Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors
PDF

Keywords

CDK
flavopiridol
bioinformatics
structure
drug design

How to Cite

Canduri, F., da Silveira, N. J. F., Câmera Junior, J. C., & de Azevedo Júnior, W. F. (2003). Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors. Eclética Química, 28(1), 45–53. https://doi.org/10.26850/1678-4618eqj.v28.1.2003.p45-53

Abstract

The present work describes molecular models for the binary complexes CDK9, CDK5 and
CDK1 complexed with Flavopiridol and Roscovitine. These structural models indicate that the inhibitors
strongly bind to the ATP-binding pocket of CDKs and the structural comparison with the complexes
CDK2:Flavopiridol and CDK2:Roscovitine correlates the structural differences with differences in
inhibition of these CDKs by the inhibitors. These structures open the possibility of testing new inhibitor
families, in addition to new substituents for the already known lead structures such as flavones and
adenine derivatives.
https://doi.org/10.26850/1678-4618eqj.v28.1.2003.p45-53
PDF

References

ALVAREZ, A.; TORO, R.; CÁCERES, A.; MACCIONI,

R. B. Inhibition of tau phosphorylating protein kinase cdk5

prevents beta-amyloid-induced neuronal death. FEBS Lett,

v. 459, n. 3, p. 421-426, 1999.

ARRIS, C. E.; BOYLE, F. T.; CALVERT, A. H.;

CURTIN, N. J.; ENDICOTT, J. A.; GARMAN, E. F.;

GIBSON, A. E.; GOLDING, B. T.; GRANT, S.; GRIFFIN,

R. J.; JEWSBURY, P.; JOHNSON, L. N.; LAWRIE, A. M.;

NEWELL, D. R.; NOBLE, M. E.; SAUSVILLE, E. A.;

SCHULTZ, R.; YU, W. Identification of novel purine and

pyrimidine cyclin-dependent kinase inhibitors with distinct

molecular interactions and tumor cell growth inhibition

profiles. J. Med. Chem., v. 43, n. 15, p. 2797-2804, 2000.

BLUNDELL, T. L.; CARNEY, D.; GARDNER, S.;

HAYES, F.; HOWLIN, B.; HUBBARD, T.; OVERINGTON,

J.; SINGH, D. A.; SIBANDA, B. L.; SUTCLIFFE, M. 18th

Krebs, Hans lecture – knowledge-based protein modeling

and design. Eur. J. Biochem., v. 172, n. 3, p. 513-520,

BLUNDELL, T. L.; SIBANDA, B. L.; STERNBERG,

M. J.; THORNTON, J. M. Knowledge-based prediction of

protein structures and the design of novel molecules. Na-

ture, v. 326, n. 6111, p. 347-352, 1987.

BRAUN, W.; GO, N. Calculation of protein conforma-

tions by proton-proton distance constraints. A new effi-

cient algorithm. J. Mol. Biol., v. 186, n. 3, p. 611-626,

BROOKS, B. R.; BRUCCOLERI, R. E.; OLAFSON, B.

D.; STATES, D. J.; SWAMINATHAN, S.; KARPLUS, M.

CHARMM: a program for macromolecular energy mini-

mization and dynamics calculations. J. Comp. Chem., v. 4,

p. 187-217, 1983.

CANDURI, F.; TEODORO, L. G. V. L.; LORENZI, C.

C. B.; HIAL, V.; GOMES, R. A. S.; RUGGIERO NETO, J.;

DE AZEVEDO, W. F. JR. Crystal structure of human uropep-

sin at 2.45Å resolution. Acta Crystallogr., v. D57, p. 1560-

, 2001.

CARLSON, B.A.; LAHUSEN, T.; SINGH, S.; LOAIZA-

PEREZ, A.; WORLAND, P. J.; PESTELL, R.; ALBANESE,

C.; SAUSVILLE, E. A.; SENDEROWICZ, A. M.

Downregulation of cyclin D1 by transcriptional repression

in MCF-7 human breast carcinoma cells induced by

flavopiridol. Cancer Res., v. 59, p. 4634-4641, 1999.

CHAO, S. H.; FUJINAGA, K.; MARION, J. E.; TAUBE,

R.; SAUSVILLE, E. A.; SENDEROWICZ, A. M.;

PETERLIN, B. M; PRICE, D. H. J. Flavopiridol inhibits P-

TEFb and blocks HIV-1 replication. J. Biol. Chem., v. 275,

n. 37, p. 28345-28348, 2000.

CLARE, P. M.; POORMAN, R. A.; KELLEY, L. C.;

WATENPAUGH, K. D.; BANNOW, C. A.; LEACH, K. L.

The cyclin-dependent kinases cdk2 and cdk5 act by a ran-

dom, anticooperative kinetic mechanism. J. Biol. Chem.,

v. 276, p. 48292-48299, 2001.

COLLABORATIVE computational project n. 4. The

CCP4 suite: programs for protein crystallography. Acta

Crystallogr., v. D50, p. 760-763, 1994.

CORPET, F. Multiple sequence alignment with

hierarchical clustering. Nucl. Acids Res., v. 16, n. 22,

p.10881-10890, 1988.

DE AZEVEDO, W. F. JR.; CANDURI, F.; FADEL, V.;

TEODORO, L. G. V. L.; HIAL, V.; GOMES, R. A. S. Mo-

lecular model for the binary complex of uropepsin and

pepstatin. Biochem. Biophys. Res. Commun., v. 287, n.

, p. 277-281, 2001.

DE AZEVEDO, W. F. JR.; CANDURI, F.; SILVEIRA,

N. J. F. Structural basis for inhibition of cyclin-dependent

kinase 9 by flavopiridol. Biochem Biophys. Res. Commun.,

v. 293, p. 566-571, 2002.

DE AZEVEDO, W. F. JR.; GASPAR, R. T.; CANDURI,

F.; CAMERA, J. C. JR.; SILVEIRA, N. J. F. Molecular model

of cyclin-dependent kinase 5 complexed with roscovitine.

Biochem. Biophys. Res. Commun., v. 297, p. 1154-1158,

DE AZEVEDO, W. F. JR.; LECLERC, S.; MEIJER, L.;

HAVLICEK, L.; STRNAD, M.; KIM, S.-H. Inhibition of

cyclin-dependent kinases by purine analogues: crystal struc-

ture of human CDK2 complexed with roscovitine. Eur. J.

Biochem., v. 243,

p. 518-526, 1997.

DE AZEVEDO, W. F. JR.; MUELLER-DIECKMANN,

H.;J.; SCHULZE-GAHMEN, U.; WORLAND, P. J.;

SAUSVILLE, E.; KIM S.-H. Structural basis for specificity

and potency of a flavonoid inhibitor of human CDK2, a

cell cycle kinase. Proc. Natl. Acad. Sci. USA., v. 93, n. 7, p.

-2740, 1996.

DEBONDT, H. L.; ROSENBLATT, J.; JANCARIK,

J.; JONES, H. D.; MORGAN, D. O.; KIM, S.-H. Crystal

structural of cyclin-dependent kinase 2. Nature, v. 363,

p. 595-602, 1993.

DESAI, D.; GU, Y.; MORGAN, D. O. Activation of

human cyclin-dependent kinases in vitro. Mol. Biol. Cell, v.

, p. 571-582, 1992.

GRAY, N.; DETIVAUD, L.; DOERIG, C.; MEIJER, L.

ATP-site directed inhibitors of cyclin-dependent kinases. Curr. Med. Chem. v. 6, n. 9, p. 859-875, 1999.

GRAY, N. S.; WODICKA, L.; THUNNIESSEN, A. M.;

NORMAN, T. C.; KWON, S.; ESPINOZA, F. H.; MOR-

GAN, D. O.; BARNES, G.; LECLERC, S.; MEIJER, L.; KIM,

S. H.; LOCKHART, D. J.; SCHULTZ, P. G. Exploiting chemi-

cal libraries, structure, and genomics in the search for kinase

inhibitors. Science, v. 281, p. 533-538, 1998.

HOESSEL, R.; LECLERC, S.; ENDICOTT, J. A.;

NOBEL, M. E.; LAWRIE, A.; TUNNAH, P.; LEOST, M.;

DAMIENS, E.; MARIE, D.; MARKO, D.; NIEDERBERGER,

E.; TANG, W.; EISENBRAND, G.; MEIJER, L. Indirubin,

the active constituent of a chinese antileukaemia medicine,

inhibits cyclin-dependent kinases. Nat. Cell Biol., v. 1, n. 1,

p. 60-67, 1999.

KIM, S.-H.; SCHULZE-GAHMEN, U.; BRANDSEN,

J.; DE AZEVEDO, W. F. JR. Structural basis for chemical

inhibitor of CDK2. Prog. Cell Cycle Res., v. 2, p. 137-145,

KRAULIS, P. MOLSCRIPT: a program to produce both

detailed and schematic plots of proteins. J. App. Cryst., v.

, p. 946-950, 1991.

KROEMER, R. T.; DOUGHTY, S. W.; ROBINSON, A.

J.; RICHARDS, W. G. Prediction of the three-dimensional

structure of human interleukin-7 by homology modeling.

Protein Eng., v. 9, n. 6, p. 493-498, 1996.

LASKOWSKI, R. A.; MACARTHUR, M. W.; SMITH,

D. K.; JONES, D. T.; HUTCHINSON, E. G.; MORRIS, A, L.;

NAYLOR, D.; MOSS, D. S.; THORTON, J. M. PROCHECK

v.3.0: program to check the stereochemistry quality of

protein structures - operating instructions, [s.l.:s.n.], 1994.

LAWRIE, A. M.; NOBLE, M. E.; TUNNAH, P.;

BROWN, N. R.; JOHNSON, L. N.; ENDICOTT, J. A. Pro-

tein kinase inhibition by staurosporine revealed in details of

the molecular interaction with CDK2. Nat. Struct. Biol., v.

, p. 796, 1997.

MEIJER, L.; BORGNE, A.; MULNER, O.; CHONG, J.

P.; BLOW, J. J.; INAGAKI, N. Biochemical and cellular

effects of roscovitine, a patent and selective inhibitor of the

cyclin-dependent kinases CDK2 and CDK5. Eur. J. Biochem.,

v. 243, p. 527-536, 1997.

MEIJER, L.; THUNNISSEN, A. M.; WHITE, A. W.;

GARNIER, M.; NIKOLIC, M.; TSAI, L. H.; WALTER, J.;

CLEVERLEY, K. E.; SALINAS, P. C.; WU, Y. Z.; BIERNAT,

J.; MANDELKOW, E. M.; KIM, S.-H.; PETTIT, G. R. Inhi-

bition of cyclin-dependent kinases, GSK-3beta and CK1 by

hymenialdisine, a marine sponge constituent. Chem. Biol.,

v. 7, n. 1, p. 51-63, 2000.

NICHOLLS, A.; SHARP, K. A.; HONIG, B. Protein

folding and association: insights from the interfacial and

thermodynamic properties of hydrocarbons. Proteins, v. 11,

n. 4, p. 281-296, 1991.

NORBURY, C.; NURSE, P. Animal cell cycles and their

control. Annu. Rev. Biochem., v. 61, p. 441-470, 1992.

OIKONOMAKOS, N. G.; SCHNIER, J. B.;

ZOGRAPHOS, S. E.; SKAMNAKI, V. T.; TSITSANOU, K.

E.; JOHNSON, L. N. Flavopiridol inhibits glycogen phos-

phorylase by binding at the inhibitor site. J. Biol. Chem., v.

, n. 44, p. 34566-34573, 2000.

PATRICK, G. N.; ZUKERBERG, L.; NIKOLIC, M.;

DE LA MONTE, S.; DIKKES, P.; TSAI, L. H. Conversion

of p35 to p25 deregulates Cdk5 activity and promotes

neurodegeneration. Nature, v. 402, n. 6762, p. 615-22, 1999.

RICHARDSON, H. E.; STUELAND, C. S.; THOMAS,

J.; RUSSEL, P.; REED, S. I. Human cDNAs encoding ho-

mologs of the small p34Cdc28/Cdc2-associated protein of

Saccharomyces cerevisiae and Schizosaccharomyces pombe.

Genes Dev., v. 4, p. 1332-1344, 1990.

SALI, A. Modeling mutations and homologous pro-

teins. Curr. Opin. Biotechnol., v. 6, n. 4, p. 437-451, 1995.

SALI, A.; BLUNDELL, T. L. Comparative protein

modelling by satisfaction of spatial restraints. J. Mol. Biol.,

v. 234, p. 779-815, 1993.

SALI, A.; OVERINGTON, J. P. Derivation of rules for

comparative protein modeling from a database of protein

structure alignments. Protein Sci., v. 3, n. 9, p. 1582-1596,

SALI, A.; POTTERTON, L.; YUAN, F.; VAN VLIJMEN,

H.; KARPLUS, M. Evaluation of comparative protein mod-

eling by MODELLER. Proteins, v. 23, n. 3, p. 318-326,

SCHULTZE-GAHMEN, U.; BRANDSEN, J.; JONES,

H. D.; MORGAN, D. O.; MEIJER, I.; VESELY, J. Multiple

modes of ligand recognition: crystal structures of cyclin-

dependent protein kinase 2 in the complex with ATP and

two inhibitors, olomoucine and isopentenyladenine. Pro-

teins, v. 22, p. 378-391, 1995.

SENDEROWICZ, A. M.; SAUSVILLE, E. A. Preclini-

cal and clinical development of cyclin-dependent kinase

modulators. J. Natl. Cancer Inst., v. 92, n. 5, p. 376-387,

SEROTA, S.; RADSIO-ANDZELM, E. Three protein

kinase structures define a common motif. Structure, v. 2, p.

-355, 1994.

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Copyright (c) 2018 Eclética Química Journal

Metrics

PDF views
64
Jan 2004Jul 2004Jan 2005Jul 2005Jan 2006Jul 2006Jan 2007Jul 2007Jan 2008Jul 2008Jan 2009Jul 2009Jan 2010Jul 2010Jan 2011Jul 2011Jan 2012Jul 2012Jan 2013Jul 2013Jan 2014Jul 2014Jan 2015Jul 2015Jan 2016Jul 2016Jan 2017Jul 2017Jan 2018Jul 2018Jan 2019Jul 2019Jan 2020Jul 2020Jan 2021Jul 2021Jan 2022Jul 2022Jan 2023Jul 2023Jan 2024Jul 2024Jan 2025Jul 2025Jan 20266.0
|