RNA-targeted therapeutics: Prospects and promise

Expert Opinion on Therapeutic Patents

Volumn 12, Issue 9, 2002, Pages 1367-1374

  Griffey, Richard H ^a   Swayze, Eric E ^a  

^a ISIS PHARMACEUTICALS   (United States)

Author keywords

Aminoglycosides; RNA; RNA drug discovery

Indexed keywords

1,2,3 TRIAZINE DERIVATIVE; 2 DEOXYSTREPTAMINE; AMIKACIN; AMINOGLYCOSIDE ANTIBIOTIC AGENT; BACTERIAL RNA; CARBAMIC ACID DERIVATIVE; FURAN DERIVATIVE; GENTAMICIN; KANAMYCIN; LIGAND; LINEZOLID; NEAMINE; NEOMYCIN; OXAZOLIDINONE DERIVATIVE; PAROMOMYCIN; PEPTIDE DERIVATIVE; PIBENZIMOL; RNA BINDING PROTEIN; STREPTOMYCIN; TOBRAMYCIN; TRANSACTIVATOR PROTEIN; UREA DERIVATIVE; VIRUS RNA;

AEROSOL; ANTIBACTERIAL ACTIVITY; ANTIVIRAL ACTIVITY; CYSTIC FIBROSIS; DRUG FORMULATION; DRUG MECHANISM; DRUG RESEARCH; DRUG SCREENING; DRUG SPECIFICITY; DRUG STRUCTURE; GENE TARGETING; HEPATITIS B; HUMAN; LUNG INFECTION; NEPHROTOXICITY; NUCLEAR MAGNETIC RESONANCE; OTOTOXICITY; PATENT; PROTEIN STRUCTURE; REVIEW; RNA ANALYSIS; RNA STRUCTURE; TUBERCULOSIS; X RAY CRYSTALLOGRAPHY;

EID: 0036737560     PISSN: 13543776     EISSN: None     Source Type: Journal    
DOI: 10.1517/13543776.12.9.1367     Document Type: Review

References (41)

1. Hermann T. Strategies for the design of drugs targeting RNA and RNA-protein complexes. Angewandte Chemie, Int. Ed. (2000) 39:1891-1905.
2. Ban N, Nissen P, Hansen J et al: The complete atomic structure of the large ribosomal subunit at 2.4Å resolution. Science (2000) 289:905-920.
3. Wimberly BT, Broderson DE, Clemons WM et al: Structure of the 30S ribosomal subunit. Nature (2000) 407:327-339.
4. Hermann T, Patel DJ: Stitching together RNA tertiary architectures. J. Mol. Biol. (1999) 294:829-849.
5. Moore PB: Structural motifs in RNA. Ann. Rev. Biochem. (1999) 67:287-300.
6. Moazed D, Noller HF: Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature (1987) 327:389-394.
7. 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.
8. 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.
9. Fourmy D, Recht MI, Blanchard SC et al: Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science (1996) 274:1367-1371.
10. 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.
11. Sannes-Lowery KA, Mei 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.
12. Wang S, Huber PW, Cui 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.
13. Kirk SR, Luedtke NW, Tor Y: Neomycin-acridine conjugate: a potent inhibitor of Rev-RRE binding. J. Am. Chem. Soc. (2000) 122:980-981.
14. 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.
15. Schroeder R, Waldsich C, Wank H: Modulation of RNA function by aminoglycoside antibiotics. EMBO J. (2000) 19:1-9.
16. 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.
17. Zhang Y, Bell A, Perlman PS et al.: Pentamidine inhibits mitochondrial intron splicing and translation in Saccharomyces cerevisiae. RIVA (2000) 6:937-951.
18. Cheng AC, Calabro V, Frankel AD: Design of RNA-binding proteins and ligands. Curr. Opin. Struct. Biol. (2001) 11:478-484.
19. 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.
20. Shuker SB, Hajduk PJ, Meadows RP et al: Discovering high-affinity ligands for proteins: SAR by NMR. Science (1996) 274:1531-1534.
21. 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.
22. Hofstadler SA, Griffey RH: Mass spectrometry as a drug discovery platform against RNA targets. Curr. Opin. Drug Discovery Dev. (2000) 3:423-431.
23. 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.
24. 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.
25. Griffey RH, Sannes-Lowery KA, Drader JJ et al.: Characterization of low-affinity complexes between RNA and small molecules using electrospray ionization mass spectrometry. J. Am. Chem. Soc. (2000) 122:9933-9938.
26. 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.
27. Tamilarasu N, Huq I, Rana TM: Targeting RNA with peptidomimetic oligomers in human cells. Bioorg. Med. Chem. Lett. (2001) 11:505-507.
28. Klimkait T, Felder ER, Albrecht G et al: Rational optimization of a HIV-1 tat inhibitor: rapid progress on combinatorial lead structures. Biotechnol. Bioeng. (1998) 61:155-168.
29. 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.
30. 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.
31. 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 in vitro inhibition of translation. J. Am. Chem. Soc. (1999) 121:6527-6541.
32. 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. J. Am. Chem. Soc. (1998) 120:8319-8327.
33. 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.
34. Barrett JF: Linezolid pharmacia corp. Curr. Opin. Invest. Drugs (2000) 1:181-187.
35. 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.
36. Li K, Davis TM, Bailly C et al.: A heterocyclic inhibitor of the Rev-RRE complex binds to RRE as a dimer. Biochemistry (2001) 40:1150-1158.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.