Novel ligands for a purine riboswitch discovered by RNA-ligand docking.
作者： Peter Daldrop , Francis E. Reyes , David A. Robinson , Colin M. Hammond , David M. Lilley
DOI: 10.1016/J.CHEMBIOL.2010.12.020
关键词:
摘要: The increasing number of RNA crystal structures enables a structure-based approach to the discovery new RNA-binding ligands. To develop poorly explored area RNA-ligand docking, we have conducted virtual screening exercise for purine riboswitch probe strengths and weaknesses docking. Using standard protein-ligand docking program with only minor modifications, four ligands binding affinities in micromolar range were identified, including two compounds based on molecular scaffolds not resembling known performed comparably indicating that this is promising option explore wealth ligand design.
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Zbyszek Otwinowski, Wladek Minor, Processing of X-ray diffraction data collected in oscillation mode Methods in Enzymology. ,vol. 276, pp. 307- 326 ,(1997) , 10.1016/S0076-6879(97)76066-X
Ajay N. Jain, Ligand-Based Structural Hypotheses for Virtual Screening Journal of Medicinal Chemistry. ,vol. 47, pp. 947- 961 ,(2004) , 10.1021/JM030520F
Christophe Guilbert, Thomas L. James, Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets Journal of Chemical Information and Modeling. ,vol. 48, pp. 1257- 1268 ,(2008) , 10.1021/CI8000327
Chidochangu P Mpamhanga, Daniel Spinks, Lindsay B Tulloch, Emma J Shanks, David A Robinson, Iain T Collie, Alan H Fairlamb, Paul G Wyatt, Julie A Frearson, William N Hunter, Ian H Gilbert, Ruth Brenk, None, One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening Journal of Medicinal Chemistry. ,vol. 52, pp. 4454- 4465 ,(2009) , 10.1021/JM900414X
So-Jung Park, Young Hoon Jung, Yang-Gyun Kim, Hyun-Ju Park, Identification of novel ligands for the RNA pseudoknot that regulate -1 ribosomal frameshifting. Bioorganic & Medicinal Chemistry. ,vol. 16, pp. 4676- 4684 ,(2008) , 10.1016/J.BMC.2008.02.025
Binqing Q. Wei, Walter A. Baase, Larry H. Weaver, Brian W. Matthews, Brian K. Shoichet, A Model Binding Site for Testing Scoring Functions in Molecular Docking Journal of Molecular Biology. ,vol. 322, pp. 339- 355 ,(2002) , 10.1016/S0022-2836(02)00777-5
Caterina Bissantz, Bernd Kuhn, Martin Stahl, A Medicinal Chemist’s Guide to Molecular Interactions Journal of Medicinal Chemistry. ,vol. 53, pp. 5061- 5084 ,(2010) , 10.1021/JM100112J
Alexander Serganov, Determination of riboswitch structures: light at the end of the tunnel? RNA Biology. ,vol. 7, pp. 98- 103 ,(2010) , 10.4161/RNA.7.1.10756
Khaled Bodoor, Vamsi Boyapati, Vikram Gopu, Marietta Boisdore, Kiran Allam, Janae Miller, W. Dale Treleaven, Thomas Weldeghiorghis, Fareed Aboul-ela, Design and implementation of an ribonucleic acid (RNA) directed fragment library. Journal of Medicinal Chemistry. ,vol. 52, pp. 3753- 3761 ,(2009) , 10.1021/JM9000659
Sunny D Gilbert, Francis E Reyes, Andrea L Edwards, Robert T Batey, None, Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure. ,vol. 17, pp. 857- 868 ,(2009) , 10.1016/J.STR.2009.04.009