Breaking the dogma of the metal-coordinating carboxylate group in integrin ligands: Introducing hydroxamic acids to the MIDAS to tune potency and selectivity

Full text of DOI:10.1002/anie.200900206

Communications
DOI: 10.1002/anie.200900206
Integrin Ligands
Breaking the Dogma of the Metal-Coordinating Carboxylate Group in
Integrin Ligands: Introducing Hydroxamic Acids to the MIDAS To
Tune Potency and Selectivity**
Dominik Heckmann, Burkhardt Laufer, Luciana Marinelli, Vittorio Limongelli,
Ettore Novellino, Grit Zahn, Roland Stragies, and Horst Kessler*
The inhibition of cell adhesion by integrin ligands is a
promising target for drug design. All integrins contain a
metal-ion-dependent adhesion site (MIDAS), in which the
metal ion is coordinated through five of six possible coordi-
nation sites. The extracellular matrix ligand provides the sixth
binding site, for example the carboxyl group of an aspartic
acid in the well-known RGD tripeptide sequence. So far all
proteins and small peptidic and non-peptidic ligands have
contained a carboxyl group for the metal-ion binding. All
attempts to mimic this carboxyl group by “isosteric” groups
have failed so far. Herein, we report that hydroxamic acids
can be used successfully for this purpose, and that the binding
affinity of the new ligands is retained or modulated. This is of
special importance because the carboxyl group, which is
ionized under neutral pH conditions, accounts for a strong
barrier in the pharmaco-dynamic behavior of the integrin
ligands. In contrast, hydroxamic acids are not ionized under
the same conditions.
Integrins constitute a family of heterodimeric, transmem-
brane, bidirectional adhesion receptors, which connect cells to
the scaffolding proteins of the extracellular matrix.[1] Dis-
turbance of integrin function is connected to a large variety of
pathological processes such as thrombosis,[2] cancer,[3] osteo-
porosis,[4] and inflammation,[5] which makes integrins attrac-
tive targets for pharmacological research. Of the 24 different
heterodimers known, the integrins avb3, avb5, and a5b1 have
attracted particular interest: They are key factors of angio-
genesis (the formation and maturation of new blood vessels),
a process that plays an important role in tumor progression
and metastasis.[3,6] The natural ligands of the three integrins
share the common tripeptidic recognition motif arginine–
glycine–aspartate (RGD).[7] The fact that particular integrins
are able to selectively bind different spatial presentations of
one binding motif along with their great medical relevance
has inspired researchers to design a vast number of different
peptidic and non-peptidic integrin ligands.[8] As an example,
the potent avb3 ligand, the cyclic peptide Cilengitide[9]
(cyclo(RGDfNMeV)) is currently in phase III clinical trials
for patients with glioblastoma multiforme, while the pepti-
domimetic aIIbb3 binder Tirofiban[10] is an approved anti-
coagulant drug. However, the application of RGD-based
drugs is hampered by their poor pharmacological properties,
which may to some extent be the result of the zwitterionic
nature of the RGD motif. Recent research efforts have
focused on improving the pharmacological parameters mainly
by altering the polarity and rigidity of the scaffold and the
nature of the basic moiety and through the synthesis of
prodrugs.[11]
While the guanidine group of the arginine has been
replaced by countless basic heterocycles during the develop-
ment of peptidomimetics, the carboxylic acid function of the
aspartate is the most conserved feature of all known integrin
ligands up to now. Indeed, to our knowledge, the successful
replacement of the carboxylic acid moiety has never been
reported. The acid is involved in the crucial coordination of
the bivalent metal cation at the MIDAS site, which is present
in all integrins.[12] Although the metal ion has not yet been
identified (Ca2+, Mg2+, and Mn2+ are under discussion), the
importance of the cation–carboxylate interaction is indisput-
able.[13] In our previous research we could demonstrate how
the selectivity between the integrins a5b1 and avb3—the
most important integrins in angiogenesis—can be switched in
either direction by changing the ligand length and altering
sterically demanding moieties close to the metal-coordination
site.[14] Even though this site seems to be very sensitive
towards modifications—several attempts to replace the
carboxylate by tetrazole or sulfonic acids failed in the
past—we thought about alternatives to a carboxylic acid
that would lead to another binding mode and thus to an
alteration in the selectivity profile.
[*] Dr. D. Heckmann,[+] M. Sc. B. Laufer,[+] Prof. Dr. H. Kessler
Institute for Advanced Study, TU Mꢀnchen, Department Chemie
Lichtenbergstrasse 4, 85747 Garching (Germany)
Fax: (+49)89-2891-3210
E-mail: kessler@ch.tum.de
Prof. Dr. L. Marinelli, Dr. V. Limongelli, Prof. Dr. E. Novellino
Dipartimento di Chimica Farmaceutica e Tossicologica
Universitꢁ di Napoli “Federico II”
Via D. Montesano, 49-80131 Napoli (Italy)
Dr. G. Zahn, Dr. R. Stragies
Jerini AG
Invalidenstrasse 130, 10115 Berlin (Germany)
[+] These authors contributed equally to this work.
[**] The authors gratefully acknowledge financial support from the
Deutsche Forschungsgemeinschaft (SFB 563), the Center for
Integrated Protein Science Munich (CIPSM), and the International
Graduate School for Science and Engineering (IGSSE) and technical
assistance by M. Wolff, B. Cordes, J. Thielmann, and Dr. W. Spahl.
We investigated hydroxamic acids, which seemed promis-
ing candidates as they can coordinate metals in a bi- or
monodentate fashion depending on the environment, and in
fact they are known to coordinate many different metal
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200900206.
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Chemie
ions.[15] We first examined the ligands 2 (see Scheme 1) as
proof of principle (2a: IC50: 60 nm for a5b1 and 131 nm for
avb3) and observed that for 2c the IC50 towards a5b1
increased to 6700 nm, while the corresponding value for avb3
decreased to 53 nm. These findings motivated us to system-
atically elucidate the potential of hydroxamic acids as integrin
ligands as well as the structural and electronic aspects of the
observed selectivity. In our previous studies we found that the
spatial orientation of the aromatic moiety in the vicinity of the
carboxylic acid determines the selectivity of the ligand; a
mesitylene carboxamide unit led to a5b1 selectivity, while a
sulfonamide group yielded biselective ligands.[14b–d] We were
expecting that the replacement of the carboxylate by a
hydroxamate should have a high impact on the positioning of
this group, so six pairs of ligands, all containing a 2-amino-
yridine group as the basic moiety, were synthesized and
evaluated for their activity and selectivity profile. Further-
more, we prepared the hydroxamate analogue of an avb3
selective ligand based on an elongated b-homotyrosine. We
also preapared another compound library based on a lead
structure comprising a tetrahydropyrimidine as the basic
moiety and a benzosulfonamide substituent, which was
previously found to give ligands with high affinity for avb3
and moderate affinity for a5b1.[14b,c] Variations of the
carboxylic acid function including an ester, amide, acylhy-
drazine, and N-methyl hydroxamic acid should reveal,
whether other carboxylic acid derivatives lead to changes in
affinity and selectivity comparable to hydroxamic acids.
The synthesis of all the ligands started from known
precursors (1, 3, 4, and 11).[14b,c] After Boc removal with
diluted aqueous HCl in dioxane, the resulting amines were
acylated with either aromatic carboxylic acids or aromatic
sulfonyl chlorides according to the desired selectivity profile.
While saponification of the methyl ester with LiOH in
methanol/water gave the carboxylic acids, a feasible way to
prepare the corresponding hydroxamic acids was the addition
of an excess of hydroxylamine to the saponification mix-
ture.[16] A previously examined procedure, the KCN-catalyzed
aminolysis of methyl esters (11!12b; see Scheme 2), was
abandoned because of lower yields and longer reaction times.
In contrast to the other hydroxamic acid ligands, 2b was
prepared by coupling of the free acid to O-benzylhydroxyl-
amine followed by hydrogenolysis. This reaction was found to
be difficult to control as sometimes overreduction to the
amide takes place, and it was therefore also not applied in the
synthesis of other hydroxamate ligands (Scheme 1). The
second series of ligands started from precursor 11, which was
transformed into the derivatives 12a–f (Scheme 2). All
ligands were purified by reverse-phase HPLC and evaluated
in an enzyme-linked immunosorbent assay (ELISA) using the
immobilized natural integrin ligands fibronectin and vitro-
nectin and the soluble integrins a5b1 and avb3, respectively.
Computational studies were performed to understand the
selectivity of the inhibition of avb3 or a5b1 integrin receptors
by ligands 5–9. Table 1 shows that the different metal-
coordinating groups together with the bulky substituent in
the a position are the major determinants for the inhibitory
activity as well as for the receptor selectivity. Thus, to address
this issue, the inhibitors were automatically docked, with the
Scheme 1. Synthesis of hydroxamic acid and carboxylic acid ligands 5–
10. Reagents and conditions: a) HCl/H2O/dioxane; then b) PhCOCl,
NaHCO3, THF/H2O, or MesCOOH, HATU, DIPEA, DMF, or ArSO2Cl,
DIPEA, DMF; c) LiOH, MeOH/H2O (acids) or LiOH, NH2OH (aq.),
MeOH/H2O (hydroxamates). All compounds were purified by RP-
HPLC using MeCN/H2O + 0.1% TFA as eluent. For reaction details
and analytical data see the Supporting Information. Bn=benzyl,
Boc=tert-butoxycarbonyl, DIPEA=diisopropylethylamine, HATU=2-
(1H-7-azabenzotriazo-1-yl)-1,1,3,3-tetramethyluronium hexaphosphate,
Mes=2,4,6-trimethylphenyl, TFA=trifluoroacetic acid.
Scheme 2. Synthesis of ligands 12a–f. Reagents and conditions:
a) HCl/dioxane; b) PhSO2Cl, DIPEA, DMF; c) H2/Pd/C, MeOH;
d) KCN, NH2OH, MeOH/H2O; e) LiOH, MeOH/H2O; f) Rink amide
resin, TBTU, HOBt, DIPEA, NMP, then 95% TFA; g) NH2NHBoc,
TBTU/HOBt, DMF; h) LiOH, NHMeOH, MeOH/H2O. For reaction
details and analytical data see the Supporting Information. HOBt=1-
hydroxy-1H-benzotriazole, NMP=N-methylpyrrolidinone, TBTU=2-
(1H-benzotriazo-1-yl)-1,1,3,3-tetramethyluronium tetrafluoroborate.
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Communications
Table 1: IC50 values of integrin ligands for a5b1 and avb3.
Cmpd
R2
n
R1
IC50 [nm]
a5b1[a]
IC50 [nm]
avb3[a]
5a
5b
-OH
-NHOH
243
2470
207
14
0
0
6a
6b
-OH
-NHOH
2.5
1244
703
72
7a
7b
-OH
-NHOH
284
296
1.9
11
0
0
8a
8b
-OH
-NHOH
46
132
3.4
4.8
9a
9b
-OH
-NHOH
1
40
279
13.5
0
1
Figure 1. Structure of 9a (pink) docked in the a5b1 integrin binding
pocket. The a5 and b1 subunits are represented by the yellow and
green surfaces, respectively. In both subunits the amino acid side
chains important for the ligand binding are represented as sticks. The
metal ion in the MIDAS region is represented by a magenta sphere.
10a
10b
-OH
-NHOH
264
4500
1.2
12
[a] IC50 values were derived from competitive ELISA using the immobi-
lized natural integrin ligands fibronectin and vitronectin and the soluble
integrins a5b1 and avb3, respectively (for details see the Supporting
Information).
scaffold of 9a was found in proximity to (a5)-Phe187,
allowing the basic moiety to form a bifurcated salt bridge
with the highly conserved (a5)-Asp227. Clearly, all of these
interactions are responsible for the subnanomolar activity of
9a towards the a5b1 receptor, while its decreased affinity
(1000-fold) for avb3 has been previously attributed by us to
the steric clashes between the isopropyloxyphenyl moiety of
9a and the (b3)-Arg214 side chain.[14b,c]
aid of AutoDock4 (AD4), in our published homology model
of the a5b1 integrin[14a] and in the X-ray structure of the avb3
receptor in complex with Cilengitide (PDB code: 1L5G)[17]
after removal of the cocrystallized inhibitor. As the docking
results using AD4 with the default charges (Gasteiger) on the
ligands and the protein were not entirely satisfactory in
reproducing the coordination geometry of the metal-coordi-
nating groups, we performed preliminary ab initio calcula-
tions on the manganese ion in the MIDAS region, on its
coordinating amino acids (Mn subsite), and on the ligands
themselves (see the Supporting Information for details). The
charges obtained through these calculations were used to give
a more accurate reproduction of the experimental binding
geometry of Cilengitide, and this was a prerequisite for the
docking of compounds 5–9.
According to our docking results, compound 9a coordi-
nates the metal ion in integrin a5b1 with one of the two
oxygens of the carboxylate group, while the other forms a
hydrogen bond with the backbone NH group of (b1)-Asn218;
this coordination mode is similar that of the Cilengitide
carboxylic group in the X-ray crystal structure (Figure 1). The
isopropyloxyphenyl moiety fits well in the b1 region where it
is involved in a p–p interaction with (b1)-Tyr127 (distance
between the centroids of the rings: 6.1 ꢀ). In this arrange-
ment, the p-isopropyloxy group is in proximity to the (b1)-
Ser171 side chain (distance between the two oxygens: 3.6 ꢀ),
which protrudes from the (b1)-SDL (specificity-determining
loop), and a hydrogen bond is likely formed. The tyrosine
Interestingly, in the docking the hydroxamic acid ana-
logue 9b into avb3, either a bidentate (O,O)-chelating mode
or a monodentate (O)-coordination mode were found.
However, unexpectedly, the bidentate (O,O)-chelating
mode, which is most commonly observed in biological
systems, is rarely found in our docking study and did not
result in any reasonable binding mode. Indeed, if a bidentate
(O,O)-chelating mode is considered, owing to the shape of the
binding site and the presence of (b3)-Ser121, (b3)-Glu220,
and (b3)-Ser123, which directly coordinate the metal in the
MIDAS, the basic moiety of the ligand cannot be properly
inserted into the narrow groove at the top of the propeller
domain of av, where contacts with (b3)-Asp218 and/or (b3)-
Asp150 are expected to occur. In contrast, one of the
monodentate coordination modes calculated by the AD4
program, was highly meaningful; it positioned the ligand in a
proper manner to form a p–p interaction with the (av)-Tyr178
(through its tyrosine scaffold), a hydrophobic interaction with
the (b3)-Tyr122 through the isopropyloxyphenyl moiety, and
also a bifurcated salt bridge between the basic moiety and the
(av)-Asp218, in addition to the coordination of the metal in
the MIDAS region (Figure 2).
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Figure 2. Structure of structure of 9b (blue) docked in the avb3
integrin binding pocket. The av and b3 subunits are represented by
the yellow and green surfaces, respectively. In both subunits the amino
acid side chains important for the ligand binding are represented as
sticks. The metal ion in the MIDAS region is represented by a magenta
sphere.
Figure 3. Superposition of the binding mode of 9b (blue) docked in
avb3 and that of 9a (pink) docked in a5b1. For clarity only the surface
of a5b1 is shown.
previous docking experiments indicated that the presence of
the sulfonamide allows the mesitylene group to fold back
towards the a subunit endowing the ligand an inhibitory
activity toward both receptors. The slightly higher activity of
8a for avb3 can be attributed to polar contacts between the
sulfonamide oxygens and the guanidine group of (b3)-
Arg214. Consequently, the hydroxamate analogue 8b has a
lower affinity for the a5b1 integrin than its carboxylate
analogue 8a, and the reason again seems to reside in the
greater distance between the metal-coordinating oxygen and
the basic moiety. Regarding the selectivity profile of com-
pound 8b, an issue similar to that of compound 9b can be
assumed.
To investigate whether other derivatives of carboxylic
acids and hydroxamic acids are capable of integrin binding,
we compared six different C termini of one ligand, which was
supposed to display high avb3 activity in its carboxylic acid
form 12c. Table 2 shows the outstanding high affinity of the
hydroxamic acid 12b in contrast to the other derivatives.
Remarkably, despite their reduced acidity [(pKa(N-hydroxy-
acetamide) = 9.40 compared to acetic acid (4.76)],[18] the
hydroxamates are still able to complex the metal ion
efficiently. The low affinity of 12e is the result of the
replacement of the MIDAS-binding oxygen by a hydrazone
NH2 group with poor coordination properties; an even more
drastic effect can be observed for the amide 12d. Similar to
12e, residual binding affinity can still be observed for the
methyl ester 12a. The sensitivity of the binding mode towards
additional substituents is demonstrated by the low affinity of
the N-methylated hydroxamic acid 12 f.
The results shown in Table 1 outline that in 9a the
replacement of the carboxylic group by the hydroxamate
moiety allows 9b to regain the activity for avb3 receptor. If
the binding mode observed for 9a (in a5b1, Figure 1) is
superimposed on that of 9b (in avb3, Figure 2), a down-
shifting of the isopropyloxyphenyl moiety is observed for the
hydroxamate derivative (Figure 3), which would account for
the activity for avb3. Moreover, as a result of the structural
difference between the carboxylic and the hydroxamic acids
(the latter has a larger distance between the two oxygen
atoms), the distance between the metal-coordinating oxygen
and the bulky substituent in the a position is greater in 9b
than in 9a. As a consequence, the coordination made by the
hydroxamate compound 9b allows a shifting of the isopropy-
loxyphenyl moiety towards the a subunit and an orientation
that allows the isopropyloxyphenyl group to form hydro-
phobic interactions with (b3)-Tyr122 (Figure 3). Another
intriguing point is the inverted selectivity of compound 9b
with respect to 9a. In fact, compound 9b slightly prefers
inhibiting the avb3 receptor over the a5b1 receptor. Accord-
ing to our results, this is a consequence of the increased
distance between the acidic and the basic groups, as a result of
the presence of the hydroxamate moiety in 9b (see above). In
fact, in line with our recently published results,[14b,c] the
mutation of (av)-Thr212 to (a5)-Gln221 in the a5b1 receptor
reduces the space available for the binding of the ligandꢁs
basic moiety, and, consequently, compounds with shorter
chains are preferred to bind to the a5b1 receptor. Accord-
ingly, compound 10b, whose length is increased by one
methylene group in addition to the hydroxamate, additionally,
shows no activity for a5b1. Concerning compound 8a,
Based on a homology model of the integrin a5b1 and
previous studies on the structure–activity relationship, we
report the first replacement of the ubiquitous carboxylic acid
function in integrin ligands. Extensive modeling of the
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Cmpd
R
IC50 [nm] a5b1[a]
IC50 [nm] avb3[a]
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12a
12b
12c
12d
12e
12 f
-COOMe
-CONHOH
-COOH
-CONH2
-CONHNH2
-CONCH3OH
2366
85
79
419
5.3
4.2
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>20000
9000
5216
>1000
290
359
[a] IC50 values were derived from competitive ELISA using the immobi-
lized natural integrin ligands fibronectin and vitronectin and the soluble
integrins a5b1 and avb3, respectively (for details see the Supporting
Information).
MIDAS region of avb3 and a5b1 helped to determine the
binding mode of this new class of ligands and to rationalize
the observed selectivities for the integrin avb3. Our findings
break with the dogma of carboxylic acid functionalized RGD
mimetics and may yield novel lead structures for pharma-
ceutical research.
Received: January 13, 2009
Published online: April 2, 2009
Keywords: antitumor agents · hydroxamic acids ·
.
integrin ligands · molecular modeling · structure–
activity relationship
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