Structure-guided development of selective RabGGTase inhibitors

Article abstract of DOI:10.1002/anie.201101210

Designing for selectivity: A combination of protein crystal-structure analysis, virtual screening, and synthetic chemistry has been used to develop noncytotoxic inhibitors of RabGGTase (IC₅₀: 42nM for the example shown; red O, blue N, yellow S)

Full text of DOI:10.1002/anie.201101210

DOI: 10.1002/anie.201101210
Inhibitor Design
Structure-Guided Development of Selective RabGGTase Inhibitors**
Robin S. Bon, Zhong Guo, E. Anouk Stigter, Stefan Wetzel, Sascha Menninger, Alexander Wolf,
Axel Choidas, Kirill Alexandrov, Wulf Blankenfeldt, Roger S. Goody, and Herbert Waldmann*
Rab guanosine triphosphatases (GTPases) are key players in
the regulation of eukaryotic intracellular trafficking events
such as the formation, motility, targeting, and docking of
vesicles.[1] The reversible association of Rab GTPases with
intracellular membranes and other proteins is essential for
their function, and is mediated by geranylgeranyl (GG)
group(s) covalently attached to C-terminal cysteine residues.
This modification, known as prenylation, is mediated by the
enzyme Rab geranylgeranyl transferase (RabGGTase) in
concert with the accessory Rab escort protein (REP).[2]
The overexpression of RabGGTase and its substrates such
as Rab5a, Rab7, and Rab25 in several cancer types[3] and the
finding that RabGGTase inhibition leads to p53-independent
apoptosis[4] validate RabGGTase as a promising anticancer
target. Whereas numerous inhibitors of the related CaaX
prenyl transferases, farnesyl transferase (FTase),[5] and ge-
ranylgeranyl transferase I (GGTase I)[6] have been developed
and have even reached clinical trials,[7] in most cases their
cellular targets are not known with certainty. Very few
RabGGTase inhibitors are known to date,[8] many of which
are either nonselective with respect to FTase or show only
moderate inhibition of cellular Rab prenylation.
The most potent of the currently available RabGGTase
inhibitors, BMS3, was originally designed as an FTase
inhibitor.[4] Since BMS3 lacks selectivity with respect to
FTase, both in vitro[4] and in cells,[9] its pro-apoptotic effect
could only be attributed to RabGGTase inhibition indirectly.
Selective inhibitors of RabGGTase would be valuable for
analysis of the effects of selective inhibition of Rab trafficking
on the proliferation of transformed cells, for the elucidation of
side effects related to FTase inhibition, and, in general, for the
analysis of Rab-mediated cellular processes. With these goals
in mind, we chose to generate cocrystal structures of
RabGGTase and FTase with BMS3 and use this structural
information to design RabGGTase-specific inhibitors.
Herein we report the structure-guided design of selective
RabGGTase inhibitors with potent cellular activities. The
inhibitors target the RabGGTase-specific tunnel adjacent to
the GGPP binding site (TAG tunnel), which was recently
found in a cocrystal structure of an RabGGTase-peptide-
based inhibitor.[8b] Since this TAG tunnel is a unique feature
that distinguishes RabGGTase from FTase and GGTase I, it
provides a rational molecular basis to achieve selectivity.
To enable rational design of the inhibitor, we synthesized
BMS3, soaked it into both RabGGTase and FTase, and solved
the binary RabGGTase:BMS3, the ternary RabGGT-
ase:BMS3:GGPP, and the ternary FTase:BMS3:FPP cocrys-
tal structures (Figure 1).
[*] Dr. R. S. Bon,[+] E. A. Stigter,[+] Dr. S. Wetzel, Prof. Dr. H. Waldmann
Max-Planck-Institut fꢀr molekulare Physiologie
Abt. Chemische Biologie
Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
and
TU Dortmund, Fakultꢁt Chemie, 44227 Dortmund (Germany)
Fax: (+49)231-133-2499
E-mail: herbert.waldmann@mpi-dortmund.mpg.de
Dr. Z. Guo,[+] Prof. Dr. K. Alexandrov, Dr. W. Blankenfeldt,
Prof. Dr. R. S. Goody
Max-Planck-Institut fꢀr molekulare Physiologie
Abt. Physikalische Biochemie
Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
Dr. S. Menninger, Dr. A. Wolf, Dr. A. Choidas
Lead Discovery Center GmbH
Emil-Figge-Strasse 76a, 44227 Dortmund (Germany)
Dr. R. S. Bon[+]
Current address: School of Chemistry and Biomedical and Health
Research Centre, University of Leeds, Leeds, LS2 9JT (UK)
Dr. S. Wetzel
Current address: Quantitative Biology, Developmental and Molec-
ular Pathways, Novartis Institutes of Biomedical Research
Basel (Switzerland)
Dr. Z. Guo,[+] Prof. Dr. K. Alexandrov
Current address: Institute for Molecular Bioscience
The University of Queensland, Brisbane, Queensland (Australia)
Dr. W. Blankenfeldt
Current address: University of Bayreuth, Bayreuth (Germany)
[+] These authors contributed equally.
The binding modes and conformations of BMS3 in these
structures are highly similar. In both enzymes the imidazole
ring coordinates to the catalytic zinc ion, whilst the phenyl
ring of the tetrahydrobenzodiazepine (THB) core p stacks
with the Tyr361 or the Phe289 residue. The 3-benzyl moiety
extends toward the lipid binding sites in both enzymes and is
involved in extensive T stacking with hydrophobic residues of
the enzymes (Figure 1). These common interaction patterns
result in the twisted form of the central 3-benzyl-THB unit
that is observed in both enzymes. The anisylsulfonyl sub-
stituent adopts a pseudoaxial position and is involved in
internal p-stacking interactions. In RabGGTase, an additional
[**] We thank the X-ray communities of the Max-Planck-Institut fꢀr
molekulare Physiologie (Dortmund, Germany) and the Max-Planck-
Institut fꢀr medizinische Forschung (Heidelberg, Germany) for
collecting diffraction data at the Swiss Light Source of the Paul
Scherrer Institute (Villigen, Switzerland) and for giving us generous
access to and support with station X10SA. This work was supported
in part by DFG grants to H.W. and R.S.G. (grant no.: SFB642), and
by the Zentrum fꢀr Angewandte Chemische Genomik. R.S.B. thanks
the Alexander von Humboldt Stiftung for a fellowship. E.A.S thanks
the IMPRS-CB for a PhD scholarship.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201101210.
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Communications
and decided to retain it to ensure the positive internal p-
stacking interaction.
Since the TAG tunnel is a unique feature of RabGGTase,
the introduction of moieties larger than the nitrile at
position B were expected to fit well in to the RabGGTase
TAG tunnel but would clash with the FTase surface.
Furthermore, we envisioned that hydrogen-bond acceptors
would interact with the nearby Tyr30 (see also Figure S2b in
the Supporting Information).
The 3-benzyl group of BMS3 approaches the lipid binding
sites (LBSs) of both enzymes. In FTase, the bulky Trp102,
which ensures the selectivity for FPP over GGPP, is close to
the 3-benzyl moiety and is involved in T-stacking interactions.
In RabGGTase, this tryptophan residue is replaced by a small
serine residue and, therefore, forms a larger binding cavity
(see Figure S2a in the Supporting Information). We predicted
that the introduction of larger groups at position A (Fig-
ure 1c) would result in selectivity for RabGGTase over FTase
as a result of an expected steric clash with Trp102.
Thus, we envisioned that extension of BMS3 at posi-
tions A and B (Figure 1c) would lead to selective inhibitors of
RabGGTase. A virtual high-throughput screening (VHS) was
conducted to identify promising substituents.[11] The virtual
library was enumerated by decorating the core scaffold with
different substituents at positions A and B, and was screened
with both enzymes (for details, see the Supporting Informa-
tion). The docking scores were compared, and compounds
that gave good results for RabGGTase and poor results for
FTase were selected. These promising candidates were
evaluated further, prioritized by individual docking, and
selected for synthesis.
Two general building blocks, 3a and 3b, were synthesized
according to modified literature procedures.[10] A condensa-
tion of 5-bromoisatoic anhydride (1) and d-tyrosine methyl
ester resulted in the benzodiazepine core, with the phenolic
hydroxy group and the bromo substituents introduced as
versatile synthetic handles for modification (Scheme 1).
Subsequent reduction with borane afforded 2a, and a
subsequent copper-catalyzed cyanation resulted in 2b. Selec-
tive N-sulfonylation with 4-methoxybenzenesulfonyl chloride
in pyridine and reductive amination with 4-imidazocarbox-
Figure 1. Cocrystal structures of BMS3: a) Surface representation of
the active site of the BMS3:RabGGTase:GGPP complex (PDB access
code: 3PZ2). The imidazole ring coordinates to the zinc ion, whereas
the sulfonamide forms hydrogen bonds with Tyr44. The 3-benzyl
moiety interacts with Trp52 and Phe289 by T stacking, whereas the
tetrahydrobenzodiazepine (THB) moiety p stacks with Phe289. The
conformation is further stabilized by internal p stacking of the THB
with the anisolylsulfonyl group. The nitrile points toward the TAG
tunnel. The orientation of BMS3 in the binary complex BMS3:Rab-
GGTase is depicted in brown lines (PDB access code: 3PZ1). The
black dashed lines indicate interactions between the ligand and the
enzyme. b) Surface representation of the active site of the BMS3:FTa-
se:FPP complex (PDB access code: 3PZ4); the imidazole ring coordi-
nates to the zinc ion. The 3-benzyl moiety interacts with Trp102 and
Trp106 by T stacking. The THB moiety interacts with Tyr361 and is
further involved in internal p stacking with the anisylsulfonyl group,
which is mainly exposed to solvent. The black dashed lines indicate
interactions between the ligand and the enzyme. c) Schematic repre-
sentation of the common binding modes of BMS3 in Figure 1a and b.
hydrogen-bond interaction is formed between the sulfonyl
group and Tyr44, whereas this group is mostly solvent exposed
in FTase. In RabGGTase:BMS3:GGPP, the nitrile group of
BMS3 is close to the TAG tunnel, whereas this group is close
to the protein surface in FTase:BMS3:FPP, where it is merely
involved in dipolar interactions with hydrophobic residues.
The shared binding interactions are reflected in similar
inhibition data for FTase and RabGGTase, as reported in
the literature (in vitro radiometric assay: IC50 = 1.4 nm and
16 nm, respectively[4] and inhibition of cellular prenylation:
Ki = 7 nm and 50 nm, respectively[9]). These data confirm that
BMS3 is a highly potent dual inhibitor of FTase and
RabGGTase.
To obtain selective RabGGTase inhibitors, we considered
several structure-guided modifications of BMS3. We decided
to keep the anisylsulfonyl and imidazole substituents of
BMS3 in our analogues. The imidazole was kept because it
represents the crucial zinc binding group. The anisylsulfonyl
moiety was already shown to be highly variable in FTase
without leading to significant changes in activity,[10] whereas
this group is involved in hydrogen bonding to Tyr44 in
RabGGTase. Therefore, we expected to observe no signifi-
cant gain in selectivity for RabGGTase by varying this group,
Scheme 1. Synthesis of general building blocks. a) d-Tyr-OMe·HCl,
DMAP, pyridine, 3 days, reflux; b) BH3 in THF, 16 h, reflux (62%,
2 steps); c) CuCN, DMF, 0.5 h, microwaves 2108C (67%); d) 4-
methoxybenzenesulfonylchloride, pyridine, 16 h, RT (61–71%); e) N-
methylimidazole-5-carboxaldehyde, TFA, TFAA, Et3SiH, CH2Cl2, 16 h,
RT (80–83%). DMAP=4-dimethylaminopyridine, TFA=trifluoroacetic
acid.
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aldehyde in the presence of trifluoroacetic anhydride (TFAA)
as a water scavenger[12] resulted in building blocks 3a and 3b
in 38 and 26% overall yield, respectively. Substituents meant
to target the hydrophobic binding pocket (R2) were attached
by alkylation or aminocarbonylation, (Scheme 2, com-
pounds 4–7). Groups meant to target the TAG tunnel (R1)
were introduced by substitution of the aryl bromide under
Suzuki coupling conditions (Scheme 2, compounds 8–12) in
30–80% overall yield and high purity.
expected clash with Trp102 in the LBS of FTase resulted in
a one–threefold decrease in FTase inhibition, but did not lead
to a loss of activity. Therefore, it is likely that the inhibitors
and/or FTase adapt their binding conformation to the newly
introduced moieties.
Modification at R1 showed a sharper inhibition profile.
Whereas 9 and 10 showed moderate to good RabGGTase
inhibitory activity, 8 showed very poor inhibition. The 4-
chlorophenyl substituent could result in a clash with the
RabGGTase surface, if it is assumed that the THB–core
binding mode is very rigid (Figure 2a). This clash was
Scheme 2. Modification of 3a,b.
Figure 2. a) Individual docking results of 8 as well as an overlay with
the structure of BMS3:RabGGTase:GGPP. Assuming a rigid THB–core
binding arrangement, the para-chlorophenyl group cannot adjust its
position toward the TAG tunnel, and clashes with the binding pocket.
b) Cocrystal structure of 14:RabGGTase (PDB access code: 3PZ3); the
furanaldehyde substituent is located in the entrance of the TAG tunnel,
but does not show the expected hydrogen-bond interaction with Tyr30.
The benzylcarbamate group is situated in the LBS and T stacks with
Phe147. The 3-benzyl moiety is reoriented and T stacks with Trp244.
The black dashed lines indicate interactions between the ligand and
the enzyme.
The collection was screened using fluorometric FTase[13]
and RabGGTase assays.[14] These fluorometric assays are
continuous and less-laborious alternatives to the correspond-
ing radioactivity-based assays. For BMS3, we determined an
IC50 value of 724 nm for RabGGTase and an IC50 value of
6 nm for FTase (Table 1). The pronounced difference in
IC50 values for these enzymes compared to previously
reported values from radiometric assays[4] is related to the
use of artificial fluorescent substrates in these assays. There-
fore, we introduced the improvement factor (IF) to indicate
the improvement in selectivity for RabGGTase, compared to
the dual inhibitor BMS3 (see above). In addition IC50 values
for GGTase I were measured to evaluate the selectivity of our
THB-based inhibitors with respect to all three prenyl trans-
ferases.
successfully circumvented by the introduction of a slightly
smaller five-membered ring, which indeed resulted in an
increase in selectivity. Although an increase in selectivity was
reached by modifying one side of BMS3 (4–7, 9–11), and
variation of R2 contributed more to a gain in selectivity than
did variation of R1, the single modifications we explored did
not result in full selectivity. However, the combination of
modification III or IV and A resulted in fully selective
RabGGTase inhibitors 14 and 15.
As expected on the basis of VHS, modification at R2 led to
a general increase in selectivity for RabGGTase. The
The RabGGTase:14 cocrystal structure shows that 14
binds in a mode similar to BMS3, with the imidazole ring
coordinating to the catalytic zinc ion and the THB core of 14,
although it is slightly twisted compared to BMS3. It also
p stacks with Phe289. In agreement with the predictions from
docking studies, the benzyl carbamate occupies the lipophilic
substrate binding site of RabGGTase, while the furanal
substituent approaches the TAG tunnel. The arrangement of
the benzylcarbamate in the LBS results in an extra T stacking
to Phe147, as well as a conformational change of the 3-benzyl
substituent, which now T stacks with Trp244 instead of with
Phe289 and Trp52. Surprisingly, the aldehyde moiety is not
involved in a hydrogen-bonding interaction with Tyr30, but
points into the TAG tunnel.
Table 1: In vitro activity of the THB library.
Cmpd R1 R2 RabGGTase IC50
FTase
IC50 [nm] IC50 [nm]
GGTase I IF[a]
[nm]
BMS3 CN
H
A
B
C
D
724Æ321
72Æ2
6Æ3
<5[b]
<5[b]
10Æ7
15Æ8
>99500
>99500
1
<8
4
5
6
7
CN
CN
CN
CN
I
38Æ7
2020Æ384 <16
162Æ10
39Æ10
>99500
>99500
7
46
8
OH >9500
OH 1302Æ478
194Æ78 >99500
<2
4
9
II
42Æ10 >99500
10
11
12
13
14
15
III OH 206Æ13
7Æ3
>99500
>99500
4
25
IV OH 63Æ2
13Æ3
II
II
III
IV
A
C
A
A
2264Æ844
6515Æ1839
141Æ26
123Æ24 >99500
>9700 >99500
>9700 >99500
>9700 >99500
7
>180
>8301
>27868
42Æ13
To determine whether the compounds inhibit Rab pren-
ylation in cellular systems, cultured HeLa cells were incu-
bated with the inhibitors for 6 h and then lysed. The lysate was
subjected to in vitro reprenylation with recombinant RabGG-
[a] The improvement factor (IF) shows the relative increase in selectivity
for RabGGTase versus FTase compared to the original compound BMS3,
for which this value is 1 by definition. [b] Lower detection limit.
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Tase, REP, and biotin-GPP (a GGPP analogue), and then the
inhibitor, is also the most potent inhibitor of cancer cell
proliferation. The inhibition of cancer cell proliferation (both
Ras-transformed and non-Ras-transformed) by the highly
selective RabGGTase inhibitors 14 and 15 is in accordance
with the finding that RabGGTase siRNA, but not FTase
siRNA, induces increased apoptosis in C. elegans and A549
cells.[4] Therefore, these results emphasize that RabGGTase
should be considered an anticancer target.
In conclusion, by applying protein/inhibitor cocrystal
structure analysis, VHS, individual docking, and synthesis
we have identified potent and selective RabGGTase inhib-
itors that inhibit proliferation of several cancer cell lines
without displaying cytotoxicity in PBMC cells. Guided by the
well-defined binding mode and conformation of BMS3 in
RabGGTase and FTase in the cocrystal structures, we have
shown that it is possible to make BMS3 analogues that are
selective for RabGGTase. This has been achieved by exploit-
ing recently identified structural features of the RabGGTase
active site such as a combination of the TAG tunnel and lipid
binding site. These results also indicate that RabGGTase-
THB cocrystal structures might be a valuable starting point
for more extensive structure-based design of selective
RabGGTase inhibitors, for example by using computational
methods based on fragment docking and growing/linking
approaches.
Rab-biotin-GPP conjugates were detected by Western blot-
ting (see the Supporting Information).[9] Compounds 4–7, 9–
11, 14, and 15 all caused increased labeling of endogenous
Rab proteins with biotin-GPP, thus indicating inhibition of
cellular prenylation, with IC50 values in the nanomolar range
(Table 2).[15] Furthermore, the cellular IC50 values roughly
follow the in vitro data, thus indicating that the modifications
did not significantly affect the bioavailability. As expected,
compound 8, which was inactive in vitro, did not inhibit
cellular Rab prenylation.
Table 2: Reprenylation assay results of THB library compounds.
Cmpd Reprenylation rel. IC50
Cmpd Reprenylation rel. IC50
[nm][a]
[nm][a]
BMS3 74Æ34
9
201Æ78
93Æ42
11Æ5
4
5
6
7
8
81Æ32
343Æ29
307Æ40
43Æ12
>30000
10
11
14
15
311Æ193
49Æ32
[a] For the calculation of relative IC50 values, the signal obtained from the
positive control (1 mm BMS3, which gives a saturated reprenylation
signal) was set as 100% RabGGTase inhibition.
Received: February 17, 2011
Published online: April 21, 2011
Next, we studied the effect of several inhibitors on the
viability of mammalian cancer cell lines and peripheral blood
mononuclear cells (PBMC; Table 3). In these experiments,
cultured cells were incubated with a THB for 72 h, followed
by incubation with resazurin. Viable cells reduce resazurin to
the fluorescent resorufin. Therefore, fluorescence intensity is
a measure of cell viability.[15]
Keywords: antitumor agents · drug design · inhibitors ·
.
protein modification · transferases
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A2780
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63Æ8
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>10000
>10000
>10000
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