Structure based approaches for targeting non-coding RNAs with small molecules
Tài liệu tham khảo
Guan, 2012, Recent advances in developing small molecules targeting RNA, ACS Chem Biol, 7, 73, 10.1021/cb200447r
Thomas, 2008, Targeting RNA with small molecules, Chem Rev, 108, 1171, 10.1021/cr0681546
Ling, 2013, microRNAs and other non-coding RNAs as targets for anticancer drug development, Nat Rev Drug Discov, 12, 847, 10.1038/nrd4140
Wilson, 2014, Ribosome-targeting antibiotics and mechanisms of bacterial resistance, Nat Rev Microbiol, 12, 35, 10.1038/nrmicro3155
Blount, 2006, Riboswitches as antibacterial drug targets, Nat Biotechnol, 24, 1558, 10.1038/nbt1268
Warner, 2014, Structural basis for activity of highly efficient RNA mimics of green fluorescent protein, Nat Struct Mol Biol, 21, 658, 10.1038/nsmb.2865
Fabian, 2010, Regulation of mRNA translation and stability by microRNAs, Annu Rev Biochem, 79, 351, 10.1146/annurev-biochem-060308-103103
Di Leva, 2014, MicroRNAs in cancer, Annu Rev Pathol, 9, 287, 10.1146/annurev-pathol-012513-104715
Schöniger, 2013, Perspectives in targeting miRNA function, Bioorg Med Chem, 21, 6115, 10.1016/j.bmc.2013.03.040
Zhang, 2010, Targeting microRNAs with small molecules: from dream to reality, Clin Pharmacol Ther, 87, 754, 10.1038/clpt.2010.46
Gumireddy, 2008, Small-molecule inhibitors of microRNA miR-21 function, Angew Chem Int Ed Engl, 47, 7482, 10.1002/anie.200801555
Young, 2010, Small molecule modifiers of microRNA miR-122 function for the treatment of hepatitis C virus infection and hepatocellular carcinoma, J Am Chem Soc, 132, 7976, 10.1021/ja910275u
Watashi, 2010, Identification of small molecules that suppress microRNA function and reverse tumorigenesis, J Biol Chem, 285, 24707, 10.1074/jbc.M109.062976
Shi, 2013, AC1MMYR2, an inhibitor of dicer-mediated biogenesis of Oncomir miR-21, reverses epithelial–mesenchymal transition and suppresses tumor growth and progression, Cancer Res, 73, 5519, 10.1158/0008-5472.CAN-13-0280
Klinge, 2012, miRNAs and estrogen action, Trends Endocrinol Metab, 23, 223, 10.1016/j.tem.2012.03.002
Murata, 2013, Fluorescent indicator displacement assay of ligands targeting 10 microRNA precursors, Bioorg Med Chem, 21, 7101, 10.1016/j.bmc.2013.09.007
Chandrasekhar, 2012, aza-Flavanones as potent cross-species microRNA inhibitors that arrest cell cycle, Bioorg Med Chem Lett, 22, 645, 10.1016/j.bmcl.2011.10.061
Hagiwara, 2012, Stilbene derivatives promote Ago2-dependent tumour-suppressive microRNA activity, Sci Rep, 2, 314, 10.1038/srep00314
Jiang, 2012, Identification of links between small molecules and miRNAs in human cancers based on transcriptional responses, Sci Rep, 2, 282, 10.1038/srep00282
Quarles, 2013, Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site, Biochemistry, 52, 795, 10.1021/bi301452a
Trabucchi, 2010, KSRP promotes the maturation of a group of miRNA precursors, Adv Exp Med Biol, 700, 36, 10.1007/978-1-4419-7823-3_4
Trabucchi, 2009, The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs, Nature, 459, 1010, 10.1038/nature08025
Michlewski, 2008, Posttranscriptional regulation of miRNAs harboring conserved terminal loops, Mol Cell, 32, 383, 10.1016/j.molcel.2008.10.013
Kloosterman, 2007, Targeted inhibition of miRNA maturation with morpholinos reveals a role for miR-375 in pancreatic islet development, PLoS Biol, 5, e203, 10.1371/journal.pbio.0050203
Velagapudi, 2014, Two-dimensional combinatorial screening enables the bottom-up design of a microRNA-10b inhibitor, Chem Commun (Camb), 50, 3027, 10.1039/c3cc00173c
Bose, 2012, The tuberculosis drug streptomycin as a potential cancer therapeutic: inhibition of miR-21 function by directly targeting its precursor, Angew Chem Int Ed Engl, 51, 1019, 10.1002/anie.201106455
Maiti, 2012, Pre-microRNA binding aminoglycosides and antitumor drugs as inhibitors of Dicer catalyzed microRNA processing, Bioorg Med Chem Lett, 22, 1709, 10.1016/j.bmcl.2011.12.103
François, 2005, Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding, Nucleic Acids Res, 33, 5677, 10.1093/nar/gki862
Velagapudi, 2014, Sequence-based design of bioactive small molecules that target precursor microRNAs, Nat Chem Biol, 10, 291, 10.1038/nchembio.1452
Chirayil, 2009, Discovering ligands for a microRNA precursor with peptoid microarrays, Nucleic Acids Res, 37, 5486, 10.1093/nar/gkp549
Diaz, 2014, Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha, RNA, 20, 528, 10.1261/rna.042911.113
Chirayil, 2014, NMR characterization of an oligonucleotide model of the miR-21 pre-element, PLOS ONE, 9, e108231, 10.1371/journal.pone.0108231
Hamy, 1997, An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication, Proc Natl Acad Sci U S A, 94, 3548, 10.1073/pnas.94.8.3548
La Spada, 2010, Repeat expansion disease: progress and puzzles in disease pathogenesis, Nat Rev Genet, 11, 247, 10.1038/nrg2748
Mooers, 2005, The structural basis of myotonic dystrophy from the crystal structure of CUG repeats, Proc Natl Acad Sci U S A, 102, 16626, 10.1073/pnas.0505873102
Warf, 2009, Pentamidine reverses the splicing defects associated with myotonic dystrophy, Proc Natl Acad Sci U S A, 106, 18551, 10.1073/pnas.0903234106
Coonrod, 2013, Reducing levels of toxic RNA with small molecules, ACS Chem Biol, 8, 2528, 10.1021/cb400431f
Lee, 2009, Controlling the specificity of modularly assembled small molecules for RNA via ligand module spacing: targeting the RNAs that cause myotonic muscular dystrophy, J Am Chem Soc, 131, 17464, 10.1021/ja906877y
Lee, 2009, Rational and modular design of potent ligands targeting the RNA that causes myotonic dystrophy 2, ACS Chem Biol, 4, 345, 10.1021/cb900025w
Pushechnikov, 2009, Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3, J Am Chem Soc, 131, 9767, 10.1021/ja9020149
Disney, 2010, The role of flexibility in the rational design of modularly assembled ligands targeting the RNAs that cause the myotonic dystrophies, ChemBioChem, 11, 375, 10.1002/cbic.200900716
Childs-Disney, 2012, Rational design of bioactive, modularly assembled aminoglycosides targeting the RNA that causes myotonic dystrophy type 1, ACS Chem Biol, 7, 1984, 10.1021/cb3001606
Childs-Disney, 2012, Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive, ACS Chem Biol, 7, 856, 10.1021/cb200408a
Disney, 2012, A small molecule that targets r(CGG)(exp) and improves defects in fragile X-associated tremor ataxia syndrome, ACS Chem Biol, 7, 1711, 10.1021/cb300135h
Parkesh, 2012, Design of a bioactive small molecule that targets the myotonic dystrophy type 1 RNA via an RNA motif-ligand database and chemical similarity searching, J Am Chem Soc, 134, 4731, 10.1021/ja210088v
Disney, 2013, Rational design of chemical genetic probes of RNA function and lead therapeutics targeting repeating transcripts, Drug Discov Today, 18, 1228, 10.1016/j.drudis.2013.07.024
Childs-Disney, 2014, Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity, ACS Chem Biol, 9, 538, 10.1021/cb4007387
Colak, 2014, Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome, Science, 343, 1002, 10.1126/science.1245831
Hoskins, 2014, Lomofungin and dilomofungin: inhibitors of MBNL1-CUG RNA binding with distinct cellular effects, Nucleic Acids Res, 42, 6591, 10.1093/nar/gku275
Su, 2014, Discovery of a biomarker and lead small molecules to target r(GGGGCC)-associated defects in c9FTD/ALS, Neuron, 83, 1043, 10.1016/j.neuron.2014.07.041
Tran, 2014, Targeting the r(CGG) repeats that cause FXTAS with modularly assembled small molecules and oligonucleotides, ACS Chem Biol, 9, 904, 10.1021/cb400875u
Disney, 2008, Two-dimensional combinatorial screening identifies specific aminoglycoside-RNA internal loop partners, J Am Chem Soc, 130, 11185, 10.1021/ja803234t
Velagapudi, 2010, Structure–activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules, Angew Chem Int Ed Engl, 49, 3816, 10.1002/anie.200907257
Wong, 2014, Targeting toxic RNAs that cause myotonic dystrophy type 1 (DM1) with a bisamidinium inhibitor, J Am Chem Soc, 136, 6355, 10.1021/ja5012146
Arambula, 2009, A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding, Proc Natl Acad Sci U S A, 106, 16068, 10.1073/pnas.0901824106
Jahromi, 2013, A novel CUG(exp)·MBNL1 inhibitor with therapeutic potential for myotonic dystrophy type 1, ACS Chem Biol, 8, 1037, 10.1021/cb400046u
Jahromi, 2013, Developing bivalent ligands to target CUG triplet repeats, the causative agent of myotonic dystrophy type 1, J Med Chem, 56, 9471, 10.1021/jm400794z
Gelus, 1999, Molecular basis of HIV-1 TAR RNA specific recognition by an acridine tat-antagonist, Bioorg Med Chem, 7, 1075, 10.1016/S0968-0896(99)00030-9
Marcheschi, 2011, Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication, ACS Chem Biol, 6, 857, 10.1021/cb200082d
Garavís, 2014, Discovery of selective ligands for telomeric RNA G-quadruplexes (TERRA) through 19F-NMR based fragment screening, ACS Chem Biol, 9, 1559, 10.1021/cb500100z
Walter, 1999, Aminoglycoside–RNA interactions, Curr Opin Chem Biol, 3, 694, 10.1016/S1367-5931(99)00028-9
Dibrov, 2014, Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site, J Med Chem, 57, 1694, 10.1021/jm401312n
Dibrov, 2012, Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches, Proc Natl Acad Sci U S A, 109, 5223, 10.1073/pnas.1118699109
Davidson, 2009, Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein, Proc Natl Acad Sci U S A, 106, 11931, 10.1073/pnas.0900629106
Stelzer, 2011, Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble, Nat Chem Biol, 7, 553, 10.1038/nchembio.596
Sztuba-Solinska, 2014, Identification of biologically active. HIV TAR RNA-binding small molecules using small molecule microarrays, J Am Chem Soc, 136, 8402, 10.1021/ja502754f
Zhou, 2013, Screening for inhibitors of the hepatitis C virus internal ribosome entry site RNA, Bioorg Med Chem, 21, 6139, 10.1016/j.bmc.2013.03.054
Tsai, 2008, Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity, Proc Natl Acad Sci U S A, 105, 3041, 10.1073/pnas.0711741105
Bollag, 2010, Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma, Nature, 467, 596, 10.1038/nature09454
Chen, 2010, A fragment-based approach to identifying ligands for riboswitches, ACS Chem Biol, 5, 355, 10.1021/cb9003139
Warner, 2014, Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically, Chem Biol, 21, 591, 10.1016/j.chembiol.2014.03.007
Chung, 2007, NMR-guided fragment-based approach for the design of tRNA(Lys3) ligands, Angew Chem Int Ed Engl, 46, 4489, 10.1002/anie.200605201
Davidson, 2011, A small-molecule probe induces a conformation in HIV TAR RNA capable of binding drug-like fragments, J Mol Biol, 410, 984, 10.1016/j.jmb.2011.03.039
Lee, 2014, A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication, Chem Commun (Camb), 50, 368, 10.1039/C3CC46973E
Baell, 2010, New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays, J Med Chem, 53, 2719, 10.1021/jm901137j
Hopkins, 2014, The role of ligand efficiency metrics in drug discovery, Nat Rev Drug Discov, 13, 105, 10.1038/nrd4163
Davis, 2004, Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic “hot spots”, J Mol Biol, 336, 343, 10.1016/j.jmb.2003.12.046
Murchie, 2004, Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA, J Mol Biol, 336, 625, 10.1016/j.jmb.2003.12.028