Small molecule targeting of biologically relevant RNA tertiary and quaternary structures
Tài liệu tham khảo
Abdulle, 2019, MALAT1 as a diagnostic and therapeutic target in diabetes-related complications: a promising long-noncoding RNA, Int. J. Med. Sci., 16, 548, 10.7150/ijms.30097
Abulwerdi, 2019, Selective small-molecule targeting of a triple helix encoded by the long noncoding RNA, MALAT1, ACS Chem. Biol., 14, 223, 10.1021/acschembio.8b00807
Ahn, 2011, Interference of ribosomal frameshifting by antisense peptide nucleic acids suppresses SARS coronavirus replication, Antivir. Res., 91, 1, 10.1016/j.antiviral.2011.04.009
Arora, 2009, Differential biophysical behavior of human telomeric RNA and DNA quadruplex, J. Phys. Chem. B, 113, 10515, 10.1021/jp810638n
Bao, 2018, Investigation of higher-order RNA G-quadruplex structures in vitro and in living cells by 19F NMR spectroscopy, Nat. Protoc., 13, 652, 10.1038/nprot.2017.156
Bhattacharyya, 2015, An independently folding RNA G-quadruplex domain directly recruits the 40S ribosomal subunit, Biochemistry, 54, 1879, 10.1021/acs.biochem.5b00091
Biffi, 2012, An intramolecular G-quadruplex structure is required for binding of telomeric repeat-containing RNA to the telomeric protein TRF2, J. Am. Chem. Soc., 134, 11974, 10.1021/ja305734x
Biffi, 2014, Elevated levels of G-quadruplex formation in human stomach and liver cancer tissues, PLoS One, 9, e102711, 10.1371/journal.pone.0102711
Blount, 2006, Riboswitches as antibacterial drug targets, Nat. Biotechnol., 24, 1558, 10.1038/nbt1268
Breaker, 2012, Riboswitches and the RNA world, Cold Spring Harb Perspect. Biol., 4, a003566, 10.1101/cshperspect.a003566
Brown, 2020, Unraveling the structure and biological functions of RNA triple helices, WIREs RNA, 11, e1598, 10.1002/wrna.1598
Brown, 2014, Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix, Nat. Struct. Mol. Biol., 21, 633, 10.1038/nsmb.2844
Bugaut, 2012, 5'-UTR RNA G-quadruplexes: translation regulation and targeting, Nucleic Acids Res., 40, 4727, 10.1093/nar/gks068
Butcher, 2011, The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks, Acc. Chem. Res., 44, 1302, 10.1021/ar200098t
Campagne, 2019, Structural basis of a small molecule targeting RNA for a specific splicing correction, Nat. Chem. Biol., 15, 1191, 10.1038/s41589-019-0384-5
Cech, 2014, The noncoding RNA revolution—trashing old rules to forge new ones, Cell, 157, 77, 10.1016/j.cell.2014.03.008
Chaires, 2004, Structural selectivity of aromatic diamidines, J. Med. Chem., 47, 5729, 10.1021/jm049491e
Chen, 2018, Tracking the dynamic folding and unfolding of RNA G-quadruplexes in live cells, Angew. Chem. Int. Ed., 57, 4702, 10.1002/anie.201801999
Connelly, 2019, Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure, Nat. Commun., 10, 1501, 10.1038/s41467-019-09493-3
Conrad, 2014, The emerging role of triple helices in RNA biology, WIREs RNA, 5, 15, 10.1002/wrna.1194
Costales, 2020, How we think about targeting RNA with small molecules, J. Med. Chem., 63, 8880, 10.1021/acs.jmedchem.9b01927
Cressina, 2011, Fragment screening against the thiamine pyrophosphate riboswitchthiM, Chem. Sci., 2, 157, 10.1039/C0SC00406E
Dai, 2015, Discovery of small molecules for up-regulating the translation of antiamyloidogenic secretase, a disintegrin and metalloproteinase 10 (ADAM10), by binding to the G-quadruplex-forming sequence in the 5' untranslated region (UTR) of its mRNA, J. Med. Chem., 58, 3875, 10.1021/acs.jmedchem.5b00139
Darras, 2015, Chapter 8 - spinal muscular atrophies, 117
Davila-Calderon, 2020, IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex, Nat. Commun., 11, 4775, 10.1038/s41467-020-18594-3
Dinman, 1998, Translating old drugs into new treatments: ribosomal frameshifting as a target for antiviral agents, Trends Biotechnol., 16, 190, 10.1016/S0167-7799(97)01167-0
Donlic, 2018, Discovery of small molecule ligands for MALAT1 by tuning an RNA-binding scaffold, Angew. Chem. Int. Ed., 57, 13242, 10.1002/anie.201808823
Donlic, 2020, Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans, Nucleic Acids Res., 48, 7653, 10.1093/nar/gkaa585
Fedorova, 2018, Small molecules that target group II introns are potent antifungal agents, Nat. Chem. Biol., 14, 1073, 10.1038/s41589-018-0142-0
Furukawa, 2012, Identification of ligand analogues that control c-di-GMP riboswitches, ACS Chem. Biol., 7, 1436, 10.1021/cb300138n
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
Hong, 2014, Antibiotic drugs targeting bacterial RNAs, Acta Pharm. Sin B, 4, 258, 10.1016/j.apsb.2014.06.012
Howe, 2015, Selective small-molecule inhibition of an RNA structural element, Nature, 526, 672, 10.1038/nature15542
Hu, 2018, Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis, Oncotarget, 9, 18648, 10.18632/oncotarget.24307
Hung, 2016, Additive promotion of viral internal ribosome entry site-mediated translation by far upstream element-binding protein 1 and an enterovirus 71-induced cleavage product, PLoS Pathog., 12, e1005959, 10.1371/journal.ppat.1005959
Jones, 2015, RNA quaternary structure and global symmetry, Trends Biochem. Sci., 40, 211, 10.1016/j.tibs.2015.02.004
Katsuda, 2016, A small molecule that represses translation of G-quadruplex-containing mRNA, J. Am. Chem. Soc., 138, 9037, 10.1021/jacs.6b04506
Kim, 2007, Different levels of alternative splicing among eukaryotes, Nucleic Acids Res., 35, 125, 10.1093/nar/gkl924
Kole, 2012, RNA therapeutics: beyond RNA interference and antisense oligonucleotides, Nat. Rev. Drug Discov., 11, 125, 10.1038/nrd3625
Lammich, 2011, Translational repression of the disintegrin and metalloprotease ADAM10 by a stable G-quadruplex secondary structure in its 5'-untranslated region, J. Biol. Chem., 286, 45063, 10.1074/jbc.M111.296921
Machtel, 2016, Emerging applications of riboswitches – from antibacterial targets to molecular tools, J. Appl. Genet., 57, 531, 10.1007/s13353-016-0341-x
Mihalusova, 2011, Functional importance of telomerase pseudoknot revealed by single-molecule analysis, Proc. Natl. Acad. Sci., 108, 20339, 10.1073/pnas.1017686108
Motika, 2020, A gram-negative antibiotic active through inhibition of an essential riboswitch, J. Am. Chem. Soc., 142, 10856, 10.1021/jacs.0c04427
Mulhbacher, 2010, Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways, Plos Pathog., 6, e1000865, 10.1371/journal.ppat.1000865
Mullard, 2020, FDA approves RNA-targeting small molecule, Nat. Rev. Drug Discov., 19, 659
Mustoe, 2019, RNA base-pairing complexity in living cells visualized by correlated chemical probing, Proc. Natl. Acad. Sci. U S A, 116, 24574, 10.1073/pnas.1905491116
Naryshkin, 2014, Motor neuron disease. SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy, Science, 345, 688, 10.1126/science.1250127
Palacino, 2015, SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice, Nat. Chem. Biol., 11, 511, 10.1038/nchembio.1837
Panchal, 2021, Riboswitches as drug targets for antibiotics, Antibiotics, 10, 45, 10.3390/antibiotics10010045
Park, 2011, Identification of RNA pseudoknot-binding ligand that inhibits the −1 ribosomal frameshifting of SARS-coronavirus by structure-based virtual screening, J. Am. Chem. Soc., 133, 10094, 10.1021/ja1098325
Patwardhan, 2017, Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR, Medchemcomm, 8, 1022, 10.1039/C6MD00729E
Plant, 2010, Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins, J. Virol., 84, 4330, 10.1128/JVI.02480-09
Pleij, 1985, A new principle of RNA folding based on pseudoknotting, Nucleic Acids Res., 13, 1717, 10.1093/nar/13.5.1717
Pyle, 2010, The tertiary structure of group II introns: implications for biological function and evolution, Crit. Rev. Biochem. Mol. Biol., 45, 215, 10.3109/10409231003796523
Ren, 2019, Targeted design and identification of AC1NOD4Q to block activity of HOTAIR by abrogating the scaffold interaction with EZH2, Clin. Epigenetics, 11, 29, 10.1186/s13148-019-0624-2
Ritchie, 2014, Anti-frameshifting ligand reduces the conformational plasticity of the SARS virus pseudoknot, J. Am. Chem. Soc., 136, 2196, 10.1021/ja410344b
Rizvi, 2018, Discovery of selective RNA-binding small molecules by affinity-selection mass spectrometry, ACS Chem. Biol., 13, 820, 10.1021/acschembio.7b01013
Schmitt, 2013, Gene regulation: long RNAs wire up cancer growth, Nature, 500, 536, 10.1038/nature12548
Serganov, 2013, A decade of riboswitches, Cell, 152, 17, 10.1016/j.cell.2012.12.024
Shen, 2017, Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs, Nucleic Acids Res., 46, 1584, 10.1093/nar/gkx1239
Siddiqui-Jain, 2002, Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress cMYC transcription, Proc. Natl. Acad. Sci., 99, 11593, 10.1073/pnas.182256799
Sivaramakrishnan, 2017, Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers, Nat. Commun., 8, 1476, 10.1038/s41467-017-01559-4
Tazi, 2009, Alternative splicing and disease, Biochim. Biophys. Acta, 1792, 14, 10.1016/j.bbadis.2008.09.017
Thulson, 2020, An RNA pseudoknot stimulates HTLV-1 pro-pol programmed -1 ribosomal frameshifting, RNA, 26, 512, 10.1261/rna.070490.119
Tomezsko, 2020, Determination of RNA structural diversity and its role in HIV-1 RNA splicing, Nature, 582, 438, 10.1038/s41586-020-2253-5
Tran, 2020, Parallel discovery strategies provide a basis for riboswitch ligand design, Cell Chem. Biol., 27, 1241, 10.1016/j.chembiol.2020.07.021
Varshney, 2020, The regulation and functions of DNA and RNA G-quadruplexes, Nat. Rev. Mol. Cell Biol., 21, 459, 10.1038/s41580-020-0236-x
Vicens, 2018, Structure-activity relationship of flavin analogues that target the flavin mononucleotide riboswitch, ACS Chem. Biol., 13, 2908, 10.1021/acschembio.8b00533
Wang, 2017, Dual-targeting small-molecule inhibitors of the Staphylococcus aureus FMN riboswitch disrupt riboflavin homeostasis in an infectious setting, Cell Chem. Biol., 24, 576, 10.1016/j.chembiol.2017.03.014
Wang, 2017, Discovery of small molecules for repressing cap-independent translation of human vascular endothelial growth factor (hVEGF) as novel antitumor agents, J. Med. Chem., 60, 5306, 10.1021/acs.jmedchem.6b01444
Warner, 2018, Principles for targeting RNA with drug-like small molecules, Nat. Rev. Drug Discov., 17, 547, 10.1038/nrd.2018.93
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
Watters, 2016, Cotranscriptional folding of a riboswitch at nucleotide resolution, Nat. Struct. Mol. Biol., 23, 1124, 10.1038/nsmb.3316
Wilusz, 2012, A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails, Genes Dev., 26, 2392, 10.1101/gad.204438.112
Wurster, 2018, Antisense oligonucleotides in neurological disorders, Ther. Adv. Neurol. Disord., 11, 10.1177/1756286418776932
Yang, 2018, Transcriptome-wide identification of transient RNA G-quadruplexes in human cells, Nat. Commun., 9, 4730, 10.1038/s41467-018-07224-8
Zhang, 2017, Interaction of quindoline derivative with telomeric repeat–containing RNA induces telomeric DNA-damage response in cancer cells through inhibition of telomeric repeat factor 2, Biochim. Biophys. Acta, 1861, 3246, 10.1016/j.bbagen.2017.09.015