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J. Biol. Chem., Vol. 280, Issue 14, 13793-13800, April 8, 2005
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¶

**
From the
Centre de Recherches de Biochimie Macromoléculaire, Department of Molecular Biophysics and Therapeutics, FRE-2593 CNRS, 1919 Route de Mende, 34293 Montpellier, France and ||Stem Cell Sciences Limited, P. O. Box 8224, Monash University L. P. O., Clayton, Victoria 3168, Australia
Received for publication, December 6, 2004 , and in revised form, January 11, 2005.
| ABSTRACT |
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5 helix of cyclin A. We demonstrate that this peptide does not interfere with complex formation but forms stable complexes with CDK2-cyclin A. The C4 peptide significantly inhibits kinase activity of complexes harboring CDK2 in a competitive fashion with respect to substrates but does not behave as an ATP antagonist. Moreover, when coupled with the protein transduction domain of Tat, the C4 peptide blocks the proliferation of tumor cell lines, thereby constituting a potent lead for the development of specific CDK-cyclin inhibitors. | INTRODUCTION |
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Determination of the crystal structure of several CDK and CDK-cyclin complexes has provided essential information on the mechanism of formation and activation of these protein kinases (15). Upon binding to CDK2, cyclin A induces a marked structural reorganization of the catalytic kinase subunit (16), which involves rearrangement of the PSTAIRE helix and repositioning of the relative orientation of the N- and C-terminal lobes. The
3 and
5 helices of cyclin A clamp the PSTAIRE at its center through hydrogen bonds, thereby promoting reconfiguration of the ATP-binding site. The cyclin also interacts with the T-loop of CDK2, causing this loop to move away from the active site. A fully active complex is finally generated through the phosphorylation of CDK2 on Thr160, which induces further changes in the orientation of the T-loop and promotes additional contacts with cyclin A. In contrast, comparison of the crystal structures of cyclin A in its free (17) and CDK2-bound state (16) indicates that this regulatory subunit does not undergo any conformational changes upon complex formation.
We have recently demonstrated that the molecular mechanism of CDK2-cyclin A complex formation is a two-step process (18). The first step involves the rapid association between the PSTAIRE helix of CDK2 and helices
3 and
5 of the cyclin to yield a non-processive intermediate complex. Two residues in the PSTAIRE helix, Ile49 and Arg50, located in a hydrophobic pocket in close contact with the side chains of Lys263, Lys266, and Phe267 and those of Leu299 and Leu306 within the
3 and
5 helices of cyclin A, respectively, are essential for the initial assembly of the CDK-cyclin complex. The second step involves additional contacts between the C-lobe of the CDK and the N-terminal helix of the cyclin, which induce subsequent isomerization of the CDK into a fully mature form by promoting exposure of the T-loop for phosphorylation by the CDK-activating kinase (CAK) as well as formation of the substrate-binding site. Both the conformational changes of the nonprocessive intermediate and phosphorylation have been reported to control the selectivity of the CDK for its cyclin partner (19, 20). We suggest that the steps of assembly and the activation of CDK-cyclin complexes both constitute key targets for the development of specific inhibitors.
In the present work, we propose a new strategy to selectively inhibit kinase activity of CDK-cyclin complexes by targeting the protein/protein interface between the two subunits. We have designed a peptide of 22 residues derived from the
5 helix of cyclin A that forms stable complexes with CDK2-cyclin A. We demonstrate that this peptide inhibits CDK2 kinase activity in a competitive fashion with respect to protein substrates. Moreover, when coupled to the protein transduction domain of Tat, this peptide blocks proliferation of tumor cell lines and therefore constitutes a potent lead for the development of specific CDK-cyclin inhibitors.
| EXPERIMENTAL PROCEDURES |
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Peptide Synthesis and PurificationAll peptides were synthesized using an Fmoc continuous flow apparatus (PioneerTM; Applied Biosystems) starting from Fmoc-peptide amide liner-polyethylene glycol-polystyrene resins at a 0.2-mmol scale. The coupling reactions were performed with 0.5 M HATU in the presence of 1 M DIEA. Protecting group removal and final cleavage from the resin were carried out with trifluoroacetic acid/phenol/H2O/thioanisol/ethanedithiol (82.5:5:5:5:2.5%) for 4 h and 20 min for peptides C1, C3, and C7 and with trifluoroacetic acid/phenol/H2O/triisopropylsilane (88:5:5:2%) for 4 h in the case of C5, C4, and C8. Crude peptides were purified by semi-preparative reverse phase high performance liquid chromatography on a C18 column (Interchrom UP5 WOD/25 M Uptisphere 300, 5 ODB, 250 x 21.2 mm) and identified by electrospray mass spectrometry. Tat, C2, C6, and C9 peptides were obtained from NeoMPS (Strasbourg-France). The C4 peptide was conjugated to the Tat peptide GRKKRRQRRR-C through a disulfide bond using the cysteamide function at the C terminus of C4. All peptides were dissolved with deionized water to make a stock solution of 500 µM except for C1 and C8 which, because of their poor solubility in water, were first dissolved in dimethyl sulfoxide. Peptides were then diluted in phosphate-buffered saline (8.1 mM Na2HPO4, 1.47 mM KH2PO4, 2.67 mM KCl, and 138 mM NaCl).
Protein Expression and PurificationThe GST-retinoblastoma fusion protein (GST-Rb), harboring residues 792 to 928, was provided by C. Sardet (IGMM, Montpellier, France). CDK2-cyclin E and CDK1-cyclin B1 complexes were purified from baculovirus-infected insect cell lysates as described previously (21, 22). Human CDK2 phosphorylated on Thr160 was produced in Escherichia coli (BL21) by coexpression of GST-CDK2 and Saccharomyces cerevisiae GST-CIV1 (a gift from J. Endicott, Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, Oxford, UK). Full-length human cyclin A was expressed as an untagged or a GST-tagged protein in E. coli. Monomeric proteins as well as the CDK2-cyclin A complex were purified according to Brown et al. (17). Briefly, cells expressing GST-CDK2 or cyclin A were lysed by sonication on ice. The clarified lysate of GST-CDK2 was applied onto a glutathione-Sepharose column (Amersham Biosciences) equilibrated in buffer A (40 mM HEPES, pH 7.0, 200 mM NaCl, and 0.01% (v/v) monothioglycerol) and extensively washed. The clarified lysate of cyclin A was then applied onto the CDK2-bound glutathione-Sepharose column. The GST-CDK2-cyclin A complex was eluted with buffer A containing 20 mM glutathione (Sigma). Following cleavage of the GST tag with protease 3C (1:50) (w/w) at 4 °C for 12 h, CDK2-cyclin A was purified by size exclusion chromatography on a HiLoad 16/60 Superdex 75 column (Amersham Biosciences). Fractions containing CDK2-cyclin A were pooled and further purified by exclusion from glutathione-Sepharose.
Kinase AssaysCDK kinase assays were carried out in a final volume of 30 µl containing 3 µM histone H1 (H4524; Sigma) or GST-Rb or 0.4 mM peptide substrate (histone H1-derived peptide PKTPKKAKKL; Promega Corporation, Madison, WI), 50 µM cold ATP, and 0.15 µCi [
-32P]ATP (3000 Ci/mmol; Amersham Biosciences). The kinase concentration used was 20 nM. Reactions were performed for 15 min at 25 °C and then quenched by the addition of 2x SDS buffer. Phosphorylated products were separated by 15% SDS-PAGE and analyzed on a PhosphorImager. Reaction samples performed with the peptide substrate were spotted onto Whatman P81 phosphocellulose paper, washed five times in 0.5% phosphoric acid, and dried. Incorporation of 32P was then quantified by Cerenkov counting.
Kinetic experiments were performed under the same conditions, except that the reaction was performed for 1 min. Reaction samples were spotted onto Whatman P81 phosphocellulose paper. Four different concentrations of histone H1 (2, 3, 5, and 10 µM) were used in the kinetic analysis of enzyme inhibition. For each substrate concentration, three concentrations of C4 peptide (0, 1, and 1.5 µM) were used, and the concentration of ATP was maintained constant at 0.1 mM. Similarly, when the concentration of ATP was varied (5, 10, 20, 30, 50, and 100 µM), C4 peptide concentrations were 0, 0.5, and 1 µM, and the concentration of histone H1 was kept constant at 15 µM. Using the Graphit Erithacus software, analysis of kinetic data for the inhibition of CDK2-cyclin A phosphorylation was performed by fitting the data to Equations 1 (non-competitive inhibition) and 2 (competitive inhibition),
![]() | (Eq. 1) |
![]() | (Eq. 2) |
Peptide-CDK Binding Assays8 µg of preformed GST-CDK2-cyclin A or CDK2-GST-cyclin A complexes were incubated in buffer A with increasing concentrations of C4 or C6 peptides (corresponding to
20, 40, and 90-fold the concentration of complex) at 25 °C for 30 min. GST complexes were then pulled down with glutathione-Sepharose beads and washed and eluted with buffer A containing 20 mM glutathione. Both the flow-through and the elution were analyzed by SDS-PAGE and Western blotting using antibodies against CDK2 (affinity-purified PSTAIRE polyclonal antibody) and cyclin A (H-432; Santa Cruz Biotechnology, Santa Cruz, CA).
CD ExperimentsFar UV CD spectra were recorded on a JASCO J-810 spectropolarimeter (JASCO Corporation, Tokyo, Japan) using a quartz cuvette with a path length of 1 mm. Spectra were corrected from the baseline buffer spectrum and smoothed with JASCO software. Peptides were dissolved to a fixed concentration of 50 µM in water or phosphate-buffered solution. CD spectra were collected at 23 °C, and each spectrum represents the average of four scans.
Cell Culture and Growth Inhibition AssaysMCF-7, HepG2, and MDA-MB-231 cell lines were cultured at 37 °C and 5% CO2 in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum (Invitrogen). The human Jurkat lymphoma T cell line was cultured in RPMI 1640 complete medium. Cells were seeded at 2 x 104 cells/well in 24-well dishes and incubated overnight at 37 °C. Cells were then treated with increasing concentrations of peptides in 300 µl of Opti-MEM for adherent cells and RPMI for Jurkat cells. After 45 min, 300 µl of medium containing 20% serum was added. After 48 h, cells were counted on a Coulter counter. The total number of cells was calculated as the percentage of treated to untreated cells. Concentrations of peptides indicated in each experiment correspond to those added in the 300 µl of OptiMEM during the first 45 min of treatment.
Surface Plasmon Resonance ExperimentsAll experiments were performed at 25 °C using a Biacore 3000 (Biacore AB). CDK2, cyclin A, and complexes were immobilized on a carboxymethyl dextran sensor chip by N-hydrosuccinimide/1-ethyl-3-(3'-dimethylaminopropyl)carbodiimide hydrochloride (NHS/EDC) coupling as described by the manufacturer. Peptide samples were prepared at different concentrations in the range of 50 to 1000 nM in 50 mM Tris HCl (pH 8.0) buffer containing 150 mM NaCl, 2 mM EDTA, and 50 mM KCl and were injected (30 µl) over the sensor surface at a flow rate of 10 µl·s1. After completion of the injection phase, dissociation was performed for 200 s at the same flow rate. The apparent association and dissociation rate constants were calculated using BIA Evaluation version 3.0, and binding curves were fitted using a simple 1:1 Langmuir two-state reaction model.
Molecular Graphics Representation of the Crystal StructureCoordinates of crystal structures used were downloaded from the Brookhaven Protein Data Bank (PDB code 1QMZ [PDB] ) (20, 23). The modeling package Discover/Insight II (MSI Inc.; San Diego, CA) and DeLano Scientific LLC PyMol software version 0.93 (DeLano Scientific, San Carlos CA) were used to analyze the structure of CDK2-cyclin A.
| RESULTS |
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3 and
5 of cyclin A, followed by a slow conformational change of the complex involving interactions between the N-terminal helix of cyclin A and the C-lobe of CDK2.
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5 helix of cyclin A encompassing residues Thr285 to Leu306 (Table I). Although contacts between PSTAIRE and the
5 helix of cyclin A are common to all CDK-cyclin complexes (26), the primary sequence of C1 is only partially conserved between different cyclins (Fig. 1).
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5 helix of cyclin A. The ability of the different peptides (C1C9) to affect the phosphorylation of histone H1 by CDK2-cyclin A is reported in Table I. Noteworthily, the peptide corresponding to part of C1 extended at its N terminus (C7) does not exhibit any inhibitory activity. Similarly, the addition of amino acids to the C-terminal Leu306 decreases the inhibitory potential of the peptide (C8), suggesting that the integrity of C1 is required for robust inhibition. However, the three first N-terminal residues of the C1 peptide are not essential (C9), in contrast to residues 293 to 296, which appear to play a key role in the functional integrity of C1 (except for Glu295 which is conserved between cyclins A, B, and E) (Fig. 1). Moreover, the greatest inhibition of kinase activity is obtained when Glu295 is mutated to an alanine (C4), a mutation that increases the solubility of the peptide. Additional residues, which are not directly involved in the interface with CDK2, are also required for inhibition, such as Leu299 (C6) and Met294 (C3). Taken together, these results suggest that the region in the peptide that contributes primarily to kinase inhibition is located between residues 293 and 306. Given that C4 exhibited the greatest potential to inhibit CDK2-cyclin A activity, it was chosen as the main focus for the rest of the study. The C4 peptide prevents phosphorylation of histone H1, GST-Rb, and the small peptide substrate derived from histone H1 by CDK2-cyclin A with estimated IC50 values of 1.8 ± 0.1, 16.7 ± 0.6, and 1.1 ± 0.3 µM, respectively.
To evaluate the selectivity of the C4 peptide for the CDK2 isoform, we tested its ability to inhibit other CDK complexes, including CDK2-cyclin E and CDK1-cyclin B. The C4 peptide inhibits the kinase activity of CDK2 associated with either cyclin A (IC50 of 1.8 ± 0.1 µM) or cyclin E (IC50 of 1.5 ± 0.3 µM) to a similar extent, but it does not significantly affect CDK1-cyclin B kinase activity (IC50 > 200 µM). In addition, C4 was not found to inhibit protein kinase A or protein kinase C (data not shown), suggesting that this peptide is specific to the CDK-cyclin complex and does not affect other protein kinases.
Structural Characterization of the Inhibitory Peptides by Circular DichroismTo determine whether the inhibitory potential of the different peptides was associated with structural constraints, we examined their secondary structure by circular dichroism. Peptides are not folded in water solution. Each peptide was dissolved in the same phosphate buffer used for kinase activity assays at a final concentration of 50 µM. Peptides were divided into three classes based on their secondary structures as follows: (i) peptides C3, C6, C7, and C8, which are predominantly random coiled (Fig. 3A); (ii) peptides C2 and C9, which aggregate into
-structure, characterized by a positive contribution at 198 nm and a large negative band near 220 nm (Fig. 3B); and (iii) C4, which tends to adopt an
-helical structure characterized by two minima at 208 and 222 nm, respectively. The spectrum of C5 peptide is suggestive of a mixture of different structures.
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5-helix of cyclin A and the N-terminal
-sheet of CDK2 are essentially hydrophobic. Thus the
-helical structure of C4 peptide, which is stabilized in the presence of salt, may favor hydrophobic interactions with CDK2-cyclin A associated with its inhibitory potential. Mechanism of Inhibition of CDK2 Activity by the C4 PeptideC4-mediated inhibition of CDK2 can result from either direct competition with cyclin A for CDK2 or from the binding of the peptide to the preformed CDK2-cyclin A complex. To discriminate between these two hypotheses, we performed direct competition experiments in which various concentrations of peptide (inhibiting kinase activity by 90%) were added to a mixture of either GST-CDK2 and cyclin A or GST-cyclin A and CDK2 (Fig. 4). The different CDK2-cyclin A complexes were isolated with glutathione-Sepharose beads. Levels of cyclin A associated with GST-CDK2 or CDK2 bound to GST-cyclin A were determined by Western blotting, and kinase activity of these complexes toward histone H1 was evaluated. As shown in Fig. 4, the addition of C4 strongly inhibits kinase activity of CDK2 without inducing dissociation of cyclin A from CDK2, irrespective of the method used. Moreover, similar kinase inhibition was obtained by adding the peptide either before or after reconstitution of the CDK2-cyclin A complex (data not shown). Based on these experiments, we infer that the C4 peptide maintains CDK2-cyclin A in an inactive or nonprocessive conformation but does not disrupt the complex.
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3 helix (Ala264 and Phe267) and the loop connecting the
3 and
4 helices (Ile270 and Tyr271) of cyclin A (Fig. 7).
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25 µM), whereas the C6 and C7 peptides had no effect after 48 h of treatment, which is consistent with the in vitro kinase assays. We attributed the 20-fold lower efficiency of C4 in cell culture in comparison to its in vitro kinase inhibition to inefficient cellular uptake of the peptide. To increase the cellular uptake of C4, we therefore covalently linked it to the protein transduction domain derived from the human immunodeficiency virus Tat protein through a disulfide bond (28). The conjugation of C4 to the carrier peptide Tat did not affect its in vitro inhibitory activity (IC50 = 2.2 ± 0.1 µM) but significantly improved its efficiency on cultured cells. MDA-MB-231 cells were incubated in the presence of various concentrations of C4-Tat, C4, and Tat ranging from 5 to 30 µM, and cell proliferation was examined after 48 h. As shown in Fig. 8, C4-Tat inhibits cell proliferation in a dose-dependent manner with an IC50 3-fold greater than that of free peptide (7.5 ± 0.3 µM). As a control, we verified that the Tat peptide did not affect cell growth in the range of concentrations used. We evaluated the effect of C4-Tat peptide on several human tumor cell lines and found that proliferation of all the cell lines was affected by C4-Tat in the low micromolar range. IC50 values of 2.0 ± 0.6, 11.9 ± 0.1, and 14.2 ± 0.3 µM were obtained for Jurkat, MCF-7, and HepG2 cell lines, respectively (Table II).
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| DISCUSSION |
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As both the structure and the mechanism of CDK2-cyclin A have been extensively characterized, we chose to target this complex as a proof of principle. Crystal structures of cyclin A in its free (17) and CDK2-bound state (16) reveal that the cyclin box (residues 209310) constitutes the main interface with CDK2 through interactions with the PSTAIRE helix and contacts with the T-loop as well as with the N-terminal
-sheet of CDK2. The major contacts involve the
3,
4, and
5 helices of cyclin A, which are critical for the first step of complex formation (18). With the aim of specifically targeting the protein-protein interface between CDK2 and cyclin A, we therefore designed and characterized a series of peptides derived from the
5 helix of cyclin A.
We have identified a peptide of 22 residues (C4) which, in contrast to the majority of the CDK-cyclin ATP antagonist inhibitors described so far, neither competes with ATP nor affects activity of other protein kinases. C4 peptide is highly specific for complexes harboring CDK2 and inhibits its kinase activity at low concentrations (Ki = 340 nM) in a competitive fashion with respect to the phosphoacceptor substrate. We have shown that C4 peptide adopts an
-helical structure, which is consistent with the idea that the conformational constraint imposed by an
-helix allows key contacts between C4 and the CDK2-cyclin A complex.
Several competitive peptide inhibitors of CDKs have been described previously (11). A large majority are based on the CBM, a consensus sequence common to a number of substrates and inhibitors of mammalian CDKs. The CBM sequence is essential for substrate recognition and interacts with a hydrophobic patch on the surface of cyclin A (30, 31). This docking site on cyclin A is known to be critical for the phosphorylation of substrates containing the CBM, such as Rb, but unlike histone H1. Inhibitory peptides derived from the C terminus of the CDK inhibitor p21WAF1 or the transcription factor E2F1 compete directly with Rb for binding to the hydrophobic patch on the cyclin and, therefore, inhibit phosphorylation of other substrates like histone H1 quite poorly. On the other hand, peptide aptamers isolated from a combinatorial library behave as competitive inhibitors of CDK2 with respect to histone H1 but do not interfere with the phosphorylation of substrates interacting with the recruitment binding site on cyclin A, such as Rb (32). In contrast to these two families of peptide inhibitors, the C4 peptide blocks phosphorylation of both histone H1 and Rb. This being said, C4-mediated inhibition is 10-fold greater for histone H1 (IC50 = 1.8 ± 0.1 µM) than for Rb (IC50 = 16.7 ± 0.6 µM), suggesting that C4 does not interact with the hydrophobic pocket of cyclin A. Moreover, given that C4 peptide competitively inhibits the phosphorylation of the small histone H1-derived peptide, it is likely that its binding site overlaps with the substrate-binding site.
We have demonstrated that the C4 peptide does not compete with cyclin A for the interaction with CDK2 but instead forms stable complexes with CDK2-cyclin A. Brown et al. (23) have reported that the short substrate peptide (HHASPRK) binds the catalytic site essentially through contacts with the C-terminal lobe of CDK2. By docking longer peptides onto the structure of CDK2-cyclin A, we have shown that residues in
3 and in the loop connecting the
3 and
4 helices of cyclin A make close contacts with the peptide substrate and should therefore be considered as part of the substrate-binding site. Taking these results together with the finding that C4 associates with cyclin A but not with monomeric CDK2, we suggest that the binding of cyclin induces a conformational change in CDK2 that exposes the docking site on the CDK, thereby facilitating binding of the C4 peptide across the catalytic cleft of CDK2. We believe that the P + 1 loop of CDKs that is involved in organizing the catalytic site of these kinases, being stabilized upon the binding of cyclin, is a good candidate interaction site for C4 (26). A growing number of studies suggest that the protein kinase docking sites that mediate substrate phosphorylation may represent effective targets for inhibitor design. Recently, peptides derived from a high affinity site on CDK2 required for p53 phosphorylation were shown to successfully inhibit p53 phosphorylation in a melanoma cell line (33). Peptides based on the c-Jun N-terminal kinase (JNK)-binding domain (JIP1) of JNK I were shown to inhibit JNK activity both in vitro and in vivo when associated with a cell-penetrating peptide (34, 35).
In conclusion, we have described a new class of small peptide inhibitors of cell cycle progression that target essential conformational changes involved in CDK2-cyclin A activation. In contrast to most kinase inhibitors described in the last few years, the prototype peptide of this study (C4) neither competes with ATP nor binds the hydrophobic patch of cyclin A. We have validated the efficacy of this peptide strategy in cellulo by demonstrating that tumor cell proliferation is blocked in a dose-dependent fashion when the C4 peptide is coupled to the cell-penetrating carrier Tat. Additional studies are in progress to characterize the mechanism of action and to identify the precise binding site of the C4 peptide on CDK2-cyclin A.
| FOOTNOTES |
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Supported by a grants from HMR-Aventis, Sidaction. ![]()
¶ Supported by European Commission Grant QLK2-CT-2001-01451. ![]()
** To whom correspondence should be addressed. Tel.: 33-04-6761-3392; Fax: 33-04-6752-1559; E-mail: gilles.divita{at}crbm.cnrs.fr.
1 The abbreviations used are: CDK, cyclin-dependent kinase; CBM, cyclin binding motif; CD, circular dichroism; Fmoc, N-(9-fluorenyl)methoxycarbonyl; GST, glutathione S-transferase; Rb, retinoblastoma. ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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