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Volumn 394, Issue , 2005, Pages 571-587

Discovery of ligands by a combination of computational and NMR-based screening: RNA as an example target

(2)  Mayer, Moriz a   James, Thomas L a  

a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; LIGAND; ORGANIC COMPOUND; PYRIMIDINE; RNA; UNCLASSIFIED DRUG; WATER;

EID: 16244416482     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)94024-X     Document Type: Article
Times cited : (13)

References (65)
  • 1
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R., Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:1994;983-1002
    • (1994) J. Mol. Biol. , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 2
    • 84986522918 scopus 로고
    • ICM - A new method for protein modeling and design - Applications to docking and structure prediction from the distorted native conformation
    • Abagyan R.A., Totrov M.M., Kuznetsov D.N. ICM - a new method for protein modeling and design - applications to docking and structure prediction from the distorted native conformation. J. Comp. Chem. 15:1994;488-506
    • (1994) J. Comp. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.A.1    Totrov, M.M.2    Kuznetsov, D.N.3
  • 3
    • 0036835460 scopus 로고    scopus 로고
    • Integration of virtual and high-throughput screening
    • Bajorath F. Integration of virtual and high-throughput screening. Nat. Rev. Drug Discov. 1:2002;882-894
    • (2002) Nat. Rev. Drug Discov. , vol.1 , pp. 882-894
    • Bajorath, F.1
  • 5
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
    • Bissantz C., Folkers G., Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 43:2000;4759-4767
    • (2000) J. Med. Chem. , vol.43 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 6
    • 0030954877 scopus 로고    scopus 로고
    • Structure-based discovery of ligands targeted to the RNA double helix
    • Chen Q., Shafer R.H., Kuntz I.D. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry. 36:1997;11402-11407
    • (1997) Biochemistry , vol.36 , pp. 11402-11407
    • Chen, Q.1    Shafer, R.H.2    Kuntz, I.D.3
  • 9
    • 0036903969 scopus 로고    scopus 로고
    • The ternary complex of cytochrome F and cytochrome C: Identification of a second binding site and competition for plastocyanin binding
    • Crowley P.B., Rabe K.S., Worrall J.A., Canters G.W., Ubbink M. The ternary complex of cytochrome F and cytochrome C: Identification of a second binding site and competition for plastocyanin binding. Chembiochem. 3:2002;526-533
    • (2002) Chembiochem. , vol.3 , pp. 526-533
    • Crowley, P.B.1    Rabe, K.S.2    Worrall, J.A.3    Canters, G.W.4    Ubbink, M.5
  • 10
    • 0033789206 scopus 로고    scopus 로고
    • Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water
    • Dalvit C., Pevarello P., Tato M., Veronesi M., Vulpetti A., Sundstrom M. Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J. Biomol. NMR. 18:2000;65-68
    • (2000) J. Biomol. NMR , vol.18 , pp. 65-68
    • Dalvit, C.1    Pevarello, P.2    Tato, M.3    Veronesi, M.4    Vulpetti, A.5    Sundstrom, M.6
  • 11
    • 0035692794 scopus 로고    scopus 로고
    • Waterlogsy as a method for primary NMR screening: Practical aspects and range of applicability
    • Dalvit C., Fogliatto G., Stewart A., Veronesi M., Stockman B. Waterlogsy as a method for primary NMR screening: Practical aspects and range of applicability. J. Biomol. NMR. 21:2001;349-359
    • (2001) J. Biomol. NMR , vol.21 , pp. 349-359
    • Dalvit, C.1    Fogliatto, G.2    Stewart, A.3    Veronesi, M.4    Stockman, B.5
  • 13
    • 0038336897 scopus 로고    scopus 로고
    • Application and limitations of X-ray crystallographic data in structure-based ligand and drug design
    • Davis A.M., Teague S.J., Kleywegt G.J. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem. Int. Ed. 42:2003;2718-2736
    • (2003) Angew. Chem. Int. Ed. , vol.42 , pp. 2718-2736
    • Davis, A.M.1    Teague, S.J.2    Kleywegt, G.J.3
  • 15
    • 0019333899 scopus 로고
    • Proton nuclear magnetic resonance studies of the effects of ligand binding on tryptophan residues of selectively deuterated dihydrofolate reductase from Lactobacillus casei
    • Feeney J., Roberts G.C., Thomson J.W., King R.W., Griffiths D.V., Burgen A.S. Proton nuclear magnetic resonance studies of the effects of ligand binding on tryptophan residues of selectively deuterated dihydrofolate reductase from Lactobacillus casei. Biochemistry. 19:1980;2316-2321
    • (1980) Biochemistry , vol.19 , pp. 2316-2321
    • Feeney, J.1    Roberts, G.C.2    Thomson, J.W.3    King, R.W.4    Griffiths, D.V.5    Burgen, A.S.6
  • 16
    • 0033213957 scopus 로고    scopus 로고
    • The shapes strategy: An NMR-based approach for lead generation in drug discovery
    • Fejzo J., Lepre C.A., Peng J.W., Bemis G.W., Ajay Murcko, M. A., Moore J.M. The shapes strategy: An NMR-based approach for lead generation in drug discovery. Chem. Biol. 6:1999;755-769
    • (1999) Chem. Biol. , vol.6 , pp. 755-769
    • Fejzo, J.1    Lepre, C.A.2    Peng, J.W.3    Bemis, G.W.4    Ajay, M.M.A.5    Moore, J.M.6
  • 18
    • 1342343126 scopus 로고    scopus 로고
    • A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site
    • Foloppe N., Chen I.J., Davis B., Hold A., Morley D., Howes R. A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site. Bioorg. Med. Chem. 12:2004;935-947
    • (2004) Bioorg. Med. Chem. , vol.12 , pp. 935-947
    • Foloppe, N.1    Chen, I.J.2    Davis, B.3    Hold, A.4    Morley, D.5    Howes, R.6
  • 19
    • 0029825658 scopus 로고    scopus 로고
    • Structure of the a site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic
    • 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. 274:1996;1367-1371
    • (1996) Science , vol.274 , pp. 1367-1371
    • Fourmy, D.1    Recht, M.I.2    Blanchard, S.C.3    Puglisi, J.D.4
  • 20
    • 0032571359 scopus 로고    scopus 로고
    • Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA
    • Fourmy D., Yoshizawa S., Puglisi J.D. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J. Mol. Biol. 277:1998;333-345
    • (1998) J. Mol. Biol. , vol.277 , pp. 333-345
    • Fourmy, D.1    Yoshizawa, S.2    Puglisi, J.D.3
  • 21
    • 0034783659 scopus 로고    scopus 로고
    • Targeting RNA with small-molecule drugs: Therapeutic promise and chemical challenges
    • Gallego J., Varani G. Targeting RNA with small-molecule drugs: Therapeutic promise and chemical challenges. Acc. Chem. Res. 34:2001;836-843
    • (2001) Acc. Chem. Res. , vol.34 , pp. 836-843
    • Gallego, J.1    Varani, G.2
  • 24
    • 0034618541 scopus 로고    scopus 로고
    • Privileged molecules for protein binding identified from NMR-based screening
    • Hajduk P.J., Bures M., Praestgaard J., Fesik S.W. Privileged molecules for protein binding identified from NMR-based screening. J. Med. Chem. 43:2000;3443-3447
    • (2000) J. Med. Chem. , vol.43 , pp. 3443-3447
    • Hajduk, P.J.1    Bures, M.2    Praestgaard, J.3    Fesik, S.W.4
  • 25
    • 0011776731 scopus 로고    scopus 로고
    • A strategy for high-throughput assay development using leads derived from nuclear magnetic resonance-based screening
    • Hajduk P.J., Betz S.F., Mack J., Ruan X., Towne D.L., Lerner C.G., Beutel B.A., Fesik S.W. A strategy for high-throughput assay development using leads derived from nuclear magnetic resonance-based screening. J. Biomol. Screen. 7:2002;429-432
    • (2002) J. Biomol. Screen , vol.7 , pp. 429-432
    • Hajduk, P.J.1    Betz, S.F.2    MacK, J.3    Ruan, X.4    Towne, D.L.5    Lerner, C.G.6    Beutel, B.A.7    Fesik, S.W.8
  • 26
    • 0034595705 scopus 로고    scopus 로고
    • Strategies for the design of drugs targeting RNA and RNA-protein complexes
    • Hermann T. Strategies for the design of drugs targeting RNA and RNA-protein complexes. Angew. Chem. Int. Ed. 39:2000;1891-1905
    • (2000) Angew. Chem. Int. Ed. , vol.39 , pp. 1891-1905
    • Hermann, T.1
  • 27
    • 0036761206 scopus 로고    scopus 로고
    • Rational ligand design for RNA: The role of static structure and conformational flexibility in target recognition
    • Hermann T. Rational ligand design for RNA: The role of static structure and conformational flexibility in target recognition. Biochimie. 84:2002;869-875
    • (2002) Biochimie , vol.84 , pp. 869-875
    • Hermann, T.1
  • 28
    • 0041836268 scopus 로고    scopus 로고
    • Chemical and functional diversity of small molecule ligands for RNA
    • Hermann T. Chemical and functional diversity of small molecule ligands for RNA. Biopolymers. 70:2003;4-18
    • (2003) Biopolymers , vol.70 , pp. 4-18
    • Hermann, T.1
  • 30
    • 3142623157 scopus 로고    scopus 로고
    • Corcema refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities
    • Jayalakshmi V., Rama Krishna N. Corcema refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities. J. Magn. Reson. 168:2004;36-45
    • (2004) J. Magn. Reson. , vol.168 , pp. 36-45
    • Jayalakshmi, V.1    Rama Krishna, N.2
  • 32
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones G., Willett P., Glen R.C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 245:1995;43-53
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 34
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the flexx incremental construction algorithm for protein-ligand docking
    • Kramer B., Rarey M., Lengauer T. Evaluation of the flexx incremental construction algorithm for protein-ligand docking. Proteins. 37:1999;228-241
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 35
    • 0042307439 scopus 로고    scopus 로고
    • Selective incorporation of 19F-labeled Trp side chains for NMR-spectroscopy-based ligand-protein interaction studies
    • Leone M., Rodriguez-Mias R.A., Pellecchia M. Selective incorporation of 19F-labeled Trp side chains for NMR-spectroscopy-based ligand-protein interaction studies. Chembiochem. 4:2003;649-650
    • (2003) Chembiochem. , vol.4 , pp. 649-650
    • Leone, M.1    Rodriguez-Mias, R.A.2    Pellecchia, M.3
  • 36
    • 0035252844 scopus 로고    scopus 로고
    • Library design for NMR-based screening
    • Lepre C.A. Library design for NMR-based screening. Drug Discov. Today. 6:2001;133-140
    • (2001) Drug Discov. Today , vol.6 , pp. 133-140
    • Lepre, C.A.1
  • 38
    • 0028673158 scopus 로고
    • Protein-ligand interactions: Exchange processes and determination of ligand conformation and protein-ligand contacts
    • Lian L.Y., Barsukov I.L., Sutcliffe M.J., Sze K.H., Roberts G.C. Protein-ligand interactions: Exchange processes and determination of ligand conformation and protein-ligand contacts. Methods Enzymol. 239:1994;657-700
    • (1994) Methods Enzymol. , vol.239 , pp. 657-700
    • Lian, L.Y.1    Barsukov, I.L.2    Sutcliffe, M.J.3    Sze, K.H.4    Roberts, G.C.5
  • 39
    • 0036008846 scopus 로고    scopus 로고
    • Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA
    • Lind K.E., Du Z., Fujinaga K., Peterlin B.M., James T.L. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chem. Biol. 9:2002;185-193
    • (2002) Chem. Biol. , vol.9 , pp. 185-193
    • Lind, K.E.1    Du, Z.2    Fujinaga, K.3    Peterlin, B.M.4    James, T.L.5
  • 40
    • 0034461768 scopus 로고    scopus 로고
    • Drug-like properties and the causes of poor solubility and poor permeability
    • Lipinski C.A. Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods. 44:2000;235-249
    • (2000) J. Pharmacol. Toxicol. Methods , vol.44 , pp. 235-249
    • Lipinski, C.A.1
  • 41
    • 0041836262 scopus 로고    scopus 로고
    • Fluorescence-based methods for evaluating the RNA affinity and specificity of HIV-1 rev-RRE inhibitors
    • Luedtke N.W., Tor Y. Fluorescence-based methods for evaluating the RNA affinity and specificity of HIV-1 rev-RRE inhibitors. Biopolymers. 70:2003;103-119
    • (2003) Biopolymers , vol.70 , pp. 103-119
    • Luedtke, N.W.1    Tor, Y.2
  • 42
    • 0034085501 scopus 로고    scopus 로고
    • Biochemical and nuclear magnetic resonance studies of aminoglycoside-RNA complexes
    • Lynch S.R., Recht M.I., Puglisi J.D. Biochemical and nuclear magnetic resonance studies of aminoglycoside-RNA complexes. Methods Enzymol. 317:2000;240-261
    • (2000) Methods Enzymol. , vol.317 , pp. 240-261
    • Lynch, S.R.1    Recht, M.I.2    Puglisi, J.D.3
  • 43
    • 0037229886 scopus 로고    scopus 로고
    • Comparison of X-ray crystal structure of the 30s subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex
    • Lynch S.R., Gonzalez R.L., Puglisi J.D. Comparison of X-ray crystal structure of the 30s subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Structure (Camb.). 11:2003;43-53
    • (2003) Structure (Camb.) , vol.11 , pp. 43-53
    • Lynch, S.R.1    Gonzalez, R.L.2    Puglisi, J.D.3
  • 44
    • 0037107887 scopus 로고    scopus 로고
    • Structure-based virtual screening: An overview
    • Lyne P.D. Structure-based virtual screening: An overview. Drug Discov. Today. 7:2002;1047-1055
    • (2002) Drug Discov. Today , vol.7 , pp. 1047-1055
    • Lyne, P.D.1
  • 46
    • 0037073160 scopus 로고    scopus 로고
    • Detecting ligand binding to a small RNA target via saturation transfer difference NMR experiments in D(2)O and H(2)O
    • Mayer M., James T.L. Detecting ligand binding to a small RNA target via saturation transfer difference NMR experiments in D(2)O and H(2)O. J. Am. Chem. Soc. 124:2002;13376-13377
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 13376-13377
    • Mayer, M.1    James, T.L.2
  • 47
    • 1842450536 scopus 로고    scopus 로고
    • NMR-based characterization of phenothiazines as a RNA binding scaffold
    • Mayer M., James T.L. NMR-based characterization of phenothiazines as a RNA binding scaffold. J. Am. Chem. Soc. 126:2004;4453-4460
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 4453-4460
    • Mayer, M.1    James, T.L.2
  • 48
    • 0033553844 scopus 로고    scopus 로고
    • Characterization of ligand binding by saturation transfer difference NMR spectroscopy
    • Mayer M., Meyer B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew. Chem. Int. Ed. 38:1999;1784-1788
    • (1999) Angew. Chem. Int. Ed. , vol.38 , pp. 1784-1788
    • Mayer, M.1    Meyer, B.2
  • 49
    • 0032491152 scopus 로고    scopus 로고
    • Inhibitors of protein-RNA complexation that target the RNA: Specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules
    • Mei H.-Y., Cui M., Heldsinger A., Lemrow S.M., Loo J.A., Sannes-Lowery K.A., Sharmeen L., Czarnik A.W. Inhibitors of protein-RNA complexation that target the RNA: Specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. Biochemistry. 37:1998;14204-14212
    • (1998) Biochemistry , vol.37 , pp. 14204-14212
    • Mei, H.-Y.1    Cui, M.2    Heldsinger, A.3    Lemrow, S.M.4    Loo, J.A.5    Sannes-Lowery, K.A.6    Sharmeen, L.7    Czarnik, A.W.8
  • 50
    • 0037463033 scopus 로고    scopus 로고
    • NMR Spectroscopy techniques for screening and identifying ligand binding to protein receptors
    • Meyer B., Peters T. NMR Spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. 42:2003;864-890
    • (2003) Angew. Chem. Int. Ed. , vol.42 , pp. 864-890
    • Meyer, B.1    Peters, T.2
  • 51
    • 0020484756 scopus 로고
    • Binding of 5-fluorotryptamine to polynucleotides as a model for protein-nucleic acid interactions: Fluorine-19 nuclear magnetic resonance, absorption, and fluorescence studies
    • Mirau P.A., Shafer R.H., James T.L. Binding of 5-fluorotryptamine to polynucleotides as a model for protein-nucleic acid interactions: Fluorine-19 nuclear magnetic resonance, absorption, and fluorescence studies. Biochemistry. 21:1982;615-620
    • (1982) Biochemistry , vol.21 , pp. 615-620
    • Mirau, P.A.1    Shafer, R.H.2    James, T.L.3
  • 52
    • 2142690682 scopus 로고    scopus 로고
    • Leveraging structural approaches: Applications of NMR-based screening and X-ray crystallography for inhibitor design
    • Moore J., Abdul-Manan N., Fejzo J., Jacobs M., Lepre C., Peng J., Xie X. Leveraging structural approaches: Applications of NMR-based screening and X-ray crystallography for inhibitor design. J. Synchrotron Radiat. 11:2004;97-100
    • (2004) J. Synchrotron Radiat. , vol.11 , pp. 97-100
    • Moore, J.1    Abdul-Manan, N.2    Fejzo, J.3    Jacobs, M.4    Lepre, C.5    Peng, J.6    Xie, X.7
  • 55
    • 0034923647 scopus 로고    scopus 로고
    • Nuclear magnetic resonance-based approaches for lead generation in drug discovery
    • Peng J.W., Lepre C.A., Fejzo J., Abdul-Manan N., Moore J.M. Nuclear magnetic resonance-based approaches for lead generation in drug discovery. Methods Enzymol. 338:2001;202-230
    • (2001) Methods Enzymol. , vol.338 , pp. 202-230
    • Peng, J.W.1    Lepre, C.A.2    Fejzo, J.3    Abdul-Manan, N.4    Moore, J.M.5
  • 56
    • 1642377999 scopus 로고    scopus 로고
    • O. Zerbe. Weinheim, Germany: Wiley-VCH
    • Roberts G.C. Zerbe O. "BioNMR in Drug Research" 2002;309-319 Wiley-VCH, Weinheim, Germany
    • (2002) "bioNMR in Drug Research" , pp. 309-319
    • Roberts, G.C.1
  • 58
    • 0035966871 scopus 로고    scopus 로고
    • Detailed analysis of scoring functions for virtual screening
    • Stahl M., Rarey M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 44:2001;1035-1042
    • (2001) J. Med. Chem. , vol.44 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 60
    • 0034237264 scopus 로고    scopus 로고
    • Diversity screening versus focussed screening in drug discovery
    • Valler M.J., Green D. Diversity screening versus focussed screening in drug discovery. Drug Discov. Today. 5:2000;286-293
    • (2000) Drug Discov. Today , vol.5 , pp. 286-293
    • Valler, M.J.1    Green, D.2
  • 65
    • 0037448895 scopus 로고    scopus 로고
    • Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA
    • Yu L., Oost T.K., Schkeryantz J.M., Yang J., Janowick D., Fesik S.W. Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA. J. Am. Chem. Soc. 125:2003;4444-4450
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 4444-4450
    • Yu, L.1    Oost, T.K.2    Schkeryantz, J.M.3    Yang, J.4    Janowick, D.5    Fesik, S.W.6


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