Novel ligands for a purine riboswitch discovered by RNA-ligand docking

Chemistry and Biology

Volumn 18, Issue 3, 2011, Pages 324-335

  Daldrop, Peter ^a   Reyes, Francis E ^b   Robinson, David A ^a   Hammond, Colin M ^a   Lilley, David M ^a   Batey, Robert T ^b   Brenk, Ruth ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PURINE; PURINE DERIVATIVE; RNA;

ARTICLE; BINDING SITE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; RIBOSWITCH; X RAY CRYSTALLOGRAPHY;

BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; LIGANDS; NUCLEIC ACID CONFORMATION; PURINES; RIBOSWITCH; RNA;

EID: 79953067257     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2010.12.020     Document Type: Article

References (62)

1. F. Barbault, L.R. Zhang, L.H. Zhang, and B.T. Fan Parametrization of a specific free energy function for automated docking against RNA targets using neural networks Chemom. Intell. Lab. Syst. 82 2006 269 275
2. R.T. Batey, S.D. Gilbert, and R.K. Montange Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine Nature 432 2004 411 415 (Pubitemid 39551677)
3. C. Bissantz, B. Kuhn, and M. Stahl A medicinal chemist's guide to molecular interactions J. Med. Chem. 53 2010 5061 5084
4. K.F. Blount, and R.R. Breaker Riboswitches as antibacterial drug targets Nat. Biotechnol. 24 2006 1558 1564 (Pubitemid 44967480)
5. K. Bodoor, V. Boyapati, V. Gopu, M. Boisdore, K. Allam, J. Miller, W.D. Treleaven, T. Weldeghiorghis, and F. Aboul-Ela Design and implementation of an ribonucleic acid (RNA) directed fragment library J. Med. Chem. 52 2009 3753 3761
6. R. Brenk, S.W. Vetter, S.E. Boyce, D.B. Goodin, and B.K. Shoichet Probing molecular docking in a charged model binding site J. Mol. Biol. 357 2006 1449 1470
7. R. Brenk, A. Schipani, D. James, A. Krasowski, I.H. Gilbert, J. Frearson, and P.G. Wyatt Lessons learnt from assembling screening libraries for drug discovery for neglected diseases ChemMedChem 3 2008 435 444
8. CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
9. L. Chen, E. Cressina, F.J. Leeper, A.G. Smith, and C. Abell A fragment-based approach to identifying ligands for riboswitches ACS Chem. Biol. 5 2010 355 358
10. C. Detering, and G. Varani Validation of automated docking programs for docking and database screening against RNA drug targets J. Med. Chem. 47 2004 4188 4201 (Pubitemid 39045426)
11. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
12. P. Englebienne, and N. Moitessier Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? J. Chem. Inf. Model. 49 2009 1568 1580
13. F. Franceschi, and E.M. Duffy Structure-based drug design meets the ribosome Biochem. Pharmacol. 71 2006 1016 1025
14. S. Fulle, and H. Gohlke Molecular recognition of RNA: challenges for modelling interactions and plasticity J. Mol. Recognit. 23 2010 220 231
15. P.R. Gerber, and K. Muller MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry J. Comput. Aided Mol. Des. 9 1995 251 268
16. S.D. Gilbert, S.J. Mediatore, and R.T. Batey Modified pyrimidines specifically bind the purine riboswitch J. Am. Chem. Soc. 128 2006 14214 14215 (Pubitemid 44707704)
17. S.D. Gilbert, C.D. Stoddard, S.J. Wise, and R.T. Batey Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain J. Mol. Biol. 359 2006 754 768 (Pubitemid 43767264)
18. S.D. Gilbert, F.E. Reyes, A.L. Edwards, and R.T. Batey Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs Structure 17 2009 857 868
19. H. Gohlke, and G. Klebe Statistical potentials and scoring functions applied to protein-ligand binding Curr. Opin. Struct. Biol. 11 2001 231 235 (Pubitemid 32289427)
20. B. Gorelik, and A. Goldblum High quality binding modes in docking ligands to proteins Proteins 71 2008 1373 1386 (Pubitemid 351564059)
21. C. Guilbert, and T.L. James Docking to RNA via root-mean-square- deviation-driven energy minimization with flexible ligands and flexible targets J. Chem. Inf. Model. 48 2008 1257 1268
22. T. Hermann Strategies for the Design of Drugs Targeting RNA and RNA-Protein Complexes Angew. Chem. Int. Ed. Engl. 39 2000 1890 1904
23. S.R. Holbrook RNA structure: the long and the short of it Curr. Opin. Struct. Biol. 15 2005 302 308 (Pubitemid 40826449)
24. A.N. Jain Ligand-based structural hypotheses for virtual screening J. Med. Chem. 47 2004 947 961 (Pubitemid 38176797)
25. T. Kalliokoski, H.S. Salo, M. Lahtela-Kakkonen, and A. Poso The effect of ligand-based tautomer and protomer prediction on structure-based virtual screening J. Chem. Inf. Model. 49 2009 2742 2748
26. X. Kang, R.H. Shafer, and I.D. Kuntz Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK Biopolymers 73 2004 192 204 (Pubitemid 38220378)
27. J.N. Kim, K.F. Blount, J. Lim, K.H. Link, and R. Breaker Design and antimicrobial action of purine analogs that bind guanine riboswitches ACS Chem. Biol. 4 2009 915 927
28. G. Klebe Virtual ligand screening: strategies, perspectives and limitations Drug Discov. Today 11 2006 580 594
29. P. Kolb, and J.J. Irwin Docking screens: right for the right reasons? Curr. Top. Med. Chem. 9 2009 755 770
30. P.T. Lang, S.R. Brozell, S. Mukherjee, E.F. Pettersen, E.C. Meng, V. Thomas, R.C. Rizzo, D.A. Case, T.L. James, and I.D. Kuntz DOCK 6: combining techniques to model RNA-small molecule complexes RNA 15 2009 1219 1230
31. E.R. Lee, K.F. Blount, and R.R. Breaker Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression RNA Biol. 6 2009 187 194
32. J.F. Lemay, J.C. Penedo, R. Tremblay, D.M. Lilley, and D.A. Lafontaine Folding of the adenine riboswitch Chem. Biol. 13 2006 857 868 (Pubitemid 44247776)
33. X. Li, Y. Li, T. Cheng, Z. Liu, and R. Wang Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes J. Comput. Chem. 31 2010 2109 2125
34. Y. Li, J. Shen, X. Sun, W. Li, G. Liu, and Y. Tang Accuracy assessment of protein-based docking programs against RNA targets J. Chem. Inf. Model. 50 2010 1134 1146
35. C. Liao, and M.C. Nicklaus Comparison of nine programs predicting pK(a) values of pharmaceutical substances J. Chem. Inf. Model. 49 2009 2801 2812
36. K.E. Lind, Z. Du, K. Fujinaga, B.M. Peterlin, and T.L. James Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA Chem. Biol. 9 2002 185 193 (Pubitemid 34196656)
37. D.M. Lorber, and B.K. Shoichet Flexible ligand docking using conformational ensembles Protein Sci. 7 1998 938 950 (Pubitemid 28216535)
38. R.L. Mancera Molecular modeling of hydration in drug design Curr. Opin. Drug Discov. Dev. 10 2007 275 280 (Pubitemid 46800221)
39. J. Manchester, G. Walkup, O. Rivin, and Z. You Evaluation of pKa estimation methods on 211 druglike compounds J. Chem. Inf. Model. 50 2010 565 571
40. M. Mandal, and R.R. Breaker Adenine riboswitches and gene activation by disruption of a transcription terminator Nat. Struct. Mol. Biol. 11 2004 29 35 (Pubitemid 38173438)
41. D. Moazed, and H.F. Noller Interaction of antibiotics with functional sites in 16S ribosomal RNA Nature 327 1987 389 394 (Pubitemid 17075811)
42. N. Moitessier, E. Westhof, and S. Hanessian Docking of aminoglycosides to hydrated and flexible RNA J. Med. Chem. 49 2006 1023 1033 (Pubitemid 43221650)
43. S.D. Morley, and M. Afshar Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock J. Comput. Aided Mol. Des. 18 2004 189 208 (Pubitemid 39069414)
44. C.P. Mpamhanga, D. Spinks, L.B. Tulloch, E.J. Shanks, D.A. Robinson, I.T. Collie, A.H. Fairlamb, P.G. Wyatt, J.A. Frearson, and W.N. Hunter One scaffold, three binding modes: novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening J. Med. Chem. 52 2009 4454 4465
45. J. Mulhbacher, E. Brouillette, M. Allard, L.C. Fortier, F. Malouin, and D.A. Lafontaine Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways PLoS Pathog. 6 2010 e1000865
46. E. Ott, J. Stolz, M. Lehmann, and M. Mack The RFN riboswitch of Bacillus subtilis is a target for the antibiotic roseoflavin produced by Streptomyces davawensis RNA Biol. 6 2009 276 280
47. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Macromol.Crystallogr. Pt. A 276 1997 307 326 (Pubitemid 27085611)
48. S.J. Park, Y.H. Jung, Y.G. Kim, and H.J. Park Identification of novel ligands for the RNA pseudoknot that regulate -1 ribosomal frameshifting Bioorg. Med. Chem. 16 2008 4676 4684 (Pubitemid 351539015)
49. P. Pfeffer, and H. Gohlke DrugScoreRNA-knowledge-based scoring function to predict RNA-ligand interactions J. Chem. Inf. Model. 47 2007 1868 1876 (Pubitemid 47561134)
50. G. Schneider Virtual screening: an endless staircase? Nat. Rev. Drug Discov. 9 2010 273 276
51. A.W. Schuttelkopf, and D.M. van Aalten PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D Biol. Crystallogr. 60 2004 1355 1363 (Pubitemid 41079731)
52. H. Schwalbe, J. Buck, B. Furtig, J. Noeske, and J. Wohnert Structures of RNA switches: insight into molecular recognition and tertiary structure Angew. Chem. Int. Ed. Engl. 46 2007 1212 1219 (Pubitemid 46981366)
53. A. Serganov Determination of riboswitch structures: light at the end of the tunnel? RNA Biol. 7 2010 98 103
54. A. Serganov, Y.R. Yuan, O. Pikovskaya, A. Polonskaia, L. Malinina, A.T. Phan, C. Hobartner, R. Micura, R.R. Breaker, and D.J. Patel Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs Chem. Biol. 11 2004 1729 1741 (Pubitemid 39651306)
55. E. Stjernschantz, and C. Oostenbrink Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes Biophys. J. 98 2010 2682 2691
56. J.R. Thomas, and P.J. Hergenrother Targeting RNA with small molecules Chem. Rev. 108 2008 1171 1224 (Pubitemid 351638813)
57. A. Vagin, and A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallogr. 30 1997 1022 1025 (Pubitemid 127485985)
58. A.A. Vagin, R.A. Steiner, A.A. Lebedev, L. Potterton, S. McNicholas, F. Long, and G.N. Murshudov REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use Acta Crystallogr. D Biol. Crystallogr. 60 2004 2184 2195 (Pubitemid 41742770)
59. M.L. Verdonk, V. Berdini, M.J. Hartshorn, W.T. Mooij, C.W. Murray, R.D. Taylor, and P. Watson Virtual screening using protein-ligand docking: avoiding artificial enrichment J. Chem. Inf. Comput. Sci. 44 2004 793 806
60. J.M. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
61. B.Q. Wei, W.A. Baase, L.H. Weaver, B.W. Matthews, and B.K. Shoichet A model binding site for testing scoring functions in molecular docking J. Mol. Biol. 322 2002 339 355
62. K. Yan, E. Hunt, J. Berge, E. May, R.A. Copeland, and R.R. Gontarek Fluorescence polarization method to characterize macrolide-ribosome interactions Antimicrob. Agents Chemother. 49 2005 3367 3372 (Pubitemid 41060584)