RNA-targeted therapeutics: prospects and promise

Bibliography

• HERMANN T: Strategies for the design of drugs targeting RNA and RNA-protein complexes. Angewandte Chenne, Int. Ed. (2000) 39:1891–1905.
   Google Scholar
• BAN N, NISSENP, HANSEN J et al.: The complete atomic structure of the large ribosomal subunit at 2.4A resolution. Science (2000) 289:905–920.
   Google Scholar
• WIMBERLY BT, BRODERSON DE, CLEMONS WM et al: Structure of the 30S ribosomal subunit. Nature (2000) 407:327–339.
   PubMed Web of Science ®Google Scholar
• •Crystal structure of the 16S subunit with bound arninoglycosides, showing contacts at atomic resolution.
   Google Scholar
• HERMANN T, PATEL DJ: Stitching together RNA tertiary architectures. J. Ma Biol. (1999) 294:829–849.
   Google Scholar
• MOORE PB: Structural motifs in RNA. Ann. Rev Biochem. (1999) 67:287–300.
   Google Scholar
• MOAZED D, NOLLER HF: Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature (1987) 327:389–394.
   PubMed Web of Science ®Google Scholar
• •Early paper demonstrating that 16S rRNA is the site of action for aminoglycoside antibiotics.
   Google Scholar
• MOAZED D, NOLLER HF: Chloramphenicol, erythromycin, carbomycin and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA. Biochimie (1987) 69:879–884.
   PubMed Web of Science ®Google Scholar
• •Paper demonstrating that 23S rRNA is the binding site for macrolide antibiotics.
   Google Scholar
• MATASSOVA NB, RODNINA R, ENDERMANN HP et al.: Ribosomal RNA is the target for oxazolidinones, a novel class of translational inhibitors. RNA (1999) 7:939–946.
   Google Scholar
• FOURMY D, RECHT MI, BLAN CHARD SC et al.: Structure of the A site of Escherichia coil 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science (1996) 274:1367–1371.
   Google Scholar
• GRIFFEY RH, HOFSTADLER SA, SANNES-LOWERY KA et al.: Determinants of aminoglycoside-binding specificity for rRNA by using mass spectrometry. Proc. Natl. Acad. Sci. USA (1999) 96:10129–10133.
   PubMed Web of Science ®Google Scholar
• SANNES-LOWERY KA, MET H-Y, LOO JA: Studying aminoglycoside antibiotic binding to HIV-1 TAR RNA by electrospray ionization mass spectrometry. Int. J. Mass Spectrom. (1999) 193:115–122.
   Google Scholar
• WANG S, HUBER PW, CUT M et al.: Binding of neomycin to the TAR element of HIV-1 RNA induces dissociation of tat protein by an allostericm mechanism. Biochemistry (1998) 37:5549–5557.
   PubMed Web of Science ®Google Scholar
• KIRK SR, LUEDTKE NW, TORY: Neomycin-acne conjugate: a potent inhibitor of Rev-RRE binding. I Am. Chem. Soc. (2000) 122:980–981.
   Web of Science ®Google Scholar
• SULLIVAN JM, GOODISMAN J, DABROWIAK JC: Absorption studies on aminoglycoside binding to the packaging region of human immunodeficiency virus Type-1. Bioorg. Med. Chem. Lett. (2002) 12:615–618.
   PubMedGoogle Scholar
• SCHROEDER R, WALDSICH C, WANK H: Modulation of RNA function by aminoglycoside antibiotics. EMBO (2000) 19:1–9.
   PubMed Web of Science ®Google Scholar
• MILETTI KE, LEIBOWITZ MJ: Pentamidine inhibition of Group I Intron splicing in Candida albicans correlates with growth inhibition. Antimicrob. Agents Chemother. (2000) 44:958–966.
   PubMed Web of Science ®Google Scholar
• ZHANG Y, BELL A, PERLMAN PS et al.: Pentamidine inhibits mitochondrial intron splicing and translation in Saccharomyces cerevisiae. RNA (2000) 6:937–951.
   PubMed Web of Science ®Google Scholar
• CHENG AC, CALABRO V, FRANKEL AD: Design of RNA-binding proteins and ligands. Can: Opin. Strad. Biol. (2001) 11:478–484.
   PubMed Web of Science ®Google Scholar
• HAJDUK PJ, SHEPPARD G, NETTESHEIM DG et al.: Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR. J. Am. Chem. Soc. (1997) 119:5818–5827.
   Web of Science ®Google Scholar
• SHUKER SB, HAJDUK PJ, MEADOWS RP et at Discovering high-affinity ligands for proteins: SAR by NMR. Science (1996) 274:1531–1534.
   PubMed Web of Science ®Google Scholar
• LYNCH SR, PUGLISI JD: Application of residual dipolar coupling measurements to identify conformational changes in RNA induced by antibiotics. J. Am. Chem. Soc. (2000) 122:7853–7854.
   Google Scholar
• HOFSTADLER SA, GRIFFEY RH: Mass spectrometry as a drug discovery platform against RNA targets. Carr. Opin. Drug Discovery Dev. (2000) 3:423–431.
   PubMedGoogle Scholar
• SANNES-LOWERY KA, DRADER JJ, GRIFFEY RH et al.: Fourier transform ion cyclotron resonance mass spectrometry as a high throughput affinity screen to identify RNA-binding ligands. TrAC, Trends Anal. Chem. (2000) 19:481–491.
   Google Scholar
• SANNES-LOWERY KA, GRIFFEY RH, HOFSTADLER SA: Measuring dissociation constants of RNA and aminoglycoside antibiotics by electrospray ionization mass spectrometry. Anal. Biochem. (2000) 280:264–271.
   PubMedGoogle Scholar
• GRIFFEY RH, SANNES-LOWERY KA, DRADER JJ et al.: Characterization of low-affinity complexes between RNA and small molecules using electrospray ionization mass spectrometry. Am. Chem. Soc. (2000) 122:9933–9938.
   Google Scholar
• SWAYZE EE, JEFFERSON EA, SANNES-LOWERY KA et al.: SAR by MS: a ligand based technique for drug lead discovery against structured RNA targets. J. Med. Chem. (2002) 45:3816–3819.
   PubMed Web of Science ®Google Scholar
• TAMILARASU N, HUQ I, RANA TM: Targeting RNA with peptidomimetic oligomers in human cells. Bioorg. Med. Chem. Lett. (2001) 11:505–507.
   PubMed Web of Science ®Google Scholar
• KLIMKAIT T, FELDER ER, ALBRECHT G et al: Rational optimization of a HIV-1 tatinhibitor: rapid progress on combinatorial lead structures. Biotechnol Bioeng. (1998) 61:155–168.
   PubMedGoogle Scholar
• SUCHECK SJ, GREENBERG WA, TOLBERT TJ et al.: Design of small molecules that recognize RNA: development of aminoglycosides as potential antitumor agents that target oncogenic RNA sequences. Angew. Chem. Int. Ed. (2000) 39:1080–1084.
   PubMedGoogle Scholar
• SUCHECK SJ, WONG AL, KOELLER KM et al.: Design of bifunctional antibiotics that target bacterial rRNA and inhibit resistance-causing enzymes. J. Am. Chem. Soc. (2000) 122:5230–5231.
   Google Scholar
• GREENBERG WA, PRIESTLEY ES, SEARS PS et al.: Design and synthesis of new aminoglycoside antibiotics containing neamine as an optimal core structure: correlation of antibiotic activity with M vitro inhibition of translation. J. Am. Chem. Soc. (1999) 121:6527–6541.
   Google Scholar
• WONG C-H, HENDRIX M, MANNING DD et al.: A library approach to the discovery of small molecules that recognize RNA: use of a 1,3-hydroxyamine motif as core.' Am. Chem. Soc. (1998) 120:8319–8327.
   Google Scholar
• HADDAD J, KOTRA LP, LLANO-SOTELO B et al.: Design of novel antibiotics that bind to the ribosomal acyltransfer site. J. Am. Chem. Soc. (2002) 124:3229–3237.
   PubMedGoogle Scholar
• BARRETT JF: Linezolid pharmacia corp. Carr. Opin. Invest. Drugs(2000) 1:181–187.
   PubMedGoogle Scholar
• ZAPP ML, YOUNG DW, KUMAR A et al: Modulation of the Rev-RRE interaction by aromatic heterocyclic compounds. Bioorg. Med. Chem. (1997) 5:1149–1155.
   PubMedGoogle Scholar
• LI K, DAVIS TM, BAILLY C et at: A heterocyclic inhibitor of the Rev-RRE complex binds to RRE as a dimer. Biochemistry (2001) 40:1150–1158.
   PubMedGoogle Scholar
• HORI Y, BICHENKOVA EV, WILTON AN et al.: Synthetic inhibitors of the processing of pretransfer RNA by the ribonuclease P ribozyme: enzyme inhibitors which act by binding to substrate. Biochemistry (2001) 40:603–608.
   PubMedGoogle Scholar
• HAMY F, BRONDANI V, FLORSHEIMER A et al.: A new class of HIV-1 tat antagonist acting through tat-TAR inhibition. Biochemistry (1998) 37:5086–5095.
   PubMed Web of Science ®Google Scholar
• MEI H-Y, MACK DP, GALAN AA et al.: Discovery of selective, small-molecule inhibitors of RNA complexes - I. The tat protein/TAR RNA complexes required for HIV-1 transcription. Bioorg. Med. Chem. (1997) 5:1173–1184.
   Google Scholar
• •One of the earliest efforts to identify small molecules that bind to RNA targets.
   Google Scholar
• MEI H-Y, CUI M, LEMROW SM et al: Discovery of selective, small-molecule inhibitors of RNA complexes - II. Self-splicing group I intron ribozyme. Bioorg. Med. Chem. (1997) 5:1185–1195.
   PubMedGoogle Scholar
• MEI HY, CUI M, HELDSINGER A 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. Biochemistry (1998) 37:14204–14212.
   PubMed Web of Science ®Google Scholar