Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble (original) (raw)
Cooper, T.A., Wan, L. & Dreyfuss, G. RNA and disease. Cell136, 777–793 (2009). ArticleCAS Google Scholar
Parsons, J. et al. Conformational inhibition of the hepatitis C virus internal ribosome entry site RNA. Nat. Chem. Biol.5, 823–825 (2009). ArticleCAS Google Scholar
Blount, K.F. & Breaker, R.R. Riboswitches as antibacterial drug targets. Nat. Biotechnol.24, 1558–1564 (2006). ArticleCAS Google Scholar
Thomas, J.R. & Hergenrother, P.J. Targeting RNA with small molecules. Chem. Rev.108, 1171–1224 (2008). ArticleCAS Google Scholar
Kuntz, I.D. Structure-based strategies for drug design and discovery. Science257, 1078–1082 (1992). ArticleCAS Google Scholar
Filikov, A.V. et al. Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J. Comput. Aided Mol. Des.14, 593–610 (2000). ArticleCAS Google Scholar
Hermann, T. Rational ligand design for RNA: the role of static structure and conformational flexibility in target recognition. Biochimie84, 869–875 (2002). ArticleCAS Google Scholar
Cruz, J.A. & Westhof, E. The dynamic landscapes of RNA architecture. Cell136, 604–609 (2009). ArticleCAS Google Scholar
Fulle, S. & Gohlke, H. Molecular recognition of RNA: challenges for modelling interactions and plasticity. J. Mol. Recognit.23, 220–231 (2010). CASPubMed Google Scholar
Zhang, Q., Sun, X., Watt, E.D. & Al-Hashimi, H.M. Resolving the motional modes that code for RNA adaptation. Science311, 653–656 (2006). ArticleCAS Google Scholar
Frank, A.T., Stelzer, A.C., Al-Hashimi, H.M. & Andricioaei, I. Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition. Nucleic Acids Res.37, 3670–3679 (2009). ArticleCAS Google Scholar
Puglisi, J.D., Tan, R., Calnan, B.J., Frankel, A.D. & Williamson, J.R. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science257, 76–80 (1992). ArticleCAS Google Scholar
Williamson, J.R. Induced fit in RNA-protein recognition. Nat. Struct. Biol.7, 834–837 (2000). ArticleCAS Google Scholar
Leulliot, N. & Varani, G. Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture. Biochemistry40, 7947–7956 (2001). ArticleCAS Google Scholar
Latham, M.P., Zimmermann, G.R. & Pardi, A. NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer. J. Am. Chem. Soc.131, 5052–5053 (2009). ArticleCAS Google Scholar
Vaiana, A.C. & Sanbonmatsu, K.Y. Stochastic gating and drug-ribosome interactions. J. Mol. Biol.386, 648–661 (2009). ArticleCAS Google Scholar
Chen, Y., Campbell, S.L. & Dokholyan, N.V. Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophys. J.93, 2300–2306 (2007). ArticleCAS Google Scholar
Clore, G.M. & Schwieters, C.D. Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry43, 10678–10691 (2004). ArticleCAS Google Scholar
Abagyan, R., Totrov, M. & Kuznetsov, D. ICM—a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem.15, 488–506 (1994). ArticleCAS Google Scholar
Lang, P.T. et al. DOCK 6: combining techniques to model RNA-small molecule complexes. RNA15, 1219–1230 (2009). ArticleCAS Google Scholar
Cheng, T., Li, X., Li, Y., Liu, Z. & Wang, R. Comparative assessment of scoring functions on a diverse test set. J. Chem. Inf. Model.49, 1079–1093 (2009). ArticleCAS Google Scholar
Guilbert, C. & James, T.L. Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. J. Chem. Inf. Model.48, 1257–1268 (2008). ArticleCAS Google Scholar
Ippolito, J.A. & Steitz, T.A. A 1.3-Å resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation. Proc. Natl. Acad. Sci. USA95, 9819–9824 (1998). ArticleCAS Google Scholar
Aboul-ela, F., Karn, J. & Varani, G. Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res.24, 3974–3981 (1996). ArticleCAS Google Scholar
Yang, M. Discoveries of Tat-TAR interaction inhibitors for HIV-1. Curr. Drug Targets Infect. Disord.5, 433–444 (2005). ArticleCAS Google Scholar
Bradrick, T.D. & Marino, J.P. Ligand-induced changes in 2-aminopurine fluorescence as a probe for small molecule binding to HIV-1 TAR RNA. RNA10, 1459–1468 (2004). ArticleCAS Google Scholar
Matsumoto, C., Hamasaki, K., Mihara, H. & Ueno, A. A high-throughput screening utilizing intramolecular fluorescence resonance energy transfer for the discovery of the molecules that bind HIV-1 TAR RNA specifically. Bioorg. Med. Chem. Lett.10, 1857–1861 (2000). ArticleCAS Google Scholar
Davidson, A., Patora-Komisarska, K., Robinson, J.A. & Varani, G. Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein. Nucleic Acids Res.39, 248–256 (2011). ArticleCAS Google Scholar
Davidson, A. et al. Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein. Proc. Natl. Acad. Sci. USA106, 11931–11936 (2009). ArticleCAS Google Scholar
White, R.J. & Durr, F.E. Development of mitoxantrone. Invest. New Drugs3, 85–93 (1985). ArticleCAS Google Scholar
Parolin, C. et al. New anti-human immunodeficiency virus type 1 6-aminoquinolones: mechanism of action. Antimicrob. Agents Chemother.47, 889–896 (2003). ArticleCAS Google Scholar
Blount, K.F., Tor, Y., Hamasaki, K. & Ueno, A. Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding aminoglycoside antibiotics, neamine and its derivatives as potent inhibitors for the RNA-protein interactions derived from HIV-1 activators. Nucleic Acids Res.31, 5490–5500 (2003). ArticleCAS Google Scholar
DeJong, E.S., Chang, C.E., Gilson, M.K. & Marino, J.P. Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1. Biochemistry42, 8035–8046 (2003). ArticleCAS Google Scholar
Kaul, M., Barbieri, C.M. & Pilch, D.S. Fluorescence-based approach for detecting and characterizing anti biotic-induced conformational changes in ribosomal RNA: Comparing aminoglycoside binding to prokaryotic and eukaryotic ribosomal RNA sequences. J. Am. Chem. Soc.126, 3447–3453 (2004). ArticleCAS Google Scholar
Stelzer, A.C., Kratz, J.D., Zhang, Q. & Al-Hashimi, H.M. RNA dynamics by design: biasing ensembles towards the ligand-bound state. Angew. Chem. Int. Ed. Engl.49, 5731–5733 (2010). ArticleCAS Google Scholar
Lapidot, A., Berchanski, A. & Borkow, G. Insight into the mechanisms of aminoglycoside derivatives interaction with HIV-1 entry steps and viral gene transcription. FEBS J.275, 5236–5257 (2008). ArticleCAS Google Scholar
Lapidot, A., Vijayabaskar, V., Litovchick, A., Yu, J.G. & James, T.L. Structure-activity relationships of amino glyco side-arginine conjugates that bind HIV-1 RNAs as determined by fluorescence and NMR spectroscopy. FEBS Lett.577, 415–421 (2004). ArticleCAS Google Scholar
Faber, C., Sticht, H., Schweimer, K. & Rosch, P. Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B. J. Biol. Chem.275, 20660–20666 (2000). ArticleCAS Google Scholar
Cabrera, C. et al. Anti-HIV activity of a novel aminoglycoside-arginine conjugate. Antiviral Res.53, 1–8 (2002). ArticleCAS Google Scholar
Blount, K.F., Zhao, F., Hermann, T. & Tor, Y. Conformational constraint as a means for understanding RNA-aminoglycoside specificity. J. Am. Chem. Soc.127, 9818–9829 (2005). ArticleCAS Google Scholar
Boehr, D.D., Nussinov, R. & Wright, P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol.5, 789–796 (2009). ArticleCAS Google Scholar
Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on unix pipes. J. Biomol. NMR6, 277–293 (1995). ArticleCAS Google Scholar