MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by targeting a mRNA for degradation or translational repression. Not surprisingly, aberrant miRNA expression can cause disease, in particular cancers. Herein, we propose a series of investigations to explore the therapeutic potential of compounds that bind a miRNA precursor associated with breast cancer and inhibit its biogenesis in breast cancer cells. These compounds were developed as a direct result of our currently funded R01 grant (R01- GM097455) in which we proposed to develop computational methods to design small molecules that avidly and selectively bind miRNA precursors. These studies have the potential to advance new anti-cancer therapies to the clinic and to enable development of general strategies to target miRNAs that cause other diseases such as Hepatitis C infections, Alzheimer's disease, and heart disease, among others. Our parent R01 grant proposes to: (i) establish a computational approach to identify lead small molecules for a desired RNA target using a database of RNA motif-small molecule interactions and to identify novel RNA targets from transcriptomes;and (ii) use these computational tools to identify lead small molecules that bind human miRNAs and evaluate them for inhibiting biogenesis in mammalian cell lines. Indeed, this approach was employed to rationally design a small molecule that selectively binds an oncogenic miRNA precursor, miR- 96, and inhibits its biogenesis in breast cancer cells. Importantly, miRNA profiling studies reveal that our small molecule is more selective than an antagomir, the state-of-the-art miRNA targeting modality! Thus, this small molecule is an exemplary case to push forward into animal models of cancer and test the hypothesis that small molecules can indeed drug """"""""undruggable"""""""" RNA targets.
The Specific Aims are:
Aim 1 : Evaluate the therapeutic potential of our designed pri-miR-96 small molecule in models of triple negative and metastatic breast cancer.
Aim 2 : Validate in vivo targets, compound selectivity and mechanism of action of our designer compounds. Previously, our group has shown that small molecules can be designed to react with RNA targets in live cells. This covalent approach significantly improves bioactivity (>2500-fold) and can be used to validate the cellular targets of small molecules.
Aim 3 : Evaluate a dimeric small molecule that simultaneously binds the Drosha processing site and an adjacent internal loop in pri-miR-96. We have designed a potent dimeric small molecule that targets pri-miR-96 in vitro (~500-fold more potent than our lead monomeric small molecule). We will evaluate the therapeutic potential of this compound in MDA-MB-231 breast cancer cells and metastatic and drug-resistant variants, using orthotopic xenograft models.

Public Health Relevance

We have designed a small molecule that binds an oncogenic microRNA and inhibits its function in breast cancer cells. We propose to determine the therapeutic potential of this compound and optimize it for bioactivity using two methods established in our laboratory. These studies could result in new cancer therapeutics and a general strategy to target RNAs that cause cancer and other diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM097455-03S1
Application #
8761317
Study Section
Drug Discovery and Molecular Pharmacology Study Section (DMP)
Program Officer
Preusch, Peter
Project Start
2012-04-05
Project End
2016-03-31
Budget Start
2014-07-01
Budget End
2015-03-31
Support Year
3
Fiscal Year
2014
Total Cost
$269,325
Indirect Cost
$126,825
Name
Scripps Florida
Department
Type
DUNS #
148230662
City
Jupiter
State
FL
Country
United States
Zip Code
33458
Childs-Disney, Jessica L; Disney, Matthew D (2016) Small Molecule Targeting of a MicroRNA Associated with Hepatocellular Carcinoma. ACS Chem Biol 11:375-80
Disney, Matthew D; Winkelsas, Audrey M; Velagapudi, Sai Pradeep et al. (2016) Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs. ACS Chem Biol 11:1720-8
Park, HaJeung; Tran, Tuan; Lee, Jun Hyuck et al. (2016) Controlled dehydration improves the diffraction quality of two RNA crystals. BMC Struct Biol 16:19
Liu, Biao; Childs-Disney, Jessica L; Znosko, Brent M et al. (2016) Analysis of secondary structural elements in human microRNA hairpin precursors. BMC Bioinformatics 17:112
Childs-Disney, Jessica L; Disney, Matthew D (2016) Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells. Annu Rev Pharmacol Toxicol 56:123-40
Yang, Wang-Yong; Wilson, Henry D; Velagapudi, Sai Pradeep et al. (2015) Inhibition of Non-ATG Translational Events in Cells via Covalent Small Molecules Targeting RNA. J Am Chem Soc 137:5336-45
Velagapudi, Sai Pradeep; Vummidi, Balayeshwanth R; Disney, Matthew D (2015) Small molecule chemical probes of microRNA function. Curr Opin Chem Biol 24:97-103
Bernat, Viachaslau; Disney, Matthew D (2015) RNA Structures as Mediators of Neurological Diseases and as Drug Targets. Neuron 87:28-46
Haga, Christopher L; Velagapudi, Sai Pradeep; Strivelli, Jacqueline R et al. (2015) Small Molecule Inhibition of miR-544 Biogenesis Disrupts Adaptive Responses to Hypoxia by Modulating ATM-mTOR Signaling. ACS Chem Biol 10:2267-76
Yildirim, Ilyas; Chakraborty, Debayan; Disney, Matthew D et al. (2015) Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1. J Chem Theory Comput 11:4943-58

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