A pinboard by
Matthew Costales

Graduate Student, The Scripps Research Institute, Florida


I am investigating small molecule modulators of RNA implicated in disease.

A bald patient, sitting in a sterilized environment under dull fluorescent lighting, in a padded chair connected to an IV machine. An image far too familiar for those who have seen a loved one or even been the one undergoing chemotherapy in that seat. Is there a way to avoid such a tragedy? Can we cancer be targeted in an effective manner? Current therapies for cancer tend to be non-selective between healthy and diseased cells. In order to reduce the suffering of side effects for these patients already afflicted with such a terrible disease, precision medicine is the key. Many drugs target either rapidly dividing DNA or proteins commonly seen on the surface of cancer cells and these treatments have been effective, but at a cost. They work, but since they non-selectively target healthy cells (such as hair roots) as well as cancer cells, these treatments drastically affect the quality of life of the patient. In order to overcome this problem, precision medicine in the key. While other labs are developing new methods to target DNA or protein, my research is investigating ways to exploit RNA as a target for cancer therapy. Given that RNA is so similar to DNA, many have previously thought it was impossible to differentiate between the two without using a DNA mimic. The main difference between RNA and DNA is that RNA has only one strand and does not form the signature double helix structure of DNA. Being single stranded, RNA tends to fold onto itself and form its own unique structures. We take advantage of this folded structure and attempt to use small molecules that can bind to and fit into specific RNA structures. In particular, one class of RNA is called microRNA (miRNAs). These miRNAs play an important regulatory role in maintaining the delicate balance of the human body, acting as dimmer switches to adjust gene expression throughout the entire body. In cancer, these miRNAs can become mutated and cause rampant cell growth that results in a tumor. Since these miRNAs are only highly expressed in the diseased cancer cells, my aim is to use small molecules to target and fit into the specific structure of these cancer causing miRNAs. As my research involves chemistry to probe biology, this field of RNA Chemical Biology, one needs extensive training in both fields. Fortunately, my synthetic chemistry research in college and immunology research at the FDA has prepared me for this research and the chance to share my passion for the topic at a renowned conference.


Design of a small molecule against an oncogenic noncoding RNA

Abstract: 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.

Pub.: 11 May '16, Pinned: 07 Jul '17

Small Molecule Inhibition of microRNA-210 Reprograms an Oncogenic Hypoxic Circuit.

Abstract: A hypoxic state is critical to the metastatic and invasive characteristics of cancer. Numerous pathways play critical roles in cancer maintenance, many of which include noncoding RNAs such as microRNA (miR)-210 that regulates hypoxia inducible factors (HIFs). Herein, we describe the identification of a small molecule named Targapremir-210 that binds to the Dicer site of the miR-210 hairpin precursor. This interaction inhibits production of the mature miRNA, derepresses glycerol-3-phosphate dehydrogenase 1-like enzyme (GPD1L), a hypoxia-associated protein negatively regulated by miR-210, decreases HIF-1α, and triggers apoptosis of triple negative breast cancer cells only under hypoxic conditions. Further, Targapremir-210 inhibits tumorigenesis in a mouse xenograft model of hypoxic triple negative breast cancer. Many factors govern molecular recognition of biological targets by small molecules. For protein, chemoproteomics and activity-based protein profiling are invaluable tools to study small molecule target engagement and selectivity in cells. Such approaches are lacking for RNA, leaving a void in the understanding of its druggability. We applied Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP) to study the cellular selectivity and the on- and off-targets of Targapremir-210. Targapremir-210 selectively recognizes the miR-210 precursor and can differentially recognize RNAs in cells that have the same target motif but have different expression levels, revealing this important feature for selectively drugging RNAs for the first time. These studies show that small molecules can be rapidly designed to selectively target RNAs and affect cellular responses to environmental conditions, resulting in favorable benefits against cancer. Further, they help define rules for identifying druggable targets in the transcriptome.

Pub.: 28 Feb '17, Pinned: 07 Jul '17