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Volumn 56, Issue 1, 2004, Pages 52-66

Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations

Author keywords

Binding site mobility; Conformational sampling; Protein conformations; Protein ligand interactions; Structure based drug design

Indexed keywords

ALDEHYDE REDUCTASE; ALDOSE REDUCTASE INHIBITOR; ALRESTATIN; AMINO ACID; CACODYLIC ACID; CITRIC ACID; GLUCOSE 6 PHOSPHATE; HISTIDINE; IDD 594; LEUCINE; LIGAND; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; SORBINIL; TOLRESTAT; TYROSINE; UNCLASSIFIED DRUG; ZENARESTAT;

EID: 2642569349     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20021     Document Type: Article
Times cited : (79)

References (38)
  • 1
    • 0036369809 scopus 로고    scopus 로고
    • Polyol pathway and diabetic peripheral neuropathy
    • Oates PJ. Polyol pathway and diabetic peripheral neuropathy. Int Rev Neurobiol 2002;50:325-392.
    • (2002) Int Rev Neurobiol , vol.50 , pp. 325-392
    • Oates, P.J.1
  • 2
    • 0031920049 scopus 로고    scopus 로고
    • Aldose reductase in glucose toxicity: A potential target for the prevention of diabetic complications
    • Yabe-Nishimura C. Aldose reductase in glucose toxicity: a potential target for the prevention of diabetic complications. Pharmacol Rev 1998;50:21-33.
    • (1998) Pharmacol Rev , vol.50 , pp. 21-33
    • Yabe-Nishimura, C.1
  • 3
    • 0036113742 scopus 로고    scopus 로고
    • Recent advances in aldose reductase inhibitors: Potential agents for the treatment of diabetic complications
    • Miyamoto S. Recent advances in aldose reductase inhibitors: potential agents for the treatment of diabetic complications. Expert Opin Ther Patents 2002;12:621-631.
    • (2002) Expert Opin Ther Patents , vol.12 , pp. 621-631
    • Miyamoto, S.1
  • 4
    • 0033915678 scopus 로고    scopus 로고
    • Recent developments in structure-based drug design
    • Klebe G. Recent developments in structure-based drug design. J Mol Med 2000;78:269-281.
    • (2000) J Mol Med , vol.78 , pp. 269-281
    • Klebe, G.1
  • 5
    • 0035942512 scopus 로고    scopus 로고
    • Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis
    • Iwata Y, Arisawa M, Hamada R, Kita Y, Mizutani MY, Tomioka N, Itai A, Miyamoto S. Discovery of novel aldose reductase inhibitors using a protein structure-based approach: 3D-database search followed by design and synthesis. J Med Chem 2001;44:1718-1728.
    • (2001) J Med Chem , vol.44 , pp. 1718-1728
    • Iwata, Y.1    Arisawa, M.2    Hamada, R.3    Kita, Y.4    Mizutani, M.Y.5    Tomioka, N.6    Itai, A.7    Miyamoto, S.8
  • 6
    • 0036191826 scopus 로고    scopus 로고
    • Discovery of new inhibitors of aldose reductase from molecular docking and database screening
    • Rastelli G, Ferrari AM, Costantino L, Gamberini MC. Discovery of new inhibitors of aldose reductase from molecular docking and database screening. Bioorg Med Chem 2002;10:1437-1450.
    • (2002) Bioorg Med Chem , vol.10 , pp. 1437-1450
    • Rastelli, G.1    Ferrari, A.M.2    Costantino, L.3    Gamberini, M.C.4
  • 7
    • 2642573060 scopus 로고    scopus 로고
    • Virtual screening for inhibitors of aldose reductase
    • Accepted for publication
    • Kraemer O, Hazemann J, Podjarny AD, Klebe G. Virtual screening for inhibitors of aldose reductase. Proteins; Accepted for publication.
    • Proteins
    • Kraemer, O.1    Hazemann, J.2    Podjarny, A.D.3    Klebe, G.4
  • 8
    • 0036680063 scopus 로고    scopus 로고
    • Protein flexibility and drug design: How to hit a moving target
    • Carlson HA. Protein flexibility and drug design: how to hit a moving target. Curr Opin Chem Biol 2002;6:447-452.
    • (2002) Curr Opin Chem Biol , vol.6 , pp. 447-452
    • Carlson, H.A.1
  • 9
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Mol Pharmacol 2000;57:213-218.
    • (2000) Mol Pharmacol , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 10
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 11
    • 0001731266 scopus 로고    scopus 로고
    • Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects
    • Bergner A, Günther J, Hendlich M, Klebe G, Verdonk M. Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects. Biopolymers 2001;61:99-110.
    • (2001) Biopolymers , vol.61 , pp. 99-110
    • Bergner, A.1    Günther, J.2    Hendlich, M.3    Klebe, G.4    Verdonk, M.5
  • 12
    • 0037436333 scopus 로고    scopus 로고
    • Utilising structural knowledge in drug design strategies: Applications using Relibase+
    • Günther J, Bergner A, Hendlich M, Klebe G. Utilising structural knowledge in drug design strategies: applications using Relibase+. J Mol Biol 2003;326:621-636.
    • (2003) J Mol Biol , vol.326 , pp. 621-636
    • Günther, J.1    Bergner, A.2    Hendlich, M.3    Klebe, G.4
  • 13
    • 0037436339 scopus 로고    scopus 로고
    • Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
    • Hendlich M, Bergner A, Günther J, Klebe G. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 2003;326:607-620.
    • (2003) J Mol Biol , vol.326 , pp. 607-620
    • Hendlich, M.1    Bergner, A.2    Günther, J.3    Klebe, G.4
  • 15
    • 0032539837 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the structure of aldose reductase complexed with the inhibitor tolrestat
    • Rastelli G, Costantino L. Molecular dynamics simulations of the structure of aldose reductase complexed with the inhibitor tolrestat. Bioorg Med Chem Lett 1998;8:641-646.
    • (1998) Bioorg Med Chem Lett , vol.8 , pp. 641-646
    • Rastelli, G.1    Costantino, L.2
  • 16
    • 0037325805 scopus 로고    scopus 로고
    • Hydrogen-bonding interactions between aldose reductase complexed with NADP(H) and inhibitor tolrestat studied by molecular dynamics simulations and binding assay
    • Lee YS, Hodoscek M, Kador PF, Sugiyama K. Hydrogen-bonding interactions between aldose reductase complexed with NADP(H) and inhibitor tolrestat studied by molecular dynamics simulations and binding assay. Chem Biol Interact 2003;143-144:307-316.
    • (2003) Chem Biol Interact , vol.143-144 , pp. 307-316
    • Lee, Y.S.1    Hodoscek, M.2    Kador, P.F.3    Sugiyama, K.4
  • 17
    • 0036285985 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M. Molecular dynamics simulations of biomolecules (Editorial). Acc Chem Res 2002;35:321-323.
    • (2002) Acc Chem Res , vol.35 , pp. 321-323
    • Karplus, M.1
  • 23
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000;21:1049-1074.
    • (2000) J Comput Chem , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 25
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly CI, Cieplak P, Cornell WP, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 1993;97: 10269-10280.
    • (1993) J Phys Chem , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.P.3    Kollman, P.A.4
  • 26
    • 0000667030 scopus 로고
    • Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
    • Cornell WP, Cieplak P, Bayly CI, Kollman PA. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J Am Chem Soc 1993;115:9620-9631.
    • (1993) J Am Chem Soc , vol.115 , pp. 9620-9631
    • Cornell, W.P.1    Cieplak, P.2    Bayly, C.I.3    Kollman, P.A.4
  • 29
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 30
    • 33846823909 scopus 로고
    • Particle Mesh Ewald - An N. log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L. Particle Mesh Ewald-an N.log(N) method for Ewald sums in large systems. J Chem Phys 1993;98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 34
    • 0031570301 scopus 로고    scopus 로고
    • A "specificity" pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil
    • Urzhumtsev A, Tete-Favier F, Mitschler A, Barbanton J, Barth P, Urzhumtseva L, Biellmann JF, Podjarny A, Moras D. A "specificity" pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil. Structure 1997;5:601-612.
    • (1997) Structure , vol.5 , pp. 601-612
    • Urzhumtsev, A.1    Tete-Favier, F.2    Mitschler, A.3    Barbanton, J.4    Barth, P.5    Urzhumtseva, L.6    Biellmann, J.F.7    Podjarny, A.8    Moras, D.9
  • 35
    • 0033642945 scopus 로고    scopus 로고
    • Structural stability of binding sites: Consequences for binding affinity and allosteric effects
    • Luque I, Freire E. Structural stability of binding sites: consequences for binding affinity and allosteric effects. Proteins Suppl 2000;4:63-71.
    • (2000) Proteins Suppl , vol.4 , pp. 63-71
    • Luque, I.1    Freire, E.2
  • 36
    • 0031746754 scopus 로고    scopus 로고
    • Statistical thermodynamic linkage between conformational and binding equilibria
    • Freire E. Statistical thermodynamic linkage between conformational and binding equilibria. Adv Protein Chem 1998;51:255-279.
    • (1998) Adv Protein Chem , vol.51 , pp. 255-279
    • Freire, E.1
  • 38
    • 0035957528 scopus 로고    scopus 로고
    • FlexE: Efficient molecular docking considering protein structure variations
    • Claussen H, Buning C, Rarey M, Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 2001;308:377-395.
    • (2001) J Mol Biol , vol.308 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.