Terphenyl-based helical mimetics that disrupt the p53/HDM2 interaction

Article abstract of DOI:10.1002/anie.200462316

(Chemical Equation Presented) HDM2 regulates p53 by binding to its transactivation domain and promoting its ubiquitin-dependent degradation. Crystallographic analysis of the HDM2/p53 complex revealed that three hydrophobic residues (F19, W23, L26) along one face of the p53 helical peptide are essential for binding (see picture). Terphenyl-based antagonists mimic the α-helical region of p53 and disrupt HDM2/p53 complexation.

Full text of DOI:10.1002/anie.200462316

Communications
Protein–Protein Interactions
Terphenyl-Based Helical Mimetics That Disrupt
the p53/HDM2 Interaction**
Hang Yin, Gui-in Lee, Hyung Soon Park,
Gregory A. Payne, Johanna M. Rodriguez,
Said M. Sebti, and Andrew D. Hamilton*
The p53 protein plays a key role in the apoptosis pathway.[1]
Increased expression of wild-type p53 in stressed cells leads to
cell-cycle arrest or apoptosis,[2] whereas in normal cells p53 is
present at very low levels owing to regulation by human
double minute 2 (HDM2), which promotes the degradation of
p53 through an ubiquitin-dependent proteasome pathway.[3]
The p53 protein is found in a mutated or inactive state in over
50% of cancerous tumors.[4] Moreover, overexpression of
HDM2 has been implicated in the development of cancerous
tumors, such as human osteogenic sarcomas and soft-tissue
sarcomas,[5] as the overexpressed HDM2 abrogates the ability
of p53 to induce cell-cycle arrest and apoptosis.[2] For these
reasons, disruption of the p53/HDM2 interaction by using
small-molecule agents has become an important goal for
anticancer-drug development.[6]
HDM2 regulates p53 by complex formation that involves
amino acid residues 18–102 of HDM2 and a helical region of
p53 (amino acids 16–28).[7] Crystallographic analysis of the
HDM2/p53 complex has revealed that three hydrophobic
residues (F19, W23, L26) along one face of the p53 helical
peptide are essential for binding (Figure 1a).[8] Several groups
[*] H. Yin, G.-i. Lee, H. S. Park, G. A. Payne, J. M. Rodriguez,
Prof. A. D. Hamilton
Department of Chemistry, Yale University
P.O. Box 208107, New Haven, CT 06520-8107 (USA)
Fax: (+1)203-432-6144
E-mail: andrew.hamilton@yale.edu
Prof. S. M. Sebti
Drug Discovery Program
H. Lee Moffitt Cancer Center and Research Institute
Departments of Oncology and Biochemistry and Molecular Biology
University of South Florida
Tampa, FL 33612 (USA)
[**] We thank the National Institutes of Health for support of this work
(GM35208 and GM69850). The HDM2 pQE40 construct was kindly
provided by Dr. Christian Klein (Hoffmann-La Roche, Inc.).
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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DOI: 10.1002/anie.200462316
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method.[13] To test the validity of this assay, we used non-
labeled p53 peptide as the competitive inhibitor to bind
HDM2, giving a Ki of 3.51 Æ 0.11 mm, which closely matches
the Kd value (3.02 Æ 0.33 mm) obtained from saturation
titration experiments.
Good in vitro inhibition potencies in disrupting the p53/
HDM2 heterodimerization were observed for certain com-
pounds within the terphenyl series (Table 1). The terphenyl 14
with an isobutyl, 2-naphthylmethylene, isobutyl side-chain
sequence showed a Ki value of 0.182 Æ 0.020 mm for displacing
p53 binding to HDM2. Terphenyls 16, 20, 21 bear only some
of the key side chains of 14, and their affinities for HDM2 are
significantly lower. These results confirmed the importance of
all three key side chains. The role of these side chains is
further emphasized by the weak binding of control com-
pounds (9 and 17), which indicated that there is no nonspecific
hydrophobic interaction between the terphenyl backbone and
the protein surface. Comparison of 1 (Ki = 3.83 mm) and 4
(Ki = 297 mm), which have reverse side-chain sequences,
indicated that the orientation of the terphenyl backbone is
critical in the binding. The terphenyl compounds with 2’,6’-
dimethyl substituents showed improved affinities, as seen in
the comparison of 1 and 10, which may be due to the
increased rigidity of the terphenyl backbone and the lowered
entropic penalty on binding.
Figure 1. a) X-ray crystal structure of the HDM2/p53 complex. The key
side chains of F19, W23, and L26 are shown in stick representation.
b) a-Helical mimicry based on a terphenyl scaffold.
The displacement of the p53 peptide from the surface of
HDM2 in the fluorescence experiment strongly suggested
that the potent terphenyl compounds bind to the same cleft
on the HMD2 surface. This location of the binding domain
was further confirmed by computational and NMR spectros-
copy experiments. The binding surface of p53 is dominated by
a triad of p53 amino acids (F19, W23, and L26) that interacts
with a hydrophobic cleft on the HDM2 surface (Figure 1a).[8]
In this classification, the F19-pocket is defined by R65, Y67,
E69, H73, I74, V75, M62, and V93 residues of HDM2, the
W23-pocket comprises S92, V93, L54, G58, Y60, V93, and
F91, the L26-pocket is composed of Y100, T101, and V53. To
study the binding mode of the terphenyl derivatives, we
conducted computational simulations with the Autodock
program.[14] The top-ranked docking results for terphenyl 14
(shown in Figure 2) suggested that the terphenyl compounds
target the same surface area where p53 binds, inserting their
side chains into the F19, W23, and L26-pockets.
We mapped the binding surface of the terphenyl com-
pounds on HDM2 using 15N HSQC NMR experiments. The
chemical shift perturbation of the HDM2 amide backbone
was monitored upon addition of six different terphenyl
compounds: 1, 3, 6, 11, 12, and 14 (results shown in
Table 2). All six compounds consistently induced chemical-
shift changes at residues V28, F55, G58, V93, and/or K94,
which all lie in the p53-binding pocket (with an exception of
V28, whose shift is possibly due to the global conformational
change of the protein). The chemical-shift changes at these
positions were also observed in the binding of the p53 peptide
and HDM2,[15] demonstrating that these terphenyl derivatives
recognize the protein surface in a similar manner to the p53
peptide. Further analysis of 3, 12, and 14 demonstrated that
bulkier side chains at the R2 position resulted in more-
significant chemical shifts at the F55, L57, V93, and K94
have reported small-molecule agents that disrupt p53/HDM2
dimerization. For example, Vassilev et al. identified cis-
imidazoline analogues as low-molecular-weight antagonists
of HDM2 in a high-throughput screening.[9] Most recently,
peptidomimetics of the helical region of p53 based on a
b hairpin[10] and 14-helix scaffolds[11] that disrupt the p53/
HDM2 complexation were developed by the groups of
Robinson and Schepartz, respectively. These studies serve
as the proof-of-principle that the protein–protein interface of
the HDM2/p53 complex provides a sound target for small-
molecule agents.
Previously, we showed that terphenyl derivatives can
mimic one face of a a-helical peptide (Figure 1b).[12] By
substituting the appropriate alkyl or aryl substituents on the
three ortho- positions of the terphenyl scaffold, the side
chains are projected in an analogous way to the i, i + 4, and
i + 7 residues of an a helix. Herein we report the use of this
strategy in which a group of terphenyl-based antagonists
mimic the a-helical region of the p53 peptide and disrupt the
HDM2/p53 complexation.
We prepared an extensive library of terphenyl inhibitors
through a synthesis involving sequential Suzuki couplings of
the appropriate ortho-substituted methoxyphenylboronate
and phenyltriflate. A previously reported fluorescence polar-
ization (FP) competition assay with a fluorescein-labeled p53
peptide, which contains residues 15–31 of p53 with a cysteine
residue appended to the C-terminus (SQETFSDLWKLL-
PENNVC), was used to assess the binding affinities of these
terphenyl derivatives to HDM2.[11] Displacement of this
probe through competitive binding of the terphenyl into the
hydrophobic cleft of HDM2 leads to a decrease in its
fluorescence polarization. Regression analysis was conducted
to determine the Ki values by using the previously reported
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Table 1: Results of the fluorescence polarization assays.
Structure
Ligand
R1
R2
R3
Ki ÆS.D. [mm][a]
1
2
3
4
5
6
7
8
Bn
Me
iBu
Me
iBu
Bn
Bn
Bn
Me
Me
Me
Me
Me
Me
Me
Me
Me
iBu
iBu
Bn
Bn
Bn
iPr
3.83Æ0.70
35.3Æ4.4
2.97Æ0.15
297Æ92
2.83Æ0.63
2.17Æ0.14
13.1Æ3.8
6.25Æ1.50
iBu
9
H
H
H
>1000
10
11
12
13
14
15
16
Bn
Bn
iBu
iBu
Me
Bn
Bn
Me
iBu
iBu
iBu
iBu
iBu
H
12.6Æ2.1
0.978Æ0.171
3.50Æ1.00
25.7Æ11.9
0.182Æ0.020
11.6Æ2.1
CH2(1-Naph)
CH2(2-Naph)
iBu
iBu
CH2(1-Naph)
iBu
CH2(1-Naph)
82.0Æ8.6
Figure 2. Results of the 15N HSQC NMR spectroscopy
and the molecular-docking experiments of terphenyl 14
binding to HDM2. a) The residues that showed signifi-
cant and moderate chemical-shift changes upon addi-
tion of the terphenyl compounds are shown in
magenta and orange, respectively. b) Overlay of the
top-ranked docking result of 14 and the p53 peptide
(green). The key hydrophobic side chains of F19, W23,
and L26 are shown in stick representations.
>1000
17
18
19
H
iPr
iPr
H
Me
iBu
H
Me
iBu
>1000
1.89Æ0.30
terphenyl derivatives are successful p53 mim-
etics and that these compounds present side
chains into the F19, W23, and L26 binding
pockets of HDM2.
20
21
Bn
Me
Me
Me
70.8Æ9.8
479Æ144
A critical issue in the design of small-
molecule a-helix mimetics is the selectivity of
these compounds among different helix-binding
proteins.[16] Nature frequently uses general sec-
ondary-structure modules, such as a helices, to
recognize different protein targets and achieves
high specificity through spatial and charge
[a] The Ki and standard deviation (S.D.) values were obtained from three independent titrations.
positions. Terphenyl 14, which shows the strongest binding
(Ki = 0.182 Æ 0.020 mm), induced significant peak shifts for all
these residues. In addition, a residue deep inside the W23
pocket, L85, is affected by 14, suggesting that the 2-naphthyl-
methylene side chain inserts into the W23 pocket, thus
resulting in a stronger binding (Figure 2b). Terphenyl 11,
which has a benzyl side chain at the R1 position, clearly
affected the residues M62 and H73 in the F19 pocket on
HDM2, whereas 12 (iBu at R1) does not, which indicates that
11 inserts the benzyl side chain into the F19 pocket as p53
does. Taking all these results together, we concluded that the
complementarity.[17] Previous studies have shown that the
p53 peptide selectively binds to HDM2 over other oncogenic
proteins, such as Bcl-xL and Bcl-2, which both complex with
the a-helical Bak BH3 domain.[18] In a similar manner to the
p53/HDM2 interaction, the Bak peptide also projects key side
chains at the i, i + 4, and i + 7 positions (V74, L78, and I81)
into hydrophobic clefts on the targeted protein surfaces.[19]
Comparison of terphenyl isomers 13 and 14, which bear 1- and
2-naphthylmethylene side chains, respectively, on the middle
phenyl rings, showed that terphenyl derivatives can selec-
tively bind to different helix-binding proteins (Table 3).
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[6] P. Chene, Nat. Rev. Cancer 2003, 3, 102.
Table 2: Summary of the amino acid residues of HDM2 that showed
chemical-shift changes upon addition of terphenyl inhibitors.
[7] J. D. Oliner, J. A. Pietenpol, S. Thiagalingam, J. Gvuris, K. W.
Kinzler, B. Vogelstein, Nature 1993, 362, 857.
Ligand Significantly shifted
residues[a]
Moderately shifted
residues[a]
[8] P. H. Kussie, S. Gorina, V. Marechal, B. Elenbaas, J. Moreau,
A. J. Levine, N. P. Pavletich, Science 1996, 274, 948.
[9] L. T. Vassilev, B. T. Vu, B. Graves, D. Carvajal, F. Podlaski, Z.
Filipovic, N. Kong, U. Kammlott, C. Lukacs, C. Klein, N. Fotouhi,
E. A. Liu, Science 2004, 303, 844.
1
S22, V28, F55, L57, G58, I61, T26, L35, E52, V53, D68
K94, K98, Y104
3
6
G12, T15, S22, V28, G58
R29, L35, F55, I74, S92, K94
[10] R. Fasan, R. L. A. Dias, K. Moehle, O. Zerbe, J. W. Vrijbloed, D.
Obrecht, J. A. Robinson, Angew. Chem. 2004, 116, 2161; Angew.
Chem. Int. Ed. 2004, 43, 2109.
[11] J. A. Kritzer, J. D. Lear, M. E. Hodsdon, A. Schepartz, J. Am.
Chem. Soc. 2004, 126, 9468.
V8, G12, S22, V28, K51, V53,
Y56, M62, V93
L33, L35, E52, F55, T63, K70,
H73, L82, L85, F91, S92, H96
11
12
14
G12, T15, V28, K51, G58, H73, S22, K45, I61, M62, I74, V75,
[12] O. Kutzki, H. S. Park, J. T. Ernst, B. P. Orner, H. Yin, A. D.
Hamilton, J. Am. Chem. Soc. 2002, 124, 11838; J. T. Ernst, O.
Kutzki, A. K. Debnath, S. Jiang, H. Lu, A. D. Hamilton, Angew.
Chem. 2002, 114, 288; Angew. Chem. Int. Ed. 2002, 41, 278; B. P.
Orner, J. T. Ernst, A. D. Hamilton, J. Am. Chem. Soc. 2001, 123,
5382.
[13] T. Wohland, K. Friedrich, R. Hovius, H. Vogel, Biochemistry
1999, 38, 8671; see the Supporting Information for the analysis
protocol.
[14] R. Stoll, C. Renner, S. Hansen, S. Palme, C. Klein, A. Belling, W.
Zeslawski, M. Kamionka, T. Rehm, P. Muhlhahn, R. Schu-
macher, F. Hesse, B. Kaluza, W. Voelter, R. A. Engh, T. A.
Holak, Biochemistry 2001, 40, 336.
[15] O. Schon, A. Friedler, S. Freund, A. R. Fersht, J. Mol. Biol. 2004,
336, 197; O. Schon, A. Friedler, M. Bycroft, S. M. V. Freund,
A. R. Fersht, J. Mol. Biol. 2002, 323, 491.
F91, S92, V93
K94, K98, I99, L107
V8, T15, S22, V28, F55, L57,
I74, F91, E95
R29, Y60, Y67, K70, S92
V8, G12, T15, S22, V28, F55,
G58, K70, L85, V93, K94, Y100
L38, M62, T63, D68
[a] See Supporting Information.
Table 3: Comparison of terphenyl derivatives 13 and 14 in inhibition of
different protein–protein complexes.
Ki [mm]
HDM2/p53
Bcl-xL/Bak
Bcl-2/Bak
13
14
25.7
0.182
0.114
2.50
0.121
15.0
[16] J. W. Harbour, T. G. Murray in Ophthalmic Surgery: Principles
and Techniques (Ed.: D. Albert), Blackwell Publishers, Maden,
MA, 1998, pp. 682.
[17] W. E. Stites, Chem. Rev. 1997, 97, 1233.
[18] J. W. Harbour, L. Worley, D. D. Ma, M. Cohen, Arch. Ophtalmol.
2002, 120, 1341.
[19] M. Sattler, H. Liang, D. Nettesheim, R. P. Meadows, J. E.
Harlan, M. Eberstadt, H. S. Yoon, S. B. Shuker, B. S. Chang,
A. J. Minn, C. B. Thompson, S. W. Fesik, Science 1997, 275, 983.
Terphenyl 14 binds to HDM2 over 100-fold more strongly
than 13 and has a 14:82 fold selectivity over Bcl-xL/Bcl-2. This
is consistent with the deeper pocket in HDM2 for W23 at the
i + 4 position compared to the L78-pocket of Bcl-xL or Bcl-2.
These results confirm the generality of the terphenyl scaffold
as a mimic of the side-chain-induced selectivity of a helices
and provides a useful tool for the rational design of protein-
binding agents. Evaluation of the inhibitory effects of
terphenyl derivatives in whole cells is currently underway.
Received: October 15, 2004
Published online: March 14, 2005
Keywords: drug design · helical structures · inhibitors ·
.
protein–protein interactions · proteins
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