Bivalent diketopiperazine-based tropomysin receptor kinase C (TrkC) antagonists

Article abstract of DOI:10.1021/jm100148d

Bivalent molecules containing two β-turn mimics with side chains that correspond to hot-spots on the neurotrophin NT-3 were prepared. Binding assays showed the mimetics to be selective TrkC ligands, and biological assays showed one mimetic to be an antago

Full text of DOI:10.1021/jm100148d

5044 J. Med. Chem. 2010, 53, 5044–5048
DOI: 10.1021/jm100148d
Bivalent Diketopiperazine-Based Tropomysin Receptor Kinase C (TrkC) Antagonists
Jing Liu,† Fouad Brahimi,‡ H. Uri Saragovi,*,‡ and Kevin Burgess*,†
†Department of Chemistry, Texas A&M University, Box 30012, College Station, Texas 77842-3012, and ‡Lady Davis Institute-Jewish
ꢀ
General Hospital, Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
Received February 5, 2010
Bivalent molecules containing two β-turn mimics with side chains that correspond to hot-spots on the
neurotrophin NT-3 were prepared. Binding assays showed the mimetics to be selective TrkC ligands,
and biological assays showed one mimetic to be an antagonist of the TrkC receptor.
Introduction
Neurotrophin growth factors have activities that might be
useful in clinical settings, particularly with respect to maladies
that affect the nervous system such as neurodegeneration or
pain.1,2 These growth factors are also implicated in cancer pro-
gression (e.g., TrkCa in breast cancer). However, even apart
from the usual problems associated with protein-based pharma-
ceuticals (e.g., cost, proteolytic and metabolic stabilities, immune
responses), there are side-effects and potential toxicity factors
that could logically be attributed to the fact that the neurotro-
phins are not entirely selective for their corresponding Trk
receptors, and they all bind the p75 receptor.3 Binding to the
latter is particularly undesirable because it tends to cause very
different effects to activation of the Trk receptors.4 For these
reasons, there is a pressing need for the development of small
molecules that selectively bind to and regulate the function of
Trk receptors.
Our approach to the design of Trk ligands has been to mimic
the β-turn regions of the parent neurotrophins.5-7 Cyclic mono-
valent compounds (one turn mimic) have proven to be useful
Figure 1. (a) Key distance of Cβ-separations of the i þ 1 to i þ 2
Trk agonists (or partial agonists)8 or antagonists.9 Bivalent
compounds based on two macrocyclic turn mimics in one
molecule10 have been identified as TrkA antagonists,11 or TrkC
agonists.12 Selectivities for the TrkA and C receptors were
achieved by using amino acid side chains corresponding to
β-turns in the parent neurotrophin ligands that constitute hot-
spots for the interactions of these with their Trk receptors.
However, the factors that determine if the ligand is an agonist
or an antagonist are more subtle. Two key molecular para-
meters that influence this are likely to be the scaffold used to
form the turn mimic, and the spacing between them in the
bivalent constructs.
residues of a type I β-turn and of the monovalent turn mimics A and
B featured here; (b) comparative overlay of the two types of 2,5-
DKP mimics (colored) onto a type I β-turn (blue).
This communication introduces a new type of turn mimic A
based on diketopiperazines (DKPs), a scaffold that is more
commonly used for forming compounds of the type B. A
strategy for making bivalent molecules containing two type-A
units at variable spacings is also described. Cell-based binding
and biological and biochemical signal transduction assays
indicate that one of these bivalent molecules is one of the first
small molecule TrkC antagonists to be reported to date.9
Results and Discussion
*To whom correspondence should be addressed. For K.B.: phone, (979)
845-4345; fax, (979) 845-8839; E-mail, Burgess@tamu.edu. For H.U.S.:
phone, (514) 340-8222 ext 5055; E-mail, horacio.saragovi@mcgill.ca.
a Abbreviations: TrkC, Tropomysin receptor kinase C; DKP, diketopi-
perazine; EDCI, 1-ethyl-(3-dimethylaminopropyl) carbodiimide hydro-
chloride; HOBt, 1-hydroxybenzotriazole; NMM, N-methylmorpholine;
TFA, trifluoroacetic acid; MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-
tetrazolium bromide; FACS, fluorescence activated cell sorting; IGF-1R,
insulin-like growth factor 1 receptor; SFM, serum-free media; NT-3,
neurotrophin-3; pTyr, phosphotyrosine; Erk, extracellular signal-regulated
kinase; MAPK, mitogen-activated protein kinase; mAb, monoclonal anti-
body; NGF, nerve growth factor.
The guiding hypothesis behind our latest designs of β-turn
mimics12,13 is that the separation between the Cβ atoms is
critical. Figure 1 shows this distance for an ideal type I turn is
˚
ca. 5.2 A. Recently we reported β-turn mimics that could
readily attain conformations with Cβ-separations corre-
sponding to this distance, even though they were not the
global minimum.12,13 Modeling shows that DKPs B have
˚
Cβ-separations of almost 5.5 A, i.e., a little too long. In any
case, these molecules are well represented in many compound
r
pubs.acs.org/jmc
Published on Web 06/11/2010
2010 American Chemical Society

Brief Article
Journal of Medicinal Chemistry, 2010, Vol. 53, No. 13 5045
Table 1. Monovalent Peptidomimetics 4a-h
Scheme 1. Solution Phase Synthesis of Monomeric DKP-
Based Peptidomimetics: (a,b) Refer to Syntheses of the Mono-
valent Scaffolds, (c) Deals with Functionalization of These with
Linker Fragmentsa
Parts a and b of Scheme 1 illustrate two approaches used to
make the target type A DKPs (full details are given in the
Supporting Information). Two approaches were necessary to
make it possible to use the most readily available protected
amino acids and the appropriate side-chain masking groups.
The key difference between the two routes is that in the first,
acid-based deprotection of Boc groups (without removing the
tert-butyl ester)17 is involved early in the synthesis, whereas
this is replaced by hydrogenolysis of Cbz protection in the
second.
Scheme 1c illustrates how “short” s and “long” l piperazine-
based linkers were coupled to the different peptidomimetics. At
the conclusion of the synthesis, four different monovalent pepti-
domimetics were generated, each of these was functionalized with
the short s and long l linker systems to give a total of eight
monovalent starting materials (Table 1). The short linker was
chosen because it is a compact structure formed from a hetero-
cycle that is common in drug design. Simple modeling experi-
ments showed that when two long linkers of the type shown were
combined then this would give a spacing of the turn mimics that
is appropriate for the largest separations of the turns in the
neurotrophins. Combinations of the long and short linkers would
span appropriate intermediate distances.
The next step in syntheses was to form a library of bivalent
molecules 6 from the eight key monovalent systems 4. Solution
phase methodology for doing this type of combination has been
published by us.13 Briefly, this relies on suppression of the rate of
SNAr reactions in apolar solvents to stop the initial reaction after
one displacement, then completion of the reaction in a more
polar solvent. Scheme 2 shows how this method was used to
form compounds 4.
a Reagents and conditions for part (a): (a) 1-ethyl-(3-dimethylamino-
propyl)carbodiimide hydrochloride (EDCI), 1-hydroxybenzotriazole
(HOBt), N-methylmorpholine (NMM), CH2Cl2, 25 °C, 12 h; (b) tri-
fluoroacetic acid (TFA)/CH2Cl2, 0-25 °C, 2 h; (c) bromoacetyl bro-
mide, 0.5 M K2CO3 (aq), CH2Cl2, 0 °C, 2 h; (d) 50% NaOH(aq),
CH2Cl2, 25 °C, 12 h; (e) TFA, iPr3SiH, CH2Cl2, 25 °C, 10 h. Reagents
and conditions for part (b): (a) EDCI, HOBt, NMM, CH2Cl2, 25 °C,
12 h; (b) H2, Pd/C, MeOH, 25 °C, 12 h; (c) bromoacetyl bromide, 0.5 M
K2CO3 (aq), CH2Cl2, 0 °C, 2 h; (d) 50% NaOH (aq), CH2Cl2, 25 °C,
12 h; (e) Me3SnOH, 1,2-dichloroethane, 80 °C, 6 h. Reagents and
conditions for part (c): for 4a and 4e: 3a, (a) (i) short or long linker,
EDCI, HOBt, NMM, CH2Cl2, 25 °C, 12 h, (ii) H2, Pd/C, MeOH, 25 °C,
16 h, (iii) Boc anhydride, Et3N, CH2Cl2, 25 °C, 12 h; for 4b and 4f: 3b,
(b) (i) short or long linker, EDCI, HOBt, NMM, CH2Cl2, 25 °C, 12 h,
(ii) H2, Pd/C, MeOH, 25 °C, 16 h; for 4c,d and 4g,h: 3c or 3d, (c) short or
long linker, EDCI, HOBt, NMM, CH2Cl2, 25 °C, 12 h.
Methods used in Scheme 2 mean that a triazine forms the
core of every bivalent molecule 6. However, this heterocycle
can be used; it has a substitution site for a “third group” to
facilitate in vitro assays (or for other purposes, not relevant
here). In this study, biotin derivatives were chosen to occupy
this position (“biotin tag”) because they facilitate direct
collections.14 Consequently, the less common substitution
pattern in A was considered.11,15,16 Here the Cβ-spacing,
˚
5.1-5.2 A, matches type I turns closely, and the structures
explore a different region of diversity space.

5046 Journal of Medicinal Chemistry, 2010, Vol. 53, No. 13
Liu et al.
Scheme 2. Solution Phase Synthesis of Biotin-Labeled Bivalent
Table 2. HPLC Purities of the Bivalent Turn Mimics 6 Prepared from
Monovalent Mimics 4a-h as Assessed by UV Detectiona
Peptidomimetic Librarya
a “i” stands for morpholine, which was used as “cap” in place of the
monovalent peptidomimetics to give control compounds that have none
or one peptidomimetic and biotin.
a Reagents and conditions: (a) 1:1 TFA/CH2Cl2, 25 °C, 10 h; (b) (i) 1:1
TFA/CH2Cl2, 25 °C, 10 h, (ii) DTAB, K2CO3, DMSO, 25 °C, 2 h;
(c) K2CO3, DMSO, 25 °C, 5-7 d.
binding assays via fluorescence activated cell sorting (FACS),
tend to increase the water solubilities of the molecules but
do not impact the measured outputs from other assays (e.g.,
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
{MTT} in cell survival assays).
Table 2 shows the purities obtained for the library of crude
samplesfrom Scheme2. All the compoundswere then purified
via preparative reverse phase HPLC (RP-HPLC) to give
samples that were more than 95% pure in all cases.
The compounds in the DKP library described above were
assayed in binding assays, biological assays, and biochemical
signal transduction assays as described previously.18 In the
binding studies, the biotinylated compounds were assayed by
flow cytometry FACS, using avidin conjugated with fluor-
escein isothiocyanate for detection. FACS assays measuring
the direct binding to NIH-3T3 cells stably transfected to
express TrkC. As controls, NIH-3T3 cells were stably trans-
fected to express neurotrophin receptors TrkA, or p75, or a
different receptor tyrosine kinase, insulin-like growth factor 1
receptor (IGF-1R). Of the 45 compounds scanned by FACS,
one compound, the one made from combination of depro-
Figure 2. Direct binding of biotin-peptidomimetic 6dh to TrkC-
expressing cells. Cells expressing the indicated receptor were first bound
at 4 °C with test ligand (50 μM), followed by fluorescein-avidin. After
washing, cells were analyzed by FACScan/CellQuest. The background
mean channel fluorescence (MCF) of NIH-IGF-1R were subtracted to
analyze the specific MCF binding to test cells. Results shown are fluore-
scence (standard error of mean (SEM), n=3independentexperiments.
tected forms of 4d and 4h, hereafter called 6dh, showed
selective TrkC binding (Figure 2). This compound binds
selectively to TrkC-expressing cells, but it does not bind to

Brief Article
Journal of Medicinal Chemistry, 2010, Vol. 53, No. 13 5047
Figure 4. Effect of 6dh on TrkC receptor phosphorylation and
MAPK activation in NIH3T3 TrkC cells. Cells were exposed to
the indicated peptidomimetic (20 μM) and growth factor (2 nM) for
20 min. Detergent lysates were analyzed by Western blotting with
anti-pTyr monoclonal antibody (mAb) 4G10 or antiphospho-
MAPK. Membranes were reblotted with anti-actin to verify protein
loading. Blots were quantified by densitometry.
Figure 3. Mimetic 6dh antagonizes NT-3 action in cell survival
assays. NIH-3T3 cells expressing either TrkA or TrkC or IGF-1R
were cultured in SFM supplemented with optimal ((a) 10 nM) or
suboptimal ((b) 0.2 nM) concentrations of the appropriate growth
factor (GF) ( peptidomimetic (20 μM). Survival was measured in
MTT assays and was calculated relative to optimal growth factor-
mediated survival (100%). Results shown are average ( SD.
functional TrkC-NT-3 interactions, and not due to selective
cytotoxicity.
Biochemical assays of signal transduction were also per-
formed on the lead compound, 6dh. The phosphotyrosine
(pTyr) content of TrkC can be used as a measure of activation
because this receptor is a receptor tyrosine kinase. Moreover,
the phosphorylated state of the downstream signaling protein
with extracellular signal-regulated kinase (Erk) 1,2 can also be
measured; as it is known to be activated by TrkC-signals
(Figure4).19 Cellswere exposed togrowth factor (2 nM) for 20
min ( 6dh (20 μM), and detergent lysates were analyzed by
Western blotting with antibodies directed to phospho-tyro-
sine or to phospho-Erk1,2. Antibodies directed to actin
demonstrated equal protein loading and this signal is used
to standardize the results.
In NIH3T3-TrkC cells, 6dh significantly blocked (40%) the
level of TrkC-pTyr that was stimulated by NT-3 (Figure 4a).
No significant effect was observed in NIH3T3-TrkA cells
stimulated with NGF (Figure 4b) or in NIH3T3-IGF-1R cells
stimulated with IGF-1 (Figure 4c). Together, these data
indicate 6dh is a selective inhibitor of NT-3-mediated activa-
tion leading to TrkC phosphotyrosinylation.
NIH-3T3 cells expressing TrkA or p75 (Figure 2), or IGF-1R
(not shown).
The effects of the peptidomimetics on receptor-mediated
cell survival of NIH-3T3 cells expressing TrkA, TrkC or IGF-
1R were also tested. Biological assays tested cell survival in
quantitative MTT assays. When cells were placed in serum-
free media (SFM), they died by apoptosis. In these conditions,
cell death can be prevented by their appropriate growth
factors (NIH-TrkA is protected by NGF, NIH-TrkC is
protected by neurotrophin-3 {NT-3}, NIH-IGF-1R is pro-
tected by IGF-1). Growth factor protection of cells from
apoptosis in SFM is dose-dependent, and suboptimal doses
of growth factor can be used that result quantitatively and
consistently in reduced survival.
Compound 6dh at 20 μM was significantly antagonistic to
TrkC-NT-3 functional interactions. It reduced the trophic
activity of optimal (10 nM) NT-3 to ∼70% (Figure 3a).
Antagonism was TrkC selective because this mimetic did
not antagonize the protective function of NGF upon TrkA
cells or the function of IGF-1 on IGF-1R (Figure 3a).
For comparison, suboptimal doses of NT-3 (0.2 nM) which
affords ∼40-50% of maximal cell survival were also tested.
The data show the effects of NT-3 on TrkC cells is antagonized
more easily by 6dh under these conditions, but also in a selective
manner (Figure 3b). In addition, control cell cytotoxicity assays
demonstrated 6dh were nontoxic at all doses tested (data not
shown) indicating selective antagonism is due to antagonism of
Conclusions
The inhibition of TrkC-pTyr correlates with the inhibi-
tion of the phosphorylation of the mitogen-activated
protein kinase (MAPK) Erk1,2 protein, which is a major
signal transduction pathway activated by neurotrophin
receptor. Mimic 6dh blocks the activation of MAPK by

5048 Journal of Medicinal Chemistry, 2010, Vol. 53, No. 13
Liu et al.
TrkC (70%) (Figure 4a) but not by TrkA or by IGF-1R
(Figure 4b,c).
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There are relatively few small molecule ligands for the
neurotrophin receptors.8,20-26 One of the earliest, a com-
pound we call D3 was designed to mimic putative β-turn
hot-spots in the nerve growth factor (NGF).6,7,27 In vitro and
in vivo tests on D3 indicate this is a partial TrkA agonist, that
has no significant binding to the other Trk receptors. This
compound shows promise for the treatment of stroke and
glaucoma. Whereas similar compounds from our laboratories
have been shown to be agonists or partial agonists for the
TrkC receptor (the one that has greatest affinity for NT-
3),18,28 this paper demonstrates a molecule that contains not
one but two β-turn mimics at an optimized separation can
serve as a TrkC antagonist. The most active of the molecules 6
(ie 6dh, the one from 4d and 4h) contains two DKPs with side
chains from Glu and Lys (EK); this mimics the sequence
DEKQ corresponding to murine NGF and not NT-3, but the
molecule was active on TrkC and not on TrkA. The 92-95
turn region of NT-3 (human or mouse) contains the ENNK
motif. Consequently, it is possible that this compound mimics
the i and i þ 3 residues of this turn rather than the i þ 1 and i þ
2 regions.
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In summary, peptidomimetic 6dh is a ligand of TrkC, and
an antagonist of TrkC-NT-3 activity. Our findings further
demonstrate that peptidomimetic molecules can be made to
act specifically on certain Trk receptors. Finding a small,
stable molecule with selective agonist/antagonistic activity
may be useful as a therapeutic agent.
Acknowledgment. We thank the National Institutes of
Health (MH070040, GM076261), and the Robert A. Welch
Foundation (A-1121) to K.B., and by the Canadian Institutes
of Health Research grant 1192060 to H.U.S. TAMU/LBMS-
Applications Laboratory provided mass spectrometric sup-
port. We thank Eunhwa Ko for taking the NMR data for
mimic 6dh. The NMR instrumentation in the Biomolecular
NMR Laboratory at Texas A&M University was supported by
a grant from the National Science Foundation (DBI-9970232)
and the Texas A&M University System.
Supporting Information Available: Details of the compound
purities, procedure for syntheses of compounds 1-6, and char-
acterization of representative dimers. This material is available
free of charge via the Internet at http://pubs.acs.org.
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