메뉴 건너뛰기




Volumn 3, Issue 4, 2000, Pages 423-431

Mass spectrometry as a drug discovery platform against RNA targets

Author keywords

Electrospray ionization; High throughput screening; Mass spectrometry; RNA

Indexed keywords

COMPLEMENTARY RNA; RNA;

EID: 0033925478     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (29)

References (35)
  • 1
    • 0034603154 scopus 로고    scopus 로고
    • Adaptive recognition by nucleic acid aptamers
    • Patel DJ: 820-825.
    • Hermann T, Patel DJ: Adaptive recognition by nucleic acid aptamers. Science (2000) 287:820-825.
    • (2000) Science , vol.287
    • Hermann, T.1
  • 2
    • 0024424033 scopus 로고
    • Mutations in 16S ribosomal RNA disrupt antibiotic - RNA interactions
    • Moazed D, Noller HF, Dahlberg AE: 1213-1216.
    • De Stasio EA, Moazed D, Noller HF, Dahlberg AE: Mutations in 16S ribosomal RNA disrupt antibiotic - RNA interactions. E/WBOJ(1989) 8:1213-1216.
    • (1989) E/WBOJ , vol.8
    • De Stasio, E.A.1
  • 3
    • 0004615149 scopus 로고
    • Mechanisms of action of aminoglycoside antibiotics
    • Sande MA (Eds), Churchill Livingstone, NY, USA 17-35.
    • Bryan LE: Mechanisms of action of aminoglycoside antibiotics. In: New Dimensions in Antimicrobial Therapy. Root RK, Sande MA (Eds), Churchill Livingstone, NY, USA (1984)1:17-35.
    • (1984) In: New Dimensions in Antimicrobial Therapy. Root RK , vol.1
    • Bryan, L.E.1
  • 4
    • 0032126750 scopus 로고    scopus 로고
    • Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA
    • Hendrix M, Priestley ES, Greenberg WA: 397-406.
    • Wong C-H, Hendrix M, Priestley ES, Greenberg WA: Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA. Chem B/o/(1998) 5:397-406.
    • (1998) Chem B/o/ , vol.5
    • Wong, C.-H.1
  • 5
    • 0039926756 scopus 로고
    • Principles and practice of electrospray ionization - Mass-spectrometry for large polypeptides and proteins
    • Loo JA, Loo RR, Busman M, Udseth HR: 359-451. A good introduction to ESI-MS - highlights a number of analytical and biological applications of the technique.
    • Smith RD, Loo JA, Loo RR, Busman M, Udseth HR: Principles and practice of electrospray ionization - mass-spectrometry for large polypeptides and proteins. Mass Spectrom fiev(1991) 10:359-451. A good introduction to ESI-MS - highlights a number of analytical and biological applications of the technique.
    • (1991) Mass Spectrom Fiev , vol.10
    • Smith, R.D.1
  • 6
    • 0042403082 scopus 로고
    • Multiply charged ions
    • 195-225.
    • Vekey K: Multiply charged ions. Mass Spectrom Rev (1995) 14:195-225.
    • (1995) Mass Spectrom Rev , vol.14
    • Vekey, K.1
  • 7
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Mann M, Meng CK, Wong SF, Whitehouse CM: 64-71.
    • Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM: Electrospray ionization for mass spectrometry of large biomolecules. Sc/ence(1989) 246:64-71.
    • (1989) Sc/ence , vol.246
    • Fenn, J.B.1
  • 8
    • 0001413545 scopus 로고
    • Detection of noncovalent receptor-ligand complexes by mass spectrometry
    • Li Y-T, Henion JD: 6294-6296. First published example of a specific non-covalent complex characterized by ESI-MS, which demonstrates that under appropriate interface and solution conditions, macromolecular complexes are amenable to mass spectrometric characterization.
    • Ganem B, Li Y-T, Henion JD: Detection of noncovalent receptor-ligand complexes by mass spectrometry. J Am Chem Soc(1991) 113:6294-6296. First published example of a specific non-covalent complex characterized by ESI-MS, which demonstrates that under appropriate interface and solution conditions, macromolecular complexes are amenable to mass spectrometric characterization.
    • (1991) J Am Chem Soc , vol.113
    • Ganem, B.1
  • 9
    • 84989026523 scopus 로고
    • Preservation of noncovalent associations in electrospray Ionization massspectrometry - Multily charged polypeptide and protein dimers
    • Light-Wahl KJ, Winger BE, Loo JA: 811-821.
    • Smith RD, Light-Wahl KJ, Winger BE, Loo JA: Preservation of noncovalent associations in electrospray Ionization massspectrometry - multily charged polypeptide and protein dimers. Org Mass Spectrom (1992) 27:811-821.
    • (1992) Org Mass Spectrom , vol.27
    • Smith, R.D.1
  • 10
    • 0001598080 scopus 로고
    • Mass spectrometric studies on noncovalent dimers of leucine zipper peptides
    • Hsieh YL, Henion JD, Senko MW, McLafferty FW, Ganem B: 8409-8413.
    • Li YT, Hsieh YL, Henion JD, Senko MW, McLafferty FW, Ganem B: Mass spectrometric studies on noncovalent dimers of leucine zipper peptides. J Am Chem Soc (1993) 115:8409-8413.
    • (1993) J Am Chem Soc , vol.115
    • Li, Y.T.1
  • 11
    • 0027274976 scopus 로고
    • Studies of the ras-GDP and ras-GTP noncovalent complexes by electrospray mass spectrometry
    • Pramanik BN, Huang EC, Tsarbopoulos A, Girijavallabhan VM, Libertés S: 7985-7996.
    • Ganguly AK, Pramanik BN, Huang EC, Tsarbopoulos A, Girijavallabhan VM, Libertés S: Studies of the ras-GDP and ras-GTP noncovalent complexes by electrospray mass spectrometry. Tetrahedron (1993) 49:7985-7996.
    • (1993) Tetrahedron , vol.49
    • Ganguly, A.K.1
  • 12
    • 0000391707 scopus 로고
    • Observation of a noncovalent ribonuclease S-protein/S-peptide complex by electrospray ionization mass spectrometry
    • Goodlet DR, Smith RD, Loo JA: 4391-4392.
    • Ogorzalek-Loo RR, Goodlet DR, Smith RD, Loo JA: Observation of a noncovalent ribonuclease S-protein/S-peptide complex by electrospray ionization mass spectrometry. JAm Chem Soc (1993) 115:4391-4392.
    • (1993) JAm Chem Soc , vol.115
    • Ogorzalek-Loo, R.R.1
  • 13
    • 0028500350 scopus 로고
    • Investigation of protein-protein noncovalent interactions in soybean agglutinin by electrospray ionization time-of-f light mass spectrometry
    • Brewer CF, Saha S, Chemushevich I, Ens W, Standing KG: 750-754.
    • Tang XJ, Brewer CF, Saha S, Chemushevich I, Ens W, Standing KG: Investigation of protein-protein noncovalent interactions in soybean agglutinin by electrospray ionization time-of-f light mass spectrometry. Rapid Commun Mass Spectrom (1994) 8:750-754.
    • (1994) Rapid Commun Mass Spectrom , vol.8
    • Tang, X.J.1
  • 14
    • 0001367661 scopus 로고
    • Application of electrospray mass spectrometry in probing protein- Protein and protein-ligand noncovalent interactions
    • Pramanik BN, Tsarbopoulos A, Reichert P, Ganguly AK, Trotta PP, Nagabhushan TL, Covey TR: 624-630.
    • Huang EC, Pramanik BN, Tsarbopoulos A, Reichert P, Ganguly AK, Trotta PP, Nagabhushan TL, Covey TR: Application of electrospray mass spectrometry in probing protein- protein and protein-ligand noncovalent interactions. JAm Soc Mass Spectrom (1993) 4:624-630.
    • (1993) JAm Soc Mass Spectrom , vol.4
    • Huang, E.C.1
  • 15
    • 0000391704 scopus 로고
    • Observation of a small oligonucleotide duplex by electrospray ionization massspectrometry
    • Springer DL, Winger BE, Edmonds CG, Camp DG, Thrall BD, Smith RD: 803-804.
    • Light-Wahl KJ, Springer DL, Winger BE, Edmonds CG, Camp DG, Thrall BD, Smith RD: Observation of a small oligonucleotide duplex by electrospray ionization massspectrometry. J Am Chem Soc (1993) 115:803-804.
    • (1993) J Am Chem Soc , vol.115
    • Light-Wahl, K.J.1
  • 16
    • 0028774392 scopus 로고
    • Accumulation and storage of ionized duplex DNA molecules in a quadrupole ion trap
    • Habibi-Goudarzi S, McLuckey SA: 3416-3422.
    • Doktycz MJ, Habibi-Goudarzi S, McLuckey SA: Accumulation and storage of ionized duplex DNA molecules in a quadrupole ion trap. Anal Chem (1994) 66:3416-3422.
    • (1994) Anal Chem , vol.66
    • Doktycz, M.J.1
  • 17
    • 0032491152 scopus 로고    scopus 로고
    • Inhibitors of proteinRNA complexation that target the RNA: Specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules
    • Cui M, Heldsinger A, Lemrow SM, Loo JA, SannesLowery KA, Sharmeen L, Czarnik AW: 14204-14212. ESI-MS and other methods are used to study the binding of three ligands which bind HIV-1 TAR RNA. It is demonstrated that ESI-MS can be used to study the differential binding of ligands to TAR variants (eg, a construct in which the hexanucleotide loop is replaced with a polyethylene glycol linker).
    • Mei HY, Cui M, Heldsinger A, Lemrow SM, Loo JA, SannesLowery KA, Sharmeen L, Czarnik AW: Inhibitors of proteinRNA complexation that target the RNA: Specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. Biochemistry (1998) 37:14204-14212. ESI-MS and other methods are used to study the binding of three ligands which bind HIV-1 TAR RNA. It is demonstrated that ESI-MS can be used to study the differential binding of ligands to TAR variants (eg, a construct in which the hexanucleotide loop is replaced with a polyethylene glycol linker).
    • (1998) Biochemistry , vol.37
    • Mei, H.Y.1
  • 18
    • 0041289883 scopus 로고    scopus 로고
    • Studying noncovalent small molecule interactions with protein and RNA targets by mass spectrometry
    • Thanabal V, Mei H-Y: 73-90.
    • Loo JA, Thanabal V, Mei H-Y: Studying noncovalent small molecule interactions with protein and RNA targets by mass spectrometry. Mass Spectrom Biol Med (2000):73-90.
    • (2000) Mass Spectrom Biol Med
    • Loo, J.A.1
  • 19
    • 0033590014 scopus 로고    scopus 로고
    • Studying aminoglycoside antibiotic binding to HIV-1 TAR RNA by electrospray ionization mass spectrometry
    • Mei H-Y, Loo JA: 115-122.
    • 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.
    • (1999) Int J Mass Spectrom , vol.193
    • Sannes-Lowery, K.A.1
  • 21
    • 0029825658 scopus 로고    scopus 로고
    • Structure of the a site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic
    • Recht Ml, Blanchard SC, Puglisi JD: 1367-1371.
    • Fourmy D, Recht Ml, Blanchard SC, Puglisi JD: Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science (1996)274:1367-1371.
    • (1996) Science , vol.274
    • Fourmy, D.1
  • 22
    • 0032538956 scopus 로고    scopus 로고
    • Structural origins of gentamicin antibiotic action
    • Fourmy D, Puglisi JD: 6437-6448
    • Yoshizawa S, Fourmy D, Puglisi JD: Structural origins of gentamicin antibiotic action. EMBO J(1998) 17:6437-6448
    • (1998) EMBO J , vol.17
    • Yoshizawa, S.1
  • 23
    • 0033566617 scopus 로고    scopus 로고
    • Multiplexed screening of neutral mass tagged RNA targets against ligand libraries with electrospray ionization FTICR MS: A paradigm for high-throughput affinity screening
    • Sannes-Lowery KA, Crooke ST, Ecker DJ, Sasmor H, Manalili S, Griffey RH: 3436-3440. It is shown that ESI-MS can be used as an affinity screen between compound collections and RNA constructs of similar (or identical) mass by using a neutral mass tag on one or more of the RNA targets. The neutral mass tag shifts the signal of the target, and associated complexes, to a unique region of the mass spectrum in which mass ambiguities are minimized.
    • Hofstadler SA, Sannes-Lowery KA, Crooke ST, Ecker DJ, Sasmor H, Manalili S, Griffey RH: Multiplexed screening of neutral mass tagged RNA targets against ligand libraries with electrospray ionization FTICR MS: A paradigm for high-throughput affinity screening. Anal Chem (1999) 71:3436-3440. It is shown that ESI-MS can be used as an affinity screen between compound collections and RNA constructs of similar (or identical) mass by using a neutral mass tag on one or more of the RNA targets. The neutral mass tag shifts the signal of the target, and associated complexes, to a unique region of the mass spectrum in which mass ambiguities are minimized.
    • (1999) Anal Chem , vol.71
    • Hofstadler, S.A.1
  • 24
    • 0033585581 scopus 로고    scopus 로고
    • Targeted site-specific gas-phase cleavage of oligoribonucleotides
    • Greig MJ, An H, Sasmor H, Manalili S: 474-475. Incorporation of deoxynucleotides into a chimeric oligoribonucleotide is shown to generate a series of labile sites where collisionally activated dissociation is favored. Binding of ligands at the labile sites affords protection from collisionally activated dissociation in MS-MS experiments. This mass spectrometry-based protection assay can be used to establish the binding sites for RNA binding ligands without the need for additional chemical reagents or radiolabeling of the RNA.
    • Griffey RH, Greig MJ, An H, Sasmor H, Manalili S: Targeted site-specific gas-phase cleavage of oligoribonucleotides. Application in mass spectrometry-based identification of ligand binding sites. J Am Chem Soc (1999)121:474-475. Incorporation of deoxynucleotides into a chimeric oligoribonucleotide is shown to generate a series of labile sites where collisionally activated dissociation is favored. Binding of ligands at the labile sites affords protection from collisionally activated dissociation in MS-MS experiments. This mass spectrometry-based protection assay can be used to establish the binding sites for RNA binding ligands without the need for additional chemical reagents or radiolabeling of the RNA.
    • (1999) Application in Mass Spectrometry-based Identification of Ligand Binding Sites. J Am Chem Soc , vol.121
    • Griffey, R.H.1
  • 25
    • 0033621114 scopus 로고    scopus 로고
    • Determinants of aminoglycoside-blnding specificity for rRNA by using mass spectrometry
    • Hofstadler SA, Sannes-Lowery KA, Ecker DJ, Crooke ST: 10129-10133. ESI-FTICR MS is used to characterize the binding of three classes of aminoglycoside antibiotics to the 16S and 18S rRNA Asites. In addition to determining binding affinities, the locations of the binding sites on the RNAs were identified from a protection pattern generated by fragmenting the aminoglycoside/RNA complex. Specific base substitutions were introduced in the RNA models and their impact on binding affinity and selectivity were measured.
    • Griffey RH, Hofstadler SA, Sannes-Lowery KA, Ecker DJ, Crooke ST: Determinants of aminoglycoside-blnding specificity for rRNA by using mass spectrometry. Proc Natl AcadSci USA (1999) 96:10129-10133. ESI-FTICR MS is used to characterize the binding of three classes of aminoglycoside antibiotics to the 16S and 18S rRNA Asites. In addition to determining binding affinities, the locations of the binding sites on the RNAs were identified from a protection pattern generated by fragmenting the aminoglycoside/RNA complex. Specific base substitutions were introduced in the RNA models and their impact on binding affinity and selectivity were measured.
    • (1999) Proc Natl AcadSci USA , vol.96
    • Griffey, R.H.1
  • 26
    • 0032571306 scopus 로고    scopus 로고
    • Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 rRNA
    • Recht Ml, Puglisi JD: 347-362.
    • Fourmy D, Recht Ml, Puglisi JD: Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 rRNA. J Mol B/o/(1998) 277:347-362.
    • (1998) J Mol B/o/ , vol.277
    • Fourmy, D.1
  • 27
    • 0032571359 scopus 로고    scopus 로고
    • Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA
    • Yoshizawa S, Puglisi JD: 333-345.
    • Fourmy D, Yoshizawa S, Puglisi JD: Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J Mol Biol (1998) 277:333-345.
    • (1998) J Mol Biol , vol.277
    • Fourmy, D.1
  • 28
    • 0033913682 scopus 로고    scopus 로고
    • Fourier transform Ion cyclotron resonance mass spectrometry as a high-throughput affinity screen to Identify RNA-binding ligands
    • Drader JJ, Griffey RH, Hofstadler SA
    • Sannes-Lowery KA, Drader JJ, Griffey RH, Hofstadler SA: Fourier transform Ion cyclotron resonance mass spectrometry as a high-throughput affinity screen to Identify RNA-binding ligands. Trends Anal Chem (2000) in press.
    • (2000) Trends Anal Chem
    • Sannes-Lowery, K.A.1
  • 29
    • 0032532125 scopus 로고    scopus 로고
    • Direct determination of solution binding constants for noncovalent complexes between bacterial cell wall peptide analogues and vancomycin group antibiotics by electrospray lonization mass spectrometry
    • Roepstorff P: 4427-4432.
    • Jorgensen TJ, Roepstorff P: Direct determination of solution binding constants for noncovalent complexes between bacterial cell wall peptide analogues and vancomycin group antibiotics by electrospray lonization mass spectrometry. Anal Chem (1998) 70:4427-4432.
    • (1998) Anal Chem , vol.70
    • Jorgensen, T.J.1
  • 32
    • 84969001783 scopus 로고
    • The attractions of proteins for small molecules and Ions
    • 660-572.
    • Scatchard G: The attractions of proteins for small molecules and Ions. Proc Nail Acad Soi USA (1949) 51:660-572.
    • (1949) Proc Nail Acad Soi USA , vol.51
    • Scatchard, G.1
  • 33
    • 0034646370 scopus 로고    scopus 로고
    • Combinatorial target-guided ligand assembly: Identification of potent subtype-selective c-Src Inhibitors
    • Choong 1C, Ellman JA: 2419-2424. A method for the identification of ligands to biological targets is reported in which ligands that bind with low affinity are connected by common chemical linkage groups through a set of flexible linkers to create components with enhanced binding affinity.
    • Maly DJ, Choong 1C, Ellman JA: Combinatorial target-guided ligand assembly: Identification of potent subtype-selective c-Src Inhibitors. Proc Natl Acad Sei USA (2000) 97:2419-2424. A method for the identification of ligands to biological targets is reported in which ligands that bind with low affinity are connected by common chemical linkage groups through a set of flexible linkers to create components with enhanced binding affinity.
    • (2000) Proc Natl Acad Sei USA , vol.97
    • Maly, D.J.1
  • 34
    • 0030829408 scopus 로고    scopus 로고
    • Stromelysin inhibitors designed from weakly bound fragments: Effects of linking and cooperativity
    • Hajduk PJ, Marcotte PA, Nettesheim DG, Meadows RP, Edalji R, Holzman TF, Fesik SW: 5828-5832. This work, and previous work by the same group, describes an NMR-based method for the identification of weakly bound chemical motifs. Compounds with higher target affinity are created by linking the binding motifs.
    • Olejniczak ET, Hajduk PJ, Marcotte PA, Nettesheim DG, Meadows RP, Edalji R, Holzman TF, Fesik SW: Stromelysin inhibitors designed from weakly bound fragments: Effects of linking and cooperativity. J Am Chem Soc (1997) 119:5828-5832. This work, and previous work by the same group, describes an NMR-based method for the identification of weakly bound chemical motifs. Compounds with higher target affinity are created by linking the binding motifs.
    • (1997) J Am Chem Soc , vol.119
    • Olejniczak, E.T.1
  • 35
    • 0034624996 scopus 로고    scopus 로고
    • Detection and selective dissociation of intact ribosomes in a mass spectrometer
    • Fucini P, Benjamin DR, Juenemann R, Nierhaus KH, Hartl FU, Dobson CM, Robinson CV: 5185-5190. Intact E coli ribosomes were studied using ESI-TOF instrumentation with a nano-electrospray ionization source. Individual ions with m/z in excess of 20,000 were detected and coadded to yield mass spectra of the intact 70S ribosome. A mass measurement of 852,187 + 3918 Da was obtained for the 30S subunit, in good agreement with the theoretical value of 846,681 Da calculated from the combined masses of the 21 small subunit proteins and the 165 RNA.
    • Rostom AA, Fucini P, Benjamin DR, Juenemann R, Nierhaus KH, Hartl FU, Dobson CM, Robinson CV: Detection and selective dissociation of intact ribosomes in a mass spectrometer. Proc Natl Acad Sei USA (2000) 97:5185-5190. Intact E coli ribosomes were studied using ESI-TOF instrumentation with a nano-electrospray ionization source. Individual ions with m/z in excess of 20,000 were detected and coadded to yield mass spectra of the intact 70S ribosome. A mass measurement of 852,187 + 3918 Da was obtained for the 30S subunit, in good agreement with the theoretical value of 846,681 Da calculated from the combined masses of the 21 small subunit proteins and the 165 RNA.
    • (2000) Proc Natl Acad Sei USA , vol.97
    • Rostom, A.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.