Co-reporter:Matthew G. Costales, Christopher L. Haga, Sai Pradeep Velagapudi, Jessica L. Childs-Disney, Donald G. Phinney, and Matthew D. Disney
Journal of the American Chemical Society March 8, 2017 Volume 139(Issue 9) pp:3446-3446
Publication Date(Web):February 27, 2017
DOI:10.1021/jacs.6b11273
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.
Co-reporter:Jonathan L. Chen, Damian M. VanEtten, Matthew A. Fountain, Ilyas Yildirim, and Matthew D. Disney
Biochemistry July 11, 2017 Volume 56(Issue 27) pp:3463-3463
Publication Date(Web):June 15, 2017
DOI:10.1021/acs.biochem.7b00252
RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington’s disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson–Crick/Watson–Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson–Crick/Watson–Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.
Co-reporter:Alicia J. Angelbello
Accounts of Chemical Research December 20, 2016 Volume 49(Issue 12) pp:2698-2704
Publication Date(Web):November 22, 2016
DOI:10.1021/acs.accounts.6b00326
ConspectusThe discovery of RNA catalysis in the 1980s and the dissemination of the human genome sequence at the start of this century inspired investigations of the regulatory roles of noncoding RNAs in biology. In fact, the Encyclopedia of DNA Elements (ENCODE) project has shown that only 1–2% of the human genome encodes protein, yet 75% is transcribed into RNA. Functional studies both preceding and following the ENCODE project have shown that these noncoding RNAs have important roles in regulating gene expression, developmental timing, and other critical functions. RNA’s diverse roles are often a consequence of the various folds that it adopts. The single-stranded nature of the biopolymer enables it to adopt intramolecular folds with noncanonical pairings to lower its free energy. These folds can be scaffolds to bind proteins or to form frameworks to interact with other RNAs. Not surprisingly, dysregulation of certain noncoding RNAs has been shown to be causative of disease.Given this as the background, it is easy to see why it would be useful to develop methods that target RNA and manipulate its biology in rational and predictable ways. The antisense approach has afforded strategies to target RNAs via Watson–Crick base pairing and has typically focused on targeting partially unstructured regions of RNA. Small molecule strategies to target RNA would be desirable not only because compounds could be lead optimized via medicinal chemistry but also because structured regions within an RNA of interest could be targeted to directly interfere with RNA folds that contribute to disease. Additionally, small molecules have historically been the most successful drug candidates. Until recently, the ability to design small molecules that target non-ribosomal RNAs has been elusive, creating the perception that they are “undruggable”.In this Account, approaches to demystify targeting RNA with small molecules are described. Rather than bulk screening for compounds that bind to singular targets, which is the purview of the pharmaceutical industry and academic institutions with high throughput screening facilities, we focus on methods that allow for the rational design of small molecules toward biological RNAs. One enabling and foundational technology that has been developed is two-dimensional combinatorial screening (2DCS), a library-versus-library selection approach that allows the identification of the RNA motif binding preferences of small molecules from millions of combinations. A landscape map of the 2DCS-defined and annotated RNA motif–small molecule interactions is then placed into Inforna, a computational tool that allows one to mine these interactions against an RNA of interest or an entire transcriptome. Indeed, this approach has been enabled by tools to annotate RNA structure from sequence, an invaluable asset to the RNA community and this work, and has allowed for the rational identification of “druggable” RNAs in a target agnostic fashion.
Co-reporter:Matthew D. Disney
Trends in Biochemical Sciences 2017 Volume 42, Issue 6(Issue 6) pp:
Publication Date(Web):1 June 2017
DOI:10.1016/j.tibs.2017.04.008
Historically, translational inhibitors have been confined to anti-bacterials that globally affect translation. Lintner et al. demonstrate that small molecules can specifically inhibit translation of a single disease-associated protein by stalling the ribosome’s nascent chain [1], opening up a new therapeutic strategy for ‘undruggable’ proteins.
Co-reporter:Wang-Yong Yang, Fang He, Rita L. Strack, Seok Yoon Oh, Michelle Frazer, Samie R. Jaffrey, Peter K. Todd, and Matthew D. Disney
ACS Chemical Biology 2016 Volume 11(Issue 9) pp:2456
Publication Date(Web):June 8, 2016
DOI:10.1021/acschembio.6b00147
RNA transcripts containing expanded nucleotide repeats cause many incurable diseases via various mechanisms. One such disorder, fragile X-associated tremor ataxia syndrome (FXTAS), is caused by a noncoding r(CGG) repeat expansion (r(CGG)exp) that (i) sequesters proteins involved in RNA metabolism in nuclear foci, causing dysregulation of alternative pre-mRNA splicing, and (ii) undergoes repeat associated non-ATG translation (RANT), which produces toxic homopolymeric proteins without using a start codon. Here, we describe the design of two small molecules that inhibit both modes of toxicity and the implementation of various tools to study perturbation of these cellular events. Competitive Chemical Cross Linking and Isolation by Pull Down (C-Chem-CLIP) established that compounds bind r(CGG)exp and defined small molecule occupancy of r(CGG)exp in cells, the first approach to do so. Using an RNA GFP mimic, r(CGG)exp-Spinach2, we observe that our optimal designed compound binds r(CGG)exp and affects RNA localization by disrupting preformed RNA foci. These events correlate with an improvement of pre-mRNA splicing defects caused by RNA gain of function. In addition, the compounds reduced levels of toxic homopolymeric proteins formed via RANT. Polysome profiling studies showed that small molecules decreased loading of polysomes onto r(CGG)exp, explaining decreased translation.
Co-reporter:Jessica L. Childs-Disney and Matthew D. Disney
ACS Chemical Biology 2016 Volume 11(Issue 2) pp:375
Publication Date(Web):November 9, 2015
DOI:10.1021/acschembio.5b00615
Development of precision therapeutics is of immense interest, particularly as applied to the treatment of cancer. By analyzing the preferred cellular RNA targets of small molecules, we discovered that 5″-azido neomycin B binds the Drosha processing site in the microRNA (miR)-525 precursor. MiR-525 confers invasive properties to hepatocellular carcinoma (HCC) cells. Although HCC is one of the most common cancers, treatment options are limited, making the disease often fatal. Herein, we find that addition of 5″-azido neomycin B and its FDA-approved precursor, neomycin B, to an HCC cell line selectively inhibits production of the mature miRNA, boosts a downstream protein, and inhibits invasion. Interestingly, neomycin B is a second-line agent for hepatic encephalopathy (HE) and bacterial infections due to cirrhosis. Our results provocatively suggest that neomycin B, or second-generation derivatives, may be dual functioning molecules to treat both HE and HCC. Collectively, these studies show that rational design approaches can be tailored to disease-associated RNAs to afford potential lead therapeutics.
Co-reporter:Matthew D. Disney, Audrey M. Winkelsas, Sai Pradeep Velagapudi, Mark Southern, Mohammad Fallahi, and Jessica L. Childs-Disney
ACS Chemical Biology 2016 Volume 11(Issue 6) pp:1720
Publication Date(Web):April 20, 2016
DOI:10.1021/acschembio.6b00001
The development of small molecules that target RNA is challenging yet, if successful, could advance the development of chemical probes to study RNA function or precision therapeutics to treat RNA-mediated disease. Previously, we described Inforna, an approach that can mine motifs (secondary structures) within target RNAs, which is deduced from the RNA sequence, and compare them to a database of known RNA motif–small molecule binding partners. Output generated by Inforna includes the motif found in both the database and the desired RNA target, lead small molecules for that target, and other related meta-data. Lead small molecules can then be tested for binding and affecting cellular (dys)function. Herein, we describe Inforna 2.0, which incorporates all known RNA motif–small molecule binding partners reported in the scientific literature, a chemical similarity searching feature, and an improved user interface and is freely available via an online web server. By incorporation of interactions identified by other laboratories, the database has been doubled, containing 1936 RNA motif–small molecule interactions, including 244 unique small molecules and 1331 motifs. Interestingly, chemotype analysis of the compounds that bind RNA in the database reveals features in small molecule chemotypes that are privileged for binding. Further, this updated database expanded the number of cellular RNAs to which lead compounds can be identified.
Co-reporter:Matthew David Disney
Bioorganic & Medicinal Chemistry 2016 Volume 24(Issue 17) pp:3875
Publication Date(Web):1 September 2016
DOI:10.1016/j.bmc.2016.06.049
Co-reporter:Matthew G. Costales, Suzanne G. Rzuczek, Matthew D. Disney
Bioorganic & Medicinal Chemistry Letters 2016 26(11) pp: 2605-2609
Publication Date(Web):1 June 2016
DOI:10.1016/j.bmcl.2016.04.025
Potential RNA targets for chemical probes and therapeutic modalities are pervasive in the transcriptome. Oligonucleotide-based therapeutics are commonly used to target RNA sequence. Small molecules are emerging as a modality to target RNA structures selectively, but their development is still in its infancy. In this work, we compare the activity of oligonucleotides and several classes of small molecules that target the non-coding r(CCUG) repeat expansion (r(CCUG)exp) that causes myotonic dystrophy type 2 (DM2), an incurable disease that is the second-most common cause of adult onset muscular dystrophy. Small molecule types investigated include monomers, dimers, and multivalent compounds synthesized on-site by using RNA-templated click chemistry. Oligonucleotides investigated include phosphorothioates that cleave their target and vivo-morpholinos that modulate target RNA activity via binding. We show that compounds assembled on-site that recognize structure have the highest potencies amongst small molecules and are similar in potency to a vivo-morpholino modified oligonucleotide that targets sequence. These studies are likely to impact the design of therapeutic modalities targeting other repeats expansions that cause fragile X syndrome and amyotrophic lateral sclerosis, for example.
Co-reporter:Sai Pradeep Velagapudi;Laura H. Rosenberg;Michael D. Cameron;Derek R. Duckett;Marie Lafitte;Donald G. Phinney;Christopher L. Haga
PNAS 2016 Volume 113 (Issue 21 ) pp:5898-5903
Publication Date(Web):2016-05-24
DOI:10.1073/pnas.1523975113
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.
Co-reporter:Wang-Yong Yang; Henry D. Wilson; Sai Pradeep Velagapudi
Journal of the American Chemical Society 2015 Volume 137(Issue 16) pp:5336-5345
Publication Date(Web):March 31, 2015
DOI:10.1021/ja507448y
One major class of disease-causing RNAs is expanded repeating transcripts. These RNAs cause diseases via multiple mechanisms, including: (i) gain-of-function, in which repeating RNAs bind and sequester proteins involved in RNA biogenesis and (ii) repeat associated non-ATG (RAN) translation, in which repeating transcripts are translated into toxic proteins without use of a canonical, AUG, start codon. Herein, we develop and study chemical probes that bind and react with an expanded r(CGG) repeat (r(CGG)exp) present in a 5′ untranslated region that causes fragile X-associated tremor/ataxia syndrome (FXTAS). Reactive compounds bind to r(CGG)exp in cellulo as shown with Chem-CLIP-Map, an approach to map small molecule binding sites within RNAs in cells. Compounds also potently improve FXTAS-associated pre-mRNA splicing and RAN translational defects, while not affecting translation of the downstream open reading frame. In contrast, oligonucleotides affect both RAN and canonical translation when they bind to r(CGG)exp, which is mechanistically traced to a decrease in polysome loading. Thus, designer small molecules that react with RNA targets can be used to profile the RNAs to which they bind in cells, including identification of binding sites, and can modulate several aspects of RNA-mediated disease pathology in a manner that may be more beneficial than oligonucleotides.
Co-reporter:Suzanne G. Rzuczek, Mark R. Southern, and Matthew D. Disney
ACS Chemical Biology 2015 Volume 10(Issue 12) pp:2706
Publication Date(Web):September 28, 2015
DOI:10.1021/acschembio.5b00430
There are many RNA targets in the transcriptome to which small molecule chemical probes and lead therapeutics are desired. However, identifying compounds that bind and modulate RNA function in cellulo is difficult. Although rational design approaches have been developed, they are still in their infancies and leave many RNAs “undruggable”. In an effort to develop a small molecule library that is biased for binding RNA, we computationally identified “drug-like” compounds from screening collections that have favorable properties for binding RNA and for suitability as lead drugs. As proof-of-concept, this collection was screened for binding to and modulating the cellular dysfunction of the expanded repeating RNA (r(CUG)exp) that causes myotonic dystrophy type 1. Hit compounds bind the target in cellulo, as determined by the target identification approach Competitive Chemical Cross-Linking and Isolation by Pull-down (C-ChemCLIP), and selectively improve several disease-associated defects. The best compounds identified from our 320-member library are more potent in cellulo than compounds identified by high-throughput screening (HTS) campaigns against this RNA. Furthermore, the compound collection has a higher hit rate (9% compared to 0.01–3%), and the bioactive compounds identified are not charged; thus, RNA can be “drugged” with compounds that have favorable pharmacological properties. Finally, this RNA-focused small molecule library may serve as a useful starting point to identify lead “drug-like” chemical probes that affect the biological (dys)function of other RNA targets by direct target engagement.
Co-reporter:Christopher L. Haga, Sai Pradeep Velagapudi, Jacqueline R. Strivelli, Wang-Yong Yang, Matthew D. Disney, and Donald G. Phinney
ACS Chemical Biology 2015 Volume 10(Issue 10) pp:2267
Publication Date(Web):July 16, 2015
DOI:10.1021/acschembio.5b00265
Hypoxia induces a complex circuit of gene expression that drives tumor progression and increases drug resistance. Defining these changes allows for an understanding of how hypoxia alters tumor biology and informs design of lead therapeutics. We probed the role of microRNA-544 (miR-544), which silences mammalian target of rapamycin (mTOR), in a hypoxic breast cancer model by using a small molecule (1) that selectively impedes the microRNA’s biogenesis. Application of 1 to hypoxic tumor cells selectively inhibited production of the mature microRNA, sensitized cells to 5-fluorouracil, and derepressed mRNAs affected by miR-544 in cellulo and in vivo, including boosting mTOR expression. Thus, small molecule inhibition of miR-544 reverses a tumor cell’s physiological response to hypoxia. Importantly, 1 sensitized tumor cells to hypoxia-associated apoptosis at a 25-fold lower concentration than a 2′-O-methyl RNA antagomir and was as selective. Further, the apoptotic effect of 1 was suppressed by treatment of cell with rapamycin, a well-known inhibitor of the mTOR signaling pathway, illustrating the selectivity of the compound. Thus, RNA-directed chemical probes, which could also serve as lead therapeutics, enable interrogation of complex cellular networks in cells and animals.
Co-reporter:HaJeung Park, Àlex L. González, Ilyas Yildirim, Tuan Tran, Jeremy R. Lohman, Pengfei Fang, Min Guo, and Matthew D. Disney
Biochemistry 2015 Volume 54(Issue 24) pp:3851-3859
Publication Date(Web):June 3, 2015
DOI:10.1021/acs.biochem.5b00551
Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide 5′UCU3′/3′UCU5′ internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.
Co-reporter:Sai Pradeep Velagapudi and Matthew D. Disney
Chemical Communications 2014 vol. 50(Issue 23) pp:3027-3029
Publication Date(Web):17 Jan 2014
DOI:10.1039/C3CC00173C
The RNA motifs that bind guanidinylated kanamycin A (G Kan A) and guanidinylated neomycin B (G Neo B) were identified via two-dimensional combinatorial screening (2DCS). The results of these studies enabled the “bottom-up” design of a small molecule inhibitor of oncogenic microRNA-10b.
Co-reporter:Tuan Tran, Jessica L. Childs-Disney, Biao Liu, Lirui Guan, Suzanne Rzuczek, and Matthew D. Disney
ACS Chemical Biology 2014 Volume 9(Issue 4) pp:904
Publication Date(Web):February 7, 2014
DOI:10.1021/cb400875u
We designed small molecules that bind the structure of the RNA that causes fragile X-associated tremor ataxia syndrome (FXTAS), an incurable neuromuscular disease. FXTAS is caused by an expanded r(CGG) repeat (r(CGG)exp) that inactivates a protein regulator of alternative pre-mRNA splicing. Our designed compounds modulate r(CGG)exp toxicity in cellular models of FXTAS, and pull-down experiments confirm that they bind r(CGG)exp in vivo. Importantly, compound binding does not affect translation of the downstream open reading frame (ORF). We compared molecular recognition properties of our optimal compound to oligonucleotides. Studies show that r(CGG)exp’s self-structure is a significant energetic barrier for oligonucleotide binding. A fully modified 2′-OMethyl phosphorothioate is incapable of completely reversing an FXTAS-associated splicing defect and inhibits translation of the downstream ORF, which could have deleterious effects. Taken together, these studies suggest that a small molecule that recognizes structure may be more well suited for targeting highly structured RNAs that require strand invasion by a complementary oligonucleotide.
Co-reporter:Jessica L. Childs-Disney, Ilyas Yildirim, HaJeung Park, Jeremy R. Lohman, Lirui Guan, Tuan Tran, Partha Sarkar, George C. Schatz, and Matthew D. Disney
ACS Chemical Biology 2014 Volume 9(Issue 2) pp:538
Publication Date(Web):December 9, 2013
DOI:10.1021/cb4007387
Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disorder caused by a r(CCUG) expansion (r(CCUG)exp) that folds into an extended hairpin with periodically repeating 2×2 nucleotide internal loops (5′CCUG/3′GUCC). We designed multivalent compounds that improve DM2-associated defects using information about RNA–small molecule interactions. We also report the first crystal structure of r(CCUG) repeats refined to 2.35 Å. Structural analysis of the three 5′CCUG/3′GUCC repeat internal loops (L) reveals that the CU pairs in L1 are each stabilized by one hydrogen bond and a water-mediated hydrogen bond, while CU pairs in L2 and L3 are stabilized by two hydrogen bonds. Molecular dynamics (MD) simulations reveal that the CU pairs are dynamic and stabilized by Na+ and water molecules. MD simulations of the binding of the small molecule to r(CCUG) repeats reveal that the lowest free energy binding mode occurs via the major groove, in which one C residue is unstacked and the cross-strand nucleotides are displaced. Moreover, we modeled the binding of our dimeric compound to two 5′CCUG/3′GUCC motifs, which shows that the scaffold on which the RNA-binding modules are displayed provides an optimal distance to span two adjacent loops.
Co-reporter:Matthew D. Disney, Ilyas Yildirim and Jessica L. Childs-Disney
Organic & Biomolecular Chemistry 2014 vol. 12(Issue 7) pp:1029-1039
Publication Date(Web):21 Nov 2013
DOI:10.1039/C3OB42023J
RNA is an immensely important target for small molecule therapeutics or chemical probes of function. However, methods that identify, annotate, and optimize RNA-small molecule interactions that could enable the design of compounds that modulate RNA function are in their infancies. This review describes recent approaches that have been developed to understand and optimize RNA motif-small molecule interactions, including structure–activity relationships through sequencing (StARTS), quantitative structure–activity relationships (QSAR), chemical similarity searching, structure-based design and docking, and molecular dynamics (MD) simulations. Case studies described include the design of small molecules targeting RNA expansions, the bacterial A-site, viral RNAs, and telomerase RNA. These approaches can be combined to afford a synergistic method to exploit the myriad of RNA targets in the transcriptome.
Co-reporter:Dr. Yiling Luo ; Dr. Matthew D. Disney
ChemBioChem 2014 Volume 15( Issue 14) pp:2041-2044
Publication Date(Web):
DOI:10.1002/cbic.201402069
Abstract
One challenge in chemical biology is to develop small molecules that control cellular protein content. The amount and identity of proteins are influenced by the RNAs that encode them; thus, protein content in a cell could be affected by targeting mRNA. However, RNA has been traditionally difficult to target with small molecules. In this report, we describe controlling the protein products of the mutated microtubule-associated protein tau (MAPT) mature mRNA with a small molecule. MAPT mutations in exon 10 are associated with inherited frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17), an incurable disease that is directly caused by increased inclusion of exon 10 in MAPT mRNA. Recent studies have shown that mutations within a hairpin at the MAPT exon 10–intron junction decrease the thermodynamic stability of the RNA, increasing binding to U1 snRNP and thus exon 10 inclusion. Therefore, we designed small molecules that bind and stabilize a mutant MAPT by using Inforna, a computational approach based on information about RNA–small-molecule interactions. The optimal compound selectively bound the mutant MAPT hairpin and thermodynamically stabilized its folding, facilitating exon 10 exclusion.
Co-reporter:Dr. Suzanne G. Rzuczek;Dr. HaJeung Park ;Dr. Matthew D. Disney
Angewandte Chemie International Edition 2014 Volume 53( Issue 41) pp:10956-10959
Publication Date(Web):
DOI:10.1002/anie.201406465
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 whereas 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 by a reaction that is catalyzed by binding to a target in cells expressing a genetic defect. It was shown 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 by a Huisgen 1,3-dipolar cycloaddition reaction, a variant of click chemistry.
Co-reporter:Dr. Suzanne G. Rzuczek;Dr. HaJeung Park ;Dr. Matthew D. Disney
Angewandte Chemie 2014 Volume 126( Issue 41) pp:11136-11139
Publication Date(Web):
DOI:10.1002/ange.201406465
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 whereas 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 by a reaction that is catalyzed by binding to a target in cells expressing a genetic defect. It was shown 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 by a Huisgen 1,3-dipolar cycloaddition reaction, a variant of click chemistry.
Co-reporter:Ilyas Yildirim ; HaJeung Park ; Matthew D. Disney ;George C. Schatz
Journal of the American Chemical Society 2013 Volume 135(Issue 9) pp:3528-3538
Publication Date(Web):February 26, 2013
DOI:10.1021/ja3108627
One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded CAG repeats can cause Huntington’s and other disease through translation of toxic proteins. Herein, a crystal structure of r[5′UUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that shows both anti–anti and syn–anti orientations for 1 × 1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using AMBER force field in explicit solvent were run for over 500 ns on the model systems r(5′GCGCAGCGC)2 (MS1) and r(5′CCGCAGCGG)2 (MS2). In these MD simulations, both anti–anti and syn–anti AA base pairs appear to be stable. While anti–anti AA base pairs were dynamic and sampled multiple anti–anti conformations, no syn–anti ↔ anti–anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, an explicit solvent MD simulation over 800 ns was run on r[5′GGGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn–anti conformation), transformed to anti–anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn–anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1 × 1 nucleotide AA internal loops in r(CAG) repeats is anti–anti but can adopt syn–anti depending on the environment. These results are important to understand RNA dynamic-function relationships and to develop small molecules that target RNA dynamic ensembles.
Co-reporter:Suzanne G. Rzuczek, Yu Gao, Zhen-Zhi Tang, Charles A. Thornton, Thomas Kodadek, and Matthew D. Disney
ACS Chemical Biology 2013 Volume 8(Issue 10) pp:2312
Publication Date(Web):September 13, 2013
DOI:10.1021/cb400265y
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 noncoding 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, α-peptides, β-peptides, and peptide tertiary amides (PTAs). On the basis of 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. Notably, we determined that r(CUG)exp is the target of the optimal PTA in cellular models and that the optimal PTA improves DM1-associated defects in a mouse model. Biophysical analyses were employed to investigate potential sources of bioactivity. These investigations show that modularly assembled compounds have increased residence times on their targets and faster on rates than the RNA-binding modules from which they were derived. Moreover, they have faster on rates than the protein that binds r(CUG)exp, the inactivation of which gives rise to DM1-associated defects. These studies provide information about features of small molecules that are programmable for targeting RNA, allowing for the facile optimization of therapeutics or chemical probes against other cellular RNA targets.
Co-reporter:Sai Pradeep Velagapudi, Matthew D. Disney
Bioorganic & Medicinal Chemistry 2013 Volume 21(Issue 20) pp:6132-6138
Publication Date(Web):15 October 2013
DOI:10.1016/j.bmc.2013.04.072
RNA is an extremely important target for the development of chemical probes of function or small molecule therapeutics. Aminoglycosides are the most well studied class of small molecules to target RNA. However, the RNA motifs outside of the bacterial rRNA A-site that are likely to be bound by these compounds in biological systems is largely unknown. If such information were known, it could allow for aminoglycosides to be exploited to target other RNAs and, in addition, could provide invaluable insights into potential bystander targets of these clinically used drugs. We utilized two-dimensional combinatorial screening (2DCS), a library-versus-library screening approach, to select the motifs displayed in a 3 × 3 nucleotide internal loop library and in a 6-nucleotide hairpin library that bind with high affinity and selectivity to six aminoglycoside derivatives. The selected RNA motifs were then analyzed using structure–activity relationships through sequencing (StARTS), a statistical approach that defines the privileged RNA motif space that binds a small molecule. StARTS allowed for the facile annotation of the selected RNA motif–aminoglycoside interactions in terms of affinity and selectivity. The interactions selected by 2DCS generally have nanomolar affinities, which is higher affinity than the binding of aminoglycosides to a mimic of their therapeutic target, the bacterial rRNA A-site.
Co-reporter:Dr. Lirui Guan ;Dr. Matthew D. Disney
Angewandte Chemie International Edition 2013 Volume 52( Issue 38) pp:10010-10013
Publication Date(Web):
DOI:10.1002/anie.201301639
Co-reporter:Dr. Lirui Guan ;Dr. Matthew D. Disney
Angewandte Chemie 2013 Volume 125( Issue 38) pp:10194-10197
Publication Date(Web):
DOI:10.1002/ange.201301639
Co-reporter:Dr. Lirui Guan ;Dr. Matthew D. Disney
Angewandte Chemie 2013 Volume 125( Issue 5) pp:1502-1505
Publication Date(Web):
DOI:10.1002/ange.201206888
Co-reporter:Dr. Lirui Guan ;Dr. Matthew D. Disney
Angewandte Chemie International Edition 2013 Volume 52( Issue 5) pp:1462-1465
Publication Date(Web):
DOI:10.1002/anie.201206888
Co-reporter:Raman Parkesh ; Jessica L. Childs-Disney ; Masayuki Nakamori ; Amit Kumar ; Eric Wang ; Thomas Wang ; Jason Hoskins ; Tuan Tran ; David Housman ; Charles A. Thornton
Journal of the American Chemical Society 2012 Volume 134(Issue 10) pp:4731-4742
Publication Date(Web):February 2, 2012
DOI:10.1021/ja210088v
Myotonic dystrophy type 1 (DM1) is a triplet repeating disorder caused by expanded CTG repeats in the 3′-untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. The transcribed repeats fold into an RNA hairpin with multiple copies of a 5′CUG/3′GUC motif that binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1). Sequestration of MBNL1 by expanded r(CUG) repeats causes splicing defects in a subset of pre-mRNAs including the insulin receptor, the muscle-specific chloride ion channel, sarco(endo)plasmic reticulum Ca2+ ATPase 1, and cardiac troponin T. Based on these observations, the development of small-molecule ligands that target specifically expanded DM1 repeats could be of use as therapeutics. In the present study, chemical similarity searching was employed to improve the efficacy of pentamidine and Hoechst 33258 ligands that have been shown previously to target the DM1 triplet repeat. A series of in vitro inhibitors of the RNA–protein complex were identified with low micromolar IC50’s, which are >20-fold more potent than the query compounds. Importantly, a bis-benzimidazole identified from the Hoechst query improves DM1-associated pre-mRNA splicing defects in cell and mouse models of DM1 (when dosed with 1 mM and 100 mg/kg, respectively). Since Hoechst 33258 was identified as a DM1 binder through analysis of an RNA motif–ligand database, these studies suggest that lead ligands targeting RNA with improved biological activity can be identified by using a synergistic approach that combines analysis of known RNA–ligand interactions with chemical similarity searching.
Co-reporter:Jessica L. Childs-Disney, Jason Hoskins, Suzanne G. Rzuczek, Charles A. Thornton, and Matthew D. Disney
ACS Chemical Biology 2012 Volume 7(Issue 5) pp:856
Publication Date(Web):February 14, 2012
DOI:10.1021/cb200408a
RNA is an important drug target, but it is difficult to design or discover small molecules that modulate RNA function. In the present study, we report that rationally designed, modularly assembled small molecules that bind the RNA that causes myotonic dystrophy type 1 (DM1) are potently bioactive in cell culture models. DM1 is caused when an expansion of r(CUG) repeats, or r(CUG)exp, is present in the 3′ untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) mRNA. r(CUG)exp folds into a hairpin with regularly repeating 5′CUG/3′GUC motifs and sequesters muscleblind-like 1 protein (MBNL1). A variety of defects are associated with DM1, including (i) formation of nuclear foci, (ii) decreased translation of DMPK mRNA due to its nuclear retention, and (iii) pre-mRNA splicing defects due to inactivation of MBNL1, which controls the alternative splicing of various pre-mRNAs. Previously, modularly assembled ligands targeting r(CUG)exp were designed using information in an RNA motif-ligand database. These studies showed that a bis-benzimidazole (H) binds the 5′CUG/3′GUC motif in r(CUG)exp. Therefore, we designed multivalent ligands to bind simultaneously multiple copies of this motif in r(CUG)exp. Herein, we report that the designed compounds improve DM1-associated defects including improvement of translational and pre-mRNA splicing defects and the disruption of nuclear foci. These studies may establish a foundation to exploit other RNA targets in genomic sequence.
Co-reporter:Sai Pradeep Velagapudi, Alexei Pushechnikov, Lucas P. Labuda, Jonathan M. French, and Matthew D. Disney
ACS Chemical Biology 2012 Volume 7(Issue 11) pp:1902
Publication Date(Web):September 8, 2012
DOI:10.1021/cb300213g
There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA–ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA–ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition.
Co-reporter:Matthew D. Disney, Biao Liu, Wang-Yong Yang, Chantal Sellier, Tuan Tran, Nicolas Charlet-Berguerand, and Jessica L. Childs-Disney
ACS Chemical Biology 2012 Volume 7(Issue 10) pp:1711
Publication Date(Web):September 4, 2012
DOI:10.1021/cb300135h
The development of small molecule chemical probes or therapeutics that target RNA remains a significant challenge despite the great interest in such compounds. The most significant barrier to compound development is defining which chemical and RNA motif spaces interact specifically. Herein, we describe a bioactive small molecule probe that targets expanded r(CGG) repeats, or r(CGG)exp, that causes Fragile X-associated Tremor Ataxia Syndrome (FXTAS). The compound was identified by using information on the chemotypes and RNA motifs that interact. Specifically, 9-hydroxy-5,11-dimethyl-2-(2-(piperidin-1-yl)ethyl)-6H-pyrido[4,3-b]carbazol-2-ium binds the 5′CGG/3′GGC motifs in r(CGG)exp and disrupts a toxic r(CGG)exp-protein complex in vitro. Structure–activity relationship studies determined that the alkylated pyridyl and phenolic side chains are important chemotypes that drive molecular recognition of r(CGG)exp. Importantly, the compound is efficacious in FXTAS model cellular systems as evidenced by its ability to improve FXTAS-associated pre-mRNA splicing defects and to reduce the size and number of r(CGG)exp-containing nuclear foci. This approach may establish a general strategy to identify lead ligands that target RNA while also providing a chemical probe to dissect the varied mechanisms by which r(CGG)exp promotes toxicity.
Co-reporter:Jessica L. Childs-Disney, Raman Parkesh, Masayuki Nakamori, Charles A. Thornton, and Matthew D. Disney
ACS Chemical Biology 2012 Volume 7(Issue 12) pp:1984
Publication Date(Web):November 7, 2012
DOI:10.1021/cb3001606
Myotonic dystrophy type 1 (DM1) is caused when an expanded r(CUG) repeat (r(CUG)exp) binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1) as well as other proteins. Previously, we reported that modularly assembled small molecules displaying a 6′-N-5-hexynoate kanamycin A RNA-binding module (K) on a peptoid backbone potently inhibit the binding of MBNL1 to r(CUG)exp. However, these parent compounds are not appreciably active in cell-based models of DM1. The lack of potency was traced to suboptimal cellular permeability and localization. To improve these properties, second-generation compounds that are conjugated to a d-Arg9 molecular transporter were synthesized. These modified compounds enter cells in higher concentrations than the parent compounds and are efficacious in cell-based DM1 model systems at low micromolar concentrations. In particular, they improve three defects that are the hallmarks of DM1: a translational defect due to nuclear retention of transcripts containing r(CUG)exp; pre-mRNA splicing defects due to inactivation of MBNL1; and the formation of nuclear foci. The best compound in cell-based studies was tested in a mouse model of DM1. Modest improvement of pre-mRNA splicing defects was observed. These studies suggest that a modular assembly approach can afford bioactive compounds that target RNA.
Co-reporter:Amit Kumar, Raman Parkesh, Lukasz J. Sznajder, Jessica L. Childs-Disney, Krzysztof Sobczak, and Matthew D. Disney
ACS Chemical Biology 2012 Volume 7(Issue 3) pp:496
Publication Date(Web):January 17, 2012
DOI:10.1021/cb200413a
Recently, it was reported that expanded r(CAG) triplet repeats (r(CAG)exp) associated with untreatable neurological diseases cause pre-mRNA mis-splicing likely due to sequestration of muscleblind-like 1 (MBNL1) splicing factor. Bioactive small molecules that bind the 5′CAG/3′GAC motif found in r(CAG)exp hairpin structure were identified by using RNA binding studies and virtual screening/chemical similarity searching. Specifically, a benzylguanidine-containing small molecule was found to improve pre-mRNA alternative splicing of MBNL1-sensitive exons in cells expressing the toxic r(CAG)exp. The compound was identified by first studying the binding of RNA 1×1 nucleotide internal loops to small molecules known to have affinity for nucleic acids. Those studies identified 4′,6-diamidino-2-phenylindole (DAPI) as a specific binder to RNAs with the 5′CAG/3′GAC motif. DAPI was then used as a query molecule in a shape- and chemistry alignment-based virtual screen to identify compounds with improved properties, which identified 4-guanidinophenyl 4-guanidinobenzoate, a small molecule that improves pre-mRNA splicing defects associated with the r(CAG)exp-MBNL1 complex. This compound may facilitate the development of therapeutics to treat diseases caused by r(CAG)exp and could serve as a useful chemical tool to dissect the mechanisms of r(CAG)exp toxicity. The approach used in these studies, defining the small RNA motifs that bind small molecules with known affinity for nucleic acids and then using virtual screening to optimize them for bioactivity, may be generally applicable for designing small molecules that target other RNAs in the human genomic sequence.
Co-reporter:Lirui Guan and Matthew D. Disney
ACS Chemical Biology 2012 Volume 7(Issue 1) pp:73
Publication Date(Web):December 20, 2011
DOI:10.1021/cb200447r
RNAs are underexploited targets for small molecule drugs or chemical probes of function. This may be due, in part, to a fundamental lack of understanding of the types of small molecules that bind RNA specifically and the types of RNA motifs that specifically bind small molecules. In this review, we describe recent advances in the development and design of small molecules that bind to RNA and modulate function that aim to fill this void.
Co-reporter:Sai Pradeep Velagapudi ; Steven J. Seedhouse ; Jonathan French
Journal of the American Chemical Society 2011 Volume 133(Issue 26) pp:10111-10118
Publication Date(Web):May 23, 2011
DOI:10.1021/ja200212b
RNA is an important therapeutic target; however, RNA targets are generally underexploited due to a lack of understanding of the small molecules that bind RNA and the RNA motifs that bind small molecules. Herein, we describe the identification of the RNA internal loops derived from a 4096 member 3 × 3 nucleotide loop library that are the most specific and highest affinity binders to a series of four designer, druglike benzimidazoles. These studies establish a potentially general protocol to define the highest affinity and most specific RNA motif targets for heterocyclic small molecules. Such information could be used to target functionally important RNAs in genomic sequence.
Co-reporter:
Biochemistry 2011 Volume 50(Issue 5) pp:599-601
Publication Date(Web):January 4, 2011
DOI:10.1021/bi101896j
The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single-hydrogen bond structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bond structure is the most populated one but the UU pair interconverts among zero, one, and two hydrogen bond pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins.
Co-reporter:
Biochemistry 2011 Volume 50(Issue 6) pp:962-969
Publication Date(Web):January 5, 2011
DOI:10.1021/bi101724h
In our previous study to identify the RNA internal loops that bind an aminoglycoside derivative, we determined that 6′-N-5-hexynoate kanamycin A prefers to bind 1x1 nucleotide internal loops containing C·A mismatches. In this present study, the molecular recognition between a variety of RNAs that are mutated around the C·A loop and the ligand was investigated. Studies show that both loop nucleotides and loop closing pairs affect binding affinity. Most interestingly, it was shown that there is a correlation between the thermodynamic stability of the C·A internal loops and ligand affinity. Specifically, C·A loops that had relatively high or low stability bound the ligand most weakly whereas loops with intermediate stability bound the ligand most tightly. In contrast, there is no correlation between the likelihood that a loop forms a C-A+ pair at lower pH and ligand affinity. It was also found that a 1x1 nucleotide C·A loop that bound to the ligand with the highest affinity is identical to the consensus site in RNAs that are edited by adenosine deaminases acting on RNA type 2 (ADAR2). These studies provide a detailed investigation of factors affecting small molecule recognition of internal loops containing C·A mismatches, which are present in a variety of RNAs that cause disease.
Co-reporter:Amit Kumar, HaJeung Park, Pengfei Fang, Raman Parkesh, Min Guo, Kendall W. Nettles, and Matthew D. Disney
Biochemistry 2011 Volume 50(Issue 45) pp:
Publication Date(Web):October 11, 2011
DOI:10.1021/bi2013068
RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5′CUG/3′GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5′r[UUGGGC(CUG)3GUCC]2, refined to 2.20 and 1.52 Å resolution are disclosed. Here, differences in the orientation of the 5′ dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5′ UU forms a one hydrogen-bonded pair with a 5′ UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å structure, CUGb, the 5′ UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 × 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5′ UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 × 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.
Co-reporter: Dr. Jessica L. Childs-Disney;Dr. Pavel B. Tsitovich; Dr. Matthew D. Disney
ChemBioChem 2011 Volume 12( Issue 14) pp:2143-2146
Publication Date(Web):
DOI:10.1002/cbic.201100298
Co-reporter:Dr. Amit Kumar;Dr. Pengfei Fang;Dr. Hajeung Park; Dr. Min Guo; Dr. Kendall W. Nettles; Dr. Matthew D. Disney
ChemBioChem 2011 Volume 12( Issue 14) pp:2140-2142
Publication Date(Web):
DOI:10.1002/cbic.201100337
Co-reporter:Pavel B. Tsitovich Dr.;Alexei Pushechnikov Dr.;Jonathan M. French Dr.
ChemBioChem 2010 Volume 11( Issue 12) pp:1656-1660
Publication Date(Web):
DOI:10.1002/cbic.201000300
Co-reporter:Pavel B. Tsitovich Dr.;Alexei Pushechnikov Dr.;Jonathan M. French Dr.
ChemBioChem 2010 Volume 11( Issue 12) pp:
Publication Date(Web):
DOI:10.1002/cbic.201090056
Co-reporter:Matthew D. Disney
Drug Discovery Today (December 2013) Volume 18(Issues 23–24) pp:1228-1236
Publication Date(Web):1 December 2013
DOI:10.1016/j.drudis.2013.07.024
•We describe general issues in developing RNA-targeted small molecules.•We describe methods to obtain lead small molecule–RNA motif interactions.•We describe optimization procedures for small molecules targeting RNA.•We describe advantages of small molecules for targeting RNA as compared to oligonucleotides.RNA is an important yet vastly underexploited target for small molecule chemical probes or lead therapeutics. Small molecules have been used successfully to modulate the function of the bacterial ribosome, viral RNAs and riboswitches. These RNAs are either highly expressed or can be targeted using substrate mimicry, a mainstay in the design of enzyme inhibitors. However, most cellular RNAs are neither highly expressed nor have a lead small molecule inhibitor, a significant challenge for drug discovery efforts. Herein, I describe the design of small molecules targeting expanded repeating transcripts that cause myotonic muscular dystrophy (DM). These test cases illustrate the challenges of designing small molecules that target RNA and the advantages of targeting repeating transcripts. Lastly, I discuss how small molecules might be more advantageous than oligonucleotides for targeting RNA.
Co-reporter:Viachaslau Bernat, Matthew D. Disney
Neuron (1 July 2015) Volume 87(Issue 1) pp:28-46
Publication Date(Web):1 July 2015
DOI:10.1016/j.neuron.2015.06.012
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
Co-reporter:Sai Pradeep Velagapudi and Matthew D. Disney
Chemical Communications 2014 - vol. 50(Issue 23) pp:NaN3029-3029
Publication Date(Web):2014/01/17
DOI:10.1039/C3CC00173C
The RNA motifs that bind guanidinylated kanamycin A (G Kan A) and guanidinylated neomycin B (G Neo B) were identified via two-dimensional combinatorial screening (2DCS). The results of these studies enabled the “bottom-up” design of a small molecule inhibitor of oncogenic microRNA-10b.
Co-reporter:Matthew D. Disney, Ilyas Yildirim and Jessica L. Childs-Disney
Organic & Biomolecular Chemistry 2014 - vol. 12(Issue 7) pp:NaN1039-1039
Publication Date(Web):2013/11/21
DOI:10.1039/C3OB42023J
RNA is an immensely important target for small molecule therapeutics or chemical probes of function. However, methods that identify, annotate, and optimize RNA-small molecule interactions that could enable the design of compounds that modulate RNA function are in their infancies. This review describes recent approaches that have been developed to understand and optimize RNA motif-small molecule interactions, including structure–activity relationships through sequencing (StARTS), quantitative structure–activity relationships (QSAR), chemical similarity searching, structure-based design and docking, and molecular dynamics (MD) simulations. Case studies described include the design of small molecules targeting RNA expansions, the bacterial A-site, viral RNAs, and telomerase RNA. These approaches can be combined to afford a synergistic method to exploit the myriad of RNA targets in the transcriptome.
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