Current Topics in Medicinal Chemistry, 2007, 7, 33-62
33
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
Protein Secondary Structure Elements
Mª Jesús Pérez de Vega, Mercedes Martín-Martínez and Rosario González-Muñiz*
Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
Abstract: In view of the crucial role of protein-protein intercommunication both in biological and pathological processes,
the search of modulators of protein-protein interactions (PPIs) is currently a challenging issue. The development of
rational strategies to imitate key secondary structure elements of protein interfaces is complementary to other approaches
based on the screening of synthetic or virtual libraries. In this sense, the present review provides representative examples
of compounds that are able to disturb PPIs of therapeutic relevance, through the stabilization or the imitation of peptide
hot-spots detected in contact areas of the interacting proteins. The review is divided into three sections, covering mimetics
of the three main secondary structural elements found in proteins, in general, and in protein-protein interfaces, in
particular (α–helices, β–sheets, and reverse turns). Once the secondary element has been identified, the first approach
typically involves the translation of the primary peptide structure into different cyclic analogues. This is normally
followed by gradual decrease of the peptide nature through combination of peptide and non-peptide fragments in the same
molecule. The final step usually consists in the development of pertinent organic scaffolds for appending key functional
groups in the right spatial disposition, as a means towards totally non-peptide small molecule PPI modulators.
Keywords: Protein-protein interactions, secondary structure mimetics, α–helices, β–sheets, reverse turns, peptidomimetics,
cyclic peptides, non-peptide small molecules.
1. INTRODUCTION
Protein–protein interactions, by their crucial role in most
biological processes —from intercellular communication to
programmed cell death—, represent an important group of
targets for therapeutic intervention [1-6]. Many molecular
pathways rely on the formation of stable or dynamic protein
complexes, such as antigen–antibody interactions, the
organization of active sites of oligomeric enzymes or
receptors, by participating in regulatory processes —from
signal transduction, cell–cell contacts, electron transport
systems, to DNA synthesis—, and during the formation of
skeletal cellular structures. Therefore, many human diseases
can be associated to aberrant protein–protein interactions,
either through the loss of an essential interaction or through
the formation of a protein complex at an inappropriate
concentration, time or location [7-11].
A few years ago, protein–protein systems were considered high-risk targets, difficult to address with conventional
peptides, peptidomimetics and small-molecules due to the
relatively large interaction surfaces involved [4,5,7].
However, it might not be necessary for a protein-protein
modulator to cover the entire protein binding surface. In fact,
it is known that in many cases only small segments of the
interface contribute to high-affinity binding (“hot-spot”)
[7,12,13]. Therefore, it can be thought that cavities and
protuberances defined by these hot-spots might be filled up
or mimicked, respectively, by low molecular weight
molecules. In this respect, a lot of effort is being dedicated to
the dissection of protein interaction hot-spots, the
identification of motifs common to protein interaction
*Address correspondence to this author at the Instituto de Química Médica
(CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain; Tel: +34 91 562 20 00;
Fax: +34 91 564 48 53; E-mail: [email protected]
1568-0266/07 $50.00+.00
interfaces, to mapping protein–protein contact surfaces, and
hence to the search of external modulators [12-16]. Special
attention is being paid to a number of small domains present
in various proteins with different biological functions that
are recurrent in many protein-protein interactions. Among
them, we can cite as representative examples the SH2, SH3,
PDZ, WW, RGD, PTB and NPF domains [17].
Apart from antibodies, which can block protein–protein
interactions by sequestering different members of a protein
complex [18], the prevailing approaches for the discovery of
modulators of protein–protein interactions are the structurebased design and combinatorial methods (synthetic libraries
or virtual screening), as in classical medicinal chemistry
[19]. When the three-dimensional structure of protein
complexes is unknown the search of modulators normally
starts by the selection of peptide modulators, using phagedisplay or synthetic peptide libraries [20]. When key amino
acids of a protein–protein interface have been identified, the
search for optimal peptide modulators can be performed by
evaluating biased peptide libraries in which all peptides
include these key amino acids [21]. In general, combinatorial
chemistry and particularly structurally diverse smallmolecule libraries are being developed as primary efforts to
modulate cellular signaling by inhibiting, promoting, or
mimicking protein–protein interactions, as it is compiled in a
number of reviews [19,22-25].
Concerning design approaches, we can choose to graft
essential residues involved in binding on constrained
molecular scaffolds followed by structure-guided optimizations or, alternatively, to perform computer assisted virtual
screening from existing small-molecules data bases [26,27].
Efforts to mimic features of short hot-spot peptides in
extended or precise folded conformations have been quite
successful, and some reviews have been published to this
© 2007 Bentham Science Publishers Ltd.
34
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
respect [28-34]. In fact, all types of secondary structure
(helices, β–sheets, turns and random coil) have been found in
contact areas of interacting proteins, and all of them have
individually been identified as important hot-spots in
particular complexes, as illustrated in the following sections.
In this review, we highlight recent advances in secondary
structure peptidomimetics as modulators of a range of
biologically significant protein–protein interactions. First, we
describe some examples where the stabilization of reverse
turn conformations was a successful method to obtain
protein ligands. Next, we illustrate the relevance of
β–strands/β–sheets within certain protein–protein interactions and the opportunity of imitating these structural motifs
as pharmaceutical tools. In the final section, we discuss
about suitable ways to fix or to mimic α–helix
conformations to target some therapeutically relevant
proteins. In general, starting from peptide sequences
important in protein comp-lex interfaces, and after
fixing/stabilizing the corresponding structural secondary
elements through cyclization or by the incorporation of
suitable scaffolds, is a well suited approach to proteinprotein modulators. It is well known that cyclic peptide
analogues and peptidomimetics are advantageous in
comparison with their linear counterparts, due to reduced
conformational entropy for binding, and protection of amide
bonds from proteolytic degradation. In some cases, this
rational approach followed by the gradual decrease of the
peptide character has permitted the discovery of totally nonpeptide derivatives of interest.
2. APPROACHES TO GENERATE STABILIZED
REVERSE TURNS
Reverse turns have long been accepted as important
structural elements in biomolecular recognition, including
peptide-protein and protein-protein interactions [35]. It has
recently been described that over one hundred G protein
coupled receptors bind to their respective peptide/protein
ligands through turn motifs [36]. In a similar way, turn-like
hot-spots have been recognized within several proteinprotein interaction surfaces [35,37]. Sites for antigenantibody recognition, and posttranslational modifications
like phosphorylation, glycosilation, and hydroxylation are
also frequently within turns [35]. Reverse turns are the most
prevalent type of non-repetitive secondary structure element,
and can be defined as short peptide fragments that make
possible the reversal of the peptide or protein chain direction
[35]. Main turn types can be classified as α–, β– and γ–turns,
depending on the number of residues implicated in the bend
(five, four, and three, respectively), while the subtypes
within each category are defined by the φ and ψ dihedral
angles of central residues. Turns may or may not be
stabilized by an intramolecular hydrogen bond between the
CO group of residue i and the i+4 (α), or i+3 (β), or i+2 (γ)
amide NH. Due to their structural simplicity, we and other
groups started extensive research programs aimed at
developing secondary structure peptidomimetics of these
non-repetitive motifs, specially β–turns [38-46]. Several
general reviews provide interesting overviews on amino acid
derivatives and peptide-derived scaffolds that, when
incorporated into peptide sequences could induce or force
the adoption of turn-like conformations [47-55]. In this
González-Muñiz et al.
section we will just focus on key strategies followed to fix
turn structures in compounds designed to interfere within
therapeutically relevant PPIs. As mentioned above, the initial
approach usually consisted in the preparation of cyclic
peptides, followed by gradual reduction of the peptide
character to reach forward non-peptide compounds. Investigations in the integrin adhesion inhibitors field, neurotrophin
loop mimetics, and GRB2-SH2 domain-binding ligands were
selected to illustrate this section with representative
examples.
2.1. β–Turn-Based Peptidomimetics as Antagonists of
Integrins
Integrins (INs) are a large family of α/β heterodimeric
transmembrane glycoproteins that mediate cell-cell and cellextracellular matrix proteins adhesion, and participate in a
wide range of physiological processes, such as embryogenesis, haemostasis, and the immune response [56]. INs are
also implicated in many pathological events, including
inflammation, tumor cell invasion, angiogenesis and
metastasis. Based on this, researchers from both academic
and industrial laboratories are focusing on the development
of antagonists of integrins [57]. The initial efforts were
directed to RGD-containing peptide derivatives, because
most extracellular matrix proteins and desintegrins contain
the Arg-Gly-Asp (RGD) sequence as the common integrin
binding motif.
Kessler´s group has developed different series of cyclic
RGD-containing pentapeptides as highly active and selective
ligands for the αVβ3 integrin receptor. The prototype,
cyclo(RGDfV) (1, Figure 1), displayed strongly increased
binding affinity and selectivity with respect to the
corresponding linear peptide, and was able to suppress
tumor-induced angiogenesis. Compound 1 adopts a quite
well defined conformation in solution, characterized by a
βII’/γ–turn arrangement with D-Phe in the i+1 position of the
βII’–turn and Gly as the central residue of the reverse γ–turn,
an spatial arrangement that was in some way associated with
the bioactive conformation [58]. However, the incorporation
of local modifications, as the reduced amide bond in 2 or the
N-Me group in 3, led to important changes in the peptide
backbone conformation, while maintaining or even improving the antagonist activity, respectively. Thus, compound 2
exhibits the typical βII’/γ–turn conformation, but with the DPhe residue at the central position of the γ–turn [59]. In
aqueous solution, cyclopeptide 3 adopts a conformation that
is consistent with a fast equilibrium between two inverse
γ–turns at Arg and Asp and a γ–turn at Gly [60]. Further
reduction of the flexibility of 1 was achieved by
incorporating different turn mimetics, as in 4-11 [61,62].
From cyclic peptides 4-6, only the spiro-derivative 6 led to
the desired βII’/γ–turn conformation, while in compounds 4
and 5 the Gly residue occupied the i+1 position of the
βII’–turn, and the turn motifs were shifted to the i+3 and i+4
position. The RGD sequence in compound 7 arranges in an
ensemble of different conformations, probably due to the
flexibility of the alkene moiety. The structure-activity
relationships showed inhomogeneous results, with compounds showing similar conformation having very different
activity, and vice versa. These findings suggest that the
structure determined for these peptides in solution may differ
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
from the receptor bound conformation, which is probably
adopted upon binding by an induced fit. Another attempt to
match the steric demands of integrin receptors involved the
incorporation of sugar amino acids as β–turn mimetic
replacements of the D-Phe-Val fragment in the lead structure
c(RGDfV) [63]. As hoped, the sugar-modified cyclic peptide
8 exhibited high αVβ3 activity, but unexpectedly it also
displayed nanomolar affinity at the αIIbβ3 receptor. This was
explained by a dynamic behavior in which peptide 8 is
flexible enough to adopt the kinked and stretched
conformations characteristic of selective binding to αVβ3 and
αIIbβ3 receptors.
In a similar way, Scolastico and co-workers described the
incorporation of azabicycloalkane and γ–cyclopentane amino
acids as turn mimetics. A small library of RGD-containing
cyclopentapeptide mimics, incorporating stereoisomeric 6,5and 7,5-fused bicyclic lactams, was found to contain highaffinity ligands for the αVβ3 receptor (compounds 9 and 10,
Fig. 1) [64,65]. The highly selective αVβ3/αVβ5 antagonist 10
also revealed the highest ability to adopt the proper RGD
orientation required for binding to αVβ3 integrin, as deduced
from comparison with the crystal structure of the extracellular fragment of this integrin in complex with a cyclic
pentapeptide ligand [66]. This conformation comprised an
inverse γ–turn with Asp at position i+1 and a distorted
βII’–turn with Gly and Asp at i+1 and i+2 positions. A series
of dihydroxy-, hydroxy- and deoxy γ–aminocyclopentane
carboxylic acid derivatives, grafted onto an RGD tripeptide
framework, displayed nanomolar dual binding capabilities
toward αVβ3 and αVβ5 integrin receptors, with compound 11
being the best candidate [67]. Solution NMR structural
analysis and docking to the extracellular segment of integrin
αVβ3 proved that the aminocyclopentane spacer, even if it is
a non-isosteric dipeptide replacement, allowed the tetrapeptide macrocycle to adopt appropriate conformations to
develop potent integrin blocking agents.
It has been demonstrated that a radiolabeled analogue of
compound 1, in which the Val residue was changed by a Lys
moiety functionalized at the side-chain with a (18F)-sugar, is
suitable for imaging of αVβ3 expresion and blockade
monitoring using positron emission tomography [68]. This
seems to anticipate the use of this kind of cyclic peptide
derivatives as non-invasive tools to evaluate the role of αVβ3
during tumor progression and angiogenesis, both in basic
research and in clinical studies.
Scientists at SmithKline Beecham reported on the cyclic
RGD-containing disulfide derivative 12, a highly active
antagonist of the αIIbβ3, with crystal and solution structures
characterized by an extended conformation at the Gly
residue, and C7-like conformations in the regions around Arg
and Asp residues [69]. To test this conformational features,
γ–turn mimetics were incorporated at the Asp level in nonpeptide analogues. After initial attempts with 2-azepinones
[70], extensive investigations on differently substituted 1,4benzodiazepine non-peptide analogues were carried out.
Several potent peptidomimetics were discovered, as exemplified here by the orally active αIIbβ3 antagonist 13 [71,72].
A similar approach led to the identification of non-peptide
αVβ3 antagonists, such as 14, revealing the versatility of the
benzodiazepine nucleus as a Gly-Asp mimetic [73,74].
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 35
The doubly cyclized peptide ACDCRGDCFCG (15),
with disulfide bonds between 1-4 and 2-3 Cys residues,
bound the αVβ3 and αVβ5 integrin receptors but did not bind
to other closely related integrins [75]. The solution structure
of compound 15 displayed a modified type I β–turn at the
RGD sequence, while the less potent 1-3, 2-4 cyclized
analogue formed a type βII’–turn at the same segment,
indicating that the presentation of the RGD motif is critical
for integrin recognition. A PANAM dendrimer RGD conjugate based on compound 15 has been used for identifying
integrin receptor expressing cells, through flow cytometry
and confocal microscopy [76]. It is expected that this
conjugate could be used to direct imaging agents or
chemotherapeutics to angiogenic tumor vasculature.
In the same line of action, and based on the Leu-Asp-Thr
(LDT) motif present in the N-terminal Ig-domain required
for binding to α4β7 integrins, Kesler’s group designed a
series of cyclic penta- and hexapeptides with defined
conformations. Compound 16, as well as other analogues
resulting from systematic exchange of amino acid residues
while maintaining the backbone structure, effectively inhibited the α4β7 integrin mediated cell adhesion to MAdCAM-1
[77]. A biased library of functionalized carbohydrates, as
rigid scaffolds to allow the display of the essential side
chains of peptide 16, resulted in the mannose-based antagonist 17, which mimicked the active conformation of the α4β7
selective peptides [78]. Compound 17 have improved
pharmacokinetic parameters and could represent a promising
candidate for drug development in inflammatory diseases
and autoimmune diabetes.
A bicyclic lactam, combining seven- and four-membered
rings, was envisaged as a non-peptidic scaffold mimicking
the RGD reverse turn topology, to maintain the Arg-to-Asp
spatial relationships similar to that of the RGD motif in
RGD-containing proteins [79]. Compound trans-18 was able
to disociate the α5β1 IN/fibronectin complex with an IC50
value close to that observed for RGDs. It is claimed that, due
to its non-peptide character, derivative 18 could offer a real
advantage from a therapeutic perspective [80]. Similarly, the
reduction of the peptide character of the RGD sequence
through incorporation of the carboxylic acid and amine
groups into piperidine-containing derivatives, while retaining
the β–turn-like structure of fibrinogen, led to the discovery
of the platelet aggregation inhibitor 19 [81]. This injectable
αIIbβ3 antagonist is now under clinical trials, although
research is being continued to develop orally active
analogues.
2.2. Mimetics of Neurotrophins
Neurotrophins (NTs) are highly homologous homodimeric growth factors involved in the control of cell survival,
differentiation, growth cessation, and apoptosis of sensory
neurons [82,83]. Members of this family of proteins include,
nerve growth factor (NGF), brain-derived neurotrophic
factor (BDNF), neurotrofin-3 (NT-3), neurotrophin-4/5 (NT4/5), and neurotrophin-6. Their biological actions are
mediated by two classes of cell surface receptors: three
tyrosine kinase (Trk) receptors that recognize in a selective
but not specific way the different neurotrophins (NGF for
TrkA, BDNF for TrkB, and NT-3 for TrkC), and the p75
receptor at which all neurotrophins bind with similar
36
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
affinities [84]. It has been postulated that abnormal NT
actions are relevant to neurodegeneration, pain and cancer,
providing a foundation for therapeutic intervention. However, clinical trials with these NTs have been disappointing,
due to in vivo instability and lack of selectivity that caused
non-desired effects. Following the discovery that the Trk
binding is mediated by certain discrete β–turn regions of
NTs, several approaches to develop pharmacological agents
to target neurotrophin receptors, through the search of small
and selective neurotrophin-derived peptidomimetics, have
been described [83,84].
In the late nineties, two independent groups endeavor
similar strategies which consisted in the preparation of
disulfide-bridged cyclic peptides corresponding to β–loop
regions of NGF. The group of Saragovi prepared and studied
the generation of monomeric cyclic mimetics, such as
compound 20 (Fig. 2), which displaced [125I]NGF binding to
TrkA receptors and specifically inhibited optimal NGFmediated neurite outgrowth in PC12 cells [85]. NMR studies
of this peptide antagonist showed that its solution structure is
characterized by a β–turn conformation at Asp93-Glu-LysGln96 residues, strikingly similar to that of the corresponding
region of NGF [86,87]. After the first proof-of-principle,
Longo and co-workers described a new series of NGF peptide derivatives, exemplified by the 29-35 region analogue
21, that promoted neuronal survival via a p75-dependent
mechanism [88].
From the previous data about monocyclic monomeric
peptides, and taking into account that the NTs are homodimeric proteins, the next advance was to design appropriate
dimeric mimetics that could bring about Trk receptors
homodimerization to mimic the actions of NTs. Thus, a
dimeric peptidomimetic related to 20 demonstrated NGF-like
neurotrophic activity, while a bicyclic dimeric peptide,
designed to mimic loop 2 of BDNF, behaved as partial
agonist and was particularly potent in promoting neuronal
survival in vitro [89,90].
In an attempt to diminish the size and peptide character
of the β–loops of NTs, the group of Burgess designed a
focused library of β–turn small peptidomimetics combining
peptide and non-peptide fragments. Compound 22 was
identified from this library as a selective and proteolytically
stable agonist of the TrkA receptor [91], with ability to
rescue cholinergic neurons from the cortex and the nucleus
basalis and to improve memory/learning in impaired aged
rats [92]. The next step was to produce more rigid turn
analogues by incorporation of an additional phenyl ring.
Among this new series of compounds, which adopted
conformations that approximate β–turns, the NGF mimetic
23 showed partial agonist activity at TrkC receptor and
enhanced the trophic activity of NT-3 in cell survival assays
[93]. The closely related analogue 24 selectively bound the
NT-3 receptor TrkC, displayed NT-3-like neurotrophic
activity, and induced tyrosine phosphorylation of the TrkC
receptor [94]. After the initial success, they constructed a
minilibrary with the i+1 and i+2 residues of the key β–loops
of NGF and NT-3 anchored into the bis-phenyl skeleton.
Remarkably, a high rate of hits showing neurotrophic
activities or leading to neuronal differentiation or both were
identified [95]. Authors claimed that this kind of focused
González-Muñiz et al.
libraries, designed specifically to target receptor hot-spots,
may be a general approach to discover functional ligands for
PPIs. The assembly of this kind of monomeric peptidomimetics into dimeric structures has once again been explored, leading to some homo- and heterobivalent molecules for
further investigation [96,97]. The same group at Texas
University has recently published the synthesis of interesting
triazole-based β–turn mimetics, as 25, able to favor type I
and type II β–turn conformational states, but no indication
about biological activity has yet been reported [98].
2.3. Antagonists of the SH2 Domain of Grb2
Growth factor receptor bound protein 2 (Grb2) is an
ubiquitously expressed adaptor protein possessing a single
Src homology 2 (SH2) domain flanked by two SH3 domains.
Grb2 plays a crucial role in signaling from the receptor
tyrosine kynases (RTK) to the Ras-MAPK cascade, working
as a bridging element between cell surface growth factor
receptors and the Ras protein [99,100]. An aberrant Grb2SH2 dependent Ras activation pathway has been described to
contribute to processes important for cancer development
(i.e., cell proliferation, apoptosis, and metastasis) [101,102].
Therefore, the discovery of compounds that selectively
antagonize the SH2 domain of Grb2 should be attractive in
oncology.
It is known that upon RTK activation the Grb2 SH2
domain links phosphotyrosyl peptides with the consensus
sequence pYXNX, which normally adopt folded β–turn
conformations, with the Asn residue in the i+2 position
[103]. The pioneering research by Novartis started by
evaluating phosphotyrosyl peptide libraries, which upon
optimization led to a high-affinity and selective compound
(26, Fig. 3) [104]. In this phosphopeptide the α,α–cycloamino acid stabilized the β–turn conformation required for
efficient recognition by the Grb2-SH2 domain. Further
modifications at different parts of the molecule resulted in a
series of inhibitors (27-30), some incorporating phosphonate
and malonyl phosphotyrosyl mimetics, and others indole
derivatives instead of the naphthalene moiety, which showed
potent activity in cell-based assays and improved stability to
cellular phosphatases [105-108].
A step ahead in this field was achieved by Burke’s group
through the preparation of macrocyclic variants of the linear
Grb2 SH2 domain antagonists in an attempt to tightly fix the
β–turn conformation. Using olefin metathesis reactions, they
first prepared the tripeptide mimetic 31 that exhibited a 100fold enhancement in binding potency with respect to the
linear analogue, but was largely ineffective in whole-cell
assays [109]. However, the incorporation of an extra
carboxymethyl group at the pTyr mimetic α–position of the
macrocyclic ligand, as in the linear analogue 28, afforded
compound 32 with enhanced Grb2 SH2 domain binding in
extracellular assays and high efficacy in whole-cell systems.
Peptidomimetic 32 displayed antiproliferative effects with
submicromolar IC50 values in breast cancer cell cultures
[110]. The related 5-methylindolyl-containing macrocycle 33
displayed the highest affinity yet reported for a synthetic
inhibitor against the SH2 domain [111]. This compound
blocked the association of Grb2 to erbB-2 in an effective
manner, and showed antimitogenic effects against erbB-2dependent breast tumors at non-cytotoxic concentrations.
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 37
Turn
Mimetic
X
HN
H
N
HN
O
NH2
O
N
R
HO2C
NH
O
NH
NH2
H
N
HN
O
HO2C
O
HN
NH
O
NH
O
NH
NH
Turn mimetic
O
H
S
N
1: X = O, R = H
2: X = H2 , R = H
3: X = O, R = Me
N
N
N
O
O
4
5
6
OBn
BnO
S
Me
NH
H2N
HN
O
H
N
N
N
H
N
O
O
8
9: n = 1
10: n = 2
11
O
O
NH2
CO2H
N
H
O
( )n
OBn
S
7
CO2 H
O
12
H
N
H2N
N
H
O
O
H
N
NH
NH
O
S
S
Me
R
HN
N
S
O
HO2C
N
H
HN
H
N
O
O
NH
N
H
O
R
O
O
H
N
N
H
CO2H
S
O
CO2 H
O
O
HN
N
N
N
NH
13
15
Me
14
NH2
CO2H
O
H
N
N
H
O
O
HN
O
NH
16
O
N
O
O
HN
HN
H
N
O
O
HO2C
O
O
O
NH
CO2H
O
O
N
HN
CO2H
O
N
HO
OH
N
H
O
17
Fig. (1). Turn-constrained peptidomimetics to interfere with integrin functions.
18
19
NHAc
38
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
HO
NH2
OH
O
H
N
H
N
O
N
H
O
HO2 C
H
N
CO2H
O
S
O
NH
O
O
CO2H
H
N
N
H
HN
O
H
N
H
N
N
H
O
O
O
O
O
HN
CONH2
CO2H
NH2
HO
O
O
S
S
NH
H
N
N
H
H2N
O
S
H
N
O
N
H
NH2
H2NOC
20
21
OH
NH2
R2
O
HO2C
R1
O
O
N
H
HN
HN
O
HN
O
N
H
O
N
H
HN
O
R2
O
R1
R4
O
N
H
HN
HN
O
X
CO2 H
N
N
O
N
R3
O2N
22
23: R1 = (CH2 )2CO2H, R 2 = (CH2) 4NH2,
25
R3 = NH2, R4 = CO2H, X = S
24: R1 = (CH2 )4NH2, R2 = CH2OH,
R3 = NO2, R4 = CONH2 , X = NH
Fig. (2). Representative examples of neurotrophin derived peptidomimetics.
Good biological results were also obtained after similar
macrocyclization of other linear derivatives containing
different phosphotyrosine mimetics, such as 29, but they did
not improve those encountered for 32 and 33 [112,113]. The
crystal structure of an analogue of 32, bearing a malonyl
phosphomimetic, with the Grb SH2 domain allowed to
determine the binding mode and the specific interactions
between the protein and the inhibitor, which could serve to
rationalize the future design of this kind of protein-protein
modulators [114]. To facilitate the identification of the
intracellular targets of these macrocyclic inhibitors, a potent
biotinylated analogue of macrocycle 32 has very recently
been synthesized and demonstrated to have nanomolar
affinity for the Grb2 SH2 domain [115].
A family of non-phosphorylated ligands for the Grb2
SH2 domain has been developed by Roller and co-workers
from a phage library of 10-mer thioether linked cyclic
peptides [116]. Gradual reduction of the peptide nature and
systematic SAR studies provided compound 34 as the best
Grb2 SH2 inhibitor within this series [117,118]. This cyclic
pentapeptide exhibited potent Grb2 SH2 domain binding
affinity (58 nM) and remarkable antiproliferative activity
against erbB-2-dependent breast cancer (IC50 = 19 nM).
Compounds of this family bear the YXNX sequence, which
adopts β–bend type conformations facilitated by the presence
of the β–turn inducing amino acid 1- aminocyclohexanecarboxylic acid and an R-configured sulfoxide [118,119].
Although 34 and analogues do not reach the nanomolar and
even picomolar binding affinities found in the previous
series of phosphotyrosine mimetics, they provide a novel
template for the development on non-pTyr-containing Grb2
SH2 domain antagonists with enhance bioavailability.
2.4. Miscellaneous Examples
Related to the stabilization of turns as a way for modulating PPIs, one of the first examples yet described refers to
the preparation of HIV protease inhibitors [120]. This
enzyme, a member of the aspartic protease family, processes
high molecular weight viral polyproteins into structural
proteins and enzymes. The occurrence of a Pro residue at the
P1’ position of many substrates, and the frequent appearance
of Pro in turns, drove the sequential incorporation of γ–turn
mimetics into model peptides. Peptidomimetic 35 (Fig. 4)
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 39
O
O
CONH2
N
H
HN
O
O
P
O
HN
O
N
H
O
HO
CONH2
N
H
R
Y
HO2C
X
OH
N
H
O
HN
CO2 H
CO2H
R=
N
26: X= O; Y = NHAc
27: X= CH2; Y = NHAc
H3 C
28: X= CH2; Y = CH2CO2H
29
30
O
O
CONH2
N
H
HN
H3C
HN
O
O
HO
O
O
N
H
O
Y
P
CONH2
N
H
N
HO
OH
O
N
H
P
CO2 H
OH
33
31: Y = H
32: Y = CH2CO2H
NH2
OH
CO2H
HO2C
O
H
N
HN
H
N
N
H
O
O
(R) S
O
O
H
N
H2NOC
HN
O
CONH2
O
NH
O
34
Fig. (3). Stabilized turn peptidomimetics recognized by the Grb2-SH2 domain.
discovered from this research program, showed good
inhibitory activity against the HIV protease, being 44-fold
better than the corresponding linear analogue.
Also in the HIV field, an important PPI is the interaction
between gp120 and the CD4 receptor, which is critical for
the initial steps of HIV infection. Viral entry into the target
cell is primarily mediated by the interaction of gp120 with
CD4 through highly conserved regions, followed by
conformational changes of gp41 that causes the fusion of cell
and viral membranes. The X-Ray structure of CD4 fragments
revealed that the Gln40-Phe43 adopted a surface-exposed
β–turn, and likewise mutagenesis studies attributed a
significant role to Phe43 residue for binding to gp120. Guided
by these facts, stable mimetics of the complementaritydetermining 2-like region of CD4, as compound 36, were
designed and found to possess low micromolar Kd for
human T-lymphotropic viral gp120 and reduced syncytium
formation [121,122]. A target phage-displayed library was
constructed to identify novel peptides able to inhibit gp120CD4 recognition process. A cyclic nonameric peptide,
designed from one of the best linear peptides, exhibited good
inhibitory activity (50-fold higher than that of the linear
counterpart) [123].
40
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
Bn
NH
OH
O
O
O
N
NH
H2 N
NH
O
NH2
O
O
O
HO
HN
N
N
H
H
O
35
36
CO2CH3
OH
N
H
O
H2N
N
N
H
H-Pen-Ile-Tyr-Asp-Thr-Lys-Gly-Lys-Asn-Val-Leu-Cys-OH
O
S
O
S
37
38
Pro
Asn
Asn
Ala
CO2H
O
Asn
Ala
Ac-Glu-Leu-Leu-Glu
H
N
O
Ala
H
N
N
HN
H
O
NH2
O
HN
Asn
O
H
N
N
H
Pro
As n
HN
N
H
HN
O
H
N
O
HO-Asn-Trp-Leu-Ser
O
O
HN
O
CO2H
39
40
Fig. (4). Miscelaneous examples of reverse turn-based mimetics.
The interaction between cell adhesion molecules CD2
and CD58 is critical for immune response in autoimmune
diseases. Therefore, modulation of this interaction could be
therapeutically useful, and inhibitors may function as
immunosuppressants. Based on the structure of the CD2CD58 complex, several cyclic peptides were designed to
mimic the β–turn and β–strand hot-spot regions of the CD2
protein. Some of these compounds, exemplified by 37,
showed T-cell adhesion in different assays and adopted well
defined β–turn conformations in solution that closely mimic
the turn structure of the surface epitopes of CD2 protein
[124,125]. Further studies will be required to elucidate the
real biological potential of this approach.
Non-peptide second mitochondria-derived activator of
caspase (Smac) mimetics, containing well-characterized
bicyclic indolicidine and perhydropyrrolo[1,2-a]azepine
β–turn inducers, were described as modulators of the Xlinked inhibitor of apoptosis protein (XIAP)/caspase-9
interaction involved in the regulation of apoptosis [126,127].
Compound 38 displayed a Ki of 25 nM to XIAP BIR3
domain, being 23 times more potent than the natural Smac
peptide. These peptidomimetics could have therapeutic
potential as anticancer drugs for overcoming apoptosis
resistance of cancer cells with high level of IAP proteins.
A conceptually different biological task, triggered by
conformationally constrained peptidomimetics, can be found
in the synthetic vaccines field. In this case, mimetics should
function by stimulating the immune system to produce
antibodies that recognize the intact parasite. NMR and
molecular modeling studies, as well as the recently reported
crystal structure of the NPNA-repeated region of the
circumsporozoite (CS) protein of the malaria parasite
Plasmodium falciparum revealed that this tetrapeptide motif
adopted a type-I β–turn structure, stabilized by hydrogen
bonding between the CO of the first Asn residue and the NH
of Ala [128,129]. Using this NPNA motif as a model, a few
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
cyclic peptidomimetics, such as 39, were mounted into
different template carriers and evaluated for their ability to
induce antibody responses [130,131]. Some conformationdependent very promising results were found with these
cyclic peptidomimetics, while linear peptides containing the
same sequences failed to induce a detectable cross-reactive
immune response.
A segment of gp41, containing the sequence Glu-LeuAsp-Lys-Trp-Ala, has been identified as the epitope of the
HIV-1 neutralizing human monoclonal antibody 2F5, and the
crystal structure of the complex revealed that this epitope
mainly adopt a β–turn conformation. Cyclic peptides (i.e.,
40), incorporating a side-chain to side-chain lactam bridge
between the i and i+4 residues, induced a defined reverse
β–turn, showed good antibody binding and were highly
immunogenic, although they were incapable of stimulating a
neutralizing response [132].
3. STRATEGIES TO FIX β–SHEET EPITOPES
The second major structural element found in globular
proteins is the β–sheet. This structure is built up from a
combination of several regions, named β–strands, of the
polypeptide chain. The β–strands are usually 5 to 10 residues
long and are in an almost fully extended conformation, with
amide bonds being almost coplanar and side chains
alternating above and below the plane of the peptide
backbone. β–Strands are aligned adjacent to each other in
such a way that hydrogen bonds can be formed between CO
groups of one β–strand and NH groups of an adjacent
β–strand, and vice versa, to form a pleated sheet. The amino
acids in the aligned β–strands can all run in the same
biochemical direction, parallel β–sheet, or can have
alternating directions, to form an antiparallel β–sheet.
β–Strands can also combine into mixed β–sheets with some
β–strand pairs parallel and some antiparallel. Within
β–sheets, one of the simplex supersecondary structures are
β–hairpins, which are formed between two antiparallel
β–strands connected by a β-turn.
Interactions between the hydrogen-bonding edges of
β–strands in different protein chains constitute an important
mode of PPIs, with hydrogen bonds being formed between
β–strands belonging to different protein chains. These
interactions are frequent in protein dimmers and other
quaternary structures, both in interaction among different
proteins and in protein aggregation [127]. Although these
PPIs occur in non-pathological processes, they are also
involved in a wide range of diseases, such as cancer [128],
parasitic, fungal and viral infections [129-132], inflammatory, immunological and respiratory conditions [133,134],
and cardiovascular [135] and degenerative disorders,
including Alzheimer’s disease [136].
Although there are some chemical models of protein
β–sheets, based on templates that allow the transplantation of
several β–strands onto them, there are no binding or other
biological studies on these engineered β–sheets, so their
description is out of the scope of the present review. Thus, in
this section we will focus on several β–sheets mimetics that
have shown their capacity to exert a particular biological
activity by interfering with different PPIs. We differentiate
among peptidomimetics designed to imitate the distinct
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 41
elements of the β–sheet, from the simplest β–strand
mimetics, to compounds developed to mimic β–hairpins or
to contain functional groups of more complex β–sheets.
3.1. β–Strand Mimetics as Protease Inhibitors
Although isolated β–strands are not common, they
constitute crucial structural elements recognized by, for
example, proteolytic enzymes, major histocompatibility
complex (MHC) proteins, and transferases. Moreover,
β–strands mimetics are of interest as inhibitors of β–sheets
aggregation, a phenomenon which is associated with a
number of neurological disorders, such as Alzheimer’s,
Huntington’s and Parkinson’s diseases.
The simplest approach in the design of β–strand mimetics
would be to use short peptides corresponding to strand/sheet
regions of proteins. However, it is known the disadvantage
of using short peptides, due to their conformational
flexibility and poor pharmacological profiles. Methods to
increase the conformational stability involve the restriction
of the peptide freedom by incorporation of conformational
constraints into the peptide backbone, or through different
types of cyclizations.
A major effort in the field of β–strand mimetics is related
to the search of protease inhibitors. Proteolytic enzymes are
classified by the nature of their active-site catalytic residues
as metallo (34%), serine (30%), cysteine (26%), aspartic
(4%), and the less characterized threonine (5%) proteases.
These enzymes regulate numerous biochemical, physiological and pathological processes by controlling protein
synthesis and degradation through hydrolysis of specific
amide bonds. Consequently, control over protease expression
and function can potentially be an effective strategy for
therapeutic intervention [137]. In fact, a good number of
protease inhibitors have already been marketed.
A recent review by Fairlie’s group shows the analysis of
over 1500 three dimensional crystal (X-ray) and solution
(NMR) structures of substrates, products and inhibitors
bound in the active sites of all five protease classes. This
study has shown that proteases recognize peptide and nonpeptide ligands in an extended β–strand conformation, with
only a few exceptions [138]. Moreover, reviews from the
same authors [139,140] have covered β–strand mimetics up
to 2004. Therefore, here we just illustrate the different
approaches to β–strand mimetics with examples of inhibitors
of the human immunodeficiency virus (HIV) protease
(HIVPR), and give some details of new inhibitors developed
in the last two years.
A first approach to mimic extended strands is the use of
small carbo− and heterocyclic structures to rigidify the
peptide backbone and to arrange functional groups in
approximately the orientation they have in native β–strands
[139,140]. Several examples can be found within the field of
inhibitors of HIV protease. HIV protease is an aspartic
protease essential for viral replication and infectivity [141].
Structurally, HIV protease functions as a C2-symmetric
homodimer with a single active site. Accordingly, the activesite symmetry has been the base for the design of potent and
selective inhibitors of this enzyme. Another strategy quite
frequently applied is the replacement of the scissile amide
bond by surrogates of the peptide bond. As several 3D
42
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
structures of substrates or inhibitors bound to this enzyme
are known, design criteria have also taken this into account
to improve both potency and bioavailability. Thus,
modification of an initial linear peptide through the use of
structure-based design led to the potent enzyme inhibitor 41
(IC50 = 6.1 nM, Fig. 5) [142]. In an alternative strategy, a
pyrrolinone structural motif, known to force β–strand
conformations, has been introduced into the backbone of a
known peptide inhibitor providing compound 42 [143].
Since the irreversibility of these inhibitors would confer
longer term efficacy in vivo, a series of inhibitors were
designed containing a cis-epoxide instead of the scissile
amide bond. The incorporation of an epoxide, as in
compound 43 (IC 50 = 20 nM) [144], led to inhibitors with a
time-dependent irreversible pattern, as the nucleophilic
oxygen of Asp side chain is added to a carbon of the epoxide
ring to form an ester bond with simultaneous epoxide ring
opening. Finally, it is worth pointing out that the search of
β–strand mimetics have provided a series of compounds
currently in use for the treatment of HIV infection, as
ritonavir (44). This compound was developed after intensive
studies of a series of analogues whose design was based on
the active-site symmetry of HIV-1 protease. Ritonavir
showed good antiviral activity and exceptional oral
pharmacokinetics [145].
Examples of inhibitors of other aspartic proteases
(plasmepsin II, renin), serine proteases (trypsin, pancreatic
elastase, t-plasminogen activator, coagulation factor Xa,
thrombin), metalloproteases (several matrix metalloproteinases, angitensin-converting enzyme-1, interleukin-1β
converting enzyme, adamalysin II) and cysteine proteases
(cathepsin B, papain, caspase 3) have been described. There
are also examples outside the field of proteases, as inhibitors
of farnesyl transferase (FTase), human class II MHC protein
HLA-DR1 (antigen), and protein tyrosine phosphatase
(PTPase) [139,140].
In the last two years efforts have also been directed to
find other rigid scaffolds that can be used as replacements of
segments of peptide backbones to pre-organize the molecule
in its bioactive conformation, namely β–strands for protease
ligands. Mempapsin 2 (BACE), a membrane-bound aspartic
protease, is a key enzyme associated with the processing of
amyloid precursor protein to generate β–amyloid peptide, the
causative agent of amyloid plaques in Alzheimer’s disease.
An inspection of the X-ray structure of a heptapeptide
inhibitor bound to this aspartic protease poved that the ligand
adopts a β–strand conformation [138]. A cyclopentane ring
was designed as a replacement for a segment of the
hydroxyethylene isostere in the heptapeptide derivative,
affording compound 45 (IC50 = 39 nM, Fig. 5) [146].
Previous structure-activity relationship (SAR) studies on
subsite specificity, and X-ray of the complex of the enzyme
with various inhibitors, suggested the replacement of the
cyclopentane for more polar analogues, and consequently
several compounds incorporating a variety of heterocycles
were designed. Among them, lactam derivative 46 showed
an IC50 < 10 nM, and a 7-fold increased selectivity over its
human homologue cathepsin D (Cat D).
Another recent example of protease inhibitor is related to
Plamesin (Plm) I, II and IV, the haemoglobin degrading
González-Muñiz et al.
aspartic proteases from Plasmodium vivax and Plasmodium
falciparum, protozoan parasites that cause malaria. Starting
from a series of C 2 symmetrical inhibitors with high affinities
to both Plm I and II, a 1,3,4-oxadiazole heterocycle was used
as a replacement of one or two amide bonds of the parent
peptide. This lead to the symmetrical compound 47 (Fig. 5)
with high affinity toward Plm IV (Ki = 35 nM) [147].
Other strategies in the search of proteases inhibitors have
just involved optimization of previously designed mimetics
that incorporate different heterocycles. In this sense, modified inhibitors have been developed for cathepsin K (Cat K)
[148], a cysteine proteases crucial in bone remodelling, and
plasmin [149], a serine protease that plays an important role
during endothelial cell extracellular matrix (ECM)
remodelling.
A second main approach to mimic β–strands refers to the
preparation of macrocyclic peptides able to keep the peptide
backbone or equivalent residues in an extended β–strand
conformation. The design of macrocyclic compounds has
been based on the known 3D structure of several proteins
bound to their ligands that show close proximity of
alternating amino acids side chains from the ligand. The
strategy followed was to condense together these side-chains
to generate several highly constrained macrocyclic mimics of
tri- and tetrapeptide components of linear peptides. In this
respect, an area of intensive research is the development of
HIV protease inhibitors. The HIV protease substrates AcSer-Leu-Asn-Phe-Pro-Ile-Val and Ac-Leu-Val-Phe-Phe-IleVal-NH2 were easily converted to potent competitive
inhibitors by replacing the scissile amide bond (-CONH-)
with non-cleavable transition state isosteres (i.e. –CHOHCH2-) [150]. On the base of the X-ray structure of these
derivatives bound to HIVPR, Fairlie’s group designed
several 15 and 16 member macrocycles by linking together
the side chains of the first and third amino acids, flanking
either the left or the right side of the scissile amide bond
[150,151]. The resulting C- and N-terminal macrocyclic
derivatives [48 (IC 50 = 12 nM) and 49 (IC 50 = 0.6 nM), Fig.
6] resulted in good inhibitory potencies against HIVPR.
Additionally, bis-macrocyclic inhibitors [50 (IC50 = 3 nM)]
[151,152], and macrocycles functionalized at both N- and Cterminus, suitable for addition of appendages at either end
[51 (IC50 = 0.6 nM)] [153,154], have also been designed.
Theoretically, it might be possible to independently vary
either the acyclic N- or C-terminus without affecting the
interactions between the macrocyclic C- or N-terminus,
respectively, and the enzyme. In these sense, cyclic
tripeptide mimics have been appended to some non-peptide
moieties without loss of protease activity [155].
Additionally, both N- and C-terminal macrocycles have also
been modified through focused combinatorial chemistry to
create a series of potent inhibitors that bind in a predictable
way within the active side of the enzyme [156]. When
available, the 3D structure of the complex between these
analogues and HIVPR showed that these inhibitors are
bound in an extended conformation [138]
Following a similar approach a series of macrocyclic
ligands of other proteases have been designed [139,140].
Among them, we can find aspartic proteases, as rennin,
plasmepsin II, and penicillopepsin; metalloproteases, as
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 43
OH
H
N
N
O
OH
O
O
O
HN
H
N
NH2
O
O
41
O
HN
O
42
N
S
H
N
N
N
H
O
H 2N
O
O
H
N
O
N
O
N
S
NH2
O
OH
O
N
H
O
OH
N
H
O
S
O
H2N
O
44
OH
H
N
N
H
O
43
O
O
H
N
N
H
O
OH
O
O
H
N
HN
CO2H
N
H
O
H
N
O
N
N
H
NH
O
O
45
Br
N
OH
N
46
O
O
O
O
Br
OH
N
N
47
Fig. (5). Structures of several β–strand mimetics as protease inhibitors.
Stromelysin-1 (MMP3), angiotensin converting enzyme
(ACE), aminoprotease B and tumour necrosis factor α
converting enzyme (TACE); and serine proteases as,
thrombin, trypsin and streptokinase.
Other examples of macrocyclic enzyme inhibitors have
appeared in the literature during the last two years. The first
one is related to inhibitors of plasmepsin I, II and IV, the
malarial aspartic proteases essential for parasite survival.
Since aspartic proteases usually bind substrates/inhibitors
adopting an extended β–strand conformation, and
macrocyclization has proved to be an effective constrain,
several 13 and 16-membered macrocycles were designed as
inhibitors of Plm [157]. In this case a ring-closing metathesis
methodology was used to avoid incorporation of new
hydrogen bond-accepting/donating amide groups into the
macrocycle. Among them, the 13-membered macrocyclic
compound 52 (Fig. 6) showed high affinity for Plm I, II and
IV, and high selectivity over its homologous human aspartic
protease Cat D. Other macrocyclic derivatives have recently
been designed as inhibitors of different proteases, although
authors do not explicitly mention if these compounds were
designed to mimic β–strands. In general, the design methodology towards protease inhibitors involves the incorporation of a non-hydrolizable amide bond, and/or a cyclization
between two close residues. This trend of thought has been
quite a general design criterion in the search of protease
44
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
CONH2
OH
O
OH
H
N
N
H
H
N
Pro-Ile-Val-NH2
O
H
N
Ac-Leu-Val
N
H
O
48
O
H
N
O
49
O
O
OH
O
N
H
H
N
H
N
O
O
H
N
N
H
H
N
O
BocHN
N
H
OH
O
O
50
O
O
O
N
H
CO2 Me
51
OH
OH
O
H
N
N
H
O
OH
O
52
Fig. (6). Structures of representative macrocyclic HIV protease inhibitors.
inhibitors, as mentioned above, for which the adoption of
β–strand conformations was recognized after the crystal
complex structure has been solved [138]. Thus, it is likely
that these new macrocyclic inhibitors also adopt this type of
secondary structure. Examples are related to HIV-1 protease
[158], memapsin 2 (BACE, β-secretase) [159], and chronic
hepatitis C virus (HCV) non structural 3 (NS3) protease
[160-163].
3.2. CXCR4 Antagonists by Stabilizing β–Hairpins
Chemokine receptor, CXCR4, is a seven transmembrane
G-Protein Coupled Receptor (GPCR) that transduces signals
of its endogenous ligand, the stromal cell-derived factor-1
(SDF-1). CXCR4 has been identified as a coreceptor that is
utilized in T cell line-tropic (X4-)HIV-1 entry. Besides, it is
expressed in malignant cells from different types of cancers.
Thus, this system has been involved in several diseases,
including HIV infection, cancer metastasis/progression, and
rheumatoid arthritis, making it an attractive therapeutic
target. Fujii and co-workers have found a CXCR4 antagonist, compound 53 (Fig. 7), which is an 18-residue peptide
that inhibits T-cell line-trophic HIV-infection. Peptide 53 is
also able to bind specifically to both gp120 (an envelope
protein of HIV) and CD4 (a T-cell surface protein) [164].
This compound derived from chemical modifications of selfdefense peptides of horseshoe crabs [165], and posses antiHIV activity comparable to that of AZT, currently in use for
the therapy of AIDS patients. Derivative 53 has an
antiparallel β–sheet structure with a type II β–turn, which is
maintained by two intramolecular disulfide bridges [166].
Several studies recognize the importance of the disulfide
bridges, especially the major disulfide loop, and the β–sheet
structure for the expression of high anti-HIV activity, along
with a positive charge in the side chain at the (i+1) position
of the β–turn region. In addition, Trp3 can be replaced by
other aromatic residues [Tyr, Phe and L-2-naphthylalanine
(Nal)] [164]. It has been shown that a 14 residue analogue
(54, Fig. 7), having only one disulfide bridge maintains both
the anti-HIV activity and the conformational structure of 53
[165,167,168]. SAR studies on 54 allowed the discovery of
the citruline (Cit) derivative 55 and its analogue 56 (Fig. 7)
with increased anti-HIV-1 activity and diminished cytotoxicity [167,168]. Conformational studies on 56 showed that
it adopts an antiparallel β–sheet conformation, with four
pharmacologically significant residues, Arg2, Nal 3, Tyr 5 and
Arg14. Based on this, cyclic pentapeptides were used as
molecular templates to dispose these four residues into
proximity. Among this series of cyclic pentapeptides,
compound 57 exhibited strong CXCR4 antagonist activity,
comparable to that of 56 [170]. However, solution conformational studies did not show an exact correlation of the
spatial disposition of the pharmacophore groups of 57 with
those of 56. Subsequent SAR studies on this series give an
idea about the importance of the Arg, Nal and D-Tyr
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
C
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 45
53
R
R
W
C
Y
R
K
Y
K
54
R
R
W
C
Y
R
K
dK
55
R
R
W
C
Y
R
K
56
R
R
Nal
C
Y
R
K
G
Y
C
Y
R
K
C
R-NH2
P
Y
R
K
C
R-NH2
dK
P
Y
R
Cit
C
R-OH
dK
P
Y
R
Cit
C
R-OH
NH2
HN
NH
NH
O
N
H
HN
O
O
N
H
NH
N
O
HN
O
HN
O
H2 N
H
N
N
H
NH
NH2.TFA
TFAH2. N
57
NH
58
HO
Fig. (7) . Amino acid sequences of 53 and several of its analogues, aligned based on their homology. The disulfide linkages between Cys
residues are shown by solid lines. Structure of the cyclic peptide 57, and its DKP analogue 58.
residues at position 2, 3 and 5, together with several amide
bonds [171,172]. Following the discovery of peptide 56,
other cyclic tetrapeptides, including a γ-amino acid, and
pseudopeptides cyclized through disulfide and olefin bridges,
and therefore having a smaller number of peptide bonds
compared to the parent compound, have also been prepared
[173]. Very recently, a diketopiperazine (DKP) mimetic
(compound 58, Fig. 7), having a (Z)-alkene unit instead of
the cis-amide bond of DKP, has been used by Fujii and coworkers as an scaffold able to support the important guanidyl
and naphthyl side chains of 57. Although derivative 58
showed significant CXCR4 antagonist activity (IC50 = 15.1
µM), it did not reach the potency of the parent cyclic
pentapeptide [174].
3.3. Non-Peptide β–Sheet Mimetics as ICAM-1/LFA-1
Modulators
The interaction of leukocyte function-associated antigen1 (LFA-1) with the intracellular adhesion molecule-1
(ICAM-1) is critical to lymphocyte and immune system
function, and has been implicated in numerous autoimmune
diseases such as psoriasis, asthma and rheumatoid arthritis.
Therefore, antagonists of this interaction could be of mayor
therapeutic interest. The binding region of both molecules
has been characterized by antibody binding, mutagenesis and
crystallographic studies. In particular, the binding epitote of
ICAM-1 that interact with the I domain of the αL subunit of
LFA-1 is a discontinue region, encompassing residues
spanning four β–strands comprising one β–sheet [175,176].
ICAM-1 mutagenesis studies identified six residues
important for the interaction, with Glu34 and Lys39 being
critical for LFA-1 binding [175,177]. A homology model
indicated that these residues opposed each other on two
strands of an antiparallel β–sheet [175]. Thus, the simpler
approach to mimic this situation would be to traverse from
α-carbon to α-carbon crossing the H-bond network between
the strands. This data, together with extensive SAR studies
on different inhibitors of LFA-1/ICAM binding, guided
Gadek and co-workers to design a class of nanomolar smallmolecule LFA-1 antagonists, illustrated by 59 and 60 (Fig. 8)
[178]. A comparison of the structure and molecular
functionality of these compounds with ICAM-1 led to
propose that these derivatives are mimics of ICAM-1, and
bound in a similar manner to the LFA-1 inserted domain (I
domain). In contrast, several authors, on the base of indirect
binding studies of these small molecules to LFA-1,
concluded that they bind to a different epitote on LFA-1, in
particular the β2 subunit I-like domain, triggering epitotes
changes within and across LFA-1 domains [179-181]. More
recently, a direct comparison of the binding of ICAM-1 and
that of these small molecule antagonists [182] concluded that
there are two distinct binding sites, one of high-affinity in the
αL subunit of LFA-1, overlapping the ICAM-1 binding site,
and a second of lower-affinity in the β subunit. The binding
of the ICAM-1 mimetics to this low affinity site might be
due to the sequence homology between I and I-like domains.
3.4. Miscelaneous Examples
Several approximations to mimic β–hairpins involve
transplantation of the β–hairpin loop sequences from the
native protein onto a template that fixes the N- and C-termini
46
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
S
O
O
H 2N
OH
HN
OH
HN
O
H
N
O
OH
Cl
OH
HN
O
O
Cl
Cl
O
OH
59
60
Fig. (8). Structure of β–sheet mimetics of ICAM-1.
of the loop into a β–hairpin geometry. One of these hairpininducing templates is the dipeptide D-Pro-L-Pro, extensively
used by Robinson´s group [183-188], which is able to
stabilize several attached loops in β–hairpin conformation.
This template has been applyed to retain the β–hairpin
geometry of cyclic peptide trypsin inhibitors, and of
inhibitors of the binding of Protein A to a human antibody
Fc fragment.
The premature activation of trypsin, one of the three
principal digestive proteinases, has been related to events
that lead to pancreatitis, a disease with substantial morbidity
and mortality [189]. Thus, inhibitors of this protease might
be of use in the prevention and treatment of this lifethreatening illness. A 14 amino acid cyclic peptide from
sunflower seeds has proved to be a trypsin inhibitor. From its
crystal structure in a complex with trypsin it was shown that
the inhibitor has a well-defined β–hairpin loop. To produce
conformational mimetics of this natural product with correct
geometry, either 11 or 7 residues of its hairpin were
transplanted onto a D-Pro-L-Pro template [184], leading to
mimetics 61 and 62 (Fig. 9). NMR studies of these
compounds revealed clear β–hairpin conformations in both
cases, besides the longer mimetic displayed similar potency
to the natural product, whereas the shorter analogue was nine
fold less active.
Another example of the utility of the D-Pro-L-Pro
scaffold is related to the disulfide bridged peptide FcIII
(Asp-Cys-Ala-Trp-His-Leu-Gly-Glu-Leu-Val-Trp-Cys-Thr),
which interacts with the Fc domain inhibiting its binding to
protein A. The hinge region on the Fc fragment of human
immunoglobulin G interacts with at least four different
natural protein scaffolds, including protein A [190]. Fc
binding ligands may be of value for biotechnological
applications, as replacement for recombinant proteins, such
as Protein-A, in the affinity chromatography of therapeutic
antibodies. A combination of phage display and peptidomimetic chemistry, directed to find peptides able to bind to
this fragment, resulted in the disulfide bridged peptide FcIII
[188]. The crystal structure of this peptide in complex with
the Fc domain confirmed that FcIII is constrained into a
β–hairpin conformation by the disulfide bridge. Then,
computer models, generated by transposing either nine or
thirteen residues from this peptide onto the D-Pro-L-Pro
template, afforded compounds 63 and 64, respectively (Fig.
9). This design was partially successful, as only the longer
mimetic 64 was able to adopt the desired conformation, and
it has approximately 80-fold lower affinity compared to the
starting disulfide bridged peptide.
In another example, Mayo and co-workers have used
β–hairpin mimetics to replace a β–sheet from anginex, a
peptide comprising a β–sheet formed by three β–strand.
Anginex, compound 65 in Fig. 10, is a potent antiangiogenic, which specifically inhibits vascular endothelial
cell (EC) growth [191]. The mechanism of action of anginex
is not well understood, but it has been suggested that induces
down-regulation of adhesion receptors [191]. Anginex was
identified from the study of several βpep peptides,
amphipathic β–sheet-forming peptides, which were designed
employing basic folding principles from short β–sheet
sequences of three antiangiogenic proteins, namely platelet
factor-4 (PF4), interleukin (IL)-8 and bactericidal-permeability increasing (BPI) protein [192,193]. To demonstrate the
hypothesis that the bioactive conformation of anginex was a
β–sheet, several disulphide-linked peptide analogues were
prepared. Among them, compound 66 (Fig. 10) was able to
inhibit the EC proliferation and to promote apoptosis, even
with slightly higher efficacy than anginex [194].
Peptidomimetic 67 that incorporate the β–turn mimetic
dibenzofuran (DBF), has also been prepared and shown to be
effective at inhibiting the EC growth [195]. Subsequently,
shorter analogues were made to identify the minimum
sequence required for activity. It has been shown that neither
the N-terminal nor the C-terminal hexapeptide were
essential, and thus the shorter derivative, Ser-Val-Gln-MetLys-Leu-[DBF]-Ile-Ile-Val-Lys-Leu-Asn-Asp
showed
comparable affinity with that of 67. NMR studies indicated
that the β–sheet structure is preserved in DBF analogues and,
interestingly, several of these peptidomimetics retained the
antiangiogenic activity and were able to inhibit tumor
growth.
4. ATTEMPTS TO STABILIZE/MIMIC α–HELIX
ELEMENTS
α–Helices are the most common protein secondary
structure accounting for over 40% of polypeptide amino
acids in natural proteins. α–Helices in proteins are found
when a stretch of consecutive residues all have the φ, ψ
angle pair approximately −60º and −50º. The α–helix has 3.6
residues per turn with hydrogen bonds between C=O of
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
O
O
N
N
H
HO
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 47
N
N
H
O
HO
O
NH
N
H2 N
O
O
O
O
O
HN
NH
OH
HN
O
HN
N
O
O
H2N
S
OH
S
O
O
NH
NH
HN
NH
O
O
O
N
HN
N
O
O
HN
D-Pro
L-Pro
H2N
N
NH
H
62
O
O
O
N
HN
O
N
O
N
H
D-Pro
L-Pro
H
N
61
OH
O
O
HN
O
HN
O
O
N
H
N
N
H
OH
NH
NH
O
O
NH
O
O
HN
O
N
NH
NH O
HN
HN
O
HN
S
O
N
N
N
H
HN
H
HO O
N
H
O
O
N
L-Pro
NH
O
O
O
O
S
HN
HN
NH
O
O
O
O
O
HN
NH
NH
N
H
O
O
N
H
N
N
D-Pro
63
L-Pro
D-Pro
64
Fig. (9). Structure of β–hairpin mimetics based on the D-Pro-L-Pro template.
residue i and NH of residue i+4, thus all NH and C=O
groups are connected with hydrogen bonds except for the
first NH and the last CO groups at the ends of the α–helix.
The average length of an α–helix is around 10 residues,
corresponding to three turns, and in proteins is almost always
right-handed, according to the screw direction of the chain.
All the hydrogen bonds in an α–helix point in the same
direction, so the peptide units are aligned in the same
orientation along the helical axis. Since a peptide unit has a
dipole moment arising from the different polarity of NH and
CO groups, these dipole moments are also aligned along the
helical axis. The overall effect is a significant net dipole for
the α–helix that gives a partial positive charge at the amino
end and a partial negative charge at the carboxy end. The
side-chains of amino acids, except for Pro, projects out from
the α–helix, and do not interfere with it. In general, there are
amino acids that are good α–helices formers, such as Ala,
Glu, Leu, and Met, while Pro, Gly, Tyr, and Ser are very
poor [196].
48
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
His
González-Muñiz et al.
Leu
His
Arg
Lys
Lys
Trp
Phe
Lys
Asp-CONH2
Leu
Lys
Leu
O
Arg
Lys
Lys
Trp
Phe
Lys
Ile
Leu
Leu
Ile
Leu
Ile
Ile
Ser
Lys
Ile
Lys
Ile
Met
Val
Leu
Met
Val
Met
Val
Gln
Lys
Glu
Gln
Lys
Gln
Lys
Val
Leu
Arg
Val
Leu
Val
Leu
Ser
Asn
Gly
Cys
Cys
Ser
As n
As p-CONH2
Asp
HN
O
Leu
Asp
Leu
Lys
Lys
Gly-CONH2
Lys
Ile
Ile
Ile
Asn
Asn
As n
Ala-NH3
Ala-NH3
Leu
65 (Anginex)
66
Ala-NH3
67
Fig. (10). Backbone conformation of anginex and two β–hairpin mimetics.
α–Helices play pivotal roles in many PPIs, therefore the
therapeutic potential of mimetics of this protein secondary
structure element is really enormous. However, in contrast to
other elements, such as β–turns, small molecule α–helix
mimetics have hitherto rarely been described in the literature.
There are several therapeutically relevant biological
pathways that involve PPIs in which the hot-spot is located
at an α–helix motif. Especially important is the fact that
α–helices constitute the mayor secondary structure elements
in key apoptosis regulating PPIs, (i.e., Bcl-2 family proteins,
p53/HDM2). Therefore, the disruption of these PPIs could
constitute an effective and selective way for the treatment of
cancer. This prompted several groups to focus their research
work in that direction.
4.1. Mimetics of the Amphipatic BH3 Segment of ProApoptotic Members of the Bcl-2 Family
The apoptosis process requires the cooperation of a series
of molecules, such as the caspase-cascade signaling system,
which in turn is regulated by various molecules, such as the
Bcl-2 (B-cell lymphoma-2) family proteins. Members of this
family of proteins can be divided into two groups: antiapoptotic proteins (for example Bcl-2, Bcl-xL), which
display sequence conservation in all BH domains, and proapoptotic proteins that are divided into multidomain
members (such as Bax and Bak), and BH3 only members
(such as Bid and Bad) that display sequence similarity only
to the BH3 α-helical domain. The BH3-only proteins
monitor cellular wellbeing and, when activated by cytotoxic
signals, engage pro-survival relatives by inserting the
amphipathic α–helix BH3 domain into a hydrophobic groove
on the surface of the anti-apoptotic members (Bcl-2, Bcl-xL),
priming the cell for apoptosis [197,198]. Since the BH3
domain has an α-helical conformation, preparation of
mimetics of this type of secondary structure is exciting
enormous interest.
One of the strategies used to restrict the conformational
freedom and constrain the structure of synthetic α-helical
peptides is through the incorporation of either covalent or
non-covalent linkages between amino acid side-chains. A
very new approach, in this context of fixing helicity by
cyclization, is the strategy developed by Grubbs and coworkers making use of the olefin cross-linking. They applied
the metathesis reaction to the cyclization of helices through
O-allyl serine residues located on adjacent helical turns
(Compound 68, Fig. 11), by using the methodology of
ruthenium-catalized ring-closing metathesis [199]. The
principal advantage of this chemistry is the high functional
group tolerance of the catalysts.
Verdine and co-workers developed this concept further in
order to confer stability to the α–helix, connecting residues i
and i+4, (or i+7) by introducing in that positions α,αdisubstituted amino acids containing olefin chains [200]. The
study comprised variations in the position of attachment,
stereochemistry, and cross-linker length, and concludes that
hydrocarbon cross-linking can greatly increase metabolic
stability as well as helical propensity of peptides, as shown
by circular dichroism (CD) experiments. Additional work in
this area led to the search of apoptosis promoting derivatives.
With this in mind, the group of Verdine prepared peptides
that mimicked the amphipatic BH3 segment of Bid, a proapoptotic member of the Bcl-2 family proteins. Derivatives
of α,α–disubstituted non-natural amino acids containing
olefin-bearing tethers, to generate what they named an allhydrocarbon “staple”, showed in vitro/in vivo biological
activity when tested for their ability to activate apoptosis.
This was assessed in a wide panel of leukemia cells, as well
as in mice bearing established human leukemia xenografts.
Compound 69 (SAHBA, Fig. 11) inhibited the proliferation
of leukemia cells at moderate inhibitory concentrations and
duplicated survival of the treated mice [201].
Following a very similar approach of stapling residues i
and i+4 of the α–helix, but mimicking the C=O…H−N
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 49
O
H
N
BocNH
H
N
O
O
n
O
HN
O
O
NH
O
MeO
H
N
n
N
H
O
68: n =1 or 2
O
O
Glu-Asp-Ile-Ile-Arg-Asn-Ile-Ala-Arg-His-Leu
H
N
N
H
N
H
O
O
HN
n
O
69: n=2 (SAHB A)
O
Trp-Ile-Ser-Arg-Asp
N
H
NH
n
H
N
OH
N
H
O
O
O
O
NH2
NH
O
O
NH
70 (HBS)
O
Trp-Ile-Ser-Arg-Asp
N
N
H
O
Fig. (11). Cyclic mimetics of the amphipatic BH3 segment of Bcl-2 family proteins.
hydrogen bond as closely as possible, Arora and co-workers
developed a strategy that permits at the same time the
preservation of helix surfaces. It consists in the substitution
of the hydrogen bond, by a covalent bond of the type
C=X−Y−N, were X and Y would be respectively part of the i
and i+4 residues. In general, helix stabilization methods have
relied predominantly on side-chains constraints, in methods
that either blocked solvent-exposed surfaces of the target
α–helices or removed important side-chain functionalities.
The attractiveness of this strategy of hydrogen-bond
surrogates (HBS) relies on the fact that the cross-link is
placed inside the helix, so the solvent-exposed molecular
recognition surfaces of the helix are not blocked, while
showing a high stability [202]. Derivatives such as
compound 70 (Fig. 11) were prepared as mimetics of the
BH3 domain of Bak, in order to check this hypothesis, and to
compare the ability of HBS derivatives with lactam-based
artificial helices previously reported, that failed to bind BclxL. Results of fluorescent polarization assays showed that
compound 70 was a high-affinity binder for Bcl-xL,
accessing the deep hydrophobic cleft, which validate the
initial hypothesis [203]. Further studies in order to check the
real pharmacologic potential of these derivatives remains to
be performed.
Using a different approach, the group of Gellman have
described a series of mixed α,β-peptide derivatives showing
antimicrobial activity that were design to be amphiphillic in
different helical conformations. Extended work in this area
led to the design of Bcl-xL ligands, based on structures that
50
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
combine α/β and α-peptides in different ways. Binding
assays demonstrated that some of the prepared chimeric
(α/β+α)-peptides displayed significant affinity for Bcl-xL
(compound 71, Fig. 12) [204].
binding conformation. Thus, Horwell and co-workers have
shown that compound 73 (Fig. 12) bind with micromolar
affinity to both NK1 and NK3 tachykinin receptors [206].
On the other hand, and on the basis of molecular
modeling studies Jacoby proposed 2,6,3’,5’-tetrasubstituted
biphenyls to mimic the side-chains of i, i+1, i+3, i+4
residues of an α–helix [207], although the real behavior of
such structures as α–helix mimetics has not been determined
(compound 74, Fig. 12).
Other type of molecules that display pharmacological
activity towards this target corresponds to non-peptide
structures. One of the first reported non-peptide α–helix
mimetic had the structure of a 1,6-disubstituted indane. This
scaffold was designed to mimic the orientation of two
adjacent amino acid side-chains i and i+1 (compound 72,
Fig. 12) [205]. Soon after, the corresponding 1,1,6-trisubstituted derivatives were suggested to operate as mimetics of
de i–1, i and i+1 residues, since the second substituent at the
1-position of the indane overlays with the i–1 residue [206].
This kind of template was used for the preparation of
mimetics of the endogenous neuropeptides of tachykinin
receptors (peptide-protein interaction), in order to prove their
In clear connexion with this, Hamilton and co-workers
have reported on trisubstituted terphenyls as α-helical
proteomimetics. They are able to mimic one face of the
α–helix by the spatial projection of its functionality in a
similar way to that corresponding to two turns of the
α–helix. The terphenyl is expected to adopt a staggered
conformation and closely reproduce the position and angular
orientation of functionality on the surface of an α–helix. In
O
N
H
H-Gly-Asn-Leu-Gly-Arg-Asn-Leu-Ala-Ile
O
H
N
N
H
H
N
O
O
N
H
H
N
N
H
O
COOH
O
R i-1
Ri
R i+1
72
Ri + 3
Ri-1= CH2Ph
Ri = CONH(CH2) 2Ph
Ri+ 1= CH2 Ph
R i+ 1
R i+ 4
Ri
73
R i+ 1
74
Biphenyls
NH2
CO2 H
O
O
N
CO2M e
O
HN
N
H
O
O
O
O
N
N
N
O
N
N
H
O
O
O
N
CO2H
75
76
77
O
O
Fig. (12). Quimeric and non-peptide mimetics of the amphipatic BH3 segment of Bcl-2 family proteins.
NH2
O
71
Ri
H
N
78
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
fact, the 3,2’,2”-trisubstituted terphenyls (coupled in para)
mimic the side-chains at the i, i+3 or i+4, and i+7 positions
of an α–helix, which are the positions that frequently play
key roles in mediating protein contacts, and result in
molecules that would be able to disrupt PPIs [208]. In fact,
this strategy of helix mimicry based on a terphenyl scaffold
has been applied to the design of several modulators of PPIs
in which the hot-spot is located at an α–helix. Thus, the
authors have described the capacity of the terphenyl based
α–helix derivatives (analogues of compound 75, Fig. 12) as
mimetics of the Bad/Bak BH3 peptide epitope. These
compounds were able to inhibit the interaction between BclxL (antiapoptotic protein) with the BH3 domains of the
mentioned pro-apoptotic proteins (Bad/Bak) [208,209].
However, the challenging synthesis and physical properties
of terphenyls prompted the search for simpler scaffolds that
could similarly mimic the side-chain presentation on an
α–helix. With this aim, a new set of inhibitors based on the
terephthalamide scaffold was designed. These new derivatives, exemplified by compound 76 (Fig. 12), have shown
high in vitro inhibition potencies in disrupting the BclxL/Bak BH3 domain complex, as well as a significant
improvement in water solubility relative to the terphenyl
derivatives [210-211]. In the same context, Hamilton´s group
have also designed a novel oligoamide foldamer, the
trispiridylamide scaffold 77 (Fig. 12), as an α–helix mimetic.
The new derivatives showed affinity for Bcl-xL and inhibited
its interaction with Bak, even if only in a low micromolar
range [212].
Additionally, Dömling and co-workers, prompted by
Hamilton’s terphenyl α–helix mimetic concept, and in order
to obviate the disadvantage inherent to the multi-step
synthetic approach needed for the assembly of the terphenyl
scaffold, investigated alternate scaffolds that would be
accessible by more efficient and faster synthetic methods,
such as the multicomponent reactions (MCR) [213].
Molecular modeling considerations led them to the selection
of a trisubstituted imidazole backbone (78, Fig. 12). Further
studies illustrated the ability of these compounds to mimic
the critical i, i+3 and i+7 residues of an α-helical Bad
peptide epitope, and some of them, as compound 78, were
found to disrupt the interaction of Bcl-w with Bak-BH3
peptide.
4.2. Disruption of the P53/HDM2 Protein-Protein
Interaction by α–Helix Mimetics
Protein p53 is a transcriptional activator critical for
stress-induced cell cycle arrest and apoptosis. Under stress
conditions, such as hypoxia or DNA damage, the p53 protein
accumulates in the cell nucleus, and induces the transcription
of various genes involved in cell-cycle control, apoptosis,
differentiation, etc. In the absence of stress, HDM2 (human
double minute 2) down-regulates p53 activity, interacting
with the p53 activation domain (p53AD) and exporting p53
from the nucleus. Tumor cells often overspress HDM2,
resulting in a loss of the cell’s primary response to stress,
and dealing to unchecked cell growth.
HDM2-p53 interaction is an attractive therapeutic target
in oncology, since its inhibition with synthetic molecules is a
promising approach for activating p53, leading to cell-cycle
arrest or apoptosis. Additionally, p53-HDM2 association is
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 51
well characterized at both the structural and biological level
[214,215].
One of the first attempts to reproduce the structural and
conformational features of a naturally occurring α-helical
protein epitope, the HDM2-binding domain on p53, is the
approach described by García-Echeverría and co-workers
[216]. Short peptides (linear peptides, from 8- to 12-mer)
were designed on the basis of the X-ray crystal structure of
the N-terminal domain of HDM2 bound to a 15-mer wildtype p53-derived peptide (Ac-Gln16-Glu-Thr-Phe-Ser-Asp21Leu-Trp22-Lys-Leu-Leu-Pro27-NH2). Starting from a 12-mer
derivative identified from phage display peptide libraries and
considering molecular modeling studies, they obtained, after
several modifications, a truncate derivative, 79 (Fig. 13), that
exhibited interesting values of binding affinity. The
incorporation of some conformational constraints by the
introduction of α,α-disubstituted amino acid residues was
then undertaken, as it is known that they contribute to
stabilize the helix conformation in short peptide motifs.
Additionally, modifications such as the introduction of a
phosphonate group (Pmp residue) in order to form a
stabilizing salt bridge with the ε–amino group of Lys94 of
HDM2, and above all the incorporation of a Cl atom in
position 6 of Trp, led to an important increase of the binding
affinity [216]. This was one of the first experimental
evidences about the capacity of peptide derivatives to inhibit
PPIs, and shows the possible utility of peptides as a starting
point for the development of non-peptide leads, or for the de
novo design of PPIs antagonists.
Besides, Robinson and co-workers have described a new
strategy for the preparation of α–helix mimetics based on the
use of a β–hairpin scaffold [185], also inspired by the
α–helix epitope of the HDM2 identified as the hot-spot for
its interaction with p53. Taking as reference the structure of
the complex described by Kussie [215], it can be realized
that the distance between the Cα atoms of Phe 19 and Trp 23 on
one face of the HDM2-bound p53 α–helix is close to the
distance between the Cα atoms of residues i and i+1 along
one strand of a β–hairpin. Therefore, a designed β–hairpin
mimetic can be used as scaffold to anchor in the correct
relative positions the side-chains of the residues identified as
crucial to the p53-HDM2 interaction, namely Phe19, Trp23,
and possibly also Leu26. Optimization of the series led to the
preparation of derivative 80 (Fig. 13) that showed an
improved profile with respect to the initial analogues.
Evaluation for p53/HDM2 inhibitory activity by a solution
phase competition assay, performed with a surface plasmon
resonance biosensor, proved that compound 80 exhibited
good affinity values for HDM2. Moreover, the crystal
structure of the complex 80/HDM2 confirmed the β–hairpin
conformation of the bound ligand, as well as the successful
mimicry of the location of the hot-spot residues Phe/Trp/Leu,
in relation to the binding of p53 [217]. It has to be noticed
the improvement on activity achieved by the substitution of
the Trp residue by a (6-Cl)Trp, on the basis of the work
previously described by García-Echeverria [216].
Other type of scaffold also used as α–helix mimetic are
peptoids, oligomers composed of N-substituted glycine
building blocks. The side-chain of each amino acid in
peptides is formally shifted by one position from the C-α to
52
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
Cl
HN
CO2 H
O
H
N
AcHN
O
H
N
N
H
O
O
H
N
N
H
O
O
H
N
N
H
O
NH2
N
H
O
O
SCH3
79
O
P
O
OH
NH
CO2 H
HO2C
O
O
H
N
N
NH
O
N
N
H
O
H
O
O
H
O
H
D-Pro
O
N
N
H
N
H
O
N
N
L-Pro
O
CO2H
HN
80
Cl
Fig. (13). Linear peptides and β–hairpin derivatives as mimetics of the α−helical protein epitope of p53.
the amino group nitrogen in peptoids. Comparison of the
peptide chain with the peptoid chain shows that the direction
of the peptide bond in peptoids should be reversed (retrosequence) in order to provide the same relative arrangement
of side-chain residues, R groups, and carbonyl groups (Fig.
14). Peptoids are achiral, and helical structures are favored
when bulky N-alkyl side-chains are present. Interestingly,
these helices are not stabilized by hydrogen bonds, and the
helicity depends on side-chain chirality and oligomer length
[218]. The chiral peptoid helix is similar to a type-I
polyproline helix, in which the amide bonds are cis, and the
carbonyl groups point the oxygens towards the N-terminus,
causing the electrostatic dipole moment to be the reverse of
standard α–helices. Because the helical conformation is
dictated by steric constraints, and not by hydrogen bonds, as
in regular proteins, it is able to persist both in aqueous and
non-polar solvents, as well as under a broad range of pH and
temperature conditions.
The group of Appella has very recently described a
peptoid scaffold that binds to HDM2, and in consequence is
capable of inhibiting the HDM2-p53 interaction [219]. Thus,
starting from a peptoid derivative of ten glycine subunits,
and after several structural modifications in order to improve
aqueous solubility and binding affinity, compound 81 (Fig.
14) was obtained as the derivative that showed higher
affinity for HDM2 in the series. In order to reproduce the
relative position of key residues Phe19, Trp 23 and Leu26 in a
type-I polyproline helix of the peptoid skeleton two main
questions had to be addressed. The first difference is that the
peptoid helix is more tightly bound than that of a peptide,
only 3 residues per turn compared with 3.6. This problem
was resolved by deleting one position between the Phe and
Trp residues. The other relevant structural difference
between the two helices is that the side-chains project out at
different angles. This problem was obviated by elongation in
an extra methylene group both the Phe and the Trp sidechains. Surprisingly, the best affinity results of the series
were shown by an achiral compound (81), suggesting the
possibility that non-helical conformations adopted by
peptoids can also be important for binding to proteins.
Helical β-peptides, composed of β-amino acids, have
also been used as prototypes for PPI disruption. β-Amino
acids are characterized by the presence of an additional
carbon atom between the amino and the carboxy groups. βPeptides consist of linear chains of β-amino acids, and are in
principle resistant to peptidases, as they are non-natural
folding oligomers, or foldamers. This has promoted their use
to modify the pharmacodynamic properties of peptide drug
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
O
R2
H
N
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 53
O
O
R2
H
N
O
N
N
H
N
R1
O
R3
N
R1
Peptides s equence
O
R3
Peptoid sequence
(OH)2(O)P
(p-NO2)Ph
O
N
HN
O
O
N
N
O
(p-NO2)Ph
(p-NO2 )Ph
N
N
O
O
N
N
O
O
N
N
O
(p-NO2)Ph
NH2
O
H2NO2S
(OH)2(O)P
NH
81
Cl
H
N
H2 N
H
N
O
H
N
O
H
N
O
NH2
HO
H
N
O
O
O
HN
H
N
H
N
O
H
N
O
O
H
N
OH
O
O
NH2
HO
O
82 (b53-1)
Ri
H
N
Ri +4
H
N
NC
Ri + 7
O
OH
H
N
O
O
O
83
OH
O
84
F
Fig. (14). Peptoids, β–peptides, and non-peptide mimetics of the α−helical protein epitope of p53.
candidates, in order to improve their metabolic stability. βPeptides can fold into stable helical secondary structures.
Side-chains may be attached either to Cα or to Cβ, or to both
of them, and this fact considerably influences the secondary
structure of the corresponding oligomer. Thus, acyclic
monosubstituted residues tend to fold into 14-helices, or
10/12 helices if patterned as alternating β2/β3 residues.
Cyclopentyl and cyclohexyl ring constraints promote
formation of a 12–helix and a 14–helix respectively.
Therefore, the choice of the appropriate substitution pattern
will determine the preferred helical secondary structure.
Helix formation occurs already in β-peptide hexamers, while
in the case of α-amino acids usually more than 10-12 amino
acid residues are required to form a stable helix [220].
Schepartz and co-workers realized that the side-chains
located at the i, i+4, i+7 positions on an α–helix superpose
with those at positions i, i+3, i+6 on a 14–helix, and on the
basis of that, decided to present a short α-helical functional
epitope on a well-folded 14–helix [221]. Therefore, their
efforts were concentrated on finding a strategy to stabilize
β3-peptide 14–helix in water, and on trying to reconstitute an
α-helical functional epitope, by incorporation of α-amino
acids bearing the appropriate side-chains. The approach used
for stabilization of the helical structure in solution was based
on the neutralization of the helix macrodipole, by introduction of positively charged side-chains near the N-terminus
and negatively charged side-chains near the C-terminus. This
rational led to the design and preparation of the β-peptide
foldamer 82 (Fig. 14), named β53-1, which fulfilled this
expectative. This compound was focused towards the
inhibition of the p53/HDM2 interaction. Fluorescence
polarization measures showed that β53-1 bound to the
oncoprotein HDM2 with an IC50 of 94.5 µM [221]. The
54
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
design of this β3-decapeptide series was made assuming that
if the side-chains of Phe19, Trp 23, and Leu26, were presented
at successive positions three residues apart on a stabilized
14–helix, it could mimic the functional epitope of p53AD. In
order to study deeply the 14–helical conformation stability of
these species, CD and fluorescence polarization studies were
performed [222,223].
On the other hand, Hamilton and co-workers have also
described the capacity of the terphenyl based α–helix
derivatives to mimic the α-helical region of the p53 peptide
and to disrupt the HDM2/p53 complexation, using an
analogue of compound 75 (Fig. 12) with a -CH2(2-naphtyl)
substituent instead of a -CH2(1-naphtyl) [224,225].
Worth to mention is the method recently described by
Guy and co-workers to construct inhibitors of the p53MDM2 interaction using a computational design strategy.
The method can be applied to any PPI for which a co-crystal
structure exists [226]. Thus, using the computer program
CAVEAT, an i, i+4, i+7 α−helical system was targeted,
arriving to a suitable scaffold represented in Fig. 14 by the
general formula 83. Preparation of the corresponding
proteomimetics library using synthetic solid phase protocols,
and further biological evaluation, finally led to derivative 84
as the most active compound in the series.
4.3. Miscellaneous Examples
As previously mentioned, one of the strategies used to
restrict the conformational freedom of synthetic α-helical
peptides is cyclization through the incorporation of covalent
or non-covalent linkages between amino acid side-chains.
This strategy was used by Wittliff and co-workers [227] with
the aim of preparing selective inhibitors of the interactions
between nuclear receptors (NR) and their co-activators. NR
superfamily includes the steroid receptors that regulate a
wide variety of physiological, developmental and metabolic
processes. Abundant evidence has identified NRs as
prominent etiological factors in diseases ranged from breast
and prostate cancer to diabetes and obesity. Steroid receptor
agonists bind to a buried hydrophobic pocket within the Cterminal ligand-binding domain (LBD) of the receptor. This
prompted a conformational shift causing repositioning of
helix 12, which allows for recognition of co-activator
proteins. Many co-activators contain a pentapeptide motif,
NH2
O
H2N
H
N
H2 N
O
H2 N
N
H
O
S
O
O
H
N
H2N
O
H
N
N
H
O
S
N
H
N
H
O
O
HN
O
H
O
N
H
O
N
H
O
N
H
OH
3
2TFA
NH
85 (PERM-1)
H2N
86
NH
CO2 H
CO2H
O
O
CO2H
CO2H
Ri
O
N
Ri+ 3
Ri+4
N
Ri+7
N
CO2H
87
88
CO2H
Fig. (15). Miscelaneous examples of mimetics of different α−helical protein epitopes.
89
CO2H
90
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
known as the “NR box” (LXXLL), which is responsible for
recognition of a hydrophobic groove created on the surface
of the LBD in response to repositioning of helix 12 upon
agonist binding. Previous work reported by McDonnell and
co-workers [228] with peptide sequences that mimic this NR
interaction motif showed that they could function as estrogen
receptors (ER) antagonists in cell based models. With this in
mind, the group of Wittliff designed conformationally
constrained analogues in order to best mimic the binding
face of the “NR box” domain with the ER α. They based on
previous X-ray studies which revealed that the critical Leu
residues are oriented on one face of an α–helix with the XX
side-chains on the opposite half of the amphipatic helix.
Optimization of the series led to the preparation of cyclic
compound 85 (Fig. 15), named PERM-1, a disulfide-bridged
derivative, that displayed the highest affinity for the ERs (Ki
= 25 nM), and showed at the same time the greatest helical
character in the CD study [227].
On the other hand, the group of Seebach has described a
series of β-peptides (i.e. compound 86, Fig. 15) that behaved
as inhibitors of small-intestinal cholesterol and fat
absorption. They mimicked the amphipatic α–helix binding
motif of the proteins or synthetic peptides that acted as
inhibitors of the so called scavenger receptors of class B,
type I or II (SR-BI or BII), membrane-bound proteins that
mediate the selective lipid transport through the brush-border
membrane (BBM) in the small intestine of mammals [229].
Additionally, Hamilton and co-workers have investigated
the activity of different therpenyl α–helix mimetics towards
several targets. The first report made of such a scaffold as
proteomimetic referred to inhibitors of calmodulin (CaM)
activation. Among them, compound 87 (Fig. 15) showed
improve activity over the helical peptide RS20, a 20-mer
fragment of an α-helical domain of the smooth muscle
myosin light-chain kinase (smMLCK) [230]. The same
strategy has been also successfully applied to the design of
an antagonist of gp41 core formation, with compound 88
(Fig. 15) showing inhibition of HIV-1 mediated cell-to-cell
fusion [231]. In a similar way, attempts to extend this
strategy to different scaffolds based on other aryl systems,
such as indane (as in compound 89, Fig. 15) and pyridine
(90, Fig. 15) are being explored [232,233].
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 55
achieve mimicry: (i) the stabilization of protein secondary
structures by means of different types of cyclic peptides,
including disulfide-bridged loops, head-to-tail and side-chain
to side-chain amide cyclizations, and a variety of C-C ring
closures based on the Grubb’s ring-closing alkene metathesis; (ii) the combination of peptide and non-peptide
elements in the same molecule to fix either helical structures,
β–pleated sheet or reverse turn conformations; (iii) the
development of organic non-peptide architectures able to
bear the appropriate functional groups of a given protein in
the right three-dimensional orientation.
With the demonstration that conformationally restricted
peptides can block protein interfaces, and the advances in
designing peptidomimetics from peptide sequences, it is
anticipated that mimetics based on protein-substructures
could hold great promise as valuable pharmacological tools
and as the next generation of therapeutic agents. Considering
that secondary elements show variations within proteins,
there is still a need for the development of diverse chemical
platforms to accurately imitate these particular spatial
arrangements. An ideal platform should be easily synthesized, preferably on solid-phase, in such a way that it may
then become the central scaffold for combinatorial libraries
suitable for exploring key contacts within PPIs. Although
some significant achievements have been made, as illustrated
in this review, the design aimed at mimicking peptide or
protein structural elements is still open to further progress.
We must be expectant to new learnings in this
multidisciplinary field.
ABREVIATIONS
BACE
=
Mempapsin 2
BBM
=
Brush-border membrane
Bcl-2
=
B-cell lymphoma-2
BDNF
=
Brain-derived neurotrophic factor
BH
=
Binding homology domain
BPI
=
Bactericidal-permeability increasing
protein
CaM
=
Calmodulin
Cat D
=
Cathepsin D
5. CONCLUDING REMARKS
Cat K
=
Cathepsin K
As an alternative to the screening methodologies, the
rational design of modulators (agonists, antagonists and
inhibitors) of PPIs is a hot topic in drug discovery. From the
knowledge of protein interfaces (amino acid composition and
shape), a major challenge for the discovery of druggable
modulators is to identify key secondary structure elements
decisively implicated in the PPI, and then attempt to mimic
these elements with non-peptide molecules. The secondary
structure-driven approaches, described above, have led to
restricted peptide derivatives and non-peptide compounds
with interesting biological activities in different therapeutic
areas (i.e., by targeting protein-protein systems important in
oncology, viral invasion, survival and replication, and
autoimmune diseases). Among all the reported examples,
and independently on the type of secondary element to be
mimicked, three main strategies can be distinguished to
CS
=
Circumsporozoite
DBF
=
Dibenzofurane
ECM
=
Extracellular matrix
ER
=
Estrogen receptors
ErbB2
=
Erythroblastic leukemia viral oncogene
homolog 2
Fn
=
Fibronectin
FTase
=
Farnesyl transferase
GPCR
=
Transmembrane G-protein coupling
receptor
Grb2
=
Growth factor receptor bound protein 2
HBS
=
Hydrogen-bond surrogate
56
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
González-Muñiz et al.
HDM2
=
Human double minute 2
[9]
HIVPR
=
Human immunodeficiency virus protease
[10]
ICAM-1
=
Intracelluler adhesion molecule-1
INs
=
Integrins
LBD
=
Ligand-binding domain
LFA-1
=
Leukocyte function-associated antigen-1
MDM2
=
Murine double minute 2
MHC
=
Major histocompatibility complex
MMP3
=
Stromelysin-1
NGF
=
Nerve growth factor
NR
=
Nuclear receptors
NT-3
=
Neurotrophin-3
NT-4/5
=
Neurotrophin-4/5
NTs
=
Neurotrophins
P53AD
=
p53 activation domain
PF-4
=
Platelet factor-4
Plm
=
Plamesin
PPIs
=
Protein-protein interactions
PTPase
=
Protein tyrosine phosphatase
[18]
RTK
=
Receptor tyrosine kinases
[19]
SDF-1
=
Stromal cell-derived factor-1
[20]
SH2
=
Src Homology 2
Smac
=
Second mitochondria-derived activator of
caspase
[21]
smMLCK
=
Smooth muscle myosin light-chain kinase
[22]
TACE
=
Tumor necrosis factor α converting
enzyme
[23]
[24]
Trk
=
Tyrosine kinase
XIAP
=
X-linked inhibitor of apoptosis protein
REFERENCES
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
Huang, Z. The Chemical Biology of Apoptosis: Exploring ProteinProtein Interactions and the Life and Death of Cells with Small
Molecules. Chem. Biol. 2002, 9, 1059-1072.
Nooren, I. M. A.; Thornton, J. M. Diversity of Protein-Protein
Interactions. EMBO J. 2003, 22, 3486-3492.
Dobson, C. M. Protein Folding and Disease: A View from the First
Horizon Symposium. Nature Rev. Drug Discov. 2003, 2, 154-160.
Archakov, A. I.; Govorun, V. M.; Duvanov, A. V.; Ivanov, Y. D.;
Veselovsky, A. V.; Lewi, P.; Janssen, P. Protein-Protein
Interactions as a Target for Drugs in Proteomics. Proteomics 2003,
3, 380-391.
Pommier, Y.; Cherfils, J. Interfacial Inhibition of Macromolecular
Interactions: Nature’s Paradigm for Drug Discovery. Trends
Pharm. Sci. 2005, 26, 138-145.
Ryan, D. P.; Mattews, J. M. Protein-Protein Interactions in Human
Diseases. Curr. Opin. Struct. Biol. 2005, 15, 441-446.
Veselovsky, A. V.; Ivanov, Y. D.; Ivanov, A. S.; Archakov, A. I.;
Lewi, P.; Janssen, P. Protein-Protein Interactions: Mechanisms and
Modifications by Drugs. J. Mol. Recogn. 2002, 15, 405-422.
Loregian, A.; Marsden, H. S.; Palú, G. Protein-Protein Interactions
as Targets for Antiviral Chemotherapy. Rev. Med. Virol. 2002, 12,
239-262.
[11]
[12]
[13]
[14]
[15]
[16]
[17]
[25]
[26]
[27]
[28]
[29]
[30]
[31]
[32]
Fry, D. C.; Vassilev, L. T. Targeting Protein-Protein Interactions
for Cancer Therapy. J. Mol. Med. 2005, 83, 955-963.
Loregian, A.; Palú, G. Disruption of Protein-Protein Interactions:
Towards New Targets for Chemotherapy. J. Cell. Physiol. 2005,
204, 750-762.
Arkin, M. Protein-Protein Interactions and Cancer: Small
Molecules Going in for the Kill. Curr. Opin. Chem. Biol. 2005, 9,
317-324.
DeLano, W. L. Unraveling Hot Spots in Binding Interfaces:
Progress and Challenges. Curr. Opin. Struct. Biol. 2002, 12, 14-20.
Ma, B.; Elkayam, M.; Wolfson, H.; Nussinov, R. Protein-Protein
Interactions: Structurally Conserved Residues Distinguish between
Binding Sites and Exposed Protein Surfaces. Proc. Natl. Acad. Sci.
USA. 2003, 100, 5772-5777.
Dramani, A. K.; Bunescu, R. C.; Mooney, R. J.; Marcotte, E. M.
Consolidating the Set of Known Human Protein-Protein
Interactions in Preparation of Large Scale Mapping of the Human
Interactome. Genome Biol. 2005, 6, R40.
Stelzl, U.; Worm, U.; Lalowski, M.; Haening, C.; Brembeck, F. H.;
Goehler, H.; Stroedicke, M.; Zenkner, M.; Schoenherr, A.;
Koeppen, S.; Timm, J.; Mintzlaff, S.; Abraham, C.; Bock, N.;
Kietzmann, S.; Goedde, A.; Toksöz, E.; Droege, A.; Krobitsch, S.;
Korn, B.; Birchmeier, W.; Lehrach, H.; Wanker, E. E. A Human
Protein-Protein Interaction Network: A Resource for Annotating
the Proteasome. Cell 2005, 122, 957-968.
Rhodes, D. R.; Tomlins, S. A.; Varambally, S.; Mahavisno, V.;
Barrette, T.; Kalyana-Sundaram, S.; Ghosh, D.; Pandey, A.;
Chinnaiyan, A. M. Probabilistic Model of the Human ProteinProtein Interaction Network. Nat. Biotechnol. 2005, 23, 951-958.
Ball, L.; Kühne, R.; Schneider-Mergener, J.; Oschkinat, H.
Recognition of Proline-Rich Motifs by Protein-Protein Interaction
Domains. Angew. Chem. Int. Ed. 2005, 44, 2852-2869.
Vaughan, T. J.; Osbourn, J. K.; Tempest, P. R. Human Antibodies
by Design. Nat. Biotechnol. 1998, 16, 535-539.
Gadek, T. R.; Nicholas, J. B. Small Molecule Antagonists of
Proteins. Biochem. Pharmacol. 2003, 65, 1-8.
Souroujon, M. C.; Mochly-Rosen, D. Peptide Modulators of
Protein-Protein Interactions in Intracellular Signaling. Nat.
Biotechnol. 1998, 16, 919-924.
Sillereud, L. O.; Larson, R. S. Design and Structure of Peptide and
Peptidomimetic Antagonists of Protein-Protein Interaction. Curr.
Protein Peptide Sci. 2005, 6, 151-169.
Toogood, P. L. Inhibition of Protein-Protein Association by Small
Molecules: Approaches and Progress. J. Med. Chem. 2002, 45,
1543-1558.
Berg, T. Modulation of Protein-Protein Interactions with Small
Organic Molecules. Angew. Chem. Int. Ed. 2003, 42, 2462-2481.
Boger, D. L.; Desharmais, J.; Capps, K. Solution-Phase
Combinatorial Libraries: Modulating Cellular Signaling by
Targeting Protein-Protein or Protein-DNA Interactions. Angew.
Chem. Int. Ed. 2003, 42, 4138-4176.
Yin, H.; Hamilton, A. D. Strategies for Targeting Protein-Protein
Interactions with Synthetic Agents. Angew. Chem. Int. Ed. 2005,
44, 4130-4163.
Huang, N.; Nagarsekar, A.; Xia, G.; Hayashi, J.; MacKerell, A. D.,
Jr. Identification of Non-Phosphate-Containing Small Molecular
Weight Inhibitors of the Tyrosine Kinase p56 Lck SH2 Domain via
in Silico Screening against pY+3 Binding Site. J. Med. Chem.
2004, 47, 3502-3511.
May, A.; Zacharias, M. Accounting for Global Protein
Deformability During Protein-Protein and Protein-Ligand Docking.
Biochim. Biophys. Acta 2005, 1754, 225-231.
Stigers, K. D.; Soth, M. J.; Nowick, J. S. Designed Molecules that
Fold to Mimic Protein Secondary Structures. Curr. Opin. Chem.
Biol. 1999, 3, 714-723.
Peczuh, M. W.; Hamilton, A. D. Peptide and Protein Recognition
by Designed Molecules. Chem. Rev. 2000, 100, 2479-2494.
Burgess, K. Solid-Phase Synthesis of β–Turn Analogues to Mimic
or Disrupt Protein-Protein Interactions. Acc. Chem. Res. 2001, 34,
826-835.
Preissner, R.; Goede, A.; Rother, K.; Osterkamp, F.; Koert, U.;
Froemmel, C. Matching Organic Libraries with ProteinSubstructures. J. Comp.-Aid. Mol. Des. 2001, 15, 811-817.
Cochran, A. G. Protein-Protein Interfaces: Mimics and Inhibitors.
Curr. Opin. Chem. Biol. 2001, 5, 654-659.
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
[33]
[34]
[35]
[36]
[37]
[38]
[39]
[40]
[41]
[42]
[43]
[44]
[45]
[46]
[47]
[48]
[49]
[50]
[51]
[52]
Zhao, L.; Chmielewski, J. Inhibiting Protein-Protein Interactions
using Designed Molecules. Curr. Opin. Struct. Biol. 2005, 15, 3134.
Fletcher, S.; Hamilton, A. D. Protein Surface Recognition and
Proteomimetics: Mimics of Protein Surface Structure and Function.
Curr. Opin. Chem. Biol. 2005, 9, 632-638.
Rose, G. D.; Gierasch, L. M.; Smith, J. A. Turns in Peptides and
Proteins. Adv. Protein Chem. 1985, 37, 1-109.
Tyndall, J. D. A.; Pfeiffer, B.; Abbenante, G.; Fairlie, D. P. Over
One Hundred Peptide-Activated G Protein-Coupled Receptors
Recognize Ligands with Turn Structure. Chem. Rev. 2005, 105,
793-826.
Panasik, Jr., N.; Fleming, P. J.; Rose, G. D. Hydrogen-Bonded
Turns in Proteins: The Case for a Recount. Protein Sci . 2005, 14,
2910-2914.
De la Figuera, N.; Rozas, I.; García-López, M. T.; GonzálezMuñiz, R. 2(S)-Amino-3-oxo-11b(R)-hexahydroindolizino[8,7b]indole-5(S)-carboxylate as a New Type of β–Turn Mimetic. J.
Chem. Soc. Chem. Commun. 1994, 613-614.
De la Figuera, N.; Alkorta, I.; García-López, M. T.; Herranz, R.;
González-Muñiz, R. 2-Amino-3-oxohexahydroindolizino[8,7b]indole-5-carboxylate Derivatives as New Scaffolds for
Mimicking β–Turn Secondary Structures. Molecular Dynamics and
Stereoselective Synthesis. Tetrahedron 1995, 51, 7841-7856.
Andreu, D.; Ruiz, S.; Carreño, C.; Alsina, J.; Albericio, F.;
Jiménez, A.; De la Figuera, N.; Herranz, R.; García-López, M. T.;
González-Muñiz, R. IBTM-Containing Gramicidin S Analogues:
Evidence for IBTM as a Suitable Type II' β–Turn Mimetic. J. Am.
Chem. Soc. 1997, 119, 10579-10586.
De la Figuera, N.; Martín-Martínez, M.; Herranz, R.; GarcíaLópez, M. T.; Latorre, M.; Cenarruzabeitia, E.; Del Río, J.;
González-Muñiz, R. Highly Constrained Dipeptoid Analogues
Containing a Type II' β–Turn Mimic as Novel Potent and Selective
CCK-A Receptor Ligands. Bioorg. Med. Chem. Lett. 1999, 9, 4348.
Martín-Martínez, M.; De la Figuera, N.; Latorre, M.; Herranz, R.;
García-López, M. T.; Cenarruzabeitia, E.; Del Río, J.; GonzálezMuñiz, R. β–Turned Dipeptoids as Potent and Selective CCK-1
Receptor Antagonists. J. Med. Chem. 2000, 43, 3770-3777.
González-Muñiz, R.; Martín-Martínez, M.; Granata, C.; De
Oliveira, E.; Santiveri, C. M.; González, C.; Frechilla, D.; Herranz,
R.; García-López, M. T.; Del Río, J.; Jiménez, A.; Andreu, D.
Conformationally Restricted PACAP27 Analogues Incorporating
Type II/II' β–Turn Mimetics. Synthesis, NMR Structure
Determination, and Binding Affinity. Bioorg. Med. Chem . 2001, 9,
3173-3183.
Martín-Martínez, M.; Latorre, M.; García-López, M. T.;
Cenarruzabeitia, E.; Del Río, J.; González-Muñiz, R. Effects of the
Incorporation of IBTM β–Turn Mimetics into the Dipeptoid CCK1
Receptor Agonist PD 170292. Bioorg. Med. Chem. Lett. 2002, 12,
109-112.
Gutiérrez-Rodríguez, M.; Martín-Martínez, M.; García-López,
M.T.; Herranz, R.; Polanco, C.; Rodríguez-Campos, I.;
Manzanares, I.; Cárdenas, F.; Feliz, M.; Lloyd-Williams, P.; Giralt,
E. Synthesis, Conformational Analysis, and Cytotoxicity of
Conformationally Constrained Aplidine and Tamandarine A
Analogues Incorporating a Spirolactam β–Turn Mimetic. J. Med.
Chem. 2004, 47, 5700-5712.
Martin-Martínez, M.; De la Figuera, N.; Latorre, M.; García-López,
M.T.; Cenarruzabeitia, E.; Del Río, J.; González-Muñiz, R.
Conformationally constrained CCK4 analogues incorporating
IBTM and BTD β–turn mimetics. J. Med. Chem. 2005, 48, 76677674.
Ball, J. B.; Alewood, P. F. Conformational Constrains: Nonpeptide
β–Turn Mimics. J. Mol. Recognit. 1990, 3, 55-64.
Hölzemann, G. Peptide Conformation Mimetics (Part 1). Kontakte
1991, 3-11.
Hölzemann, G. Peptide Conformation Mimetics (Part 2). Kontakte
1991, 55-63.
Kahn, M. Peptide Secondary Structure Mimetics: Recent Advances
and Future Challenges. Synthesis 1993, 821-826.
Liskamp, R. M. J. Conformationally Restricted Amino Acids and
Dipeptides, (non)Peptidomimetics and Secondary Structure
Mimetics. Recl. Trav. Chim. Pays-Bas 1994, 113, 1-19.
Hanessian, S.; McNaughton-Smith, G.; Lombart, H.-G.; Lubell, W.
D. Design and Synthesis of Conformationally Constrained Amino
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 57
[53]
[54]
[55]
[56]
[57]
[58]
[59]
[60]
[61]
[62]
[63]
[64]
[65]
[66]
[67]
[68]
[69]
[70]
Acids as Versatile Scaffolds and Peptide Mimetics. Tetrahedron
1997, 53, 12789-12854.
Kim, H.-O.; Kahn, M. A Merger of Rational Drug Design and
Combinatorial Chemistry: Development and Application of Peptide
Secondary Structure Mimetics. Comb. Chem. High T. Scr. 2000, 3,
167-183.
Souers, A. J.; Ellman, J. A. β–Turn Mimetic Library Synthesis:
Scaffolds and Applications. Tetrahedron 2001, 57, 7431-7448.
Egucji, M.; McMillan, M.; Nguyen, C.; Teo, J.-L.; Chi, E. Y.;
Henderson, W. R.; Kahn, M. Chemogenomics with Peptide
Secondary Structure Mimetics. Tetrahedron 2001, 57, 7431-7448.
Shimaoka, M.; Springer, T. A. Therapeutic antagonists and
Conformational Regulation of Integrin Function. Nature Rev. Drug
Discov. 2003, 2, 703-716.
Calzada, M. J.; Roberts, D. D. Novel Integrin Antagonists Derived
from Thrombospondins. Curr. Pharm. Design 2005, 11, 849-866.
Aumailley, M.; Gurrath, M.; Muller, G.; Calvete, J.; Timpl, R.;
Kessler, H. Arg-Gly-Asp Constrained within Cyclic Pentapeptides.
Strong and Selective Inhibitors of Cell Adhesion to Vitronectin and
Laminin Fragment P1. FEBS Lett. 1991, 291, 50-54.
Geyer, A.; Müller, G.; Kessler, H. Conformational Análysis of a
Cyclic RGD Peptide Containing a ψ[CH2-NH] Bond: A
Possitional Shift in Backbone Structure Caused by a Single
Dipeptide Mimetic. J. Am. Chem. Soc. 1994, 116, 7735-7743.
Dechantsreiter, M. A.; Planker, E.; Matha, B.; Lohof, E.;
Holzemann, G.; Jonczyk, A.; Goodman, S. L.; Kessler, H. NMethylated cyclic RGD peptides as highly active and selective
αVβ3 integrin antagonists. J. Med. Chem. 1999, 42, 3033-3040.
Haubner, R.; Schmitt, W.; Hölzemann, G.; Goodman, S. L.;
Jonczyk, A.; Kessler, H. Cyclic RGD Peptides Containing β–Turn
Mimetics. J. Am. Chem. Soc. 1996, 118, 7881-7891.
Sukkop, M.; Marinelli, L.; Séller, M.; Brandl, T.; Goodman, S. L.;
Hoffmann, R. W.; Kessler, H. Designed Beta–Turn Mimic Based
on the Allylic-Starin Concept: Evaluation of Structural and
Biological Features by Incorporation into a Cyclic RGD Peptide
(Cyclo(-L-arginylglycyl-L-α-aspartyl)). Helv. Chim. Acta 2002, 85,
4442-4452.
Lohof, E.; Planker, E.; Mang, C.; Burkhart, F.; Dechantsreiter, M.
A.; Haubner, R.; Wester, H.-J.; Schwaiger, M.; Hölzemann, G.;
Goodman, S. L.; Kessler, H. Carbohydrate Derivatives for Use in
Drug Design: Cyclic αV-Selective RGD Ppetides. Angew. Chem.
Int. Ed. 2000, 39, 2761-2764.
Belvisi, L.; Bernardi, A.; Checchia, A.; Manzoni, L.; Potenza, D.;
Scolastico, C.; Castorina, M.; Cupelli, A.; Giannini, G.; Carminati,
P.; Pisano, C. Potent Integrin Antagonists from a Small Library of
RGD-Including Cyclic Pseudopeptides. Org. Lett. 2001, 3, 10011004.
Belvisi, L.; Bernardi, A.; Colombo, M.; Manzoni, L.; Potenza, D.;
Scolastico, C.; Giannini, G.; Marcellini, M.; Riccioni, T.;
Castorina, M.; LoGiudice, P.; Pisano, C. Targeting Integrins:
Insights into Structure and Activity of Cyclic RGD Pentapeptide
Mimics Containing Azabicycloalkane Amino Acids. Bioorg. Med.
Chem. 2006, 14, 169-180.
Xiong, J.-P.; Stehle, T.; Ahang, R.; Joachimiak, A.; Frec., M.
Goodman, S. L.; Arnaout, M. A. Crystal Structure of the
Extracellular Segment of Integrin αVβ3 in Complex with an ArgGly-Asp Ligand. Science 2002, 296, 151-155.
Casiraghi, G.; Rassu, G.; Auzzas, L.; Burreddu, P.; Gaetani, E.;
Battistini, L.; Zanardi, F.; Curti, C.; Nicastro, G.; Belvisi, L.;
Motto, I.; Castorina, M.; Giannini, G.; Pisano, C. Grafting
Aminocyclopentane Carboxylic Acids onto the RGD Tripeptide
Séquence Generates Low Nanomolar αVβ3/αVβ5 Integrin Dual
Binders. J. Med. Chem. 2005, 48, 7675-7687.
Haubner, R.; Wester, H.-J.; Weber, W. A.; Mang, C.; Ziegler, S. I.;
Goodman, S. L.; Senekowitsch-Schmidtke, R.; Kessler, H.;
Scwaigner, M. Noninvasive Imaging of αVβ3 Integrin Expression
Using 18F-labeled-containing Glycopeptide and Positron Emission
Tomography. Cancer Res. 2001, 61, 1781-1785.
Kopple, K. D.; Baures, P. W.; Bean, J.W.; D’Ambrosio, C. A.;
Hughes, J. L.; Peishoff, C. E.; Eggleston, D. S. Conformations of
Arg-Gly-Asp Containing Heterodetic Cyclic Peptides: Solution and
Crystal Studies. J. Am. Chem. Soc. 1992, 114, 9615-9623.
Callahan, J. F.; Bean, J.W.; Burgess, J. L.; Eggleston, D. S.;
Hwang, S. M.; Kopple, K. D.; Koster, P. F.; Nichols, A.; Peishoff,
C. E.; Samanen, J. M.; Vasko, J. A.; Wong, A.; Huffman, W. F.
Design and Synthesis of a C7 Mimetic for the Predicted γ–Turn
58
[71]
[72]
[73]
[74]
[75]
[76]
[77]
[78]
[79]
[80]
[81]
[82]
[83]
[84]
[85]
[86]
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
Conformation Found in Several Constrained RGD Antagonists. J.
Med. Chem. 1992, 35, 3970-3972.
Ku, T. W.; Ali, F. E.; Barton, L. S.; Bean, J. W.; Bondinell, W. E.;
Burgess, J. L.; Callahan, J. F.; Calvo, R. R.; Chen, L.; Eggleston,
D. S.; Gleason, J. G.; Huffman, W. F.; Hwang, S. M.; Jakas, D. R.;
Karash, C. B.; Keenan, R. M.; Kopple, K. D.; Miller, W. H.;
Newlander, K. A.; Nichols, A.; Parker, M. F.; Peishoff, C. E.;
Samanen, J. M.; Uzinskas, I.; Venslavsky, J. W. Direct Design of a
Potent Non-peptide Fibrinogen Receptor Antagonist Based on the
Structure and Conformation of a Highly Constrained Cyclic RGD
Peptide. J. Am. Chem. Soc. 1993, 115, 8861-8862.
Samanen, J. M.; Ali, F. E.; Barton, L. S.; Bondinell, W. E.;
Burgess, J. L.; Callahan, J. F.; Calvo, R. R.; Chen, W.; Chen, L.;
Erhard, K.; Feuerstein, G.; Heys, R.; Hwang, S.-M.; Jakas, D. R.;
Keenan, R. M.; Koster, P. F.; Ku, T. W.; Kwon, C.; Lee, C.- P.;
Miller, W. H.; Newlander, K. A.; Nichols, A.; Parker, M.; Peishoff,
C. E.; Rhodes, G.; Ross, S.; Shu, A.; Simpson, R.; Takata, D.;
Vasko-Moser, J. A.; Valocik, R. E.; Yellin, T. O.; Uzinskas, I.;
Venslavsky, J. W.; Wong, A.; Yuan, C.-K.; Huffman, W. F. Potent,
Selective, Orally Active 3-Oxo-1,4-benzodiazepine GPIIb/IIIa
Integrin Antagonists. J. Med. Chem. 1996, 39, 4867-4870.
Keenan, R. M.; Miller, W. H.; Kwon, C.; Ali, F. E.; Callahan, J. F.;
Calvo, R. R.; Hwang, S. M.; Kopple, K. D.; Peishoff, C. E.;
Samanen, J. M.; Wong, A. S.; Yuan, C. K.; Huffman, W. F.
Discovery of Potent Nonpeptide Vitronectin Receptor (αVβ3)
Antagonists. J. Med. Chem. 1997, 40, 2289-2292.
Miller, W. H.; Alberts, D. P.; Bhatnagar, P. K.; Bondinell, W. E.;
Callahan, J. F.; Calvo, R. R.; Cousins, R. D.; Erhard, K. F.;
Heerding, D. A.; Keenan, R. M.; Kwon, C.; Manley, P. J.;
Newlander, K. A.; Ross, S. T.; Samanen, J. M.; Uzinskas, I. N.;
Venslavsky, J. W.; Yuan, C. C.-K.; Haltiwanger, R. C.; Gowen,
M.; Hwang, S.-M.; James, I. E.; Lark, M. W.; Rieman, D. J.;
Stroup, G. B.; Azzarano, L. M.; Salyers, K. L.; Smith, B. R.; Ward,
K. W.; Johanson, K. O.; Huffman, W. F. Discovery of Orally
Active Nonpeptide Vitronectin Receptor Antagonists Based on a 2Benzazepine Gly-Asp Mimetic. J. Med. Chem. 2000, 43, 22-26.
Assa-Munt, N.; Jia, X.; Laakkonen, P.; Ruoslahti, E. Solution
Structure and Integrin Binding Activities of an RGD Peptide with
Two Isomers. Biochemistry 2001, 40, 2373-2378.
Shukla, R.; Thomas, T. P.; Peters, J.; Kotlyar, A.; Myc, A.; Baker,
Jr., J. R. Tumor Angiogenic Vasculature Targeting with PAMAM
Dendrimer-RGD conjugates. Chem. Commun. 2005, 5739-5741.
Boer, J.; Gottschling, D.; Schuster, A.; Semmrich, M.; Holzmann,
B.; Kessler, H. Design and Synthesis of Potent and Selective α4β7
Integrin Antagonists. J. Med. Chem. 2001, 44, 2586-2592.
Locardi, E.; Boer, J.; Schuster, A.; Holzmann, B.; Kessler, H.
Synthesis and Structure-Activity Relationship of Mannose-Based
Peptidomimetics Selectively Blocking Integrin α4β7 Binding to
Mucosal Addressin Cell Adhesion Molecule-1. J. Med. Chem.
2003, 46, 5752-5762.
Leahy, D. J.; Aukhil, I.; Erickson, H.P. 2.0 Å Crystal Structure of a
Four-Domain Segment of Human Fibronectin Encompassing the
RGD Loop and Synergy Region. Cell 1996, 84, 155-164.
Bourguet, E.; Banères, J.-L.; Parello, J.; Lusinchi, X.; Girard, J.-P.;
Vidal, J.-P. Non-Peptide RGD Antagonists: A Novel Class of
Mimetics, the 5,8-Disubstituted 1-Azabicyclo[5.2.0]nonan-2-one
Lactam. Bioorg. Med. Chem. Lett. 2003, 13, 1561-1564.
Yamanaka, T.; Ohkubo, M.; Kuroda, S.; Nakamura, H.; Takahashi,
F.; Aoki, T.; Mihara, K.; Seki, J.; Kato, M. Design, Synthesis, and
Structure-Activity Relationships of Potent GPIIb/IIIa Antagonists:
Discovery of FK419. Bioorg. Med. Chem. 2005, 13, 4343-4352.
Wiesmann, C.; Vos, A. M. Nerve Growth Factor: Structure and
Function. Cell. Mol. Life Sci. 2001, 58, 748-759.
Saragovi, H. U.; Gehring, K. Development of Pharmacological
Agents for Targeting Neurotrophins and their Receptors. Trends
Pharmacol. Sci. 2000, 21, 93-98.
Pattarawarapan, M.; Burgess, K. Molecular Basis of NeurotrophinReceptor Interactions. J. Med. Chem. 2003, 46, 5277-5291.
LeSauteur, L.; Wei, L.; Gibbs, B. F.; Saragovi, H. U. Small Peptide
Mimics of Nerve Growth Factor Bind TrkA Receptors and Affect
Biological Responses. J. Biol. Chem. 1995, 270, 6564-6569.
Beglova, N.; LeSauteur, L.; Ekiel, I.; Saragovi, H. U.; Gehring, K.
Solution Structure and Internal Motion of a Bioactive Peptide
Derived from Nerve Growth Factor. J. Biol. Chem. 1998, 273,
23652-23658.
González-Muñiz et al.
[87]
[88]
[89]
[90]
[91]
[92]
[93]
[94]
[95]
[96]
[97]
[98]
[99]
[100]
[101]
[102]
[103]
[104]
[105]
[106]
[107]
Beglova, N.; Maliartchouk, S.; Ekiel, I.; Zaccaro, M. C.; Saragovi,
H. U.; Gehring, K. Design and Solution Structure of Functional
Peptide Mimetics of Nerve Growth Factor. J. Med. Chem. 2000,
43, 3530-3540.
Longo, F. M.; Manthorpe, M.; Xie, Y. M.; Varon, S. Synthetic
NGF Peptide Derivatives Prevent Neuronal Death Via a p75
Receptor-Dependent Mechanism. J. Neurosci. Res. 1997, 48, 1-17.
Xie, Y.; Tisi, M. A.; Yeo, T. T.; Longo, F. M. Nerve Growth Factor
(NGF) Loop 4 Dimeric Mimetics Activate ERK and AKT and
Promote NGF-like Neurotrophic Effects. J. Biol. Chem. 2000, 275,
29863-29874.
O’Leary, P. D.; Hughess, R. A. Design of Potent Peptide Mimetics
of Brain-Derived Neurotrophic Factor. J. Biol. Chem. 2003, 278,
25738-25744.
Maliartchouk, S.; Feng, Y.; Ivanisevic, L.; Debeir, T.; Cuello, A.
C.; Burgess, K.; Saragovi, H. U. A. Designed Peptidomimetic
Agonistic Ligand of TrkA Nerve Growth Factor Receptors. Mol.
Pharmacol. 2000, 57, 385-391.
Bruno, M. A.; Clarke, P. B. S.; Seltzer, A.; Quirion, R.; Burgess,
K.; Cuello, A. C.; Saragovi, H. U. Long-Lasting Rescue of AgeAssociated Deficits in Cognition and the CNS Cholinergic
Phenotype by a Partial Agonist Peptidomimetic Ligand of TrkA. J.
Neurosci. 2004, 24, 8009-8018.
Lee, H. B.; Zaccaro, M. C.; Pattarawarapan, M.; Roy, S.; Saragovi,
H. U.; Burgess, K. Syntheses and Activities of New C10 β–Turn
Peptidomimetics. J. Org. Chem. 2004, 69, 701-713.
Pattarawarapan, M.; Zaccaro, M. C.; Saragovi, H. U.; Burgess, K.
New Templates for Syntheses of Ring-Fused, C10 β–Turn
Peptidomimetics Leading to the First Reported Small-Molecule
Mimic of Neurotrophin-3. J. Med. Chem. 2002, 45, 4387-4390.
Zaccaro, M. C.; Lee, H. B.; Pattarawarapan, M.; Xia, Z.; Caron, A.;
L’Heureux, P.-J.; Bengio, Y.; Burgess, K.; Saragovi, H. U.
Selective Small Molecule Peptidomimetics Ligands of TrkC and
TrkA Receptors Afford Discrete or Complete Neurotrophic
Activity. Chem. Biol. 2005, 12, 1015-1028.
Zhang, A. J.; Khare, S.; Gokulan, K.; Linthicum, D. S.; Burgess, K.
Dimeric β–Turn Peptidomimetics as Ligands for the Neurotrophin
Receptor TrkC. Bioorg. Med. Chem. Lett. 2001, 11, 207-210.
Pattarawarapan, M.; Reyes, S.; Xia, Z.; Zaccaro, M. C.; Saragovi,
H. U.; Burgess, K. Selective Formation of Homo- and
Heterobivalent Peptidomimetics. J. Med. Chem. 2003, 46, 35653567.
Angell, Y.; Burgess, K. Rign Closure to β–Turn Mimics via
Copper-Catalyzed Azide/Alkyne Cycloadditions. J. Org. Chem.
2005, 70, 9595-9598.
García-Echeverría, C. Antagonists of the Src Homology 2 (SH2)
Domains of Grb2, Src, lck and ZAP-70. Curr. Med. Chem. 2001, 8,
1589-1604.
Machida, K.; Mayer, B. J. The SH2 Domain: Versatile Signaling
Module and Pharmaceutical Target. Biochim. Biophys. Acta 2005,
1747, 1-25.
Tari, A. M.; Hung, M.-C.; Li, K.; Lopez-Berestein, G. Growth
Inhibition of Breast Cancer Cells by Rgb2 Downregulation is
Correlated with Inactivation of Mitogen-Activated Protein Kinase
in EGFR, but not in ErbB2, Cells. Oncogene 1999, 18, 1325-1332.
Soriano, J. V.; Liu, N.; Gao, Y.; Yao, Z.-J.; Ishibashi, T.; Underhill,
C.; Burke, T.R., Jr.; Bottaro, D. P. Inhibition of Angiogenesis by
Growth Factor Receptor Bound Protein 2-Src Homology 2 Domain
Binding Antagonists. Mol. Cancer Ther. 2004, 3, 1289-1299.
Rahuel, J.; Gay, B.; Erdmann, D.; Strauss, A.; García-Echeverría,
C.; Furet, P.; Caravatti, G.; Fretz, H.; Schoepfer, J.; Grütter, M. G.
Structural Basis for Specificity of Grb2-SH2 Revealed by a Novel
Ligand Binding Mode. Nat. Struc. Biol. 1996, 3, 586-589.
Furet, P.; Gay, B.; Caravatti, G.; García-Echeverría, C.; Rahuel, J.;
Schoepfer, J.; Fretz, H. Structure-Based Design and Synthesis of
High Affinity Tripeptide Ligands of the Grb2-SH2 Domain. J.
Chem. Med. 1998, 41, 3442-3449.
Schoepfer, J.; Fretz, H.; Gay, B.; García-Echeverría, C.; End, N.;
Caravati, G. Highly Potent Inhibitors of the Grb2-SH2 Domain.
Bioorg. Med. Chem. Lett. 1999, 9, 221-226.
Yao, Z.-J.; King, C. R.; Cao, T.; Kelley, J.; Milne, G. W. A.; Voigt,
J.H.; Burke, T.R., Jr. Potent Inhibition of Grb2 SH2 Domain
Binding by Nonphosphate-Containing Ligands. J. Med. Chem.
1999, 42, 25-35.
Gao, Y.; Luo, J.; Yao, Z.-J.; Guo, R.; Zou, H.; Kelley, J.; Voigt,
J.H.; Yang, D.; Burke, T.R., Jr. Inhibition of Grb2 SH2 Domain
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
[108]
[109]
[110]
[111]
[112]
[113]
[114]
[115]
[116]
[117]
[118]
[119]
[120]
[121]
[122]
[123]
Binding by Non-Phosphate Containing Ligands. 2. 4-(2Malonyl)phenylalanine as a Potent Phosphotyrosyl Mimetic. J.
Med. Chem. 2000, 43, 911-920.
Wei, C.-Q.; Li, B.; Guo, R.; Yang, D.; Burke, T. R. Jr. Development of a Phosphate-Stable Phosphotyrosyl Mimetic Suitable
Protected for the Synthesis of High-Affinity Grb2 SH2 DomainBinding Ligands. Bioorg. Med. Chem. Lett. 2002, 12, 2781-2784.
Gao, Y.; Voigt, J.; Wu, J. X.; Yang, D.; Burke, T. R., Jr.
Macrocyclization in the Design of a Conformationally Constrained
Grb2 SH2 Domain Inhibitor. Bioorg. Med. Chem. Lett. 2001, 11,
1889-1892.
Wei, C.-Q.; Gao, Y.; Lee, K.; Guo, R.; Zhang, M.; Yang, D.;
Burke, Jr., T. R. Macrocyclization in the Design of Grb2 SH2
Domain-Binding Ligands Exhibiting High Potency in Whole-Cell
Systems. J. Med. Chem. 2003, 46, 244-254.
Shi, Z.-D.; Lee, K.; Liu, H.; Zhang, M.; Roberts, L. R.; Worthy, K.
M.; Fivash, M. J.; Fischer, R. J.; Yang, D.; Burke, T. R., Jr. A
Novel Macrocyclic Tetrapeptide Mimetic that Exhibits LowPicomolar Grb2 SH2 Domain-Binding Affinity. Biochem. Byophys.
Res. Commun. 2003, 310, 378-383.
Shi, Z.-Q.; Wei, C.-Q.; Lee, K.; Liu, H.; Zhang, M.; Araki, T.;
Roberts, L. R.; Worthy, K. M.; Fischer, R. J.; Neel, B. G.; Kelley,
J. A.; Yang, D.; Burke, T. R., Jr. Macrocyclization in the Design of
Non-Phosphorus-Containing Grb2 SH2 Domain-Binding Ligands.
J. Med. Chem. 2004, 47, 2166-2169.
Kang, S.-U.; Shi, Z.-Q.; Worthy, K. M.; Bindu, L. K.;
Dharmawardana, P. G.; Choyke, K. M.; Bottaro, D. P.; Fischer, R.
J.; Burke, T. R., Jr. Examination of Phosphoryl-Mimicking
Functionalities within a Macrocyclic Grb2 SH2 Domain-Binding
Platform. J. Med. Chem. 2005, 48, 3945-3948.
Phan, J.; Shi, Z.-Q.; Burke, T. R., Jr.; Waung, D. S. Crystal
Structure of High-Affinity Macrocyclic Peptide Mimetic in
Complex with the Grb2 SH2 Domain. J. Mol. Biol. 2005, 353, 104115.
Shi, Z.-Q.; Liu, H.; Zhang, M.; Worthy, K. M.; Bindu, L. K.; Yang,
D.; Fischer, R. J.; Burke, T. R., Jr. Synthesis of a C-Terminal
Biotinylated Macrocyclic Peptide Mimetic Exhibiting Grb2 SH2
Domain-Binding Affinity. Bioorg. Med. Chem. 2005, 13, 42004208.
Oligino, L.; Lung, F.-D. T.; Sastry, L.; Bigelow, J.; Cao, T.;
Curran, M.; Burke, T. R., Jr.; Wang, S.; Krag, D.; Roller, P. P.;
King, C. R. Nonphosphorylated Peptide Ligands for the Grb2 Src
Homology 2 Domain. J. Biol. Chem. 1997, 272, 29046-29052.
Long, Y.-Q.; Lung, F.-D. T.; Roller, P. P. Global Optimization of
Conformationally Constraint on Nonphosphorylated Cyclic Peptide
Antagonists of the Grb2-SH2 Domain. Bioorg. Med. Chem. 2003,
11, 3929-3936.
Son, Y.-L.; Peach, M. L.; Roller, P. P.; Qiu, S.; Wang, S.; Long,
Y.-Q. Global Optimization of Conformationally Constraint on
Nonphosphorylated Cyclic Peptide Antagonists of the Grb2-SH2
Domain. J. Med. Chem. 2006, 49, 1585-1596.
Shi, Y.-h; Song, Y.-L.; Lin, D.-h.; Tan, J.; Roller, R. P.; Li, Q.;
Long, Y.-Q.; Long, Y.-Q.; Song, G.-Q. Binding Affinity Difference
Induced by the Stereochemistry of the Sulfoxide Bridge of the
Cyclic Peptide Inhibitors of Grb2-SH2 Domain: NMR Studies for
the Structural Origin. Biochem. Biophys. Res. Commun. 2005, 330,
1254-1261.
Newlander, K. A.; Callahan, J. F.; Moore, M. L.; Tomaszek, T. A.,
Jr.; Huffman, W. F. A novel Constrained Reduced-Amide Inhibitor
of HIV-1 Protease Derived from the Sequential Incorporation of
γ–Turn Mimetics into a Model Substrate. J. Med. Chem. 1993, 36,
2321-2331.
Chen, S.; Chrusciel, R. A.; Nakanishi, H.; Raktabutr, A.; Johnson,
M. E.; Sato, A.; Weiner, D.; Hoxie, J.; Saragovi, H. U.; Greene, M.
I.; Kahn, M. Design and Synthesis of a CD4 β–Turn Mimetic that
Inhibits Human Immunodeficiency Virus Envelope Glycoprotein
gp120 Binding and Infection of Human Lymphocytes. Proc. Natl.
Acad. Sci. USA 1992, 89, 5872-5876.
Urban, J.; Qabar, M.; Sia, C.; Klein, M.; Kahn, M. Sculpted
Immunogens; B-Cell Epitope Optimization Using Constrained
Secondary Structure Libraries. Bioorg. Med. Chem. 1996, 4, 673676.
Choi, Y. H.; Rho, W. S.; Kim, N. D.; Park, S. J.; Shin, D. H.; Kim,
J. W.; Im, S. H.; Won, H. S.; Lee, C. W.; Chae, C. B.; Sung, Y. C.
Short Peptides with Induced β–Turn Inhibit the Interaction between
HIV-1 gp120 and CD4. J. Med. Chem. 2001, 44, 1356-1363.
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 59
[124]
[125]
[126]
[127]
[128]
[129]
[130]
[131]
[132]
[133]
[134]
[135]
[136]
[137]
[138]
[139]
[140]
[141]
[142]
Jining, L.; Makagiansar, I.; Yusuf-Makagiansar, H.; Chow, V. T.
K.; Siahaan, T. J.; Jois, S. D. S. Design, Structure and Biological
Activity of β–Turn Peptides of CD2 Protein for Inhibition of T-Cell
Adhesion. Eur. J. Biochem. 2004, 271, 2873-2886.
Liu, J.; Ying, J.; Chow, V. T. K.; Hruby, V. J.; Satyanarayanajois,
S. D. Structure-Activity Studies of Peptides from the “Hot-Spot”
Region of Human CD2 Protein: Development of Peptides for
Immunomodulation. J. Med. Chem. 2005, 48, 6236-6249.
Sun, H.; Nikolovska-Coleska, Z.; Yang, C.-Y.; Xu, L.; Tomita, Y.;
Krajewski, K.; Roller, P. P.; Wang, S. Structure-Based Design,
Synthesis, and Evaluation of Conformationally Constrained
Mimetics of the Second Mitochondria-Derived Activator of
Caspase that Target the X-Linked Inhibitor of Apoptosis
Protein/caspase-9 Interaction Site. J. Med. Chem. 2004, 47, 41474150.
Sun, H.; Nikolovska-Coleska, Z.; Yang, C.-Y.; Xu, Liu, M.; L.;
Tomita, Y.; Pan, H.; Yoshioka, Y.; Krajewski, K.; Roller, P. P.;
Wang, S. Structure-Based Design of Potent, Conformationally
Constrained Smac Mimetics. J. Am. Chem. Soc. 2004, 126, 1668616687.
Nanzer, A. P.; Torda, A. E.; Bisang, C.; Weber, C.; Robinson, J.
A.; Van Gunsteren, W. F. Dynamical Studies of Peptide Motifs in
the Plasmodium Falciparum Circumsporozoite Surface Protein by
Restrained and Unrestrained MD Simulations. J. Mol. Biol. 1997,
267, 1012-1025.
Ghasparian, A.; Moehle, K.; Linden, A.; Robinson, J. A. Crystal
Structure of an NPNA-Repeat Motif from the Circumsporozoite
Protein of the Malaria Parasite Plasmodium Falciparum. Chem.
Commun. 2006, 174-176.
Moreno, R.; Jiang, L.; Moehle, K.; Zurbriggen, R.; Glück, R.;
Robinson, J. A.; Pluscgke, G. Exploiting Conformationally
Constrained Peptidomimetics and an Efficient Human-Compatible
Delivery System in Synthetic Vaccine Design. ChemBioChem.
2001, 2, 838-843.
Pfeiffer, B.; Peduzzi, E. Moehler, K.; Zurbriggen, R.; Glück, R.;
Pluschke, G.; Robinson, J. A. A Virosome-Mimotope Approach to
Synthetic Vaccine Design and Optimization: Synthesis,
Conformation, and Immune Recognition of a Potential MalariaVaccine Candidate. Angew. Chem. Int. Ed. 2003, 42, 2368-2371.
McGaughey, G. B.; Citron, M.; Danzeisen, R. C.; Freidinger, R.
M.; Garsky, V. M.; Hurni, W. M.; Joyce, J. G.; Liang, X.; Miller,
M.; Shiver, J.; Bogusky, M. J. HIV-1 Vaccine Development:
Constrained Peptide Immunogens Show Improved Binding to the
Anti-HIV-1 gp41 MAb. Biochemistry 2003, 42, 3214-3223.
Hugli, T. E. Protease Inhibitors: Novel Therapeutic Application
and Development. Trends Biotechnol. 1996, 14, 409-412.
Fath, M. A.; Wu, X.; Hileman, R. E.; Linhardt, R. J.; Kashem, M.
A.; Nelson, R. M.; Wright, C. D.; Abraham, W. M. Interaction of
Secretory Leukocyte Protease Inhibitor with Heparin Inhibits
Proteases Involved in Asthma. J. Biol. Chem. 1998, 273, 1356313569.
Stubbs, M. T.; Bode, W. A Player of Many Parts: the Spotlight
Falls on Thrombin-Structure. Thromb. Res. 1993, 69, 1-58.
Selkoe, D. J. Alzheimer’s Disease: Genotypes, Phenotypes, and
Treatments. Science 1997, 275, 630-631.
Leung, D.; Abbenante, G.; Fairlie, D. P. Protease Inhibitors:
Current Status and Future Prospects. J. Med. Chem. 2000, 43, 305341.
Tyndall, J. D. A.; Tessa, N.; Fairlie, D. P. Proteases Universally
Recognize Beta Strands in their Active Sites. Chem. Rev. 2005,
105, 973-999.
Tyndall J. D.; Fairlie D. P. Macrocycles Mimic the Extended
Peptide Conformation Recognized by Aspartic, Serine, Cysteine
and Metallo Proteases. Curr. Med. Chem. 2001, 8, 893-907.
Loughlin, W. A.; Tyndall, J. D.; Glenn, M. P.; Fairlie D. P.
Beta–Strand Mimetics. Chem. Rev. 2004, 104, 6085-6118
Meek T. D.; Lambert D.M.; Dreyer G. B.; Carr, T. J.; Tomaszek, T.
A Jr; Moore, M. L.; Strickler, J. E.; Debouck C.; Hyland, L. J.;
Matthews, T. J.; Metcalf, B. W.; Petteway, S. R. Inhibition of
HIV-1 Protease in Infected T-lymphocytes by Synthetic Peptide
Analogues. Nature 1990, 343, 90-92.
Kaldor, S. W.; Dressman, B. A.; Hammond, M.; Appelt, K.;
Burgess, J. A.; Lubbehusen, P. P.; Muesing, M. A.; Hatch, S. D.;
Wiskerchen M. A.; Baxter A. J. Isophthalic Acid Derivatives:
Amino Acid Surrogates for the Inhibition of HIV-1 Protease.
Bioorg. Med. Chem. Lett. 1995, 5, 721-726.
60
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
[143]
[144]
[145]
[146]
[147]
[148]
[149]
[150]
[151]
[152]
[153]
[154]
[155]
[156]
Smith, A. B. 3rd; Hirschmann, R.; Pasternak, A.; Akaishi, R.;
Guzman, M. C.; Jones, D. R.; Keenan, T. P.; Sprengeler, P. A.;
Darke, P. L.; Emini, E. A.; Holloway, M. K.; Schleif, W. A. Design
and Synthesis of Peptidomimetic Inhibitors of HIV-1 Protease and
Renin. Evidence for Improved Transport. J. Med. Chem. 1994, 37,
215-218.
Choy, N.; Choi, H.; Jung, W. H.; Kim, C. R.; Yoon, H.; Kim, S. C.;
Lee T. G.; Koh J. S. Synthesis of Irreversible HIV-1 Protease
Inhibitors Containing Sulfonamide and Sulfone as Amide Bond
isosteres. Bioorg. Med. Chem. Lett. 1997, 7, 2635-2638
Kempf, D. J.; Marsh, K. C.; Denissen, J. F.; McDonald, E.;
Vasavanonda, S.; Flentge, C. A.; Green, B. E.; Fino, L.; Park, C.
H.; Kong, X. P.; Wideburg, N. E.; Saldiver, A.; Ruiz, L.; Kati, W.
M.; Sham, H. L.; Robins, T.; Stewarti, K. D.; Hsu, A.; Plattner, J.
J.; Leonard, M.; Norbeck, D. W. ABT-538 is a Potent Inhibitor of
Human Immunodeficiency Virus Protease and Has High Oral
Bioavailability in Humans. Proc. Natl. Acad. Sci. USA 1995, 92,
2484-2488.
Hanessian, S.; Yun, H.; Hou, Y.; Yang, G.; Bayrakdarian, M.;
Therrien, E.; Moitessier, N.; Roggo, S.; Veenstra, S.; TintelnotBlomley, M.; Rondeau, J.-M.; Ostermeier, C.; Strauss, A.; Ramage,
P.; Paganetti, P.; Neumann, U. and Betschart, C. Structure-Based
Design, Synthesis, and Memapsin 2 (BACE) Inhibitory Activity of
Carbocyclic and Heterocyclic Peptidomimetics. J. Med. Chem.
2005, 48, 5175-5190.
Ersmark, K.; Nervall, M.; Hamelink, E.; Janka, L. K.; Clemente, J.
C.; Dunn, B. M.; Blackman, M. J.; Samuelsson, B.; Åqvist, J.;
Hallberg, A. Synthesis of Malarial Plasmepsin Inhibitors and
Prediction of Binding Modes by Molecular Dynamics Simulations.
J. Med. Chem. 2005, 48, 6090-6106.
Yamashita, D. S.; Marquis, R. W.; Xie, R.; Nidamarthy, S. D.; Oh,
H.-J.; Jeong, J. U.; Erhard, K. F.; Ward, K. W.; Roethke, T. J.;
Smith, B. R.; Cheng, H-Y.; Geng, X.; Lin, F.; Offen, P. H.; Wang,
B.; Nevins, N.; Head, M. S.; Haltiwanger, R. C.; Sarjeant, A. A. N.;
Liable-Sands, L. M.; Zhao, B.; Smith, W. W.; Janson, C. A.; Gao,
E.; Tomaszek, T.; McQueney, M.; James, I. E.; Gress, C. J.;
Zembryki, D. L.; Lark, M. W.; Veber, D. F. Structure Activity
Relationships of 5-, 6-, and 7-Methyl-Substituted Azepan-3-one
Cathepsin K Inhibitors. J. Med. Chem. 2006, 49, 1597-1612.
Xue, F.; Seto, C. T. Selective Inhibitors of the Serine Protease
Plasmin: Probing the S3 and S3' Subsites Using a Combinatorial
Library. J. Med. Chem. 2005, 48, 6908-6917.
Abbenante, G.; March, D. R.; Bergman, D. A.; Hunt, P. A.;
Garnham, B.; Dancer, R. J.; Martin, J. L.; Fairlie, D. P.
Regioselective Structural and Functional Mimicry of Peptidesdesign of Hydrolytically-stable Cyclic Peptidomimetic Inhibitors of
HIV-1 Protease. J. Am. Chem. Soc. 1995, 117, 10220-10226.
Abbenante G.; Bergman D. A.; Brinkworth R. I.; March D.
R.; Reid R. C.; Hunt P. A.; James I. W.; Dancer R. J.; Garnham
B.; Stoermer M. L.; Fairlie D. P. Structure-Activity Relationships
for Macrocyclic Peptidomimetic Inhibitors of HIV-1 Protease
Bioorg. Med. Chem. Lett. 1996, 6, 2531-2536.
Martin, J. L.; Begun, J.; Schindeler, A.; Wickramasinghe, W. A.;
Alewood, D.; Alewood, P. F.; Bergman, D. A.; Brinkworth, R. I.;
Abbenante, G.; March, D. R.; Reid, R. C.; Fairlie, D. P. Molecular
Recognition of Macrocyclic Peptidomimetic Inhibitors by HIV-1
Protease. Biochemistry 1999, 38, 7978-7988.
Janetka, J. W.; Raman, P.; Satyshur, K.; Flentke, G. R.; Rich, D. H.
Novel Cyclic Biphenyl Ether Peptide β–Strand Mimetics and HIVProtease Inhibitors. J. Am. Chem. Soc. 1997, 119, 441-442.
Glenn, M. P.; Pattenden, L. K.; Reid, R. C.; Tyssen, D. P.; Tyndall,
J. D.; Birch, C. J.; Fairlie, D. P. Beta–Strand Mimicking
Macrocyclic Amino Acids: Templates for Protease Inhibitors with
Antiviral Activity. J. Med. Chem. 2002, 45, 371-381.
Tyndall, J. D.; Reid, R. C.; Tyssen, D.P.; Jardine, D. K.; Todd, B.;
Passmore, M.; March, D. R.; Pattenden, L. K.; Bergman, D. A,;
Alewood, D.; Hu, S. H.; Alewood, P. F.; Birch, C. J.; Martin, J. L.;
Fairlie, D. P. Synthesis, Stability, Antiviral Activity, and ProteaseBound Structures of Substrate-Mimicking Constrained Macrocyclic
Inhibitors of HIV-1 Protease. J. Med. Chem. 2000, 43, 3495-3504.
Reid, R. C.; Pattenden, L. K.; Tyndall, J. D. A.; Martin, J. L.;
Walsh, T.; Fairlie D. P. Countering Cooperative Effects in Protease
Inhibitors Using Constrained β-Strand-Mimicking Templates in
Focused Combinatorial Libraries. J. Med. Chem. 2004, 47 16411651.
González-Muñiz et al.
[157]
[158]
[159]
[160]
[161]
[162]
[163]
[164]
[165]
[166]
[167]
[168]
[169]
[170]
Ersmark, K.; Nervall, M.; Gutierrez-de-Teran, H.; Hamelink, E.;
Janka, L. K.; Clemente, J. C.; Dunn, B. M.; Gogoll, A.;
Samuelsson, B.; Qvist, J.; Hallberg, A. Macrocyclic Inhibitors of
the Malarial Aspartic Proteases Plasmepsin I, II, and IV. Bioorg.
Med. Chem. 2006, 14, 2197-2208.
Ghosh, A. K.; Swanson, L. M.; Cho, H.; Leshchenko, S.; Hussain,
K. A.; Kay, S.; Walters, D. E.; Koh, Y.; Mitsuya, H. StructureBased Design: Synthesis and Biological Evaluation of a Series of
Novel Cycloamide-Derived HIV-1 Protease Inhibitors. J. Med.
Chem. 2005, 48, 3576-3585.
Ghosh, A. K.; Devasamudram, T.; Hong, L.; DeZutter, C.; Xu, X.;
Weerasena, V.; Koelsch, G.; Bilcer, G.; Tang, J. Structure-Based
Design of Cycloamide-Urethane-Derived Novel Inhibitors of
Human Brain Memapsin 2 (β-Secretase). Bioorg. Med. Chem. Lett.
2005, 15, 15-20.
Venkatraman, S.; Njoroge, F. G.; Girijavallabhan, V. M.; Madison,
V. S.; Butkiewicz, N.; Pichardo, J. Design and Synthesis of
Depeptidized Macrocyclic Inhibitors of Hepatitis C NS3-4A
Protease Using Structure-Based Drug Design. J. Med. Chem. 2005,
48, 5088-5091.
Chen, K. X.; Njoroge, F. G.; Prongay, A.; Pichardo, J.; Madison,
V.; Girijavallabhan, V. Synthesis and Biological Activity of
Macrocyclic Inhibitors of Hepatitis C Virus (HCV) NS3 Protease.
Bioorg. Med. Chem. Lett. 2005, 15, 4475-4478.
Chen, K. X.; Njoroge, F. G.; Pichardo, J.; Prongay, A.; Butkiewicz,
N.; Yao, N.; Madison, V.; Girijavallabhan, V. Potent 7-Hydroxy1,2,3,4-Tetrahydroisoquinoline-3-carboxylic
Acid-Based
Macrocyclic Inhibitors of Hepatitis C Virus NS3 Protease. J. Med.
Chem. 2006, 49, 567-574.
Chen, K. X.; Njoroge, F. G.; Arasappan, A.; Venkatraman, S.;
Vibulbhan, B.; Yang, W.; Parekh, T. N.; Pichardo, J.; Prongay, A.;
Cheng, K.-C.; Butkiewicz, N.; Yao, N.; Madison, V.;
Girijavallabhan, V. Novel Potent Hepatitis C Virus NS3 Serine
Protease Inhibitors Derived from Proline-Based Macrocycles. J.
Med. Chem. 2006, 49, 995-1005.
Tamamura, H.; Imai, M.; Ishihara, T.; Masuda, M.; Funakoshi, H.;
Oyake, H.; Murakami, T.; Arakaki, R.; Nakashima, H.; Otaka, A.;
Ibuka, T.; Waki, M.; Matsumoto, A.; Yamamoto, N.; Fujii, N.
Pharmacophore Identification of a Chemokine Receptor (CXCR4)
Antagonist, T22 ([Tyr(5,12),Lys7]-Polyphemusin II), which
Specifically Blocks T Cell-line-tropic HIV-1 Infection. Bioorg.
Med. Chem. 1998, 6, 1033-1041.
Masuda, M.; Nakashima, H.; Ueda, T.; Naba, H.; Ikoma, R.; Otaka,
A.; Terakawa, Y.; Tamamura, H.; Ibuka, T.; Murakami, T.;
Koyanagi, Y.; Waki, M.; Matsumoto, A.; Yamamoto, N.;
Funakoshi S.; Fujii. N. A novel Anti-HIV Synthetic Peptide, T-22
([Tyr5,12,Lys7]-Polyphemusin II). Biochem. Biophys. Res. Commun.
1992, 189, 845-850.
Tamamura, H.; Kuroda, M.; Masuda, M.; Otaka, A.; Funakoshi, S.;
Nakashima, H.; Yamamoto, N.; Waki, M.; Matsumoto, A.;
Lancelin, J. M.; Kohda, D.; Tate, S.; Inagaki, F.; Fujii, N. A
Comparative Study of the Solution Structures of Tachyplesin I and
a Novel Anti-HIV Synthetic Peptide, T22 ([Tyr5,12, Lys7]Polyphemusin II), Determined by Nuclear Magnetic Resonance.
Biochim. Biophys. Acta 1993, 1163, 209-216.
Tamamura, H.; Arakaki, R.; Funakoshi, H.; Imai, M.; Otaka, A.;
Ibuka, T.; Nakashima, H.; Murakami, T.; Waki, M.; Matsumoto,
A.; Yamamoto, N.; Fujii, N. Effective Lowly Cytotoxic Analogs of
an HIV-Cell Fusion Inhibitor, T22 ([Tyr5,12, Lys7]-Polyphemusin
II). Bioorg. Med. Chem. 1998, 6, 231-238.
Tamamura, H.; Waki, M.; Imai, M.; Otaka, A.; Ibuka, T.; Walki,
K.; Miyamoto, K.; Matsumoto, A.; Murakami, T.; Nakashima, H.;
Yamamoto, N.; Fujii, N. Downsizing of an HIV-Cell Fusion
Inhibitor, T22 ([Tyr5,12,Lys7]-Polyphemusin II), with the
Maintenance of Anti-HIV Activity and Solution Strucutre. Bioorg.
Med. Chem. 1998, 6, 473-479.
Tamamura, H.; Xu, Y.; Hattori, T.; Zhang, X.; Arakaki, R.;
Kanbara, K.; Omagari, A.; Otaka, A.; Ibuka, T.; Yamamoto, N.;
Nakashima, H.; Fujii, N. A Low-Molecular-Weight Inhibitor
Against the Chemokine Receptor CXCR4: a Strong Anti-HIV
Peptide T140. Biochem. Biophys. Res. Commun. 1998, 253, 877882.
Fujii, N.; Oishi, S.; Hiramatsu, K.; Araki, T.; Ueda, S.; Tamamura,
H.; Otaka, A.; Kusano, S.; Terakubo, S.; Nakashima, H.; Broach, J.
A.; Trent, J. O.; Wang, Z.; Peiper, S. C. Molecular-Size Reduction
of a Potent CXCR4-Chemokine Antagonist Using Orthogonal
Modulation of Protein-Protein Interactions by Stabilizing/Mimicking
[171]
[172]
[173]
[174]
[175]
[176]
[177]
[178]
[179]
[180]
[181]
[182]
[183]
[184]
[185]
Combination of Conformation- and Sequence-Based Libraries.
Angew. Chem. Int. Ed. 2003, 42, 3251-3253.
Tamamura, H.; Esaka, A.; Ogawa, T.; Araki, T.; Ueda, S.; Wang,
Z.; Trent, J. O.; Tsutsumi, H.; Masuno, H.; Nakashima, H.;
Yamamoto, N.; Peiper, S. C.; Otaka, A.; Fujii, N. Structure-activity
Relationship Studies on CXCR4 Antagonists Having Cyclic
Pentapeptide Scaffolds. Org. Biomol. Chem. 2005, 3, 4392-4394.
Tamamura, H.; Hiramatsu, K.; Ueda, S.; Wang, Z.; Kusano, S.;
Terakubo, S.; Trent, J. O.; Peiper, S. C.; Yamamoto, N.;
Nakashima, H.; Otaka, A.; Fujii, N. Stereoselective Synthesis of
[L-Arg-L/D-3-(2-naphthyl)alanine]-type (E)-alkene Dipeptide
Isosteres and its Application to the Synthesis and Biological
Evaluation of Pseudopeptide Analogues of the CXCR4 Antagonist
FC131. J. Med. Chem. 2005, 48, 380-391.
Tamamura, H.; Araki, T.; Ueda, S.; Wang, Z.; Oishi, S.; Esaka, A.;
Trent, J. O.; Nakashima, H.; Yamamoto, N.; Peiper, S. C.; Otaka,
A.; Fujii, N. Identification of Novel Low Molecular Weight
CXCR4 Antagonists by Structural Tuning of Cyclic Tetrapeptide
Scaffolds. J. Med. Chem. 2005, 48, 3280-3289.
Niida, A.; Tanigaki, H.; Inokuchi, E.; Sasaki, Y.; Oishi, S.; Ohno,
H.; Tamamura, H.; Wang, Z.; Peiper, S. C.; Kitaura, K.; Otaka, A.;
Fujii, N. Stereoselective Synthesis of 3,6-Disubstituted-3,6dihydropyridin-2-ones as Potential Diketopiperazine Mimetics
Using Organocopper-Mediated anti-SN2' Reactions and Their Use
in the Preparation of Low-Molecule CXCR4 Antagonists. J. Org.
Chem. 2006, 71, 3942-3951.
Fisher, K. L.; Lu, J.; Riddle, L.; Kim, K. L.; Presta, L, G.; Bodary,
S. C. Identification of the Binding Site in Intercellular Adhesion
Molecule 1 for its Receptor, Leukocyte Function-Associated
Antigen 1. J. Biol. Cell 1997, 8, 501-515.
Casasnovas, J. M.; Stehle, T.; Liu, J.-H.; Wang J.-H.; Springer, T.
A. A dimeric crystal structure for the N-terminal two domains of
intercellular adhesion molecule-1. Proc. Natl. Acad. Sci. U.S.A.
1998, 95, 4134-4139.
Stauton, D. E.; Dustin, M. L.; Erickson, H. P.; Springer, T. A. The
Arrangement of the Immunoglobulin-Like Domains of ICAM-1
and the Binding Sites for LFA-1 and Rhinovirus. Cell 1990, 61,
243-254.
Gadek, T. R.; Burdick, D. J.; McDowell, R. S.; Stanley, M. S.;
Marster Jr, J. C.; Paris, K. J.; Oare, D. A.; Reynolds, M. E.; Ladner,
C.; Zioncheck, K. A.; Lee, W. P.; Gribling, P.; Dennis, M. S.;
Skelton, N. J.; Tumas, D. B.; Clark, K. R.; Keating, S. M.;
Beresini, M. H.; Tilley, J. W.; Presta, L. G. and Bodary, S. C.
Generation of an LFA-1 Antagonist by the Transfer of the ICAM-1
Immunoregulatory Epitope to a Small Molecule. Science 2002,
295, 1086-1089.
Shimaoka, M.; Salas, A.; Yang, W.; Weitz-Schmidt, G.; Springer,
T. A. Small Molecule Integrin Antagonist that Bind to the β2
Subunit I-Like Domain and Activate Signals in one Direction and
Block them in the Other. Immunity 2003, 19, 391-402.
Welzenbach, K. L.; Hommel, U.; Weithz-Schmidt, G. Small
Molecule Inhibitors Induce Conformational Changes in the I
Domain and the I-Like Domain of Lymphocyte FunctionAssociated Antigen-1. J. Biol. Chem. 2002, 277, 10590-10598.
Yank, W.; Shimaoka, M.; Salas, A.; Takagi, J.; Springer, T. A.
Intersubunit Signal Transmission in Integrins by a Receptor-Like
Interaction with a Pull Spring. Proc. Natl. Acad. Sci. 2004, 101,
2906-2911.
Keating, S. M.; Clark, K. R.; Stefanich, L. D.; Arellano, F.;
Edwards, C. P.; Bodary, S. C.; Spencer, S. A.; Gadek, T. R.;
Marsters, J. C. Jr.; Beresini, M. H. Competition Between
Intercellular Adhesion Molecule-1 and a Small-Molecule
Antagonist for a Common Binding Site on the α1 Subunit of
Lymphocyte Function-Associated Antigen-1. Protein Sci. 2006, 15,
290-303.
Favre, R.; Moehle, K.; Dhanapal, B.; Obrecht, D.; Robinson, J. A.
Structural Mimicry of Canonical Conformations in Antibody
Hypervariable Loops Using Cyclic Peptides Containing a
Heterochiral Diproline Template. J. Am. Chem. Soc. 1999, 121,
2679-2685.
Descours, A.; Moehle, K.; Renard, A.; Robinson, J. A. A New
Family of β–Hairpin Mimetics Based on a Trypsin Inhibitor from
Sunflower Seeds. ChemBioChem 2002, 3, 318-323.
Fasan, R.; Dias, R. L. A.; Moehle, K.; Zerbe, O.; Vrijbloed, J. W.;
Obrecht, D.; Robinson, J. A. Using a β–Hairpin to Mimic an
α–helix: Cyclic Peptidomimetic Inhibitors of the p53-HDM2
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1 61
[186]
[187]
[188]
[189]
[190]
[191]
[192]
[193]
[194]
[195]
[196]
[197]
[198]
[199]
[200]
[201]
[202]
[203]
[204]
[205]
Protein-Protein Interaction. Angew. Chem. Int. Ed. 2004, 43, 21092112.
Athanassiou, Z.; Dias, R. L. A.; Moehle, K.; Dobson, N.; Varani,
G.; Robinsion, J. A. Structural Mimicry of Retroviral Tat Proteins
by Constrained β–Hairpin Peptidomimetics: Ligands with High
Affinity and Selectivity for Viral TAR RNA Regulatory Elements.
J. Am. Chem. Soc. 2004, 126, 6906-6913.
Robinson, J. A.; Shankaramma, S. C.; Jetter, P.; Kienzl, U.;
Schwendener, R. A.; Vrijbloed J. W.; Obrecht D. Properties and
Structure-Activity Studies of Cyclic β-Hairpin Peptidomimetics
Based on the Cationic Antimicrobial Peptide Protegrin I. Bioorg.
Med. Chem. 2005, 13, 2055-2064.
Dias, R. L. A.; Fasan, R.; Moehle, K.; Renard, A.; Obrecht, D.;
Robinson, J. A. Protein Ligand Design: From Phage Display to
Synthetic Protein Epitope Mimetics in Human Antibody FcBinding Peptidomimetics. J. Am. Chem. Soc. 2006, 128, 27262732.
Whitcomb, D.C. Acute Pancreatitis: Molecular Biology Update, J.
Gastrointest. Surg. 2003, 7, 940-942.
DeLano, W. L.; Ultsch, M. H.; de Vos, A. M.; Wells, J. A.
Convergent Solutions to Binding at a Protein-Protein Interface.
Science 2000, 287, 1279-1283
Griffioen, A. W.; Van Der Schaft, D. W. J.; Barendsz-Janson, A.
F.; Cox, A.; Struijker Boudier, H. A. J.; Hillen, H. F. P.; Mayo, K.
H. Anginex, a Designed Peptide that Inhibits Angiogenesis.
Biochem. J. 2001, 354, 233-242.
Mayo, K. H.; Haseman, J. R.; Llyina, E.; Gray, B. Designed
β–Sheet-Forming Peptide 33mer with Potent Human
Bactericidal/Permeability Increasing Protein-like Bactericidal and
Endotoxin Neutralizing Activities. Biochim. Biophys. Acta. 1998,
1425, 81-92.
Mayo, K. H.; van der Schaft, D. W.; Griffioen, A. W. Designed
Beta–Sheet Peptides that Inhibit Proliferation and Induce Apoptosis
in Endothelial Cells. Angiogenesis 2001, 4, 45-51.
Dings, R. P. M.; Arroyo, M. M.; Lockwood, N. A.; van Eijk, L. I.;
Haseman, J. R.; Griffioen, A. W.; Mayo, K. H. β–Sheet is the
Bioactive Conformation of the Anti-angiogenic Anginex Peptide.
Biochem. J. 2003, 373, 281-288.
Mayo, K. H.; Dings, R. P. M.; Flades, C.; Nesmelova, I.; Hargittai,
B.; van del Schaft, D. W. J.; van Eijk, L. I.; Walek, D.; Haseman,
J.; Hoye, T. R.; Griffioen, A. W. Design of a Partial Peptide
Mimetic of Anginex with Antiangiogenic and Anticancer Activity.
J. Biol. Chem. 2003, 278, 45746-45752.
Introduction to Protein Structure; Branden, C.: Tooze, J. Eds.;
Garland Publishing, Inc.: New York and London, 1991; pp 12-14.
Willis, S. N.; Adams, J. M. Life in the Balance: How BH3-Only
Proteins Induce Apoptosis. Curr. Opin. Cell. Biol. 2005, 17, 617625.
Fan, T.-J.; Han, L.-H.; Cong, R.-S; Liang, J. Caspase Family
Proteases and Apoptosis. Acta Biochim. Biophys. Sin. (Shanghai)
2005, 37, 719-727.
Blackwell, H. E.; Grubbs, R. H. Highly Efficient Synthesis of
Covalently Cross-Linked Peptide Helices by Ring-Closing
Metathesis. Angew. Chem. Int. Ed. 1998, 37, 3281-3284.
Schafmeister, C. E.; Po, J.; Verdine, G. L. An All-Hydrocarbon
Cross-Linking System for Enhancing the Helicity and Metabolic
Stability of Peptides. J. Am. Chem. Soc. 2000, 122, 5891-5892.
Walensky, L. D.; Kung, A. D.; Escher, I.; Malia, T. J.; Barbuto, S.;
Wright, R. D.; Wagner, G.; Verdine, G.L.; Korsmeyer, S. J.
Activation of Apoptosis in Vivo by a Hydrocarbon-Stapled BH3
Helix Science 2004, 305, 1466-1470.
Chapman, R. N.; Dimartino, G.; Arora, P. S. A Highly Stable Short
α–Helix Constrained by a Main-Chain Hydrogen-Bond Surrogate.
J. Am. Chem. Soc. 2004, 126, 12252-12253.
Wang, D.; Liao, W.; Arora, P. S. Enhanced Metabolic Stability and
Protein-Binding Properties of Artificial α Helices Derived from a
Hydrogen-Bond Surrogate: Application to Bcl-xL. Angew. Chem.
Int. Ed. 2005, 44, 6525-6529.
Sadowsky, J. D.; Schmitt, M. A.; Lee, H.-S.; Umezawa, N.; Wang,
S.; Tomita, Y.; Gellman, S. H. Chimeric (α/β+α)-Peptide Ligands
for the BH3-Recognition Cleft of Bcl-xL: Critical Role of the
Molecular Scaffold in Protein Surface Recognition. J. Am. Chem.
Soc. 2005, 127, 11966-11968.
Nolan, W. P.; Ratcliffe, G. S.; Rees, D. C. The Synthesis of 1,6Disubstituted Indanes which Mimic the Orientation of Amino Acid
62
Current Topics in Medicinal Chemistry, 2007, Vol. 7, No. 1
[206]
[207]
[208]
[209]
[210]
[211]
[212]
[213]
[214]
[215]
[216]
[217]
[218]
Side-Chains in a Protein Alpha–Helix Motif. Tetrahedron Lett
1992, 33, 6879-6882.
Horwell, D. C.; Howson, W.; Ratcliffe, G. S.; Willems, H. M. G.
The Design of Dipeptide Helical Mimetics: The Synthesis,
Tachykinin Receptor Affinity and Conformational Analysis of
1,1,6-Trisubstituted Indanes. Bioorg. Med. Chem. 1996, 4, 33-42.
Jacoby, E. Biphenyls as Potential Mimetics of Protein α–Helix.
Bioorg. Med. Chem. Let. 2002, 12, 891-893.
Kutzki, O.; Park, H. S.; Ernst, J. T.; Orner, B. P.; Yin, H.;
Hamilton, A. D. Development of a potent Bcl-xL Antagonist Based
on α–Helix Mimicry. J. Am. Chem. Soc. 2002, 124, 11838-11839.
Yin, H.; Lee, G.; Sedey, K. A.; Kutzki, O.; Park, H. S.; Orner, B.
P.; Ernst, J. T.; Wang H.-G.; J. M.; Sebti, S. M.; Hamilton, A. D.
Terphenyl-Based Bak BH3 α-Helical Proteomimetics as LowMolecular-Weight Antagonists of Bcl-xL. J. Am. Chem. Soc. 2005,
127, 10191-10196.
Yin, H.; Lee, G.-i.; Sedey, K. A.; Rodriguez, J. M.; Wang H. G.;
J.M.; Sebti, S. M.; Hamilton, A. D. Terephthalamide Derivatives as
Mimetics of Helical Peptides: Disruption of the Bcl-xL/Bak
Interaction. J. Am. Chem. Soc. 2005, 127, 5463-5468.
Yin, H.; Hamilton, A. D. Terephthalamide Derivatives as Mimetics
of the Helical Region of Bak Peptide Target Bcl-xL Protein.
Bioorg. Med. Chem. Let. 2004, 14, 1375-1379.
Ernst, J. T.; Becerril, J.; Park, H. S.; Yin, H.; Hamilton, A. D.
Design and Application of an α–Helix-Mimetic Scaffold Based on
an Oligoamide-Foldamer Strategy: Antagonism of the Bak
BH3/Bcl-xL Complex. Angew. Chem. Int. Ed. 2003, 42, 535-539.
Antuch, W.; Menon, S.; Chen, Q.-Z.; Lu, Y.; Sakamuri, S.; Beck,
B.; Schauer-Vukasinovic, V.; Agarwal, S.; Hess, S.; Dömling, A.
Design and Modular Parallel Synthesis of a MCR Derived α–Helix
Mimetic Protein-Protein Interaction Inhibitor Scaffold. Bioorg.
Med. Chem. Let. 2006, 16, 1740-1743.
Chène, P. Inhibiting the p53-MDM-2 Interaction: an Important
Target for Cancer Therapy. Nature Rev. 2003, 3, 102-109.
Kussie, P. H.; Gorina, S.; Marechal, V.; Elenbaas, B.; Moreau, J.;
Levine, A. J.; Pavletich, N. P. Structure of the MDM2 Oncoprotein
Bound to the p53 Tumor Suppressor Transactivation Domain.
Science 1996, 274, 948-953.
García-Echeverría, C.; Chène, P.; Blommers, M. J. J.; Furet, P.
Discovery of Potent Antagonists of the Interaction Between Human
Double Minute 2 and Tumor Suppressor p53. J. Med. Chem. 2000,
43, 3205-3208.
Fasan, R.; Dias, R. L. A.; Moehle, K.; Zerbe, O.; Obrecht, D.;
Mittl, P. R. E.; Markus, G. G.; Robinson, J. A. Structure-Activity
Studies in a Family of β–Hairpin Protein Epitope Mimetic
Inhibitors of the p53-HDM2 Protein-Protein Interaction.
ChemBioChem 2006, 7, 515-526.
Peptides: Chemistry and Biology. Sewald, N.; Jakubke, H.-D.;
Eds.; Wiley-VCH: Weinheim (Germany), 2002; pp 358-359.
Received: April 20, 2006
Accepted: May 30, 2006
González-Muñiz et al.
[219]
[220]
[221]
[222]
[223]
[224]
[225]
[226]
[227]
[228]
[229]
[230]
[231]
[232]
[233]
Hara, T.; Durell, S. R.; Myers, M. C.; Appella, D. H. Probing the
Structural Requirements of Peptoids that Inhibit HDM2-p53
Interactions. J. Am. Chem. Soc. 2006, 128, 1995-2004.
Peptides: Chemistry and Biology. Sewald, N.; Jakubke, H.-D.;
Eds.; Wiley-VCH: Weinheim (Germany), 2002; pp 361-362.
Kritzer, J. A.; Stephens, O. M.; Guarracino, D. A.; Reznik, S. K.;
Schepartz, A. β-Peptides as Inhibitors of Protein-Protein
Interactions. Bioorg. Med. Chem. 2005, 13, 11-16.
Kritzer, J.A.; Hodsdon, M.E.; Schepartz, A. Solution Structure of a
β-Peptide Ligand for hDM2 J. Am. Chem. Soc. 2005, 127, 41184119.
Kritzer, J. A.; Lear, J. D.; Hodsdon, M. E.; Schepartz, A. Helical βPeptide Inhibitors of the p53-hDM2 Interaction. J. Am. Chem. Soc.
2004, 126, 9468-9469.
Yin, H.; Lee, G.-i.; Park, H. S.; Payne, G. A.; Rodriguez, J. M.;
Sebti, S. M.; Hamilton, A. D. Terphenyl-Based Helical Mimetics
that Disrupt the p53/HDM2 Interaction. Angew. Chem. Int. Ed.
2005, 44, 2704-2707.
Chen, L.; Yin, H.; Farooqi, B.; Sebti, S.; Hamilton, A. D.; Chen, J.
p53 α–Helix Mimetics Antagonize p53/MDM2 Interaction and
Activate p53. Mol. Cancer Ther. 2005, 4, 1019-1025.
Lu, F.; Chi, S.-W.; Kim, D.-H.; Han, K.-H.; Kuntz, I. D.; Guy, R.
K. Proteomimetic Libraries: Design, Synthesis, and Evaluation of
p53-MDM2 Interaction Inhibitors. J. Comb. Chem. 2006, 8, 315325.
Leduc, A.-M.; Trent, J. O.; Wittliff, J. L.; Bramlett, K. S.; Briggs,
S. L.; Chirgadze, N. Y.; Wang, Y.; Burris, T. P.; Spatola, A. F.
Helix-Stabilized Cyclic Peptides as Selective Inhibitors of Steroid
Receptor-Coactivator Interactions. Proc. Nat. Acad. Sci. USA 2003,
100, 11273-11278.
Norris, J. D.; Paige, L. A.; Christensen, D. J.; Chang, C.-Y.;
Huacani, M. R.; Fan, D.; Hamilton, P. T.; Fowlkes, D. M.:
McDonnell, D. P. Peptide Antagonists of the Human Estrogen
Receptor. Science 1999, 285, 744-746.
Werder, M.; Hauser, H.; Abele, S.; Seebach, D. β-Peptides as
Inhibitors of Small-Intestinal Cholesterol and Fat Absorption. Helv.
Chim. Acta 1999, 82, 1774-1783.
Orner, B. P.; Ernst, J. T.; Hamilton, A. D. Toward Proteomimetics:
Terphenyl Derivatives as Structural and Functional Mimics of
Extended Regions of an α–Helix. J. Am. Chem. Soc. 2001, 123,
5382-5383.
Ernst, J. T.; Kutzki, O.; Debnath, A. K.; Jiang, S.; Lu, H.;
Hamilton, A. D. Design of a Protein Surface Antagonist Based on a
α–Helix Mimicry: Inhibition of gp41 Assembly and Viral Fusion.
Angew. Chem. Int. Ed. 2002, 41, 278-281.
Kim, I. Ch.; Hamilton, A. D. Diphenylindane-Based
Proteomimetics Reproduce the Projection of the i, i+3, i+4, and i+7
Residues on an α–Helix. Org. Lett. 2006, 8, 1751-1754.
Davis, J. M.; Truong, A.; Hamilton, A. D. Synthesis of a 2,3’;6’,3”Terpyridine Scaffold as an α–Helix Mimetic. Org. Lett. 2005, 7,
5405-5408.