Targeting RNA with Small Molecules

This article is cited by 535 publications.

1. Quentin M. R. Gibaut, Jessica A. Bush, Yuquan Tong, Jared T. Baisden, Amirhossein Taghavi, Hailey Olafson, Xiyuan Yao, Jessica L. Childs-Disney, Eric T. Wang, Matthew D. Disney. Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG)exp Degrader in Myotonic Dystrophy. ACS Central Science 2023, 9 (7) , 1342-1353. https://doi.org/10.1021/acscentsci.2c01223
2. Sarah Viola Heel, Karolina Bartosik, Fabian Juen, Christoph Kreutz, Ronald Micura, Kathrin Breuker. Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer. Journal of the American Chemical Society 2023, 145 (28) , 15284-15294. https://doi.org/10.1021/jacs.3c02774
3. Shelby R. Lennon, Aleksandra J. Wierzba, Shea H. Siwik, Dorota Gryko, Amy E. Palmer, Robert T. Batey. Targeting Riboswitches with Beta-Axial-Substituted Cobalamins. ACS Chemical Biology 2023, 18 (5) , 1136-1147. https://doi.org/10.1021/acschembio.2c00939
4. Boris S. Morozov, Aleksandr S. Oshchepkov, Insa Klemt, Aleksandr M. Agafontsev, Swathi Krishna, Frank Hampel, Hong-Gui Xu, Andriy Mokhir, Dirk Guldi, Evgeny Kataev. Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences. JACS Au 2023, 3 (3) , 964-977. https://doi.org/10.1021/jacsau.2c00658
5. Daria Aristova, Roman Selin, Hannah Sophie Heil, Viktoriia Kosach, Yuriy Slominsky, Sergiy Yarmoluk, Vasyl Pekhnyo, Vladyslava Kovalska, Ricardo Henriques, Andriy Mokhir, Svitlana Chernii. Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy. ACS Omega 2022, 7 (51) , 47734-47746. https://doi.org/10.1021/acsomega.2c05231
6. Elisabeth Kallert, Tim R. Fischer, Simon Schneider, Maike Grimm, Mark Helm, Christian Kersten. Protein-Based Virtual Screening Tools Applied for RNA–Ligand Docking Identify New Binders of the preQ1-Riboswitch. Journal of Chemical Information and Modeling 2022, 62 (17) , 4134-4148. https://doi.org/10.1021/acs.jcim.2c00751
7. Stefan Crielaard, Rick Maassen, Tess Vosman, Ivy Rempkens, Willem A. Velema. Affinity-Based Profiling of the Flavin Mononucleotide Riboswitch. Journal of the American Chemical Society 2022, 144 (23) , 10462-10470. https://doi.org/10.1021/jacs.2c02685
8. Zhengguo Cai, Martina Zafferani, Olanrewaju M. Akande, Amanda E. Hargrove. Quantitative Structure–Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure. Journal of Medicinal Chemistry 2022, 65 (10) , 7262-7277. https://doi.org/10.1021/acs.jmedchem.2c00254
9. Eric Largy, Alexander König, Anirban Ghosh, Debasmita Ghosh, Sanae Benabou, Frédéric Rosu, Valérie Gabelica. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chemical Reviews 2022, 122 (8) , 7720-7839. https://doi.org/10.1021/acs.chemrev.1c00386
10. Kaijie Mu, Zhengdan Zhu, Amina Abula, Cheng Peng, Weiliang Zhu, Zhijian Xu. Halogen Bonds Exist between Noncovalent Ligands and Natural Nucleic Acids. Journal of Medicinal Chemistry 2022, 65 (6) , 4424-4435. https://doi.org/10.1021/acs.jmedchem.1c01854
11. Chloé Maucort, Duc Duy Vo, Samy Aouad, Coralie Charrat, Stéphane Azoulay, Audrey Di Giorgio, Maria Duca. Design and Implementation of Synthetic RNA Binders for the Inhibition of miR-21 Biogenesis. ACS Medicinal Chemistry Letters 2021, 12 (6) , 899-906. https://doi.org/10.1021/acsmedchemlett.0c00682
12. Dong-Hwa Lee, Sohee Oh, Kyungeun Lim, Boah Lee, Gwan-Su Yi, Young-Rok Kim, Ki-Bum Kim, Chong-Kil Lee, Seung-Wook Chi, Mi-Kyung Lee. Tertiary RNA Folding-Targeted Drug Screening Strategy Using a Protein Nanopore. Analytical Chemistry 2021, 93 (5) , 2811-2819. https://doi.org/10.1021/acs.analchem.0c03941
13. Andrew T. Chang, Lu Chen, Luo Song, Shuxing Zhang, Edward P. Nikonowicz. 2-Amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA). Biochemistry 2020, 59 (35) , 3225-3234. https://doi.org/10.1021/acs.biochem.0c00369
14. Nicole I. Orlovsky, Hashim M. Al-Hashimi, Terrence G. Oas. Exposing Hidden High-Affinity RNA Conformational States. Journal of the American Chemical Society 2020, 142 (2) , 907-921. https://doi.org/10.1021/jacs.9b10535
15. Aleksandr S. Oshchepkov, Tatiana A. Shumilova, Mario Zerson, Robert Magerle, Victor N. Khrustalev, Evgeny A. Kataev. Conformational Selection in Anion Recognition: cGMP-Selective Binding by a Naphthalimide-Functionalized Amido-Amine Macrocycle. The Journal of Organic Chemistry 2019, 84 (14) , 9034-9043. https://doi.org/10.1021/acs.joc.9b00947
16. Aline Umuhire Juru, Neeraj N. Patwardhan, Amanda E. Hargrove. Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA–Small Molecule Interactions. ACS Chemical Biology 2019, 14 (5) , 824-838. https://doi.org/10.1021/acschembio.8b00945
17. Amanda L. Garner, Daniel A. Lorenz, Jorge Sandoval, Erin E. Gallagher, Samuel A. Kerk, Tanpreet Kaur, Arya Menon. Tetracyclines as Inhibitors of Pre-microRNA Maturation: A Disconnection between RNA Binding and Inhibition. ACS Medicinal Chemistry Letters 2019, 10 (5) , 816-821. https://doi.org/10.1021/acsmedchemlett.9b00091
18. Siffeen Zehra, Thierry Roisnel, Farukh Arjmand. Enantiomeric Amino Acid Schiff Base Copper(II) Complexes as a New Class of RNA-Targeted Metallo-Intercalators: Single X-ray Crystal Structural Details, Comparative in Vitro DNA/RNA Binding Profile, Cleavage, and Cytotoxicity. ACS Omega 2019, 4 (4) , 7691-7705. https://doi.org/10.1021/acsomega.9b00131
19. Daniel L. Jasinski, Daniel W. Binzel, Peixuan Guo. One-Pot Production of RNA Nanoparticles via Automated Processing and Self-Assembly. ACS Nano 2019, 13 (4) , 4603-4612. https://doi.org/10.1021/acsnano.9b00649
20. Fardokht A. Abulwerdi, Wenbo Xu, Abeer A. Ageeli, Michael J. Yonkunas, Gayatri Arun, Hyeyeon Nam, John S. Schneekloth, Jr., Theodore Kwaku Dayie, David Spector, Nathan Baird, Stuart F. J. Le Grice. Selective Small-Molecule Targeting of a Triple Helix Encoded by the Long Noncoding RNA, MALAT1. ACS Chemical Biology 2019, 14 (2) , 223-235. https://doi.org/10.1021/acschembio.8b00807
21. Hao Yan, Mi Zhou, Umesh Bhattarai, Yabin Song, Mengmeng Zheng, Jianfeng Cai, Fu-Sen Liang. Cyclic Peptidomimetics as Inhibitor for miR-155 Biogenesis. Molecular Pharmaceutics 2019, 16 (2) , 914-920. https://doi.org/10.1021/acs.molpharmaceut.8b01247
22. Aurélie Blond, Serge Turcaud, Thomas Lecourt, Laurent Micouin. Diastereoselective Ring Homologation of Bicyclic Hydrazines: Access to cis-1,3-Diaminocyclohexitols. ACS Omega 2018, 3 (11) , 15302-15307. https://doi.org/10.1021/acsomega.8b02910
23. Hafeez S. Haniff, Amanda Graves, Matthew D. Disney. Selective Small Molecule Recognition of RNA Base Pairs. ACS Combinatorial Science 2018, 20 (8) , 482-491. https://doi.org/10.1021/acscombsci.8b00049
24. Michelle H. Moon, Thomas A. Hilimire, Allix M. Sanders, John S. Schneekloth, Jr.. Measuring RNA–Ligand Interactions with Microscale Thermophoresis. Biochemistry 2018, 57 (31) , 4638-4643. https://doi.org/10.1021/acs.biochem.7b01141
25. Shivaji A. Thadke, J. Dinithi R. Perera, V. M. Hridya, Kirti Bhatt, Ashif Y. Shaikh, Wei-Che Hsieh, Mengshen Chen, Chakicherla Gayathri, Roberto R. Gil, Gordon S. Rule, Arnab Mukherjee, Charles A. Thornton, Danith H. Ly. Design of Bivalent Nucleic Acid Ligands for Recognition of RNA-Repeated Expansion Associated with Huntington’s Disease. Biochemistry 2018, 57 (14) , 2094-2108. https://doi.org/10.1021/acs.biochem.8b00062
26. Noreen F. Rizvi, John A. Howe, Ali Nahvi, Daniel J. Klein, Thierry O. Fischmann, Hai-Young Kim, Mark A. McCoy, Scott S. Walker, Alan Hruza, Matthew P. Richards, Chad Chamberlin, Peter Saradjian, Margaret T. Butko, Gabriel Mercado, Julja Burchard, Corey Strickland, Peter J. Dandliker, Graham F. Smith, Elliott B. Nickbarg. Discovery of Selective RNA-Binding Small Molecules by Affinity-Selection Mass Spectrometry. ACS Chemical Biology 2018, 13 (3) , 820-831. https://doi.org/10.1021/acschembio.7b01013
27. Alicia J. Angelbello, Jonathan L. Chen, Jessica L. Childs-Disney, Peiyuan Zhang, Zi-Fu Wang, and Matthew D. Disney . Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Chemical Reviews 2018, 118 (4) , 1599-1663. https://doi.org/10.1021/acs.chemrev.7b00504
28. Michal H. Kolář and Oriana Tabarrini . Halogen Bonding in Nucleic Acid Complexes. Journal of Medicinal Chemistry 2017, 60 (21) , 8681-8690. https://doi.org/10.1021/acs.jmedchem.7b00329
29. Lizzette M. Gómez Ramos, Natalya N. Degtyareva, Nicholas A. Kovacs, Stefany Y. Holguin, Liuwei Jiang, Anton S. Petrov, Marcin Biesiada, Michael Y. Hu, Katarzyna J. Purzycka, Dev P. Arya, and Loren Dean Williams . Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets. Biochemistry 2017, 56 (40) , 5288-5299. https://doi.org/10.1021/acs.biochem.7b00703
30. Juan Aranda, Antonio Francés-Monerris, Iñaki Tuñón, and Daniel Roca-Sanjuán . Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations. Journal of Chemical Theory and Computation 2017, 13 (10) , 5089-5096. https://doi.org/10.1021/acs.jctc.7b00610
31. Thomas A. Hilimire, Jeffrey M. Chamberlain, Viktoriya Anokhina, Ryan P. Bennett, Oliver Swart, Jason R. Myers, John M. Ashton, Ryan A. Stewart, Aaron L. Featherston, Kathleen Gates, Eric D. Helms, Harold C. Smith, Stephen Dewhurst, Benjamin L. Miller. HIV-1 Frameshift RNA-Targeted Triazoles Inhibit Propagation of Replication-Competent and Multi-Drug-Resistant HIV in Human Cells. ACS Chemical Biology 2017, 12 (6) , 1674-1682. https://doi.org/10.1021/acschembio.7b00052
32. Guodong Hu, Aijing Ma, and Jihua Wang . Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations. Journal of Chemical Information and Modeling 2017, 57 (4) , 918-928. https://doi.org/10.1021/acs.jcim.7b00139
33. Hao Yan, Umesh Bhattarai, Zhi-Fo Guo, and Fu-Sen Liang . Regulating miRNA-21 Biogenesis By Bifunctional Small Molecules. Journal of the American Chemical Society 2017, 139 (14) , 4987-4990. https://doi.org/10.1021/jacs.7b00610
34. Sai Pradeep Velagapudi, Yiling Luo, Tuan Tran, Hafeez S. Haniff, Yoshio Nakai, Mohammad Fallahi, Gustavo J. Martinez, Jessica L. Childs-Disney, and Matthew D. Disney . Defining RNA–Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA. ACS Central Science 2017, 3 (3) , 205-216. https://doi.org/10.1021/acscentsci.7b00009
35. Colleen M. Connelly, Robert E. Boer, Michelle H. Moon, Peter Gareiss, and John S. Schneekloth, Jr. . Discovery of Inhibitors of MicroRNA-21 Processing Using Small Molecule Microarrays. ACS Chemical Biology 2017, 12 (2) , 435-443. https://doi.org/10.1021/acschembio.6b00945
36. Christopher S. Eubanks, Jordan E. Forte, Gary J. Kapral, and Amanda E. Hargrove . Small Molecule-Based Pattern Recognition To Classify RNA Structure. Journal of the American Chemical Society 2017, 139 (1) , 409-416. https://doi.org/10.1021/jacs.6b11087
37. Fardokht A. Abulwerdi, Matthew D. Shortridge, Joanna Sztuba-Solinska, Robert Wilson, Stuart F. J. Le Grice, Gabriele Varani, and John S. Schneekloth, Jr. . Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA. Journal of Medicinal Chemistry 2016, 59 (24) , 11148-11160. https://doi.org/10.1021/acs.jmedchem.6b01450
38. Brian P. Charrette, Mark A. Boerneke, and Thomas Hermann . Ligand Optimization by Improving Shape Complementarity at a Hepatitis C Virus RNA Target. ACS Chemical Biology 2016, 11 (12) , 3263-3267. https://doi.org/10.1021/acschembio.6b00687
39. Louis Zimmermann, Indrajit Das, Jérôme Désiré, Guillaume Sautrey, Vinicius Barros R. S., Micheline El Khoury, Marie-Paule Mingeot-Leclercq, and Jean-Luc Décout . New Broad-Spectrum Antibacterial Amphiphilic Aminoglycosides Active against Resistant Bacteria: From Neamine Derivatives to Smaller Neosamine Analogues. Journal of Medicinal Chemistry 2016, 59 (20) , 9350-9369. https://doi.org/10.1021/acs.jmedchem.6b00818
40. Ayesha Kabir, Devawati Dutta, Chhabinath Mandal, and Gopinatha Suresh Kumar . Molecular Recognition of tRNA with 1-Naphthyl Acetyl Spermine, Spermine, and Spermidine: A Thermodynamic, Biophysical, and Molecular Docking Investigative Approach. The Journal of Physical Chemistry B 2016, 120 (42) , 10871-10884. https://doi.org/10.1021/acs.jpcb.6b05391
41. Hua He, Zhencai Wang, Tiantian Cheng, Xu Liu, Xiaojuan Wang, Junying Wang, Hao Ren, Yawei Sun, Yanzhuo Song, Jiang Yang, Yongqing Xia, Shengjie Wang, Xiaodong Zhang, and Fang Huang . Visible and Near-Infrared Dual-Emission Carbogenic Small Molecular Complex with High RNA Selectivity and Renal Clearance for Nucleolus and Tumor Imaging. ACS Applied Materials & Interfaces 2016, 8 (42) , 28529-28537. https://doi.org/10.1021/acsami.6b10737
42. Asako Murata, Takahiro Otabe, Jinhua Zhang, and Kazuhiko Nakatani . BzDANP, a Small-Molecule Modulator of Pre-miR-29a Maturation by Dicer. ACS Chemical Biology 2016, 11 (10) , 2790-2796. https://doi.org/10.1021/acschembio.6b00214
43. Martina Roos, Ugo Pradère, Richard P. Ngondo, Alok Behera, Sara Allegrini, Gianluca Civenni, Julian A. Zagalak, Jean-Rémy Marchand, Mirjam Menzi, Harry Towbin, Jörg Scheuermann, Dario Neri, Amedeo Caflisch, Carlo V. Catapano, Constance Ciaudo, and Jonathan Hall . A Small-Molecule Inhibitor of Lin28. ACS Chemical Biology 2016, 11 (10) , 2773-2781. https://doi.org/10.1021/acschembio.6b00232
44. Donghyun Lim, Wan Gi Byun, Ja Young Koo, Hankum Park, and Seung Bum Park . Discovery of a Small-Molecule Inhibitor of Protein–MicroRNA Interaction Using Binding Assay with a Site-Specifically Labeled Lin28. Journal of the American Chemical Society 2016, 138 (41) , 13630-13638. https://doi.org/10.1021/jacs.6b06965
45. David W. Crawford, Brett D. Blakeley, Po-Han Chen, Chringma Sherpa, Stuart F.J. Le Grice, Ite A. Laird-Offringa, and Brian R. McNaughton . An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription. ACS Chemical Biology 2016, 11 (8) , 2206-2215. https://doi.org/10.1021/acschembio.6b00145
46. Matthew D. Disney, Audrey M. Winkelsas, Sai Pradeep Velagapudi, Mark Southern, Mohammad Fallahi, and Jessica L. Childs-Disney . Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs. ACS Chemical Biology 2016, 11 (6) , 1720-1728. https://doi.org/10.1021/acschembio.6b00001
47. Ester Jiménez-Moreno, Laura Montalvillo-Jiménez, Andrés G. Santana, Ana M. Gómez, Gonzalo Jiménez-Osés, Francisco Corzana, Agatha Bastida, Jesús Jiménez-Barbero, Francisco Javier Cañada, Irene Gómez-Pinto, Carlos González, and Juan Luis Asensio . Finding the Right Candidate for the Right Position: A Fast NMR-Assisted Combinatorial Method for Optimizing Nucleic Acids Binders. Journal of the American Chemical Society 2016, 138 (20) , 6463-6474. https://doi.org/10.1021/jacs.6b00328
48. Stephanie A. Barros, Ina Yoon, Sung-Eun Suh, and David M. Chenoweth . Bridgehead-Substituted Triptycenes for Discovery of Nucleic Acid Junction Binders. Organic Letters 2016, 18 (10) , 2423-2426. https://doi.org/10.1021/acs.orglett.6b00945
49. Damien Habrant, Pauline Peuziat, Thibault Colombani, Laurence Dallet, Johan Gehin, Emilie Goudeau, Bérangère Evrard, Olivier Lambert, Thomas Haudebourg, and Bruno Pitard . Design of Ionizable Lipids To Overcome the Limiting Step of Endosomal Escape: Application in the Intracellular Delivery of mRNA, DNA, and siRNA. Journal of Medicinal Chemistry 2016, 59 (7) , 3046-3062. https://doi.org/10.1021/acs.jmedchem.5b01679
50. Jun Shik Choi, So-hee Han, Hyoseok Kim, and Yong-beom Lim . Cyclic Peptide-Decorated Self-Assembled Nanohybrids for Selective Recognition and Detection of Multivalent RNAs. Bioconjugate Chemistry 2016, 27 (3) , 799-808. https://doi.org/10.1021/acs.bioconjchem.6b00017
51. Ina Yoon, Sung-Eun Suh, Stephanie A. Barros, and David M. Chenoweth . Synthesis of 9-Substituted Triptycene Building Blocks for Solid-Phase Diversification and Nucleic Acid Junction Targeting. Organic Letters 2016, 18 (5) , 1096-1099. https://doi.org/10.1021/acs.orglett.6b00169
52. Aaron T. Frank . Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA–Ligand Poses?. Journal of Chemical Information and Modeling 2016, 56 (2) , 368-376. https://doi.org/10.1021/acs.jcim.5b00593
53. Jaeyoung Pai, Soonsil Hyun, Ji Young Hyun, Seong-Hyun Park, Won-Je Kim, Sung-Hun Bae, Nak-Kyoon Kim, Jaehoon Yu, and Injae Shin . Screening of Pre-miRNA-155 Binding Peptides for Apoptosis Inducing Activity Using Peptide Microarrays. Journal of the American Chemical Society 2016, 138 (3) , 857-867. https://doi.org/10.1021/jacs.5b09216
54. Alice Sosic, Laura Sinigaglia, Marta Cappellini, Ilaria Carli, Cristina Parolin, Giuseppe Zagotto, Giuseppina Sabatino, Paolo Rovero, Dan Fabris, and Barbara Gatto . Mechanisms of HIV-1 Nucleocapsid Protein Inhibition by Lysyl-Peptidyl-Anthraquinone Conjugates. Bioconjugate Chemistry 2016, 27 (1) , 247-256. https://doi.org/10.1021/acs.bioconjchem.5b00627
55. Thomas A. Hilimire, Ryan P. Bennett, Ryan A. Stewart, Pablo Garcia-Miranda, Alex Blume, Jordan Becker, Nathan Sherer, Eric D. Helms, Samuel E. Butcher, Harold C. Smith, and Benjamin L. Miller . N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNA. ACS Chemical Biology 2016, 11 (1) , 88-94. https://doi.org/10.1021/acschembio.5b00682
56. Liang Qi, Yuan Huo, Huan Wang, Jing Zhang, Fu-Quan Dang, and Zhi-Qi Zhang . Fluorescent DNA-Protected Silver Nanoclusters for Ligand–HIV RNA Interaction Assay. Analytical Chemistry 2015, 87 (21) , 11078-11083. https://doi.org/10.1021/acs.analchem.5b03166
57. Ankur Bikash Pradhan, Lucy Haque, Sutanwi Bhuiya, Aniruddha Ganguly, and Suman Das . Deciphering the Positional Influence of the Hydroxyl Group in the Cinnamoyl Part of 3-Hydroxy Flavonoids for Structural Modification and Their Interaction with the Protonated and B Form of Calf Thymus DNA Using Spectroscopic and Molecular Modeling Studies. The Journal of Physical Chemistry B 2015, 119 (23) , 6916-6929. https://doi.org/10.1021/acs.jpcb.5b02827
58. Benedikt Klauser, Janina Atanasov, Lena K. Siewert, and Jörg S. Hartig . Ribozyme-Based Aminoglycoside Switches of Gene Expression Engineered by Genetic Selection in S. cerevisiae. ACS Synthetic Biology 2015, 4 (5) , 516-525. https://doi.org/10.1021/sb500062p
59. Jie Dai, Zhen-Quan Liu, Xiao-Qin Wang, Jing Lin, Pei-Fen Yao, Shi-Liang Huang, Tian-Miao Ou, Jia-Heng Tan, Ding Li, Lian-Quan Gu, and Zhi-Shu Huang . 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. Journal of Medicinal Chemistry 2015, 58 (9) , 3875-3891. https://doi.org/10.1021/acs.jmedchem.5b00139
60. Wang-Yong Yang, Henry D. Wilson, Sai Pradeep Velagapudi, and Matthew D. Disney . Inhibition of Non-ATG Translational Events in Cells via Covalent Small Molecules Targeting RNA. Journal of the American Chemical Society 2015, 137 (16) , 5336-5345. https://doi.org/10.1021/ja507448y
61. Gerard Artigas and Vicente Marchán . Synthesis and Tau RNA Binding Evaluation of Ametantrone-Containing Ligands. The Journal of Organic Chemistry 2015, 80 (4) , 2155-2164. https://doi.org/10.1021/jo502661j
62. Daniel A. Lorenz, James M. Song, and Amanda L. Garner . High-Throughput Platform Assay Technology for the Discovery of pre-microRNA-Selective Small Molecule Probes. Bioconjugate Chemistry 2015, 26 (1) , 19-23. https://doi.org/10.1021/bc500544v
63. Ayesha Kabir and Gopinatha Suresh Kumar . Targeting Double-Stranded RNA with Spermine, 1-Naphthylacetyl Spermine and Spermidine: A Comparative Biophysical Investigation. The Journal of Physical Chemistry B 2014, 118 (38) , 11050-11064. https://doi.org/10.1021/jp5035294
64. Jianfeng Pei, Ning Yin, Xiaomin Ma, and Luhua Lai . Systems Biology Brings New Dimensions for Structure-Based Drug Design. Journal of the American Chemical Society 2014, 136 (33) , 11556-11565. https://doi.org/10.1021/ja504810z
65. Brett D. Blakeley and Brian R. McNaughton . Synthetic RNA Recognition Motifs That Selectively Recognize HIV-1 Trans-Activation Response Element Hairpin RNA. ACS Chemical Biology 2014, 9 (6) , 1320-1329. https://doi.org/10.1021/cb500138h
66. Joanna Sztuba-Solinska, Shilpa R. Shenoy, Peter Gareiss, Lauren R. H. Krumpe, Stuart F. J. Le Grice, Barry R. O’Keefe, and John S. Schneekloth, Jr. . Identification of Biologically Active, HIV TAR RNA-Binding Small Molecules Using Small Molecule Microarrays. Journal of the American Chemical Society 2014, 136 (23) , 8402-8410. https://doi.org/10.1021/ja502754f
67. Tuan Tran, Jessica L. Childs-Disney, Biao Liu, Lirui Guan, Suzanne Rzuczek, and Matthew D. Disney . Targeting the r(CGG) Repeats That Cause FXTAS with Modularly Assembled Small Molecules and Oligonucleotides. ACS Chemical Biology 2014, 9 (4) , 904-912. https://doi.org/10.1021/cb400875u
68. Duc Duy Vo, Cathy Staedel, Laura Zehnacker, Rachid Benhida, Fabien Darfeuille, and Maria Duca . Targeting the Production of Oncogenic MicroRNAs with Multimodal Synthetic Small Molecules. ACS Chemical Biology 2014, 9 (3) , 711-721. https://doi.org/10.1021/cb400668h
69. Sergey M. Dibrov, Jerod Parsons, Maia Carnevali, Shu Zhou, Kevin D. Rynearson, Kejia Ding, Emily Garcia Sega, Nicholas D. Brunn, Mark A. Boerneke, Maria P. Castaldi, and Thomas Hermann . Hepatitis C Virus Translation Inhibitors Targeting the Internal Ribosomal Entry Site. Journal of Medicinal Chemistry 2014, 57 (5) , 1694-1707. https://doi.org/10.1021/jm401312n
70. Jessica L. Childs-Disney, Ilyas Yildirim, HaJeung Park, Jeremy R. Lohman, Lirui Guan, Tuan Tran, Partha Sarkar, George C. Schatz, and Matthew D. Disney . Structure of the Myotonic Dystrophy Type 2 RNA and Designed Small Molecules That Reduce Toxicity. ACS Chemical Biology 2014, 9 (2) , 538-550. https://doi.org/10.1021/cb4007387
71. Leslie O. Ofori, Thomas A. Hilimire, Ryan P. Bennett, Nathaniel W. Brown, Jr., Harold C. Smith, and Benjamin L. Miller . High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity. Journal of Medicinal Chemistry 2014, 57 (3) , 723-732. https://doi.org/10.1021/jm401438g
72. Neil M. Bell, Anne L’Hernault, Pierre Murat, James E. Richards, Andrew M. L. Lever, and Shankar Balasubramanian . Targeting RNA–Protein Interactions within the Human Immunodeficiency Virus Type 1 Lifecycle. Biochemistry 2013, 52 (51) , 9269-9274. https://doi.org/10.1021/bi401270d
73. Gerard Artigas and Vicente Marchán . Synthesis of Janus Compounds for the Recognition of G-U Mismatched Nucleobase Pairs. The Journal of Organic Chemistry 2013, 78 (21) , 10666-10677. https://doi.org/10.1021/jo401684j
74. Janghyun Lee, Catherine E. Vogt, Mitchell McBrairty, and Hashim M. Al-Hashimi . Influence of Dimethylsulfoxide on RNA Structure and Ligand Binding. Analytical Chemistry 2013, 85 (20) , 9692-9698. https://doi.org/10.1021/ac402038t
75. Robert-André F. Rarig, Mai N. Tran, and David M. Chenoweth . Synthesis and Conformational Dynamics of the Reported Structure of Xylopyridine A. Journal of the American Chemical Society 2013, 135 (24) , 9213-9219. https://doi.org/10.1021/ja404737q
76. Debojit Bose, Gopal Gunanathan Jayaraj, Santosh Kumar, and Souvik Maiti . A Molecular-Beacon-Based Screen for Small Molecule Inhibitors of miRNA Maturation. ACS Chemical Biology 2013, 8 (5) , 930-938. https://doi.org/10.1021/cb300650y
77. Amin Haghighat Jahromi, Lien Nguyen, Yuan Fu, Kali A. Miller, Anne M. Baranger, and Steven C. Zimmerman . A Novel CUGexp·MBNL1 Inhibitor with Therapeutic Potential for Myotonic Dystrophy Type 1. ACS Chemical Biology 2013, 8 (5) , 1037-1043. https://doi.org/10.1021/cb400046u
78. Ariadna Grau-Campistany, Anna Massaguer, Dolors Carrion-Salip, Flavia Barragán, Gerard Artigas, Paula López-Senín, Virtudes Moreno, and Vicente Marchán . Conjugation of a Ru(II) Arene Complex to Neomycin or to Guanidinoneomycin Leads to Compounds with Differential Cytotoxicities and Accumulation between Cancer and Normal Cells. Molecular Pharmaceutics 2013, 10 (5) , 1964-1976. https://doi.org/10.1021/mp300723b
79. Jia Lu, Liang Zhao, Amy Xia, Tianbing Xia, and Xin Qi . Dissect Conformational Distribution and Drug-Induced Population Shift of Prokaryotic rRNA A-Site. Biochemistry 2013, 52 (10) , 1651-1653. https://doi.org/10.1021/bi400053s
80. Jessica L. Childs-Disney, Raman Parkesh, Masayuki Nakamori, Charles A. Thornton, and Matthew D. Disney . Rational Design of Bioactive, Modularly Assembled Aminoglycosides Targeting the RNA that Causes Myotonic Dystrophy Type 1. ACS Chemical Biology 2012, 7 (12) , 1984-1993. https://doi.org/10.1021/cb3001606
81. Anthony Bugaut, Pierre Murat, and Shankar Balasubramanian . An RNA Hairpin to G-Quadruplex Conformational Transition. Journal of the American Chemical Society 2012, 134 (49) , 19953-19956. https://doi.org/10.1021/ja308665g
82. Lu Chen, George A. Calin, and Shuxing Zhang . Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery. Journal of Chemical Information and Modeling 2012, 52 (10) , 2741-2753. https://doi.org/10.1021/ci300320t
83. Douglas M. Warui and Anne M. Baranger . Identification of Small Molecule Inhibitors of the HIV-1 Nucleocapsid–Stem-Loop 3 RNA Complex. Journal of Medicinal Chemistry 2012, 55 (9) , 4132-4141. https://doi.org/10.1021/jm2007694
84. Sunil Kumar, Patrick Kellish, W. Edward Robinson, Jr., Deyun Wang, Daniel H. Appella, and Dev P. Arya . Click Dimers To Target HIV TAR RNA Conformation. Biochemistry 2012, 51 (11) , 2331-2347. https://doi.org/10.1021/bi201657k
85. David I. Bryson, Wenyu Zhang, Patrick M. McLendon, Theresa M. Reineke, and Webster L. Santos . Toward Targeting RNA Structure: Branched Peptides as Cell-Permeable Ligands to TAR RNA. ACS Chemical Biology 2012, 7 (1) , 210-217. https://doi.org/10.1021/cb200181v
86. Alethia A. Hostetter, Maire F. Osborn, and Victoria J. DeRose . RNA-Pt Adducts Following Cisplatin Treatment of Saccharomyces cerevisiae. ACS Chemical Biology 2012, 7 (1) , 218-225. https://doi.org/10.1021/cb200279p
87. Lirui Guan and Matthew D. Disney . Recent Advances in Developing Small Molecules Targeting RNA. ACS Chemical Biology 2012, 7 (1) , 73-86. https://doi.org/10.1021/cb200447r
88. Pankaj Gupta, Oluwatoyosi Muse, and Eriks Rozners . Recognition of Double-Stranded RNA by Guanidine-Modified Peptide Nucleic Acids. Biochemistry 2012, 51 (1) , 63-73. https://doi.org/10.1021/bi201570a
89. Katherine E. Deigan and Adrian R. FerrÉ-D’AmarÉ . Riboswitches: Discovery of Drugs That Target Bacterial Gene-Regulatory RNAs. Accounts of Chemical Research 2011, 44 (12) , 1329-1338. https://doi.org/10.1021/ar200039b
90. Amit Kumar, HaJeung Park, Pengfei Fang, Raman Parkesh, Min Guo, Kendall W. Nettles, and Matthew D. Disney . Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations. Biochemistry 2011, 50 (45) , 9928-9935. https://doi.org/10.1021/bi2013068
91. Crina M. Orac, Shu Zhou, John A. Means, David Boehm, Stephen C. Bergmeier, and Jennifer V. Hines . Synthesis and Stereospecificity of 4,5-Disubstituted Oxazolidinone Ligands Binding to T-box Riboswitch RNA. Journal of Medicinal Chemistry 2011, 54 (19) , 6786-6795. https://doi.org/10.1021/jm2006904
92. Catherine M. Serrano and Ryan E. Looper . Synthesis of Cytimidine through a One-Pot Copper-Mediated Amidation Cascade. Organic Letters 2011, 13 (19) , 5000-5003. https://doi.org/10.1021/ol2018196
93. Anu Kiviniemi and Pasi Virta . Synthesis of Aminoglycoside-3′-Conjugates of 2′-O-Methyl Oligoribonucleotides and Their Invasion to a 19F labeled HIV-1 TAR Model. Bioconjugate Chemistry 2011, 22 (8) , 1559-1566. https://doi.org/10.1021/bc200101r
94. Sai Pradeep Velagapudi, Steven J. Seedhouse, Jonathan French, and Matthew D. Disney . Defining the RNA Internal Loops Preferred by Benzimidazole Derivatives via 2D Combinatorial Screening and Computational Analysis. Journal of the American Chemical Society 2011, 133 (26) , 10111-10118. https://doi.org/10.1021/ja200212b
95. Shuna Liu, Ping Wu, Wen Li, Hui Zhang, and Chenxin Cai . Ultrasensitive and Selective Electrochemical Identification of Hepatitis C Virus Genotype 1b Based on Specific Endonuclease Combined with Gold Nanoparticles Signal Amplification. Analytical Chemistry 2011, 83 (12) , 4752-4758. https://doi.org/10.1021/ac200624f
96. Sunil Kumar, Liang Xue, and Dev P. Arya . Neomycin−Neomycin Dimer: An All-Carbohydrate Scaffold with High Affinity for AT-Rich DNA Duplexes. Journal of the American Chemical Society 2011, 133 (19) , 7361-7375. https://doi.org/10.1021/ja108118v
97. Raman Parkesh, Matthew Fountain, and Matthew D. Disney . NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1. Biochemistry 2011, 50 (5) , 599-601. https://doi.org/10.1021/bi101896j
98. Roba Moumné, Morgane Pasco, Elise Prost, Thomas Lecourt, Laurent Micouin, and Carine Tisné. Fluorinated Diaminocyclopentanes as Chiral Sensitive NMR Probes of RNA Structure. Journal of the American Chemical Society 2010, 132 (38) , 13111-13113. https://doi.org/10.1021/ja1037885
99. Prakash B. Palde, Leslie O. Ofori, Peter C. Gareiss, Jaclyn Lerea and Benjamin L. Miller . Strategies for Recognition of Stem−Loop RNA Structures by Synthetic Ligands: Application to the HIV-1 Frameshift Stimulatory Sequence. Journal of Medicinal Chemistry 2010, 53 (16) , 6018-6027. https://doi.org/10.1021/jm100231t
100. Ming Li, Thomas Zengeya and Eriks Rozners. Short Peptide Nucleic Acids Bind Strongly to Homopurine Tract of Double Helical RNA at pH 5.5. Journal of the American Chemical Society 2010, 132 (25) , 8676-8681. https://doi.org/10.1021/ja101384k