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Volumn 21, Issue 8, 2012, Pages 1597-1610

3D-QSAR and molecular docking studies of hydroxamic acids as peptide deformylase inhibitors

Author keywords

3D QSAR; CoMFA; CoMSIA; Docking; PDF

Indexed keywords

HYDROXAMIC ACID; PEPTIDE DEFORMYLASE; PEPTIDE DEFORMYLASE INHIBITOR;

EID: 84866070794     PISSN: 10542523     EISSN: 15548120     Source Type: Journal    
DOI: 10.1007/s00044-011-9672-7     Document Type: Article
Times cited : (10)

References (40)
  • 1
    • 0014413570 scopus 로고
    • On the release of the formyl group from nascent protein
    • Adams JM (1968) On the release of the formyl group from nascent protein. J Mol Biol 33:571-574
    • (1968) J Mol Biol , vol.33 , pp. 571-574
    • Adams, J.M.1
  • 2
    • 0013868347 scopus 로고
    • N-formylmethionyl-sRNA as the initiator of protein synthesis
    • Adams JM, Capecchi MR (1966) N-formylmethionyl-sRNA as the initiator of protein synthesis. Proc Natl Acad Sci USA 55: 147-155
    • (1966) Proc Natl Acad Sci USA , vol.55 , pp. 147-155
    • Adams, J.M.1    Capecchi, M.R.2
  • 4
    • 0027672324 scopus 로고
    • Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA
    • Bush BL, Nachbar RB (1993) Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA. J Comput Aided Mol Des 7:587-619
    • (1993) J Comput Aided Mol des , vol.7 , pp. 587-619
    • Bush, B.L.1    Nachbar, R.B.2
  • 5
    • 8844285335 scopus 로고    scopus 로고
    • Isoxazole-3-hydroxamic acid derivatives as peptide deformylase inhibitors and potential antibacterial agents
    • Calí P, Nærum L, Mukhija S, Hjelmencrantz A (2004) Isoxazole-3-hydroxamic acid derivatives as peptide deformylase inhibitors and potential antibacterial agents. Bioorg Med Chem Lett 14: 5997-6000
    • (2004) Bioorg Med Chem Lett , vol.14 , pp. 5997-6000
    • Calí, P.1    Nærum, L.2    Mukhija, S.3    Hjelmencrantz, A.4
  • 7
    • 9144268506 scopus 로고    scopus 로고
    • Peptide deformylase inhibitors as antibacterial agents: Identification of VRC3375, a proline-3-alkylsuccinyl hydroxamate derivative, by using an integrated combinatorial and medicinal chemistry approach
    • Chen D, Hackbarth C, Ni ZJ, Wu C, Wang W, Jain R, He Y, Bracken K, Weidmann B, Patel DV, Trias J, White RJ, Yuan Z (2004) Peptide deformylase inhibitors as antibacterial agents: Identification of VRC3375, a proline-3-alkylsuccinyl hydroxamate derivative, by using an integrated combinatorial and medicinal chemistry approach. Antimicrob Agents Chemother 48:250-261
    • (2004) Antimicrob Agents Chemother , vol.48 , pp. 250-261
    • Chen, D.1    Hackbarth, C.2    Ni, Z.J.3    Wu, C.4    Wang, W.5    Jain, R.6    He, Y.7    Bracken, K.8    Weidmann, B.9    Patel, D.V.10    Trias, J.11    White, R.J.12    Yuan, Z.13
  • 8
  • 10
    • 0023751431 scopus 로고
    • Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
    • Cramer RD III, Patterson DE, Bunce JD (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110:5959-5967
    • (1988) J Am Chem Soc , vol.110 , pp. 5959-5967
    • Cramer Iii, R.D.1    Patterson, D.E.2    Bunce, J.D.3
  • 12
    • 0038592455 scopus 로고    scopus 로고
    • Identifification of substrate channels and protein cavities
    • Exner T, Keil M, Moeckel G, Brickmann J (1998) Identifification of substrate channels and protein cavities. J Mol Model 4:340-343
    • (1998) J Mol Model , vol.4 , pp. 340-343
    • Exner, T.1    Keil, M.2    Moeckel, G.3    Brickmann, J.4
  • 13
    • 70349971143 scopus 로고    scopus 로고
    • New screens and targets in antibacterial drug discovery
    • Falconer SB, Brown ED (2009) New screens and targets in antibacterial drug discovery. Curr Opin Microbiol 12:497-504
    • (2009) Curr Opin Microbiol , vol.12 , pp. 497-504
    • Falconer, S.B.1    Brown, E.D.2
  • 14
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges
    • Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 36:3219-3228
    • (1980) Tetrahedron , vol.36 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 15
    • 85152373811 scopus 로고
    • Notes on the history and nature of partial least squares (PLS) modelling
    • Geladi P (1988) Notes on the history and nature of partial least squares (PLS) modelling. J Chemom 2:231-246
    • (1988) J Chemom , vol.2 , pp. 231-246
    • Geladi, P.1
  • 16
    • 0032546490 scopus 로고    scopus 로고
    • Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site
    • Groche D, Becker A, Schlichting I, Kabsch W, Schultz S et al (1998) Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site. Biochem Biophys Res Commun 246: 342-346
    • (1998) Biochem Biophys Res Commun , vol.246 , pp. 342-346
    • Groche, D.1    Becker, A.2    Schlichting, I.3    Kabsch, W.4    Schultz, S.5
  • 17
    • 34848865009 scopus 로고    scopus 로고
    • Drug forecast-The peptide deformylase inhibitors as antibacterial agents
    • Guay DRP (2007) Drug forecast-the peptide deformylase inhibitors as antibacterial agents. Ther Clin Risk Manag 3:513-525
    • (2007) Ther Clin Risk Manag , vol.3 , pp. 513-525
    • Guay, D.R.P.1
  • 19
    • 0035972911 scopus 로고    scopus 로고
    • Three-dimensional quantitative structureactivity relationship analyses of a series of cinnamamides
    • Hou TJ, Xu XJ (2001) Three-dimensional quantitative structureactivity relationship analyses of a series of cinnamamides. Chemom Intell Lab Syst 56:123-132
    • (2001) Chemom Intell Lab Syst , vol.56 , pp. 123-132
    • Hou, T.J.1    Xu, X.J.2
  • 20
    • 0034219043 scopus 로고    scopus 로고
    • Three-dimensional quantitative structure-activity relationship analysis of the new potent sulfonylureas using comparative molecular similarity indices analysis
    • Hou TJ, Li ZM, Li Z, Liu J, Xu XJ (2000) Three-dimensional quantitative structure-activity relationship analysis of the new potent sulfonylureas using comparative molecular similarity indices analysis. J Chem Inf Comput Sci 40:1002-1009
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 1002-1009
    • Hou, T.J.1    Li, Z.M.2    Li, Z.3    Liu, J.4    Xu, X.J.5
  • 21
    • 0037208314 scopus 로고    scopus 로고
    • Mapping the binding site of a large set of quinazoline type EGF-R inhibitors using molecular field analyses and molecular docking studies
    • Hou TJ, Zhu LL, Chen LR, Xu XJ (2002) Mapping the binding site of a large set of quinazoline type EGF-R inhibitors using molecular field analyses and molecular docking studies. J Chem Inf Comput Sci 43:273-287
    • (2002) J Chem Inf Comput Sci , vol.43 , pp. 273-287
    • Hou, T.J.1    Zhu, L.L.2    Chen, L.R.3    Xu, X.J.4
  • 23
    • 33846601268 scopus 로고    scopus 로고
    • Pharmacophoric features of Pseudomonas aeruginosa deacetylase LpxC inhibitors: An electronic and structural analysis
    • Kadam RU, Chavan A, Roy N (2007) Pharmacophoric features of Pseudomonas aeruginosa deacetylase LpxC inhibitors: an electronic and structural analysis. Bioorg Med Chem Lett 17:861-868
    • (2007) Bioorg Med Chem Lett , vol.17 , pp. 861-868
    • Kadam, R.U.1    Chavan, A.2    Roy, N.3
  • 24
    • 0033022163 scopus 로고    scopus 로고
    • Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries
    • Klebe G, Abraham U (1999) Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries. J Comput Aided Mol Des 13:1-10
    • (1999) J Comput Aided Mol des , vol.13 , pp. 1-10
    • Klebe, G.1    Abraham, U.2
  • 25
    • 0027944195 scopus 로고
    • Molecular Similarity Indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
    • Klebe G, Abraham U, Mietzner T (1994) Molecular Similarity Indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem 37:4130-4146
    • (1994) J Med Chem , vol.37 , pp. 4130-4146
    • Klebe, G.1    Abraham, U.2    Mietzner, T.3
  • 27
    • 33748430340 scopus 로고    scopus 로고
    • Peptide deformylase as an antibacterial target: A critical assessment
    • Leeds JA, Dean CR (2006) Peptide deformylase as an antibacterial target: a critical assessment. Curr Opin Pharmacol 6:445-452
    • (2006) Curr Opin Pharmacol , vol.6 , pp. 445-452
    • Leeds, J.A.1    Dean, C.R.2
  • 28
    • 0014441360 scopus 로고
    • Deformylation and protein biosynthesis
    • Livingston DM, Leder P (1969) Deformylation and protein biosynthesis. Biochemistry 8:435-443
    • (1969) Biochemistry , vol.8 , pp. 435-443
    • Livingston, D.M.1    Leder, P.2
  • 29
    • 0019333951 scopus 로고
    • Initiation of protein synthesis in isolated mitochondria and chloroplasts
    • Lucchini G, Bianchetti R (1980) Initiation of protein synthesis in isolated mitochondria and chloroplasts. Biochim Biophys Acta 608:54-61
    • (1980) Biochim Biophys Acta , vol.608 , pp. 54-61
    • Lucchini, G.1    Bianchetti, R.2
  • 31
    • 0022636261 scopus 로고
    • Comparative analysis of the electrostatic potentials of dibenzofuran and some dibenzo-p-dioxins
    • Murray JS, Zilles BA, Jayasuriya K, Politzer P (1986) Comparative analysis of the electrostatic potentials of dibenzofuran and some dibenzo-p-dioxins. J Am Chem Soc 108:915-918
    • (1986) J Am Chem Soc , vol.108 , pp. 915-918
    • Murray, J.S.1    Zilles, B.A.2    Jayasuriya, K.3    Politzer, P.4
  • 32
    • 0000296163 scopus 로고    scopus 로고
    • Peptide deformylase: A new type of mononuclear iron protein
    • Rajagopalan PTR, Yu XC, Pei D (1997) Peptide deformylase: a new type of mononuclear iron protein. J Am Chem Soc 119:12418-12419
    • (1997) J Am Chem Soc , vol.119 , pp. 12418-12419
    • Rajagopalan, P.T.R.1    Yu, X.C.2    Pei, D.3
  • 33
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489
    • (1996) J Mol Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 34
    • 0033949276 scopus 로고    scopus 로고
    • Receptor-based 3D QSAR analysis of estrogen receptor ligands - Merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods
    • Sippl W (2000) Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods. J Comput Aided Mol Des 14:559-572
    • (2000) J Comput Aided Mol des , vol.14 , pp. 559-572
    • Sippl, W.1
  • 35
    • 33744979775 scopus 로고    scopus 로고
    • Docking studies of nickel-peptide deformylase (PDF) inhibitors: Exploring the new binding pockets
    • Wang Q, Zhang D, Wang J, Cai Z, Xu W (2006) Docking studies of nickel-peptide deformylase (PDF) inhibitors: exploring the new binding pockets. Biophys Chem 122:43-49
    • (2006) Biophys Chem , vol.122 , pp. 43-49
    • Wang, Q.1    Zhang, D.2    Wang, J.3    Cai, Z.4    Xu, W.5
  • 36
    • 0001681052 scopus 로고
    • The collinearity problem in linear regression. The partial least squares (PLS) approach to generalized inverses
    • Wold S, Ruhe A, Wold H, Dunn WJIii (1984) The collinearity problem in linear regression. The partial least squares (PLS) approach to generalized inverses. SIAM J Sci Stat Comput 5:735-743
    • (1984) SIAM J Sci Stat Comput , vol.5 , pp. 735-743
    • Wold, S.1    Ruhe, A.2    Wold, H.3    Dunn, I.I.W.J.I.4
  • 37
    • 0035885234 scopus 로고    scopus 로고
    • Deformylase as a novel antibacterial target
    • Yuan Z, Trias J, White RJ (2001) Deformylase as a novel antibacterial target. Drug Discov Today 6:954-961
    • (2001) Drug Discov Today , vol.6 , pp. 954-961
    • Yuan, Z.1    Trias, J.2    White, R.J.3
  • 38
    • 62549145285 scopus 로고    scopus 로고
    • Design, synthesis and antibacterial activity of novel actinonin derivatives containing benzimidazole heterocycles
    • Zhang D, Wang Z, Xu W, Sun F, Tang L, Wang J (2009) Design, synthesis and antibacterial activity of novel actinonin derivatives containing benzimidazole heterocycles. Eur J Med Chem 44:2202-2210
    • (2009) Eur J Med Chem , vol.44 , pp. 2202-2210
    • Zhang, D.1    Wang, Z.2    Xu, W.3    Sun, F.4    Tang, L.5    Wang, J.6
  • 39
    • 29644438077 scopus 로고    scopus 로고
    • Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans
    • Zhou Z, Song X, Gong W (2005) Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans. J Biol Chem 280:42391-42396
    • (2005) J Biol Chem , vol.280 , pp. 42391-42396
    • Zhou, Z.1    Song, X.2    Gong, W.3
  • 40
    • 0035385131 scopus 로고    scopus 로고
    • 3D QSAR analyses of novel tyrosine kinase inhibitors based on pharmacophore alignment
    • Zhu LL, Hou TJ, Chen LR, Xu XJ (2001) 3D QSAR analyses of novel tyrosine kinase inhibitors based on pharmacophore alignment. J Chem Inf Comput Sci 41:1032-1040
    • (2001) J Chem Inf Comput Sci , vol.41 , pp. 1032-1040
    • Zhu, L.L.1    Hou, T.J.2    Chen, L.R.3    Xu, X.J.4


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