SHAPE-enabled fragment-based ligand discovery for RNA

Zeller, Meredith J.; Favorov, Oleg; Li, Kelin; Nuthanakanti, Ashok; Hussein, Dina; Michaud, Aureliane; Lafontaine, Daniel A.; Busan, Steven; Serganov, Alexander; Aube, Jeffrey; Weeks, Kevin M.

doi:10.1073/pnas.2122660119

SHAPE-enabled fragment-based ligand discovery for RNA

Journal Article · 01 May 2022 · Proc. Natl. Acad. Sci. USA

DOI:https://doi.org/10.1073/pnas.2122660119· OSTI ID:1872608

Zeller, Meredith J.; Favorov, Oleg; Li, Kelin; Nuthanakanti, Ashok; Hussein, Dina; Michaud, Aureliane; Lafontaine, Daniel A.; Busan, Steven; Serganov, Alexander; Aube, Jeffrey; Weeks, Kevin M.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIH

OSTI ID:: 1872608

Journal Information:: Proc. Natl. Acad. Sci. USA, Journal Name: Proc. Natl. Acad. Sci. USA Journal Issue: (20) Vol. 119

Country of Publication:: United States

Language:: ENGLISH

References (50)

Fragment screening against the thiamine pyrophosphate riboswitchthiM Cressina, Elena; Chen, Liuhong; Abell, Chris Chem. Sci., Vol. 2, Issue 1 https://doi.org/10.1039/C0SC00406E	journal	January 2011
Targeting noncoding RNAs in disease Adams, Brian D.; Parsons, Christine; Walker, Lisa Journal of Clinical Investigation, Vol. 127, Issue 3 https://doi.org/10.1172/JCI84424	journal	March 2017
RNAstructure: software for RNA secondary structure prediction and analysis Reuter, Jessica S.; Mathews, David H. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-129	journal	March 2010
Regulation of translation via mRNA structure in prokaryotes and eukaryotes Kozak, Marilyn Gene, Vol. 361 https://doi.org/10.1016/j.gene.2005.06.037	journal	November 2005
Monitoring RNA dynamics in native transcriptional complexes Chauvier, Adrien; St-Pierre, Patrick; Nadon, Jean-François Proceedings of the National Academy of Sciences, Vol. 118, Issue 45 https://doi.org/10.1073/pnas.2106564118	journal	November 2021
Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically Warner, Katherine Deigan; Homan, Philip; Weeks, Kevin M. Chemistry & Biology, Vol. 21, Issue 5 https://doi.org/10.1016/j.chembiol.2014.03.007	journal	May 2014
What is Cooperativity? Hunter, Christopher A.; Anderson, Harry L. Angewandte Chemie International Edition, Vol. 48, Issue 41 https://doi.org/10.1002/anie.200902490	journal	September 2009
The Centrality of RNA Sharp, Phillip A. Cell, Vol. 136, Issue 4 https://doi.org/10.1016/j.cell.2009.02.007	journal	February 2009
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Synthetic Riboswitches: From Plug and Pray toward Plug and Play Etzel, Maja; Mörl, Mario Biochemistry, Vol. 56, Issue 9 https://doi.org/10.1021/acs.biochem.6b01218	journal	February 2017
Stromelysin Inhibitors Designed from Weakly Bound Fragments: Effects of Linking and Cooperativity Olejniczak, E. T.; Hajduk, P. J.; Marcotte, P. A. Journal of the American Chemical Society, Vol. 119, Issue 25 https://doi.org/10.1021/ja9702780	journal	June 1997
The distributions, mechanisms, and structures of metabolite-binding riboswitches Barrick, Jeffrey E.; Breaker, Ronald R. Genome Biology, Vol. 8, Issue 11 https://doi.org/10.1186/gb-2007-8-11-r239	journal	January 2007
Quantitative metrics for drug–target ligandability Vukovic, Sinisa; Huggins, David J. Drug Discovery Today, Vol. 23, Issue 6 https://doi.org/10.1016/j.drudis.2018.02.015	journal	June 2018
Traversing the coordination chemistry and chemical biology of hydroxamic acids Codd, Rachel Coordination Chemistry Reviews, Vol. 252, Issue 12-14 https://doi.org/10.1016/j.ccr.2007.08.001	journal	July 2008
Riboswitches as antibacterial drug targets Blount, Kenneth F.; Breaker, Ronald R. Nature Biotechnology, Vol. 24, Issue 12 https://doi.org/10.1038/nbt1268	journal	December 2006
Principles for targeting RNA with drug-like small molecules Warner, Katherine Deigan; Hajdin, Christine E.; Weeks, Kevin M. Nature Reviews Drug Discovery, Vol. 17, Issue 8 https://doi.org/10.1038/nrd.2018.93	journal	July 2018
Fragment based search for small molecule inhibitors of HIV-1 Tat-TAR Zeiger, Mirco; Stark, Sebastian; Kalden, Elisabeth Bioorganic & Medicinal Chemistry Letters, Vol. 24, Issue 24 https://doi.org/10.1016/j.bmcl.2014.11.004	journal	December 2014
On the attribution and additivity of binding energies Jencks, W. P. Proceedings of the National Academy of Sciences, Vol. 78, Issue 7 https://doi.org/10.1073/pnas.78.7.4046	journal	July 1981
Recent Advances in Developing Small Molecules Targeting RNA Guan, Lirui; Disney, Matthew D. ACS Chemical Biology, Vol. 7, Issue 1 https://doi.org/10.1021/cb200447r	journal	December 2011
Predicting protein druggability Hajduk, Philip J.; Huth, Jeffrey R.; Tse, Christin Drug Discovery Today, Vol. 10, Issue 23-24 https://doi.org/10.1016/S1359-6446(05)03624-X	journal	December 2005
Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation Chauvier, Adrien; Picard-Jean, Frédéric; Berger-Dancause, Jean-Christophe Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms13892	journal	January 2017
The 'rule of three' for fragment-based drug discovery: where are we now? Jhoti, Harren; Williams, Glyn; Rees, David C. Nature Reviews Drug Discovery, Vol. 12, Issue 8 https://doi.org/10.1038/nrd3926-c1	journal	July 2013
Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation Bastet, Laurène; Chauvier, Adrien; Singh, Navjot Nucleic Acids Research, Vol. 45, Issue 12 https://doi.org/10.1093/nar/gkx434	journal	May 2017
The Emerging Role of RNA as a Therapeutic Target for Small Molecules Connelly, Colleen M.; Moon, Michelle H.; Schneekloth, John S. Cell Chemical Biology, Vol. 23, Issue 9 https://doi.org/10.1016/j.chembiol.2016.05.021	journal	September 2016
Structural Basis of Thiamine Pyrophosphate Analogues Binding to the Eukaryotic Riboswitch Thore, Stéphane; Frick, Christian; Ban, Nenad Journal of the American Chemical Society, Vol. 130, Issue 26 https://doi.org/10.1021/ja801708e	journal	July 2008
Non-coding RNAs as drug targets Matsui, Masayuki; Corey, David R. Nature Reviews Drug Discovery, Vol. 16, Issue 3 https://doi.org/10.1038/nrd.2016.117	journal	July 2016
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
A Fragment-Based Approach to Identifying Ligands for Riboswitches Chen, Liuhong; Cressina, Elena; Leeper, Finian J. ACS Chemical Biology, Vol. 5, Issue 4 https://doi.org/10.1021/cb9003139	journal	February 2010
Tertiary Motifs in RNA Structure and Folding Batey, Robert T.; Rambo, Robert P.; Doudna, Jennifer A. Angewandte Chemie International Edition, Vol. 38, Issue 16 https://doi.org/10.1002/(SICI)1521-3773(19990816)38:16<2326::AID-ANIE2326>3.0.CO;2-3	journal	August 1999
The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones Cech, Thomas R.; Steitz, Joan A. Cell, Vol. 157, Issue 1 https://doi.org/10.1016/j.cell.2014.03.008	journal	March 2014
Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2 Busan, Steven; Weeks, Kevin M. RNA, Vol. 24, Issue 2 https://doi.org/10.1261/rna.061945.117	journal	November 2017
Quantifying the chemical beauty of drugs Bickerton, G. Richard; Paolini, Gaia V.; Besnard, Jérémy Nature Chemistry, Vol. 4, Issue 2 https://doi.org/10.1038/nchem.1243	journal	January 2012
RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE) Merino, Edward J.; Wilkinson, Kevin A.; Coughlan, Jennifer L. Journal of the American Chemical Society, Vol. 127, Issue 12 https://doi.org/10.1021/ja043822v	journal	March 2005
Riboswitch diversity and distribution McCown, Phillip J.; Corbino, Keith A.; Stav, Shira RNA, Vol. 23, Issue 7 https://doi.org/10.1261/rna.061234.117	journal	April 2017
The ways and means of fragment-based drug design Doak, Bradley C.; Norton, Raymond S.; Scanlon, Martin J. Pharmacology & Therapeutics, Vol. 167 https://doi.org/10.1016/j.pharmthera.2016.07.003	journal	November 2016
Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors Tickner, Zachary J.; Farzan, Michael Pharmaceuticals, Vol. 14, Issue 6 https://doi.org/10.3390/ph14060554	journal	June 2021
Novel cis -Acting Element within the Capsid-Coding Region Enhances Flavivirus Viral-RNA Replication by Regulating Genome Cyclization Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao Journal of Virology, Vol. 87, Issue 12 https://doi.org/10.1128/JVI.00243-13	journal	June 2013
The rise of fragment-based drug discovery Murray, Christopher W.; Rees, David C. Nature Chemistry, Vol. 1, Issue 3 https://doi.org/10.1038/nchem.217	journal	June 2009
Compound Design by Fragment-Linking Ichihara, Osamu; Barker, John; Law, Richard J. Molecular Informatics, Vol. 30, Issue 4 https://doi.org/10.1002/minf.201000174	journal	April 2011
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) Siegfried, Nathan A.; Busan, Steven; Rice, Greggory M. Nature Methods, Vol. 11, Issue 9 https://doi.org/10.1038/nmeth.3029	journal	July 2014
The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN Riboswitch Wickiser, J. Kenneth; Winkler, Wade C.; Breaker, Ronald R. Molecular Cell, Vol. 18, Issue 1 https://doi.org/10.1016/j.molcel.2005.02.032	journal	April 2005
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Serganov, Alexander; Polonskaia, Anna; Phan, Anh Tuân Nature, Vol. 441, Issue 7097 https://doi.org/10.1038/nature04740	journal	May 2006
Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery Zeller, Meredith J.; Nuthanakanti, Ashok; Li, Kelin ACS Chemical Biology, Vol. 17, Issue 2 https://doi.org/10.1021/acschembio.1c00880	journal	January 2022
Probing riboswitch–ligand interactions using thiamine pyrophosphate analogues Chen, Liuhong; Cressina, Elena; Dixon, Neil Organic & Biomolecular Chemistry, Vol. 10, Issue 30 https://doi.org/10.1039/c2ob07116a	journal	January 2012
Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies Busan, Steven; Weidmann, Chase A.; Sengupta, Arnab Biochemistry, Vol. 58, Issue 23 https://doi.org/10.1021/acs.biochem.8b01218	journal	May 2019
Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis Smola, Matthew J.; Rice, Greggory M.; Busan, Steven Nature Protocols, Vol. 10, Issue 11 https://doi.org/10.1038/nprot.2015.103	journal	October 2015
Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome Sreeramulu, Sridhar; Richter, Christian; Berg, Hannes Angewandte Chemie International Edition, Vol. 60, Issue 35 https://doi.org/10.1002/anie.202103693	journal	August 2021
Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition Edwards, Thomas E.; Ferré-D'Amaré, Adrian R. Structure, Vol. 14, Issue 9 https://doi.org/10.1016/j.str.2006.07.008	journal	September 2006
Targeting Influenza A Virus RNA Promoter Bottini, Angel; De, Surya K.; Wu, Bainan Chemical Biology & Drug Design, Vol. 86, Issue 4 https://doi.org/10.1111/cbdd.12534	journal	March 2015
Entropic Contribution to the Linking Coefficient in Fragment Based Drug Design: A Case Study Borsi, Valentina; Calderone, Vito; Fragai, Marco Journal of Medicinal Chemistry, Vol. 53, Issue 10 https://doi.org/10.1021/jm901723z	journal	May 2010

Similar Records

Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery

Journal Article · 2022 · ACS Chemical Biology · OSTI ID:1879302

Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors

Journal Article · 2009 · Bioorg. Med. Chem. Lett. · OSTI ID:1007119

Genetically Encoded Fragment-Based Discovery of Glycopeptide Ligands for Carbohydrate-Binding Proteins

Journal Article · 2015 · J. Am. Chem. Soc. · OSTI ID:1179495

SHAPE-enabled fragment-based ligand discovery for RNA

Citation Formats

References (50)

Similar Records

Related Subjects