Abstract: Described are small molecule embodiments, ALS compounds, that bind with the (G4C2)exp RNA repeat transcription of the chromosome 9 open reading frame 72 involved in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). These ALS compounds comprise a pyridocarbazole moiety having at least one substituent. Preferred ALS compounds comprise bridged dimers of the pyridocarbazole moiety in which the bridge between the two pyridocarbazole moieties is a polyoxyethylenyl group or an aminobispolyoxyethylenyl group.

Abstract: The protein targeted medicine, Dovitinib, has been repurposed to target a non-coding RNA by using selection and computational drug design via Inforna. Selectivity was achieved for pre-miR-21 by endowing the medicine with the ability to recruit RNA quality control enzymes to cleave the target.

Abstract: Embodiments of methods are disclosed for inhibiting, regulating and/or otherwise affecting or managing the pri-miR-17-92 cluster, and certain pre-miRNA's embedded in the cluster as well as the pre-miRNA's themselves as isolated forms, as members of a library, present in oncogenic and/or polycystic cell lines and/or that are present in breast cancer, prostate cancer and/or polycystic kidney disease in animals or humans, or present in any other disease in which the pri-miR-17-92 cluster and the certain pre-miRNAs within in it cause or contribute to disease. The methods utilize compounds that target the structural feature or features of the pri-miR-17-92 cluster and/or the certain pre-miRNA's. The pre-miRNA's are members of the pre-miRNA-X group which includes one or more of pre-miR-17, pre-miR-18a, pre-miR-19a, pre-miR-19b-1, pre-miR-20a, and pre-miR-92a-1 or any combination thereof. The compounds incorporate a dimeric formula of a binding moiety for the certain pre-miRNA-X's.

Abstract: Methods and computer systems are described herein for identifying small molecules that bind to selected RNA structural features (e.g., to RNA secondary structures). Also described are compounds and compositions that modulate RNA function and/or activity.

Abstract: 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, de-represses glycerol-3-phosphate dehydrogenase 1-like enzyme (GPD1 L), a hypoxia-associated protein negatively regulated by miR-210, decreases HIF-1 a, 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. 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.

Abstract: The invention is directed to a method of identifying the interactions of RNA such as miRNA with small molecules interacting with RNA (SMIRNAs). A candidate SMIRNA group is associated with a photoaffinity diazirene group that can form a covalent complex with an RNA target site and with an alkyne group that can be used in subsequent “click chemistry’ reactions such as a “CuAAC” reaction, a copper-catalyzed alkyne-azide cy-cloaddition to yield a stable triazole ring. By this means, the RNA binding site of the small molecule can be identified via isolation of the RNA-targetSMIRNA covalent complex and reverse transcription of the RNA followed by DNA sequencing of the reverse transcription product. Sites on the RNA blocked during reverse transcription by the covalently bound SMIRNA are identified as terminations in the sequence compared to the native RNA.

Abstract: A method is described to define the binding of fragments onto RNA targets and to use this profiling to enable the design of small molecules targeting RNA. The method comprises exposing a labeled RNA target to a small molecule fragment appended with diazirine and an alkyne moiety. Exposure of the compounds to light produce a reactive intermediate from the diazirine moiety that will react with sites in the RNA that are proximal to the small molecule fragments binding site. The RNAs that are reacted with the fragments are captured by using a biotin azide or azide-displaying beads that react with the alkyne moiety in the presence of a Cu(I) catalyst using click chemistry. Biotinylated products are captured with streptavidin resin. The amount of labeled RNA captured by the resin/beads is measured, thereby identifying which fragments bind an RNA target. The binding site of the fragment is determined by RT-PCR.

Abstract: Many RNAs cause disease, however RNA is rarely exploited as a small molecule drug target. Disclosed herein are methods for identifying privileged RNA motif-small molecule interactions to enable the rational design of compounds that modulate RNA biology starting from only sequence. A massive, library-versus-library screen was completed that probed over 50 million binding events between RNA motifs and small molecules. The resulting data provide a rich encyclopedia of small molecule-RNA recognition patterns, defining chemotypes and RNA motifs that confer selective, avid binding. The resulting interaction maps were mined against the entire viral genome of hepatitis C virus (HCV). A small molecule was identified that avidly bound RNA motifs present in the HCV3? untranslated region and inhibited viral replication while having no effect on host cells. Collectively, this investigation represents the first whole genome pattern recognition between small molecules and RNA folds.

Abstract: Disclosed herein are compounds and methods to identify the direct RNA targets of small molecules in cells is described. The approach, dubbed Chemical Cross-Linking and Isolation by Pull-down to Map Small Molecule-RNA Binding Sites (Chem-CLIP-Map-Seq), appends a cross-linker and a purification tag onto a small molecule. In cells, the compound binds to RNA and undergoes a proximity-based reaction. The cross-linked RNA is purified and then amplified using a universal reverse transcription (RT) primer and gene-specific PCR primers. At nucleotides proximal to the binding site, RT “stops” are observed. This approach has broad utility in identifying and validating the RNA targets and binding sites of small molecules in the context of a complex cellular system.

Abstract: A method for the precise cellular destruction of an oncogenic non-coding RNA with a RNA-binding small molecule conjugated with bleomycin A5 is described. The method affords reversal of phenotype. Bleomycin A5 was coupled to an RNA-binding molecule that selectively binds the microRNA-96 hairpin precursor (pri-miR-96). By coupling of bleomycin A5's free amine to the RNA-binding molecule, its affinity for binding to pri-miR-96 is >100-fold stronger than to DNA. The conjugate compound selectively cleaves pri-miR-96 in triple negative breast cancer (TNBC) cells. Selective cleavage of pri-miR-96 enhances expression of FOXO1 protein, a pro-apoptotic transcription factor that miR-96 silences, and triggers apoptosis in TNBC cells. No effects were observed in healthy breast epithelial cells. This method provides programmable control for targeting RNA through the selection of an RNA-binding molecule/bleomycin A5 conjugate and provides a facile method of mapping the cellular binding sites of an RNA-binding molecule.

Abstract: Provided herein are compounds that selectively bind and cleave RNA. In various embodiments, the disclosure provides chemical compounds effective as ribonuclease targeting chimeras (RIBOTACs), that target the endogenous enzyme RNase L to selectively cleave the RNA in a living cell. These compounds are useful in the treatment of diseases, e.g., the treatment of breast cancer.

Abstract: Transcriptomes provide a myriad of potential RNAs that could be the targets of therapeutics or chemical genetic probes of function. Cell permeable small molecules, however, generally do not exploit these targets, owing to the difficulty in the design of high affinity, specific small molecules targeting RNA. As part of a general program to study RNA function using small molecules, we designed bioactive, modularly assembled small molecules that target the non-coding expanded RNA repeat that causes myotonic dystrophy type 1 (DM1), r(CUG)exp. Herein, we present a rigorous study to elucidate features in modularly assembled compounds that afford bioactivity. Different modular assembly scaffolds were investigated including polyamines, ?-peptides, ?-peptides, and peptide tertiary amides (PTAs). Based on activity as assessed by improvement of DM1-associated defects, stability against proteases, cellular permeability, and toxicity, we discovered that constrained backbones, namely PTAs, are optimal.

Abstract: Potent modulators of RNA function can be assembled in cellulo by using the cell as a reaction vessel and a disease-causing RNA as a catalyst. When designing small molecule effectors of function, a balance between permeability and potency must be struck. Low molecular weight compounds are more permeable while higher molecular weight compounds are more potent. The advantages of both types of compounds could be synergized if low molecular weight molecules could be transformed into potent, multivalent ligands via a reaction catalyzed by binding to a target in cells expressing a genetic defect. We demonstrate that this approach is indeed viable in cellulo. Small molecule modules with precisely positioned alkyne and azide moieties bind adjacent internal loops in r(CCUG)exp, the causative agent of myotonic dystrophy type 2 (DM2), and are transformed into oligomeric, potent inhibitors of DM2 RNA dysfunction via a 1,3 Huisgen dipolar cycloaddition reaction, a variant of click chemistry.

Abstract: A repeat expansion in C9ORF72 causes frontotemporal dementia and amyotrophic lateral sclerosis (c9FTD/ALS). RNA of the expanded repeat (r(GGGGCC)exp) forms nuclear foci or undergoes repeat-associated non-ATG (RAN) translation producing “c9RAN proteins”. Since neutralizing r(GGGGCC)exp could inhibit these potentially toxic events, we sought to identify small molecule binders of r(GGGGCC)exp. Chemical and enzymatic probing of r(GGGGCC)8 indicate it adopts a hairpin structure in equilibrium with a quadruplex structure. Using this model, bioactive small molecules targeting r(GGGGCC)exp were designed and found to significantly inhibit RAN translation and foci formation in cultured cells expressing r(GGGGCC)66 and neurons trans-differentiated from fibroblasts of repeat expansion carriers. Finally, we show that poly(GP) c9RAN proteins are specifically detected in c9ALS patient cerebrospinal fluid.

Abstract: Methods and computer systems are described herein for identifying small molecules that bind to selected RNA structural features (e.g., to RNA secondary structures). Also described are compounds and compositions that modulate RNA function and/or activity.

Abstract: Potent modulators of RNA function can be assembled in cellulo by using the cell as a reaction vessel and a disease-causing RNA as a catalyst. When designing small molecule effectors of function, a balance between permeability and potency must be struck. Low molecular weight compounds are more permeable while higher molecular weight compounds are more potent. The advantages of both types of compounds could be synergized if low molecular weight molecules could be transformed into potent, multivalent ligands via a reaction catalyzed by binding to a target in cells expressing a genetic defect. We demonstrate that this approach is indeed viable in cellulo. Small molecule modules with precisely positioned alkyne and azide moieties bind adjacent internal loops in r(CCUG)exp, the causative agent of myotonic dystrophy type 2 (DM2), and are transformed into oligomeric, potent inhibitors of DM2 RNA dysfunction via a 1,3 Huisgen dipolar cycloaddition reaction, a variant of click chemistry.

Abstract: Potent modulators of RNA function can be assembled in cellulo by using the cell as a reaction vessel and a disease-causing RNA as a catalyst. When designing small molecule effectors of function, a balance between permeability and potency must be struck. Low molecular weight compounds are more permeable while higher molecular weight compounds are more potent. The advantages of both types of compounds could be synergized if low molecular weight molecules could be transformed into potent, multivalent ligands via a reaction catalyzed by binding to a target in cells expressing a genetic defect. We demonstrate that this approach is indeed viable in cellulo. Small molecule modules with precisely positioned alkyne and azide moieties bind adjacent internal loops in r(CCUG)exp, the causative agent of myotonic dystrophy type 2 (DM2), and are transformed into oligomeric, potent inhibitors of DM2 RNA dysfunction via a 1,3 Huisgen dipolar cycloaddition reaction, a variant of click chemistry.

Abstract: Methods and computer systems are described herein for identifying small molecules that bind to selected RNA structural features (e.g., to RNA secondary structures). Also described are compounds and compositions that modulate RNA function and/or activity.

Abstract: A repeat expansion in C9ORF72 causes frontotemporal dementia and amyotrophic lateral sclerosis (c9FTD/ALS). RNA of the expanded repeat (r(GGGGCC)exp) forms nuclear foci or undergoes repeat-associated non-ATG (RAN) translation producing “c9RAN proteins”. Since neutralizing r(GGGGCC)exp could inhibit these potentially toxic events, we sought to identify small molecule binders of r(GGGGCC)exp. Chemical and enzymatic probing of r(GGGGCC)8 indicate it adopts a hairpin structure in equilibrium with a quadruplex structure. Using this model, bioactive small molecules targeting r(GGGGCC)exp were designed and found to significantly inhibit RAN translation and foci formation in cultured cells expressing r(GGGGCC)66 and neurons trans-differentiated from fibroblasts of repeat expansion carriers. Finally, we show that poly(GP) c9RAN proteins are specifically detected in c9ALS patient cerebrospinal fluid.

Abstract: The invention provides compounds and their pharmaceutical compositions according to Formula (I) that are useful for inhibiting RNA toxicity, such as in the treatment of myotonic dystrophy type 1, wherein W1, W2, W3, W4, L1, L2, and Cy are defined herein.