Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linkin

Zeller, Meredith J.; Nuthanakanti, Ashok; Li, Kelin; Aube, Jeffrey; Serganov, Alexander; Weeks, Kevin M.

doi:10.1021/acschembio.1c00880

Title: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linkin

Journal Article · 01 January 2022 · ACS Chem. Biol.

DOI:https://doi.org/10.1021/acschembio.1c00880· OSTI ID:1847154

Zeller, Meredith J.; Nuthanakanti, Ashok; Li, Kelin; Aube, Jeffrey; Serganov, Alexander; Weeks, Kevin M.

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH)

OSTI ID:: 1847154

Journal Information:: ACS Chem. Biol., Vol. 17, Issue (2)

Country of Publication:: United States

Language:: ENGLISH

References (52)

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
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
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 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
Discovery of Potent Nonpeptide Inhibitors of Stromelysin Using SAR by NMR Hajduk, P. J.; Sheppard, G.; Nettesheim, D. G. Journal of the American Chemical Society, Vol. 119, Issue 25 https://doi.org/10.1021/ja9702778	journal	June 1997
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
Small molecules targeting viral RNA: Small molecules targeting viral RNA Hermann, Thomas Wiley Interdisciplinary Reviews: RNA, Vol. 7, Issue 6 https://doi.org/10.1002/wrna.1373	journal	June 2016
Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA-Targeted Bioactive Ligands Morgan, Brittany S.; Forte, Jordan E.; Culver, Rebecca N. Angewandte Chemie International Edition, Vol. 56, Issue 43 https://doi.org/10.1002/anie.201707641	journal	September 2017
RNA as a small molecule druggable target Rizvi, Noreen F.; Smith, Graham F. Bioorganic & Medicinal Chemistry Letters, Vol. 27, Issue 23 https://doi.org/10.1016/j.bmcl.2017.10.052	journal	December 2017
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
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
Fragment-based design of small RNA binders: Promising developments and contribution of NMR Moumné, Roba; Catala, Marjorie; Larue, Valéry Biochimie, Vol. 94, Issue 7 https://doi.org/10.1016/j.biochi.2012.02.002	journal	July 2012
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
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
Discovery of Selective Ligands for Telomeric RNA G-quadruplexes (TERRA) through ¹⁹ F-NMR Based Fragment Screening Garavís, Miguel; López-Méndez, Blanca; Somoza, Alvaro ACS Chemical Biology, Vol. 9, Issue 7 https://doi.org/10.1021/cb500100z	journal	May 2014
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
Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design Tran, Brandon; Pichling, Patricio; Tenney, Logan Cell Chemical Biology, Vol. 27, Issue 10 https://doi.org/10.1016/j.chembiol.2020.07.021	journal	October 2020
A general fragment-based approach to identify and optimize bioactive ligands targeting RNA Suresh, Blessy M.; Li, Weichao; Zhang, Peiyuan Proceedings of the National Academy of Sciences, Vol. 117, Issue 52 https://doi.org/10.1073/pnas.2012217117	journal	December 2020
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
Cooperativity in macromolecular assembly Williamson, James R. Nature Chemical Biology, Vol. 4, Issue 8 https://doi.org/10.1038/nchembio.102	journal	July 2008
Cooperativity, allostery and synergism in ligand binding to riboswitches Peselis, Alla; Gao, Ang; Serganov, Alexander Biochimie, Vol. 117 https://doi.org/10.1016/j.biochi.2015.06.028	journal	October 2015
Cooperative and anticooperative binding to a ribozyme. Bevilacqua, P. C.; Johnson, K. A.; Turner, D. H. Proceedings of the National Academy of Sciences, Vol. 90, Issue 18 https://doi.org/10.1073/pnas.90.18.8357	journal	September 1993
Probing the Tetrahymena Group I Ribozyme Reaction in Both Directions Karbstein, Katrin; Carroll, Kate S.; Herschlag, Daniel Biochemistry, Vol. 41, Issue 37 https://doi.org/10.1021/bi0202631	journal	August 2002
Design of small molecules targeting RNA structure from sequence Ursu, Andrei; Childs-Disney, Jessica L.; Andrews, Ryan J. Chemical Society Reviews, Vol. 49, Issue 20 https://doi.org/10.1039/d0cs00455c	journal	January 2020
Discovering High-Affinity Ligands for Proteins: SAR by NMR Shuker, S. B.; Hajduk, P. J.; Meadows, R. P. Science, Vol. 274, Issue 5292, p. 1531-1534 https://doi.org/10.1126/science.274.5292.1531	journal	November 1996
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
Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity Steen, Kady-Ann; Rice, Greggory M.; Weeks, Kevin M. Journal of the American Chemical Society, Vol. 134, Issue 32 https://doi.org/10.1021/ja304027m	journal	August 2012
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
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
Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach Lang, Kathrin; Rieder, Renate; Micura, Ronald Nucleic Acids Research, Vol. 35, Issue 16 https://doi.org/10.1093/nar/gkm580	journal	August 2007
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch Kulshina, N.; Edwards, T. E.; Ferre-D'Amare, A. R. RNA, Vol. 16, Issue 1 https://doi.org/10.1261/rna.1847310	journal	November 2009
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
Monofluoro- and difluoro-methylenebisphosphonic acids: isopolar analogues of pyrophosphoric acid Blackburn, G. Michael; England, David A.; Kolkmann, Friedrich Journal of the Chemical Society, Chemical Communications, Issue 17 https://doi.org/10.1039/c39810000930	journal	January 1981
Complex Ligand-Induced Conformational Changes in tRNA ^Asp Revealed by Single-Nucleotide Resolution SHAPE Chemistry ^† Wang, Bin; Wilkinson, Kevin A.; Weeks, Kevin M. Biochemistry, Vol. 47, Issue 11 https://doi.org/10.1021/bi702372x	journal	March 2008
Identification of Biologically Active, HIV TAR RNA-Binding Small Molecules Using Small Molecule Microarrays Sztuba-Solinska, Joanna; Shenoy, Shilpa R.; Gareiss, Peter Journal of the American Chemical Society, Vol. 136, Issue 23 https://doi.org/10.1021/ja502754f	journal	May 2014
Single-molecule correlated chemical probing of RNA Homan, Philip J.; Favorov, Oleg V.; Lavender, Christopher A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 38 https://doi.org/10.1073/pnas.1407306111	journal	September 2014
RNA base-pairing complexity in living cells visualized by correlated chemical probing Mustoe, Anthony M.; Lama, Nicole N.; Irving, Patrick S. Proceedings of the National Academy of Sciences, Vol. 116, Issue 49 https://doi.org/10.1073/pnas.1905491116	journal	November 2019
Ligand efficiency as a guide in fragment hit selection and optimization Schultes, Sabine; de Graaf, Chris; Haaksma, Eric E. J. Drug Discovery Today: Technologies, Vol. 7, Issue 3 https://doi.org/10.1016/j.ddtec.2010.11.003	journal	October 2010
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Serganov, Alexander; Huang, Lili; Patel, Dinshaw J. Nature, Vol. 458, Issue 7235 https://doi.org/10.1038/nature07642	journal	January 2009
Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection Vicens, Quentin; Mondragón, Estefanía; Batey, Robert T. Nucleic Acids Research, Vol. 39, Issue 19 https://doi.org/10.1093/nar/gkr565	journal	July 2011
Structural basis of ligand binding by a c-di-GMP riboswitch Smith, Kathryn D.; Lipchock, Sarah V.; Ames, Tyler D. Nature Structural & Molecular Biology, Vol. 16, Issue 12 https://doi.org/10.1038/nsmb.1702	journal	November 2009
Structure and ligand binding of the SAM-V riboswitch Huang, Lin; Lilley, David M. J. Nucleic Acids Research, Vol. 46, Issue 13 https://doi.org/10.1093/nar/gky520	journal	June 2018
Synthesis of Stable Analogues of Thiamine Di- and Triphosphate as Tools for Probing a New Phosphorylation Pathway Klein, Emmanuel; Nghiêm, Hoàng-Oanh; Valleix, Alain Chemistry - A European Journal, Vol. 8, Issue 20 https://doi.org/10.1002/1521-3765(20021018)8:20<4649::aid-chem4649>3.0.co;2-m	journal	October 2002
Selective Monodeprotection of Phosphate, Phosphite, Phosphonate, and Phosphoramide Benzyl Esters Saady, Mourad; Lebeau, Luc; Mioskowski, Charles The Journal of Organic Chemistry, Vol. 60, Issue 9 https://doi.org/10.1021/jo00114a059	journal	May 1995
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
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
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
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/s0907444909047337	journal	January 2010
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
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures Ho, Bosco K.; Gruswitz, Franz BMC Structural Biology, Vol. 8, Issue 1 https://doi.org/10.1186/1472-6807-8-49	journal	January 2008

Similar Records

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

Journal Article · 2023 · ACS Chemical Biology · OSTI ID:1847154

Zeller, M; Nuthanakanti, A.; Li, K.; +3 more

Crystallographic Analysis of TPP Riboswitch Binding by Small-Molecule Ligands Discovered Through Fragment-Based Drug Discovery Approaches

Book · 2015 · OSTI ID:1847154

Warner, Katherine Deigan; Ferré-DAmaré, Adrian R.

Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch

Journal Article · 2011 · Molecular Cell · OSTI ID:1847154

Huang, L; Serganov, A; Patel, D

Title: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linkin

Citation Formats

References (52)

Similar Records

Related Subjects