Modeling RNA-ligand interactions: The Rev-binding element RNA- aminoglycoside complex

Journal of Medicinal Chemistry

Volumn 41, Issue 2, 1998, Pages 175-182

  Leclerc, Fabrice ^a   Cedergren, Robert ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; ANTIVIRUS AGENT; DRUG CARRIER; FRAMYCETIN; GENTAMICIN C; KANAMYCIN A; KANAMYCIN B; LIGAND; LIVIDOMYCIN; NEAMINE; OXAZOLINE DERIVATIVE; PAROMOMYCIN; RIBOSTAMYCIN; RNA; SISOMICIN; TOBRAMYCIN;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER SIMULATION; CONFORMATION; DRUG ACTIVITY; MODEL; MOLECULAR DYNAMICS; RHINOVIRUS; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

AMINOGLYCOSIDES; ANTI-BACTERIAL AGENTS; ANTIVIRAL AGENTS; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; GENE PRODUCTS, REV; HUMANS; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; RHINOVIRUS; RNA, VIRAL; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0031894779     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm970372r     Document Type: Article

References (22)

1. Zapp, M. L.; Stern, S.; Green, M. Small molecules that selectively block RNA binding of HIV-1 Rev protein inhibit Rev function and viral production. Cell 1993, 74, 969-978.
2. Werstuck, G.; Zapp, M. L.; Green, M. R. A noncanonical base pair within the human immunodeficiency virus Rev-responsive element is involved in both Rev and small molecule recognition. Chem. Biol. 1996, 3, 129-137.
3. Leclerc, F.; Cedergren, R.; Ellington, A. D. A three-dimensional model of the Rev-binding element of HIV-1 derived from analyses of aptamers. Nature Struct. Biol. 1994, 1, 293-300.
4. 1H NMR studies of the high-affinity Rev binding site of the Rev responsive element of HIV-1 mRNA: base pairing in the core binding element. Biochemistry 1994, 33, 5357-5366.
5. 13C-heteronuclear NMR. J. Biomol. NMR 1995, 6, 375-389.
6. Leclerc, F.; Srinivasan, J.; Cedergren, R. Predicting RNA structures: The model of the RNA element binding Rev meets the NMR structure. Folding Des. 1997, 2, 141-147.
7. Llorente, B.; Leclerc, F.; Cedergren, R. Using SAR and QSAR analysis to model the activity and structure of the Quinolone/ DNA complex. Bioorg. Med. Chem. 1996, 61-71.
8. Srinivasan, J.; Leclerc, F.; Xu, W.; Ellington, A. D.; Cedergren, R. A docking and modelling strategy for peptide-RNA complexes: applications to BIV Tat-TAR and HIV-RBE. Folding Des. 1996, 463-472.
9. Diana, G. D.; McKinlay, M. A.; Otto, M. J.; Akullian, V.; Oglesby, C. [[(4,5-Dihydro-2-oxazolyl)phenoxy]alkyl]isoxaxole inhibitors of picornavirus uncoating. J. Med. Chem. 1985, 1906-1910.
10. Badger, J.; Minor, I.; Kremer, M. J.; Oliveira, M. A.; Smith, T. J.; Griffith, J. P.; Guerin D. M. A.; Krishnaswamy, S.; Leo, M.; Rossmann, M. G.; McKinlay, M. A.; Diana, G. D.; Dutko, F. J.; Fancher, M.; Rueckert, R. R.; Heinz, B. A. Structural analysis of a series of antiviral agents complexed with human rhinovirus 14. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 3304-3308.
11. Klebe, G.; Abraham, U. On the prediction of binding properties of drug molecules by comparative molecular field analysis. J. Med. Chem. 1993, 36, 70-80.
12. Robinson, H.; Wang, A. H. J. Neomycin, spermine and hexaamminecobalt(III) share common structural motifs in converting B- to A-DNA. Nucleic Acid Res. 1995, 24, 3700-3706.
13. Wang, Y.; Hamasaki, K.; Rando, R. R. Specificity of aminoglycoside binding to RNA constructs derived from the 16S rRNA decoding region and the HIV-RRE activator region. Biochemistry 1997, 36, 768-779.
14. Fourmy, D.; Recht, M. I.; Blanchard, S. C.; Puglisi, J. D. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 1996, 274, 1367-1371.
15. Mattos, C.; Ringe, D. Multiple binding modes. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, 1993; pp 226-254.
16. Botto, R. E.; Coxon, B. Nitrogen-15 nuclear magnetic resonance spectroscopy of neomycin B and related aminoglycosides. J. Am. Chem. Soc. 1983, 105, 1021-1028.
17. Potential Energy Functions Consortium PEFC 1994 release; Biosym/MSI Technologies, San Diego, CA.
18. Golender, V. E.; Vorpagel, E. R. Computer-assisted pharmacophore identification. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, 1993; pp 137-149.
19. Golender, V. E.; Rozenblit, A. B. Logical and Combinatorial Algorithms in Drug Design; Research Studies Press: Letch-worth, 1983.
20. Ding, H.-Q.; Karasawa, N.; Goddard, W. A. Atomic level simulations on a million, particles: the cell multipole method for Coulomb and London nonbond interactions. J. Chem. Phys. 1992, 97, 4309-4315.
21. Mathiowetz, A. M.; Jain, A.; Karasawa, N.; Goddard, W. A. Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 1994, 20, 227-247.
22. King, G.; Barford, R. A. Calculations of association free energies. Separation of electrostatic and hydrophobic contributions. In Molecular Modeling: From Virtual Tools to Real Problems; Kumosinski, T. F., Liebman, M. N., Eds.; ACS Symp. Series 576; American Chemical Society: Washington, DC, 1994; pp 173-184.