Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.

[1]  P. Bolton,et al.  Ethidium bromide binding to transfer RNA: transfer RNA as a model system for studying drug-RNA interactions. , 1978, Biochemistry.

[2]  I. Tinoco,et al.  Ethidium ion binds more strongly to a DNA double helix with a bulged cytosine than to a regular double helix. , 1985, Biochemistry.

[3]  I. Tinoco,et al.  Absorbance melting curves of RNA. , 1989, Methods in enzymology.

[4]  O. Uhlenbeck,et al.  Synthesis of small RNAs using T7 RNA polymerase. , 1989, Methods in enzymology.

[5]  J. Karn,et al.  Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[6]  D M Crothers,et al.  Fragments of the HIV-1 Tat protein specifically bind TAR RNA. , 1990, Science.

[7]  D. Crothers,et al.  RNA recognition by Tat-derived peptides: Interaction in the major groove? , 1991, Cell.

[8]  J. Puglisi,et al.  Conformation of the TAR RNA-arginine complex by NMR spectroscopy. , 1992, Science.

[9]  M Sumner-Smith,et al.  Conserved nucleotides in the TAR RNA stem of human immunodeficiency virus type 1 are critical for Tat binding and trans activation: model for TAR RNA tertiary structure , 1992, Journal of virology.

[10]  R. Diamond.  On the multiple simultaneous superposition of molecular structures by rigid body transformations , 1992, Protein science : a publication of the Protein Society.

[11]  M. Garcia-Blanco,et al.  Unusual structure of the human immunodeficiency virus type 1 trans-activation response element , 1992, Journal of virology.

[12]  J Grasby,et al.  Hydrogen-bonding contacts in the major groove are required for human immunodeficiency virus type-1 tat protein recognition of TAR RNA. , 1993, Journal of molecular biology.

[13]  J. Karn,et al.  High affinity binding of TAR RNA by the human immunodeficiency virus type-1 tat protein requires base-pairs in the RNA stem and amino acid residues flanking the basic region. , 1993, Journal of molecular biology.

[14]  Michael J. Gait,et al.  Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins , 1994, Nucleic Acids Res..

[15]  R Diamond,et al.  Coordinate-based cluster analysis. , 1995, Acta crystallographica. Section D, Biological crystallography.

[16]  J. Karn,et al.  The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. , 1995, Journal of molecular biology.

[17]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[18]  W. Wilson,et al.  Inhibition of HIV-1 Rev-RRE interaction by diphenylfuran derivatives. , 1996, Biochemistry.

[19]  Gabriele Varani,et al.  NMR investigation of RNA structure , 1996 .

[20]  J. Karn,et al.  Human immunodeficiency virus type-1 Tat is an integral component of the activated transcription-elongation complex. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Karn,et al.  Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. , 1996, Nucleic acids research.

[22]  J. Karn,et al.  An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Williamson,et al.  Solution structure of the HIV-2 TAR-argininamide complex. , 1997, Journal of molecular biology.

[24]  J. Karn,et al.  Transfer of Tat and release of TAR RNA during the activation of the human immunodeficiency virus type‐1 transcription elongation complex , 1997, The EMBO journal.

[25]  C. Bailly,et al.  Binding of Hoechst 33258 to the TAR RNA of HIV-1. Recognition of a pyrimidine bulge-dependent structure. , 1997, Nucleic acids research.

[26]  T. Klimkait,et al.  A new class of HIV-1 Tat antagonist acting through Tat-TAR inhibition. , 1998, Biochemistry.

[27]  A. W. Czarnik,et al.  Inhibitors of protein-RNA complexation that target the RNA: specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. , 1998, Biochemistry.

[28]  J. Williamson,et al.  NMR evidence for a base triple in the HIV-2 TAR C-G.C+ mutant-argininamide complex. , 1998, Nucleic acids research.

[29]  A. W. Czarnik,et al.  Binding of neomycin to the TAR element of HIV-1 RNA induces dissociation of Tat protein by an allosteric mechanism. , 1998, Biochemistry.

[30]  T. Steitz,et al.  A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[31]  T. Klimkait,et al.  Inhibition of HIV-1 Tat-TAR interaction by diphenylfuran derivatives: effects of the terminal basic side chains. , 1999, Bioorganic & medicinal chemistry.

[32]  W. C. Still,et al.  Inhibition of gene expression in human cells through small molecule-RNA interactions. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[33]  D. Crothers,et al.  Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA. , 1999, Biochemistry.

[34]  J. Karn,et al.  Direct evidence that HIV-1 Tat stimulates RNA polymerase II carboxyl-terminal domain hyperphosphorylation during transcriptional elongation. , 1999, Journal of molecular biology.

[35]  J. Karn,et al.  Stimulation of Tat‐associated kinase‐independent transcriptional elongation from the human immunodeficiency virus type‐1 long terminal repeat by a cellular enhancer , 1999, The EMBO journal.

[36]  P. Seeburg,et al.  Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. , 2000, Science.

[37]  R. Rando,et al.  Specific binding of Hoechst 33258 to site 1 thymidylate synthase mRNA. , 2000, Nucleic acids research.

[38]  H. Sticht,et al.  Structural Rearrangements of HIV-1 Tat-responsive RNA upon Binding of Neomycin B* , 2000, The Journal of Biological Chemistry.

[39]  G. Varani,et al.  Targeting RNA with small-molecule drugs: therapeutic promise and chemical challenges. , 2001, Accounts of chemical research.

[40]  C. Bailly,et al.  A heterocyclic inhibitor of the REV-RRE complex binds to RRE as a dimer. , 2001, Biochemistry.

[41]  J. Wengel,et al.  Inhibition of HIV-1 Tat-dependent trans activation by steric block chimeric 2'-O-methyl/LNA oligoribonucleotides. , 2001, Biochemistry.

[42]  R. Gambari,et al.  Aromatic polyamidines inhibiting the Tat-induced HIV-1 transcription recognize structured TAR-RNA. , 2001, Antisense & nucleic acid drug development.

[43]  K. Hall,et al.  RNA-protein interactions. , 2002, Current opinion in structural biology.

[44]  Zhihua Du,et al.  Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening. , 2002, Chemistry & biology.

[45]  D. Patel,et al.  Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. , 2002, Journal of molecular biology.

[46]  P. Herdewijn,et al.  RNA as a target for drug design, the example of Tat-TAR interaction. , 2002, Current topics in medicinal chemistry.

[47]  R. L. Myers,et al.  Anti-TAR Polyamide Nucleotide Analog Conjugated with a Membrane-Permeating Peptide Inhibits Human Immunodeficiency Virus Type 1 Production , 2002, Journal of Virology.

[48]  J. Karn,et al.  Phosphorylation of the RNA Polymerase II Carboxyl-Terminal Domain by CDK9 Is Directly Responsible for Human Immunodeficiency Virus Type 1 Tat-Activated Transcriptional Elongation , 2002, Molecular and Cellular Biology.

[49]  Zhihua Du,et al.  Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. , 2002, Chemistry & biology.

[50]  R. Griffey,et al.  SAR by MS: a ligand based technique for drug lead discovery against structured RNA targets. , 2002, Journal of medicinal chemistry.

[51]  Mohammad Afshar,et al.  RNA as a drug target. , 2002, Progress in medicinal chemistry.

[52]  Liping Yu,et al.  Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA. , 2003, Journal of the American Chemical Society.

[53]  M. Gait,et al.  Steric inhibition of human immunodeficiency virus type-1 Tat-dependent trans-activation in vitro and in cells by oligonucleotides containing 2'-O-methyl G-clamp ribonucleoside analogues. , 2003, Nucleic acids research.