Halogen-enriched fragment libraries as leads for drug rescue of mutant p53

Article abstract of DOI:10.1021/ja301056a

The destabilizing p53 cancer mutation Y220C creates a druggable surface crevice. We developed a strategy exploiting halogen bonding for lead discovery to stabilize the mutant with small molecules. We designed halogen-enriched fragment libraries (HEFLibs)

Full text of DOI:10.1021/ja301056a

Article
pubs.acs.org/JACS
Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of
Mutant p53
Rainer Wilcken,†,‡ Xiangrui Liu,‡ Markus O. Zimmermann,† Trevor J. Rutherford,‡ Alan R. Fersht,‡
Andreas C. Joerger,*,‡ and Frank M. Boeckler*,†
†Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute
of Pharmacy, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
‡MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
S
* Supporting Information
ABSTRACT: The destabilizing p53 cancer mutation Y220C
creates a druggable surface crevice. We developed a strategy
exploiting halogen bonding for lead discovery to stabilize the
mutant with small molecules. We designed halogen-enriched
fragment libraries (HEFLibs) as starting points to complement
classical approaches. From screening of HEFLibs and
subsequent structure-guided design, we developed substituted
2-(aminomethyl)-4-ethynyl-6-iodophenols as p53-Y220C sta-
bilizers. Crystal structures of their complexes highlight two key
features: (i) a central scaffold with a robust binding mode anchored by halogen bonding of an iodine with a main-chain carbonyl
and (ii) an acetylene linker, enabling the targeting of an additional subsite in the crevice. The best binders showed induction of
apoptosis in a human cancer cell line with homozygous Y220C mutation. Our structural and biophysical data suggest a more
widespread applicability of HEFLibs in drug discovery.
of the protein.14,15 About one-third of these mutations simply
destabilize this only marginally stable domain, lowering its
INTRODUCTION
■
Halogen bonds have attracted increased interest in molecular
design recently,1,2 offering alternatives to classical polar
melting temperature so that it rapidly unfolds at body
temperature.16,17 In theory, wild-type function of these mutants
interactions such as hydrogen bonds. Halogen bonding is a
noncovalent interaction of the type R−X···Y−R′, where X is
chlorine, bromine or iodine acting as a Lewis acid and Y can be
any kind of Lewis base. Because of a deficiency in electron
density on the hind side of X along the R−X bond axis,
chlorine, bromine and iodine possess a characteristic region of
can be recovered by binding of molecules that shift the
folding−unfolding equilibrium toward the folded state and also
slow down the rate of unfolding. We have previously shown
that the cancer hotspot mutant Y220C, which accounts for
approximately 75 000 new cancer cases per year, is a
particularly suitable test case for developing and validating
positive electrostatic potential, the σ-hole, which favors
such compounds.10 The mutation destabilizes the protein by
interaction with electron donors.3 Halogen bonds involving
creating a surface crevice at a site that is distant from the
main-chain carbonyl oxygens were found to improve the
functional interfaces of the protein.18 From virtual screening,
binding of several ligands to their target protein significantly.4−7
we discovered a carbazole-based small molecule, PhiKan083,
The most frequently observed halogen bonds in protein−ligand
that binds to this crevice with a KD of 150 μM and raises the
structures are either halogen−carbonyl oxygen or halogen−π
melting temperature of the protein in vitro.19 Using halogen-
interactions.8 Quantum chemical calculations also suggest that
enriched fragment libraries (HEFLibs), we were able to exploit
halogen bonding for lead discovery and apply it to develop
biologically active small molecules that stabilize the p53 mutant
Y220C.
affinity and selectivity of ligands can be increased by directed
halogen−sulfur contacts with methionines.9 Despite this
potential of halogen moieties to contribute favorably to ligand
binding, the number of compounds containing heavy halides in
standard libraries for fragment-based screening is very low.
Here, we have designed a halogen-enriched fragment library
(HEFLib) and screened this library for molecules binding to
RESULTS AND DISCUSSION
Design of a Halogen-Enriched Fragment Library and
Lead Discovery. We used the previously solved structural
■
the Y220C mutant of the p53 tumor suppressor. p53 is
features of the mutation-induced surface crevice in Y220C as
inactivated in virtually every cancer either through direct
starting points to design new leads. The central cavity has a
mutation or through perturbation of its associated pathways.
Reactivation of p53 function in tumors has, therefore, become a
prime target for therapeutic intervention.10−13 Most oncogenic
p53 cancer mutations are located in the DNA-binding domain
Received: February 1, 2012
Published: March 22, 2012
© 2012 American Chemical Society
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Figure 1. Mutation-induced cavity in p53 Y220C. (a) Molecular surface of the p53 mutant Y220C bound to the carbazole derivative PhiKan083
(PDB code 2VUK).19 The ligand is shown as a yellow stick model. The mutation-induced cavity can be subdivided into three parts: (i) a deep but
narrow central cavity, colored in blue, which is occupied by the carbazole ring; (ii) an open rather shallow subsite 1, colored in red; and (iii) subsite
2, colored in green, which is flanked by several prolines and main-chain oxygens. The latter is not occupied by PhiKan083. (b) Ribbon diagram
showing details of the binding mode of PhiKan083, in particular the role of Leu145 at the bottom of the central cavity.19 Also shown are structural
water molecules in the ligand-free structure (PDB code 2J1X)18 that are displaced upon ligand binding. One of these water molecules sits at the
bottom of the predominantly hydrophobic central cavity and forms a hydrogen bond with the main-chain oxygen of Leu145. (c and d) Potential for
halogen-bond interactions with the carbonyl oxygen of Leu145. The iodine-interaction energy sphere is plotted onto the carbonyl oxygen of Leu145
in the Y220C-PhiKan083 structure, showing that this oxygen at the bottom of the central cavity is poised for interaction with iodine-containing
ligands with maximum binding energy. Blue regions have the lowest energy; red regions have the highest energy (see Supporting Information for
details).
number of water molecules that are displaced upon ligand
binding (Figure 1).18,19 One water molecule forms a hydrogen
bond with the main-chain oxygen of Leu145, which is
embedded within a hydrophobic environment. The carbonyl
is not saturated with hydrogen bonds in the complex of Y220C
with the carbazole-based PhiKan083 compound (Figure 1b),19
whereas other small molecules interact with this oxygen via an
amino group.20 Quantum chemical calculations at MP2/
TZVPP level revealed that the carbonyl oxygen of Leu145 is
poised for halogen-bond interactions with moieties binding to
the central cavity, in addition to formation of hydrogen bonds
(Figure 1c,d). We therefore designed a HEFLib to exploit this
additional chemical space in our search for alternative scaffolds
binding to the Y220C mutant.
and isothermal titration calorimetry (ITC). The most
promising lead obtained was 2,4-diiodo-6-((methyl(1-methyl-
piperidin-4-yl)amino)methyl)phenol 3, which bound to the
mutation-induced cavity with a dissociation constant, KD, of
184 23 μM as determined by NMR (Figure 2a).
To verify whether 3 shows halogen bonding as an essential
binding interaction and to guide our further ligand design, we
solved the crystal structure of the Y220C mutant bound to 3
(1.7-Å resolution), revealing the detailed binding mode of the
compound. The benzene moiety sits at the center of the
mutation-induced cavity in Y220C, flanked by three prolines
(Pro151, Pro222 and Pro223), Val147 and Thr150 (Figure 2b).
The two iodine atoms are facing the bottom of the cavity. One
iodine atom sits close to the sulfur atom of Cys220 (4.1-Å
distance), whereas the other is further removed from the sulfur
(5.4-Å distance) and, most importantly, forms an energetically
favorable halogen bond with the main-chain oxygen of Leu145.
The distance between the iodine and oxygen atoms is 3.0 Å,
which is significantly shorter than the sum of the van der Waals’
radii of the two atoms, consistent with quantum chemical
calculations on the nature of halogen bonds.22 The halogen-
bond angle (C−I···O) is 172°. The phenol group interacts with
a conserved structural water molecule, which in turn is
stabilized by hydrogen bonds with main-chain atoms of
Val147 and Asp228. In addition, the phenol hydroxyl forms
The HEFLib was designed using criteria for fragment
selection similar to the “rule of three” by Congreve et al.21
but employing an upper limit of the number of heavy atoms
(up to 22) rather than the original molecular weight-based
criterion (MW ≤ 300). As an additional cheminformatics
selection rule, the molecules were required to contain heavy
halides, such as bromine and, in particular, iodine. We chose 79
small, nonreactive, soluble halogenated aromatic compounds
from standard vendors, tested them using a thermal shift assay
(differential scanning fluorimetry, DSF) and performed
1
secondary screenings with H/15N-HSQC NMR spectroscopy
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Figure 2. Binding mode of 3 in the mutation-induced pocket of the
p53 mutant Y220C. (a) Overlay of 15N/1H HSQC spectra of T-p53C-
Y220C without ligand (red) and increasing concentrations of 3 (73
μM, orange; 145 μM, yellow; 291 μM, green; 582 μM, cyan; 2000 μM,
dark blue). (b) Crystal structure of the Y220C mutant bound to 3.
The mutant is shown as a gray cartoon representation, with selected
residues in the cavity shown as stick models. The ligand is shown as a
yellow stick model, and polar interactions with the protein are
highlighted with broken lines. An unbiased simulated-annealing omit
(Fo − Fc) electron-density map for the ligand is shown at a contour
level of 3.0 σ. The piperidine moiety of 3 protruding from the cavity
was not resolved in the crystal structure and has been omitted from the
model.
Figure 3. Overview of the synthetic strategy based on the initial hit 3
resulting from HEFLibs screening. Variations in the amine side chain
(3−5) were created starting from building block 1 by reductive
amination (red box). Variation in the halogen substitution pattern (6−
8) for systematically studying the strength of the halogen−oxygen
interactions was done by using different building blocks (blue box).
The established scaffold was further extended into subsite 2 by
Sonogashira coupling of 4 with different acetylenes yielding analogues
9−13 (green box).
an intramolecular hydrogen bond with the tertiary amine.
There was no clear electron density to model the binding mode
of the piperidine ring in 3, indicating a high flexibility of this
moiety in the complex (Figure 2b).
amines. The salicylic acid derivative of this building block 2
bound to the mutation-induced cavity with a KD of about 800
μM, which corresponds to a ligand efficiency23 of 0.34 kcal/mol
per non-hydrogen atom. We generated computer models of all
possible products using this building block and commercially
available amines, and docked them into the Y220C structure to
select suitable candidates for synthesis. We employed a rigid
scaffold match constraint using the binding mode of 3 to fix the
central scaffold, as halogen bonding is not generally
implemented in current docking tools. Optimizing the amine
moiety within subsite 1 (red areas in Figure 1a) by this
structure-guided design increased compound affinities moder-
ately. The two amines with highest binding affinity were 4 and
5, showing KDs measured by NMR of 104 and 87 μM,
respectively. The crystal structure of the Y220C complex with 4
Lead Optimization. With the binding mode of 3 confirmed
by X-ray crystallography, we developed a lead optimization
strategy as presented in Figure 3 to extend the ligand into
subsites 1 and 2 of the Y220C binding pocket. Dissociation
1
constants obtained by H/15N-HSQC NMR and ITC, as well
as the increase in the melting temperature measured by
differential scanning fluorimetry (DSF), are given in Table 1 for
selected compounds at different stages of the lead optimization
process. Compound 3 and its analogues are easily obtained by
reductive amination of the commercially available building
block 3,5-diiodosalicylaldehyde (1) with a range of different
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Table 1. Biophysical characterization of designed p53-
Y220C ligands
DSF ΔTm [K]
a
compound
at 250 μM
NMR KD [μM] ITC KD [μM]
2
3
4
5
6
7
8
n.d.
819 68
184 23
104 23
87 17
n.d.
225
105
78
0.55
0.97
1.10
0.31
0.03
−0.05
0.58
0.64
3.21
2.59
3.61
247 44
1040 160
4900 2300
n.d.
n.d.
n.d.
107
n.d.
15.5
20.6
9.7
9 (PhiKan5116)
10
114
8
1080 360
b
11 (PhiKan5174)
12 (PhiKan5176)
13 (PhiKan5196)
n.a.
b
n.a.
b
n.a.
a
b
ΔTm =Tm(ligand-bound protein) − Tm(free protein). For binders
with a KD in the low micromolar region, line broadening (intermediate
exchange) was observed instead of chemical shift perturbation.
showed essentially the same binding mode of the central
scaffold as observed for 3. In contrast to the crystal structure of
3, the piperidine ring was well-defined. It packs against residues
147−150, protruding from the central region of the pocket and
extending into the shallow subsite 1 and out into solvent
(Figure 4a and Supporting Information Figure S1).
To evaluate the contribution of halogen bonding to the
observed ligand affinities, we replaced the iodine moieties in 5
with the lighter halogens bromine and chlorine, which are
expected to form weaker halogen bonds based on theoretical
calculations. Comparison of data for the three ligands 6, 7 and
8 with 5 (see Figure 3) demonstrates the importance of the
iodine−oxygen halogen bond (Table 1); substituting the iodine
moiety binding to Leu145 by bromine resulted in a 4-fold
decrease in KD, while substitution with chlorine severely
impaired binding of the compound to the Y220C crevice and
resulted in a 20-fold loss in affinity. In addition to reduced
halogen bonding, reduced space filling by the smaller chlorine
compared to iodine may also affect binding affinity.
Replacement of the other iodine in position 4 by chlorine
resulted only in a 3-fold loss in affinity.
Figure 4. Crystal structures of Y220C−ligand complexes. Shown are
the binding modes of 4 (a), PhiKan5116 (b), and PhiKan5196 (c).
The protein is shown as a gray cartoon representation with selected
residues highlighted as stick models. The halogen bond between the
iodine and the carbonyl oxygen of Leu145 is indicated by a broken
magenta line; additional polar interactions with the protein are shown
as green broken lines.
Next, we extended the ligand into subsite 2 (colored in green
in Figure 1a), which required bridging the narrow gap between
Cys220 and Pro151. A significant benefit of our HEFLibs
strategy is that halogens not involved in essential interactions
with the binding site can be utilized by a multitude of Pd-based
cross-coupling reactions for developing and decorating the
original scaffold. We evaluated various possibilities in silico and
found an acetylene linker best suited to bridge this narrow gap
between the central cavity and subsite 2. The acetylene linker
was introduced by a reaction of the 4-iodo moiety on the
central scaffold with terminal acetylenes in a Sonogashira
coupling reaction.24,25 The first compound with acetylene
linker to be tested was 9 (PhiKan5116), exhibiting very similar
binding affinity to that of the parent di-iodo compound 4.
Hence, loss of the bulky 4-iodo moiety in the central scaffold is
compensated for by interactions formed by the new substituent
in 9. Surprisingly, 10, which has a propargylamine moiety
instead of the propargyl alcohol moiety in 9, bound only weakly
to p53-Y220C, possibly due to heavy desolvation penalties for
this highly polar compound (NMR KD ≈ 1.1 mM). In contrast,
its t-BOC-protected precursor, 11 (PhiKan5174), exhibited
very tight binding to the mutation-induced crevice (KD
measured from ITC = 15.5 μM) and substantially stabilized
the protein (Table 1, Figure 3). Substitution of the free
terminal hydroxyl group in 9 by a phenoxy moiety resulting in
compound 12 (PhiKan5176) led to a 10-fold increase in
binding affinity predominantly due to a favorable CH-π
stacking of the phenyl ring on Pro153. Finally, introducing an
anilinic −NH− group instead of the phenol ether resulted in 13
(PhiKan5196), the most potent Y220C stabilizer identified to
date. 13 bound to the mutation-induced cavity with a
dissociation constant of 9.7 μM as determined by ITC and
raised the melting point of the protein by about 3.6 K at 250
μM compound concentration (Figure 5).
Binding Mode of Ligands with Acetylene Linker. To
validate our ligand design results, we solved crystal structures of
a series of Y220C−ligand complexes at 1.4−1.6 Å resolution
(Figure 4 and Supporting Information Figure S2). Replacement
of the iodine facing Cys220 with an acetylene linker in our
third-generation compounds had virtually no effect on the
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Figure 5. Biophysical characterization of PhiKan5174 and PhiKan5196 by DSF and ITC. Concentration-dependent thermostabilization of the
Y220C mutant by PhiKan5174 (a) and PhiKan5196 (b) measured by DSF. Binding of PhiKan5174 (c) and PhiKan5196 (d) to Y220C as
characterized by ITC.
binding mode of the central scaffold. In all ligand-bound
protein structures, the key interactions of the central scaffold
are conserved. The iodine−oxygen halogen bond distance is
consistently between 3.0 and 3.1 Å (representing only ∼86−
89% of the sum of the van der Waals radii), and the halogen-
bond angles (C−I···O) are between 169° and 173°. This
verifies our quantum chemical calculations regarding energeti-
cally favored iodine−oxygen halogen bonds (as shown in
Figure 1c,d), which formed the basis for the design of HEFLibs.
As anticipated, the acetylene group occupies the narrowest part
of the cavity between residues Pro151, Cys220 and Pro222 that
leads into the previously unoccupied subsite 2, thus widening
the scope for additional interactions. The additional hydroxyl
group in 9, for example, forms a hydrogen bond with the main-
chain oxygen of Pro151 (Figure 4b). This oxygen is also
hydrogen bonded with the amide of PhiKan5174 (Supporting
Figure S2). Key structural features of the tightest binding
ligands include the additional hydrophobic interactions linking
Pro153 to Pro222. 12 and 13, for example, are stabilized by
packing of a benzene ring against Pro153, allowing favorable
CH−π stacking interaction, and hydrophobic interactions with
Thr150 and Pro222 (Figure 4c and Supporting Information
Figures S1 and S2). 11, however, combines a hydrogen bond
with the carbonyl group of Pro151 and hydrophobic
interactions of the tertiary butyl moiety with the aforemen-
tioned three residues (Supporting Information Figure S2). The
higher affinity of 13 compared to 12 results from an additional,
albeit weak, hydrogen bond formed between the benzamine
moiety and the carbonyl oxygen of Cys220 (hydrogen-bond
distance of 3.2 Å). Overall, the structural and biophysical data
highlight the crucial role of the acetylene linker for designing
high-affinity ligands occupying both subsites of the Y220C
binding pocket.
Apoptotic Effects of PhiKan5174 and PhiKan5196 in
Human Cancer Cell Lines. We tested the effects of 9, 11 and
13 on the human gastric cancer cell lines NUGC-3 (p53-
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Y220C+/+) and NUGC-4 (wild-type p53+/+) using a caspase 3/
7 apoptosis assay at concentrations ranging from 6.25 to 100
μM (Figure 6). 9, the weakest binder of the three ligands
Y220C mutant measured in our in vitro studies. In contrast, no
significant effect on apoptosis/caspase activity was observed in
the NUGC-4 cell line with wild-type p53 under the same
conditions, suggesting that the apoptotic effects of 11 and 13 in
the NUGC-3 cell line are mutant-specific. The compounds
showed cytotoxic effects at 50 and 100 μM in both cancer cell
lines in a Y220C-independent manner (Supporting Information
Figure S3). Future developments will be to increase the affinity
to levels that ensure target selectivity. Structure-guided scaffold
decoration, in particular to probe subsite 2 interactions (e.g.,
based on PhiKan5196, 13), should be ideally suited for this
purpose.
CONCLUSIONS
■
We have designed a new class of biologically active small-
molecule stabilizers of the p53 cancer mutant Y220C, resulting
in a significant increase in affinity compared to the carbazole-
based ligand PhiKan083 reported previously.19 This class of
compounds has two key features: (i) a central scaffold anchored
by halogen bonding and (ii) an acetylene linker which targets
an additional subsite of the mutation-induced cavity. With its
two iodine atoms, the lead fragment, 3, identified from
screening of a halogen-enriched library is perfectly suited for
the design of potent Y220C binders and provided a central
scaffold with a very robust binding mode. While one iodine
moiety facilitates ligand binding through energetically favorable
halogen bonding, the other iodine can be exploited for carbon−
carbon bond formation, such as the Sonogashira coupling
performed here, to extend the ligand into subsite 2.
We propose a general strategy that uses halogen-enriched
fragment libraries (HEFLibs) for lead discovery, in addition to
halogen bonding having been successfully employed recently
for scaffold decoration.1,2 Halogenated compounds are under-
represented in fragment libraries because of the significant
atomic weight of bromine and iodine. However, HEFLibs share
the advantages of regular fragments, and as molecular probes of
small size they can explore binding sites for favorable halogen-
bond interactions, to identify unique binding modes that are
complementary to those obtained from classical fragment-based
screening. We have demonstrated that highly directed iodine−
oxygen contacts, in particular, are stable across a multistep
structure-based design process. We therefore suggest a more
widespread use of HEFLibs in molecular design and drug
discovery. This strategy may not only be useful for tackling
novel targets but also provide alternative leads for well-
established pharmaceutically relevant target proteins and, thus,
circumvent patent restrictions.
Figure 6. Effects of compounds in human cancer cell lines. Caspase-3/
7 activities are shown at different concentrations of PhiKan5116 (a),
EXPERIMENTAL SECTION
PhiKan5174 (b), and PhiKan5196 (c) in NUGC-3 (p53-Y220C+/+
)
■
and NUGC-4 (p53-wt+/+) cell lines. While PhiKan5116 does not
induce Caspase-3/7 activation, apoptosis is induced by the more
potent binders PhiKan5174 and PhiKan5196 at high concentrations in
Y220C mutant cells but not in wild-type cells.
Molecular Modeling. All docking experiments were performed
using the GOLD v3.226 suite of programs together with the scoring
functions Goldscore27 and Chemscore28 at default parameters, as
described previously.29 The search efficiency for the genetic algorithm
was increased to 200% in automatic mode. Binding site residues were
defined automatically by providing the co-crystal structures of
PhiKan083 (PDB entry 2VUK) or 3 as a template and using flood
fill (“detect cavity” option enabled) with an active site radius of 12 Å.
For docking of halogen-bond forming compounds derived from 3, a
scaffold match constraint was used, with the central scaffold of 3 as a
template. Further details of computational methods, and a description
of the quantum chemical calculations used to plot the iodine−oxygen
interaction energy sphere (Figure 1c,d) are given in the Supporting
Information.
tested, showed no effect on caspase activity in either NUGC-3
or NUGC-4 cells after 6 h at 37 °C. The more potent binders
PhiKan5174 and PhiKan5196 (11 and 13), on the other hand,
induced apoptosis in the Y220C-containing NUGC-3 cells in a
dose-dependent manner. Onset of apoptosis with 13 was
observed at a concentration of 50 μM, whereas 11 induced
apoptosis only at 100 μM compound concentration, which is
consistent with the 2-fold higher affinity of 13 toward the
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Table 2. X-ray Data Collection and Refinement Statistics of p53-Y220C:Ligand Complexes
compound
3
4
9
11
12
13
Data Collection
Space Group
a (Å)
P212121
65.33
P212121
64.98
P212121
65.04
P212121
65.05
P212121
65.08
P212121
65.04
b (Å)
71.04
71.17
71.26
71.13
71.17
71.24
c (Å)
105.65
104.96
104.88
105.15
104.98
104.94
Molecules/AU
Resolution (Å)
2
2
2
2
2
2
a
42.4−1.70
(1.79−1.70)
54,754
35.4−1.52
(1.60−1.52)
73,697
35.4−1.60
(1.69−1.60)
64,327
35.5−1.45
(1.53−1.45)
84,513
35.4−1.50
(1.58−1.50)
79,145
29.6−1.42
(1.50−1.42)
91,185
Unique reflections
a
Completeness (%)
99.8 (99.6)
5.4 (5.4)
10.0 (31.1)
9.9 (4.3)
13.6
97.8 (94.2)
5.7 (5.5)
7.7 (39.4)
13.8 (4.1)
12.8
99.0 (97.0)
5.4 (5.3)
7.8 (31.4)
12.9 (4.4)
13.4
97.3 (93.2)
5.5 (5.7)
7.2 (31.4)
14.4 (5.0)
10.8
99.9 (99.9)
5.7 (5.5)
6.7 (22.9)
16.3 (6.7)
11.5
98.7 (94.7)
5.2 (4.7)
5.0 (38.1)
17.0 (3.8)
14.5
a
Multiplicity
a,b
R
merge(%)
a
<I/σI>
Wilson B value (Å2)
Refinement
c
No. of protein atoms
No. of water atoms
No. of zinc atoms
No. of ligand atoms
3124
638
2
3150
607
2
3160
609
2
3126
557
2
3137
577
2
3127
558
2
26
42
48
62
60
60
Overall B value (Å2)
17.9
16.3
19.3
0.007
1.0
16.2
17.3
19.7
0.006
1.1
16.8
17.6
19.3
0.005
1.0
13.6
19.4
21.6
0.006
1.1
14.2
16.8
18.7
0.006
1.1
16.8
18.0
19.5
0.006
1.1
d
R
R
cryst, (%)
d
free, (%)
rmsd bonds (Å)
rmsd angles (°)
PDB code
4AGL
4AGM
4AGN
4AGO
4AGP
4AGQ
a
b
c
d
Values in parentheses are for the highest-resolution shell. Rmerge = ∑(Ih,i − <Ih>)/∑Ih,i. Number includes alternative conformations. Rcryst and
Rfree = ∑||Fobs| − |Fcalc||/∑|Fobs| where Rfree was calculated over 5% of the amplitudes chosen at random and not used in the refinement.
Protein Expression and Purification. The stabilized DNA-
binding domain of the p53 mutant Y220C, T-p53-Y220C, was
expressed and purified as described previously.19 For the expression of
15N-labeled protein for NMR experiments, M9 minimal medium with
15NH4Cl (1 g/L) as the sole nitrogen source was used.
Chemical Compounds. Compound 2 was purchased from Sigma-
Aldrich and >99% pure. The screening compound 3 was purchased
from Chembridge (San Diego, CA) with >95% guaranteed purity. The
remaining compounds were synthesized within the framework of
custom synthesis contracts. 4 was synthesized by Enamine (Kiev,
Ukraine). Compounds 5−8 were synthesized by Chembridge (San
Diego, CA), and compounds 9−13 were synthesized by Roowin
(Romainville, France). For all compounds, compound identity and
>95% purity were guaranteed by the supplier.
of 5% (v/v) DMSO-d6 in buffer. All HSQC spectra were acquired with
8 transients per t1 data point, 1024 data points in t2, and 64 complex
data points in t1, with spectral widths of 11.0 kHz for 1H and 2.7 kHz
for 15N, and a recycle delay of 800 ms. After zero filling, forward
complex linear prediction in f1 and Fourier transformation, the digital
1
resolution was 0.01 ppm/point for H and 0.13 ppm/point for 15N.
Chemical shifts were considered significant if the average weighted
1H/15N chemical shift difference Δδ(1H/15N) = [(Δδ(1H))2
+
(Δδ(15N)/5)2]1/2 was greater than 0.04 ppm. To determine
dissociation constants, at least five 15N/1H HSQC spectra at different
compound concentrations were measured. Spectra analysis was
performed using Sparky 3.11430 and Bruker Topspin 2.0 software.
To derive KD values, a quadratic saturation binding equation was fitted
to the concentration-dependent chemical shift changes of the relevant
shifting peaks:
Differential Scanning Fluorimetry (DSF). The effect of
compounds on the melting temperature of T-p53C-Y220C was
monitored using SYPRO Orange (Invitrogen) as the fluorescent
probe, which quantitatively binds to the hydrophobic protein patches
exposed upon thermal denaturation. Real-time melt analysis was
performed using a Corbett Rotor-Gene 6000 real-time qPCR
thermocycler. Excitation and emission filters were set to 460 and
510 nm, respectively. Heating from 28 to 60 °C, a constant heating
rate of 270 K/h was applied. The protein (final concentration of 10
μM) was briefly mixed with SYPRO orange (10×) in buffer (25 mM
KPi pH 7.2, 150 mM NaCl, 1 mM TCEP), and compound (5 mM)
dissolved in DMSO was added to give a final compound concentration
of 250 μM in 5% (v/v) DMSO. The melting temperature (Tm) of the
protein (10 μM) in presence of compounds was determined from the
inflection point of the melting curve. Melting temperatures were
compared with control samples without compound (yielding ΔTm
DSF). All samples were measured in triplicate.
[L0] + [P ] + KD
−
([L0] + [P ] + KD)2 − 4·[P ]·[L0]
0
0
0
∂
= ∂max
obs
2·[P ]
0
Isothermal Titration Calorimetry (ITC). ITC experiments were
conducted using a MicroCal (Amherst) iTC200 calorimeter. Protein
samples used in the cell unit were prepared to a final concentration of
50−200 μM in 25 mM KPi, pH 7.2, 150 mM NaCl, 1 mM TCEP in
5% (v/v) DMSO. Compounds for use in the syringe unit were
dissolved in the same buffer at 5% (v/v) DMSO. Measurements were
performed at 20 °C using injection steps of 2 μL at a rate of 0.5 μL/s
(initial injection: 0.5 μL) and 120 s spacing. Data analysis was
performed using MicroCal Origin software.
X-ray Crystallography. Crystals of T-p53C-Y220C were grown
by the sitting drop vapor diffusion method as described previously.18
They were soaked in solutions of compound (30 mM or saturated
solution) in cryo buffer (19% polyethylene glycol 4000, 20% glycerol,
10 mM sodium phosphate, pH 7.2, 100 mM HEPES, pH 7.2, 150 mM
KCl, 10 mM DTT) for 1−3 h and flash frozen in liquid nitrogen. X-ray
data sets were collected at 100 K at the Diamond Light Source, Oxford
(beamlines I02, I03 and I04). The data sets were processed with either
NMR Spectroscopy. 1H/15N-HSQC spectra of uniformly 15N-
labeled T-p53-Y220C (75 μM) with and without compounds were
acquired at 20 °C on a Bruker Avance-800 spectrometer using a 5-mm
inverse cryogenic probe. Samples were prepared by adding dilutions of
compound from stock solutions in DMSO-d6 to a final concentration
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Journal of the American Chemical Society
Article
MOSFLM31 or XDS,32 and SCALA.33 The structures were solved by
rigid body refinement with PHENIX34 using the structure of the
ligand-free mutant (PDB ID 2J1X)18 as starting model. Models were
built and refined using Coot35 and PHENIX. Data collection and
refinement statistics are shown in Table 2. The atomic coordinates and
structure factors of the Y220C−ligand complexes have been deposited
in the Protein Data Bank, www.pdb.org (PDB ID codes 4AGL, 4AGM,
4AGN, 4AGO, 4AGP, and 4AGQ). Structural figures were prepared
using PyMOL (www.pymol.org).
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a mixture containing the cell-permeable protease substrate GF-AFC
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content was mixed by orbital shaking for 1 min, and cells were
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plate reader using a 400/500 nm and a 480/520 nm optic module,
respectively. Luminescence was recorded using an Orion microplate
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incubation with Caspase-Glo 3/7 reagent (100 μL/well) at room
temperature. Experiments were performed in triplicate.
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ASSOCIATED CONTENT
■
S
* Supporting Information
Supplementary computational procedures, Figures S1−S3,
spectroscopic data of compounds 4−13. This material is
available free of charge via the Internet at http://pubs.acs.org.
AUTHOR INFORMATION
■
Corresponding Author
acj2@mrc-lmb.cam.ac.uk; frank.boeckler@uni-tuebingen.de
Notes
(23) Hopkins, A. L.; Groom, C. R.; Alex, A. Drug Discovery Today
2004, 9, 430.
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS
■
We thank the staff at the Diamond Light Source for technical
assistance during data collection. This work was funded by the
ERC Advanced Grant “Tumour suppressor p53: structure,
stability and novel anti-cancer drug development” and the
federal state of Baden-Wuerttemberg, Germany.
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