaloids tetrandrine and fangchinoline) by targeting BLM642–1290 helicase. Then we explore the inhibitory mechanism of those small molecules on proliferation of MDA-MB-435 breast cancer cells. Methods Fluorescence polarization technique was used to screen small molecules which inhibited the DNA binding and unwinding of BLM642–1290 helicase. The effects of positive small molecules on the ATPase and conformation of BLM642–1290 helicase were studied by the malachite green-phosphate ammonium molybdate colorimetry and ultraviolet spectral scanning, respectively. The effects of positive small molecules on growth of MDA-MB-435 cells were studied by MTT method, colony formation and cell counting method. The mRNA and protein levels of BLM helicase in the MDA-MB-435 cells after positive small molecule treatments were examined by RT-PCR and ELISA, respectively. Results The compound HJNO (a tetrandrine derivative) was screened out which inhibited the DNA binding, unwinding and ATPase of BLM642–1290 helicase. That HJNO could bind BLM642–1290helicase to change its conformationcontribute to inhibiting the DNA binding, ATPase and DNA unwinding of BLM642–1290 helicase. In addition, HJNO showed its inhibiting the growth of MDA-MB-435 cells. The values of IC50 after drug treatments for 24 h, 48 h and 72 h were 19.9 μmol/L, 4.1 μmol/L and 10.9 μmol/L, respectively. The mRNA and protein levels of BLM helicase in MDA-MB-435 cells increased after HJNO treatment. Those showed a significant difference (P < 0.05) compared with negative control when the concentrations of HJNO were 5 μmol/L and 10 μmol/L, which might contribute to HJNO inhibiting the DNA binding, ATPase and DNA unwinding of BLM helicase. Conclusion The small molecule HJNO was screened out by targeting BLM642–1290 helicase. And it showed an inhibition on MDA-MB-435 breast cancer cells expansion.

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