Inhibitors of Leishmania N-myristoyltransferase (NMT), a potential target for the treatment of leishmaniasis, obtained from a high-throughput screen, were resynthesized to validate activity. Crystal structures bound to Leishmania major NMT were obtained, and the active diastereoisomer of one of the inhibitors was identified. On the basis of structural insights, enzyme inhibition was increased 40-fold through hybridization of two distinct binding modes, resulting in novel, highly potent Leishmania donovani NMT inhibitors with good selectivity over the human enzyme.
Inhibitors of Leishmania N-myristoyltransferase (NMT), a potential target for the treatment of leishmaniasis, obtained from a high-throughput screen, were resynthesized to validate activity. Crystal structures bound to Leishmania major NMT were obtained, and the active diastereoisomer of one of the inhibitors was identified. On the basis of structural insights, enzyme inhibition was increased 40-fold through hybridization of two distinct binding modes, resulting in novel, highly potent Leishmania donovani NMT inhibitors with good selectivity over the human enzyme.
The leishmaniases are
a spectrum of infectious diseases caused
by protozoan parasites of the genus Leishmania. Cutaneous leishmaniasis (CL), caused mainly by Leishmania
major (Lm), can lead to permanent scarring and disfiguration,
while visceral leishmaniasis (VL), caused mainly by Leishmania donovani (Ld), is often fatal due to failure
of the host immune system. The leishmaniases are endemic in 88 countries,
72 of which are low-income,[1] and is a major
health issue with an estimated 0.2–0.4 million cases of VL,
0.7–1.2 million cases of CL, and a conservative estimate of
20000–40000 deaths per year.[2] Treatment
of leishmaniasis has previously been dominated by the use of pentavalent
antimonials which are toxic, painful to administer, and require long
treatment regimens;[3] resistance has also
developed to these antimonials in India.[4] Some progress has been made in the last 10 years in the development
of safer, more easily applied therapeutics with the development of
lipid formulations of amphotericin B, miltefosine, and paromomycin.
However, side effects are common and resistance to these therapies
may still be a problem,[5] thus the need
for new antileishmanials remains high.[6,7] Despite these
issues, development of new antileishmanial drugs is limited[8] and compounded by challenges of cell permeability.
The amastigote form of the parasite most relevant to human disease
resides within an acidic parasitophorous vacuole inside host cells,[9] and the parasite bears a glycoinositolphospholipid
coat that could limit uptake of xenoantibiotics.[10]N-Myristoyltransferase (NMT), an enzyme ubiquitous
in eukaryotes, catalyzes the transfer of myristate (a 14-carbon fatty
acid) to the N-terminal glycine of target proteins,[11] either cotranslationally[12] or
post-translationally.[13] Between 0.5% and
3% of the cellular proteome is predicted to be N-myristoylated,[14] and this modification is vital for multiple
regulatory processes, including protein–protein interactions
and protein stability.[15−17] Inhibition of NMT therefore has pleiotropic effects
on cellular function. NMT has been shown to be essential in a range
of parasitic organisms including Leishmania,[18] and small-molecule cytotoxic inhibitors
have been developed for NMTs in parasitic organisms including Trypanosoma brucei(19) and Plasmodium species.[20−22] Inhibition of Leishmania NMT therefore represents a rational drug
target for development of new therapeutics for this neglected tropical
disease.[14,23,24]The
NMT enzyme operates via a Bi–Bi mechanism, with myristoyl
CoA (MyrCoA) binding to the enzyme first and inducing a conformational
change before binding of the peptide substrate. The myristate group
is then transferred to the N-terminal glycine of the peptide before
sequential release of the myristoyl peptide and reduced CoA products.[25,26] The structures of several parasitic NMTs have been reported[19,27,28] and show a conserved binding
site for MyrCoA. The peptide-binding region is less conserved between
different species and therefore presents a target for selective inhibition
of NMTs from different species.[29]A recently published high-throughput screen (HTS) of a diverse
subset of the Pfizer corporate collection against LdNMT, Plasmodium falciparum NMT, and the two human isoforms
(HsNMT1 and HsNMT2) revealed four novel series of Leishmania-selective NMT inhibitors.[30] Here we report
the development of highly potent LdNMT inhibitors based on structure-guided
fusion of two of these series; piperidinylindoles, exemplified by
PF-03393842 1, and aminoacylpyrrolidines, exemplified
by PF-03402623 2 and PF-03402619 3 (Chart 1).
Chart 1
Leishmania-Selective
Hits from Screening
of a Subset of the Pfizer Compound File[30]
Results and Discussion
Synthesis
and Validation of Hits
To validate the HTS
results, synthesis of both piperidinylindole 1 and the
most potent aminoacylpyrrolidine 2 was carried out. Synthesis
of 1 was achieved in four steps from 5-nitro indole (Scheme 1). Condensation of 5-nitro indole 4 with N-Boc-4-piperidone, followed by concurrent
reduction of the resulting double bond and nitro group, yielded amine 6.[31] Reaction with para-fluorophenylacetyl chloride followed by Boc deprotection gave piperidinylindole 1.
Reagents
and conditions: (a)
pyrrolidine, N-Boc-4-piperidone, EtOH, rt, 3 days,
80%; (b) NH4HCO2, EtOH, Pd/C, 2 h, 96%; (c) para-fluorophenylacetyl chloride, Et3N, THF,
2 h, 92%; (d) 6 M HCl, IPA, 2 h, 43%.Compound 2 was synthesized as a mixture of two diastereoisomers,
as it was unclear from the original report whether the stereochemistry
at the pyrrolidine ring in the HTS hit was relative or absolute. It
was envisaged that the preferred stereochemistry could be identified
by cocrystallization of the mixture with Leishmania NMT. The pyrrolidine core was accessed as a racemic mixture by cycloaddition
of benzyl-(methyoxymethyl)[(trimethylsilyl)methyl]amine 9 and trans-methyl 4-chlorocinnamate 8 in the presence of catalytic TFA to give trans-pyrrolidine 10 (Scheme 2).[32,33] The benzyl protecting group was removed using 1-chloroethyl chloroformate[34] to avoid the use of reductive methods in the
presence of the aromatic chlorine prior to amide coupling with acid 12 to obtain amide 13. Reduction of the ester
followed by Boc deprotection proceeded smoothly to afford 2 as a mixture of two diastereoisomers.
Scheme 2
Synthesis of Aminoacylpyrrolidine 2
Reagents and conditions: (a) 9, TFA, DCM, 0 °C to rt, 24 h, 88%; (b) (i) 1-chloroethyl
chloroformate, toluene, 110 °C, 3 h, (ii) MeOH, reflux, 30 min;
(c) 12, EDCI, HOBt, DIPEA, DMF, 4 h, 55% over 2 steps;
(d) LiBH4, THF, 3 h, 71%; (e) TFA, DCM, 2 h, 31%.
Synthesis of Aminoacylpyrrolidine 2
Reagents and conditions: (a) 9, TFA, DCM, 0 °C to rt, 24 h, 88%; (b) (i) 1-chloroethyl
chloroformate, toluene, 110 °C, 3 h, (ii) MeOH, reflux, 30 min;
(c) 12, EDCI, HOBt, DIPEA, DMF, 4 h, 55% over 2 steps;
(d) LiBH4, THF, 3 h, 71%; (e) TFA, DCM, 2 h, 31%.Testing of compounds 1 and 2 against
LdNMT and HsNMT1 in our previously reported CPM assay[35] confirmed the results of the HTS, with both compounds showing
selectivity for LdNMT over HsNMT1 (Table 1).
The hits were also tested against related LmNMT, which has been shown
to be more amenable to X-ray crystallography[19,36] and were shown to have comparable activity to LdNMT.
Table 1
Enzyme Activity Data (Results from
HTS in Brackets)[30]
compd
LdNMT IC50 (μM)
LmNMT IC50 (μM)
HsNMT1 IC50 (μM)
EC50a(μM)
LD50b (μM)
1
0.31 (0.102)
0.55
63 (73)
>30
>45
2
0.080 (0.093)
0.031
4.7 (5.2)
10–30
8–16
EC50 in extracellular
Ld amastigotes;
LD50 in bone marrow derived
mouse macrophages
EC50 in extracellular
Ld amastigotes;LD50 in bone marrow derived
mouse macrophagesCompounds
were also tested against extracellular amastigotes of Leishmania donovani and against bone marrow derived
macrophages to determine toxicity (Table 1).[37] Compound 1 displayed no cell activity
up to 30 μM, although no toxicity was observed. Compound 2 showed an EC50 between 10 and 30 μM, however,
the compound was also toxic to macrophages at this concentration.
X-ray Crystallography
Our first strategy to optimize
these NMT inhibitors was to drive down enzyme potency using structure-guided
design. To elucidate the binding mode of the HTS hits and the preferred
stereochemistry of 2, crystal structures of ternary complexes
of LmNMT (97% sequence homology with LdNMT) and myristoyl-CoA cofactor
were obtained for both resynthesized hits, as recently reported.[36] Both inhibitors were shown to bind in the peptide
binding region. The structure of compound 1 bound to
LmNMT revealed a direct interaction between the basic piperidine nitrogen
and the C-terminal carboxylate of the enzyme (Leu421) (Figure 1). This type of charge–charge interaction
has previously been observed with other NMT inhibitors in Plasmodium NMT[20,21] and via a bridging
water molecule in LmNMT.[19] The indole adopts
an equatorial position off the piperidine ring in a hydrophobic pocket,
and the amide carbonyl is orthogonal to the indole ring, forming hydrogen
bonds to Tyr345 and Asn376.
Figure 1
Inhibitor 1 (blue) bound in the
peptide binding pocket
of LmNMT (green). PDB code: 4cgn.
Inhibitor 1 (blue) bound in the
peptide binding pocket
of LmNMT (green). PDB code: 4cgn.The cocrystal structure
of 2 bound to LmNMT displays
a unique binding mode compared to previously reported NMT inhibitors;
the conformation of the inhibitor appears to be governed by a hydrophobic
collapse[38] that folds the aromatic rings
into a hairpin conformation about the flexible linker, with the chlorophenyl
substituent of the pyrrolidine ring sandwiched between the edge of
Tyr345 below and Tyr217 above. The inhibitor takes up a compact conformation
in which its surface area is almost completely buried by the protein
and MyrCoA. Interestingly, the key charge–charge interaction
between the basic amine and Leu421 is not seen (Figure 2). Instead, the primary amine is adjacent to the thioester
of MyrCoA and makes bridging contacts with the backbone carbonyl of
Thr203 and the side chain of Asn167. The hydroxyl group is actually
closest to the C-terminal leucine carboxylate (2.6 Å), and there
is a potential hydrogen bond between the amide carbonyl and Thr203
(Figure 2).
Figure 2
Inhibitor 2a (pink) bound
in the peptide binding pocket
of LmNMT (green). MyrCoA in blue. PDB code: 4cgl.
Inhibitor 2a (pink) bound
in the peptide binding pocket
of LmNMT (green). MyrCoA in blue. PDB code: 4cgl.As expected, the crystal structure shows a single
diastereoisomer
(2a, Scheme 3) bound to the enzyme.
To confirm that 2a is the most active isomer, both diastereoisomers
(2a and 2b) were synthesized separately
using enantiopure oxazolidinone 17 for the cycloaddition
reaction (Scheme 3). Cycloaddition yielded
diasteroisomers 18a and 18b, which could
be separated by column chromatography and were assigned by comparison
with reported 1H NMR data[39] (Scheme 3). Removal of the oxazolidinone gave esters 10a and 10b from which 2a and 2b were synthesized, respectively, using the route detailed
in Scheme 2.
Scheme 3
Synthesis of 2a and 2b
Reagents
and conditions: (a)
(i) oxalyl chloride, DCM, DMF, 0 °C, 30 min, (ii) 17, Et3N, LiCl, 15 h, 29%; (b) 9, TFA, DCM,
0 °C to rt, 24 h, 18a 36%, 18b 25%;
(c) CO(OMe)2, NaOMe, DCM, 15 h, 10a 48%, 10b 40%.
Synthesis of 2a and 2b
Reagents
and conditions: (a)
(i) oxalyl chloride, DCM, DMF, 0 °C, 30 min, (ii) 17, Et3N, LiCl, 15 h, 29%; (b) 9, TFA, DCM,
0 °C to rt, 24 h, 18a 36%, 18b 25%;
(c) CO(OMe)2, NaOMe, DCM, 15 h, 10a 48%, 10b 40%.Enzyme inhibition assays
confirmed that diastereoisomer 2a was more active with
an IC50 of 25 nM against LdNMT,
with 2b exhibiting 60-fold lower potency and 4-fold lower
selectivity for LdNMT over HsNMT1 (Table 2).
Table 2
Enzyme Activity Data for Diastereoisomers 2a and 2b
compd
LdNMT IC50 (μM)
HsNMT1 IC50 (μM)
2
0.080
4.7
2a
0.025
1.4
2b
1.7
24
A crystal structure was also obtained for 2b bound
to LmNMT. The structure shows a similar hydrophobic collapse of the
ligand and that the key functional groups (the primary amine and alcohol)
of both diastereoisomers are superimposed in the active site (circled,
Figure 3). However, as a result of maintaining
these interactions, the scaffold is twisted such that the amide carbonyl
no longer forms the hydrogen bond with Thr203 seen in the structure
of 2a.
Figure 3
Overlay of I 2b (cyan) and 2a (pink)
bound in the peptide binding pocket of LmNMT obtained by alignment
of the protein main chain atoms (distances in Å). PDB code for 2b: 4cyn.
Overlay of I 2b (cyan) and 2a (pink)
bound in the peptide binding pocket of LmNMT obtained by alignment
of the protein main chain atoms (distances in Å). PDB code for 2b: 4cyn.
Hybridization of Binding
Modes
Comparison of the distinct
binding modes of hits 1 and 2 showed that
the benzo-ring of the indole in 1 and the aromatic substituent
of the pyrrolidine in 2 bind in the same region (Figure 4a). For this reason, it was hypothesized that addition
of a para-fluorophenyl acetamide ortho- to the chlorine atom in this ring in compound 2 may
significantly improve potency (Figure 4b).
This could potentially introduce hydrogen bonding between the acetamide
carbonyl and Tyr345 and Asn376 and allow 2 to extend
into the same hydrophobic pocket as 1. To determine whether
an acyl group would be sufficient to increase potency by addition
of the hydrogen bond, or whether the hydrophobic bulk of the para-fluorophenyl group would be required, both the acyl
and para-fluorophenyl acetamide derivatives of 2 were synthesized (19 and 20, respectively,
Figure 4b).
Figure 4
(a) Overlay of binding modes of 1 (blue) and 2a (pink). (b) Proposed hybrid structures 19 and 20.
(a) Overlay of binding modes of 1 (blue) and 2a (pink). (b) Proposed hybrid structures 19 and 20.To allow the addition of an acetamide in the correct position,
synthesis of the pyrrolidine core was carried out using 3-nitro, 4-chloro
cinnamate 21 (Scheme 4). Selective
reduction of the nitro group with tin(II) chloride then provided an
aniline moiety for formation of the required amide bond. Both the
acyl derivative 19 and para-fluorophenyl
derivative 20 were synthesized using the route shown
in Scheme 4.
Scheme 4
Synthesis of 19 and 20
Reagents
and conditions: (a) 9, TFA, DCM, 0 °C to rt, 24
h, 79%; (b) SnCl2, EtOH, 2 h, 87% (c) R = H, Ac2O, Et3N, DCM,
2 h, 65%, R = pF-Ph para-fluorophenylacetyl
chloride, Et3N, DCM, 2 h, 42%; (d) (i) 1-chloroethyl chloroformate,
toluene, 110 °C, 3 h, (ii) MeOH, reflux, 30 min; (e) EDCI, HOBt,
DIPEA, 12, DMF, 4 h, R = H 41% over 2 steps, R = cpF-Ph 43% over 2 steps; (f) LiBH4, THF, 3 h;
(g) TFA, DCM, 2 h, R = H 61% over 2 steps, R = pF-Ph
34% over two steps.
Synthesis of 19 and 20
Reagents
and conditions: (a) 9, TFA, DCM, 0 °C to rt, 24
h, 79%; (b) SnCl2, EtOH, 2 h, 87% (c) R = H, Ac2O, Et3N, DCM,
2 h, 65%, R = pF-Ph para-fluorophenylacetyl
chloride, Et3N, DCM, 2 h, 42%; (d) (i) 1-chloroethyl chloroformate,
toluene, 110 °C, 3 h, (ii) MeOH, reflux, 30 min; (e) EDCI, HOBt,
DIPEA, 12, DMF, 4 h, R = H 41% over 2 steps, R = cpF-Ph 43% over 2 steps; (f) LiBH4, THF, 3 h;
(g) TFA, DCM, 2 h, R = H 61% over 2 steps, R = pF-Ph
34% over two steps.Testing of the hybrid
compound 19 showed that the
acyl group was tolerated but did not improve potency. However, addition
of the para-fluorophenyl group in compound 20 led to an IC50 at the lower measurement limit
of the biochemical assay. In this case, converting to Ki using the Cheng–Prusoff equation for tight binders
is more informative[40,41] (Table 3). Introduction of the para-fluorophenyl group led
to a 40-fold decrease in Ki against LdNMT
(Ki = 1.6 nM). Alignment of the X-ray
crystal structures of 20, 1, and 2 bound to LmNMT demonstrates that 20 binds as designed
and that all interactions with the enzyme are conserved (Figure 5 and Figure S1, Supporting Information).
Table 3
Enzyme and Cell Activity Data
compd
pKa
LdNMT Ki (nM)
HsNMT1 Ki (nM)
EC50a (μM)
LD50b (μM)
1
10.0
254
28505
>30
>45
2
8.9
63
2124
10–30
8–16
2a
8.9
17
631
10–30
12–24
2b
8.9
1406
10857
10–30
12–24
19
8.9
110
4910
>50
>90
20
8.9
1.6
27
10–30
12–24
43
59
1710
10–30
>24
EC50 in extracellular
Ld amastigotes (for comparison, EC50 for the widely used
antileishmanial drugs amphotericin B and miltefosine in this assay
are 50 and 7850 nM, respectively.)
LD50 in bone marrow-derived
mouse macrophages.
Figure 5
Overlay of hits 1 (blue), 2 (pink), and
hybrid 20 (white; PDB code 4cyo) bound to LmNMT obtained by alignment
of the protein main chain atoms.
EC50 in extracellular
Ld amastigotes (for comparison, EC50 for the widely used
antileishmanial drugs amphotericin B and miltefosine in this assay
are 50 and 7850 nM, respectively.)LD50 in bone marrow-derived
mouse macrophages.Overlay of hits 1 (blue), 2 (pink), and
hybrid 20 (white; PDB code 4cyo) bound to LmNMT obtained by alignment
of the protein main chain atoms.
Cell Testing
Despite the greater enzyme inhibition
achieved by hybrid compound 20, no improvement in cell-based
activity was seen (Table 3). This highlights
that simply driving down enzyme potency in this compound series is
insufficient to increase cellular activity against this challenging
target organism. The diastereoisomers of 2 were also
tested separately, and both displayed an EC50 of 10–30
μM and an LD50 of 12–24 μM, demonstrating
that both activity and toxicity are unrelated to NMT inhibition for
these compounds. We hypothesized that the lack of cell-based activity
for this series of compounds is due to lack of cellular uptake and
thus, insufficient target engagement. Compounds 1 and 2 and derivatives synthesized here all contain a basic center
(pKa 10.0 and 8.9 respectively) which
would be charged at physiological pH, with a potentially adverse effect
on membrane permeability.
Replacement of the Primary Amine
As the crystal structures
of the aminoacylpyrrolidines show that the amine does not make the
key charge–charge interaction with the C-terminal carboxylate
observed previously in other series, we considered replacing the primary
amine with a less basic moiety. It was envisaged that the amine could
be replaced with an alcohol without loss of hydrogen bonding, potentially
generating a potent, neutral NMT inhibitor. To synthesize this neutral
compound, acid 35 was synthesized from 4-chlorophenylacetyl
chloride 32. Reaction with Meldrum’s acid followed
by hydrolysis gave ketone 33, which was subsequently
reduced. Hydrolysis of the resulting ester gave the acid 35 (Scheme 5).
Scheme 5
Synthesis of Acid 35
Reagents and conditions: (a)
(i) Meldrum’s acid, pyridine, DCM, 0 °C, 30 min then
rt, 15 h, (ii) EtOH, reflux, 2 h, 70%; (b) NaBH4, MeOH,
0 °C to rt, 1.5 h, 40%; (c) LiOH, MeOH/H2O 99%.
Synthesis of Acid 35
Reagents and conditions: (a)
(i) Meldrum’s acid, pyridine, DCM, 0 °C, 30 min then
rt, 15 h, (ii) EtOH, reflux, 2 h, 70%; (b) NaBH4, MeOH,
0 °C to rt, 1.5 h, 40%; (c) LiOH, MeOH/H2O 99%.This acid was then used to synthesize the alcohol
analogue of hybrid 20 (Scheme 6). As acid 35 was synthesized as a racemic mixture,
pyrrolidine 39 was synthesized as a single enantiomer
in order to give the hybrid
alcohol 43 as a mixture of only two diastereoisomers
(Scheme 6). The hybrid alcohol 43 was tested for its enzyme activity and showed reduced activity compared
to the corresponding amine (Table 3). However,
the activity for this neutral compound is comparable to the original
primary amine hit 2, and selectivity over HsNMT1 is maintained.
Scheme 6
Synthesis of Alcohol 43
Reagents
and conditions: (a)
(i) oxalyl chloride, DCM, DMF, 0 °C, 30 min, (ii) 16, Et3N, LiCl, 15 h, 45%; (b) 9, TFA, DCM,
0 °C to rt, 24 h, 38a 40%; (c) CO(OMe)2, NaOMe, DCM, 15 h 36%; (d) SnCl2, EtOH, 2 h, quantitative;
(e) para-fluorophenylacetyl chloride, Et3N, DCM, 2 h 55%; (f) (i) 1-chloroethyl chloroformate, toluene, 110
°C, 3 h, (ii) MeOH, reflux, 30 min; (g) DMC, 35,
Et3N, DCM, 15 h, 27% over 2 steps; (h) LiBH4, THF, 2 h, 25%.
Synthesis of Alcohol 43
Reagents
and conditions: (a)
(i) oxalyl chloride, DCM, DMF, 0 °C, 30 min, (ii) 16, Et3N, LiCl, 15 h, 45%; (b) 9, TFA, DCM,
0 °C to rt, 24 h, 38a 40%; (c) CO(OMe)2, NaOMe, DCM, 15 h 36%; (d) SnCl2, EtOH, 2 h, quantitative;
(e) para-fluorophenylacetyl chloride, Et3N, DCM, 2 h 55%; (f) (i) 1-chloroethyl chloroformate, toluene, 110
°C, 3 h, (ii) MeOH, reflux, 30 min; (g) DMC, 35,
Et3N, DCM, 15 h, 27% over 2 steps; (h) LiBH4, THF, 2 h, 25%.The crystal structure of
alcohol 43 bound to LmNMT
appeared to overlay well with that of amine 20 (Figure S2, Supporting Information, PDB code 4cyq). However, closer
inspection revealed a slight difference in the position of the amine
versus the alcohol in these two structures. The primary amine of 20 forms a hydrogen bond to the backbone carbonyl group of
Thr203 at a distance of 2.9 Å. When this amine is replaced with
an alcohol in compound 43, the corresponding oxygen is
3.5 Å away, reducing its potential to hydrogen bond.Testing
against extracellular amastigotes showed no improvement
in activity for compound 43 compared with the original
hits or the hybrid amine (Table 3). Metabolic
chemical tagging[22] in Ld amastigotes (Figure S3, Supporting Information) demonstrated
that despite replacement of the primary amine, target engagement consistent
with a Ki of 59 nM was not achieved, supporting
our hypothesis that the lack of cell-based activity for these compounds
is due to poor cellular uptake.Despite the potential of NMT
as a drug target in Leishmania, these
organisms are known to be difficult
to target, due in part to their cell surface coats, a key component
of Leishmania virulence and survival.[9,10] Advances in
potency and particularly physicochemical properties will be required
to progress this series of compounds and to chemically validate Leishmania NMT as a drug target in vivo.
Conclusion
Two Leishmania NMT-selective HTS
hits have been resynthesized and their activities validated. Crystal
structures of these inhibitors identified their binding modes and,
in the case of compound 2, identified the active diastereoisomer.
The crystal structures were used to increase enzyme affinity through
hybridization of the two independent binding modes, and this led to
the discovery of a highly potent inhibitor of LdNMT. The unusual binding
mode of the aminoacylpyrrolidines allowed the replacement of the primary
amine, leading to compound 43, a potent and neutral NMT
inhibitor. Although poor uptake appears to lead to a lack of cell
activity for these compounds, elucidation of the binding modes of
these inhibitor series along with their hybridization provides a useful
starting point for the development of LdNMT inhibitors with improved
physicochemical properties.
Experimental Section
The purity of final compounds was determined by reversed-phase
LC-MS on a Waters 2767 system and was ≥95% for all tested compounds.
TFA (20 μL, 0.20 mmol) was added
to a solution of 9 (1.04 mL, 4.06 mmol) and chlorocinnamate 8 (400 mg, 2.03 mmol) in DCM (40 mL) at 0 °C, and the
solution was stirred (rt) for 24 h. Saturated aqueous NaHCO3 (40 mL) was added, and the phases were separated. The organic layer
was dried over Na2SO4 and the solvent removed
under reduced pressure. The crude residue was purified by column chromatography
(1:9 EtOAc–hexane, Rf 0.25) to
give the product 10 as a colorless oil (590 mg, 88%). 1H NMR (400 MHz,CDCl3) δ 7.41–7.27
(m, 9H), 3.76–3.68 (m, 5H), 3.68–3.63 (m, 1H), 3.16–3.03
(m, 2H), 3.02–2.96 (m, 1H), 2.86 (dd, J =
8.3, 6.4 Hz, 1H), 2.77 (dd, J = 9.4, 5.8 Hz, 1H).
1-Chloroethyl chloroformate (327 μL,
3.03 mmol) was added to a solution of 10 (500 mg, 1.51
mmol) in toluene (30 mL), and the solution was stirred at 110 °C
for 3 h. The reaction was cooled to room temperature, and the solvent
was removed under reduced pressure. The residue was dissolved in methanol
(30 mL), and the solution was heated at reflux for 30 min before cooling
to room temperature. The solvent was removed under reduced pressure
to give 513 mg of yellow oil. Then 150 mg of this oil was dissolved
in DMF (7.5 mL), and acid 12 (216 mg, 0.69 mmol) was
added, followed by EDCI (132 mg, 0.69 mmol), HOBt (93 mg, 0.69 mmol),
and DIPEA (120 μL, 0.69 mmol). The solution was stirred at room
temperature for 4 h. EtOAc (10 mL) was added, and the mixture was
washed with saturated aqueous NaHCO3 (10 mL), water (3
× 10 mL), and brine (10 mL). The solvent was removed under reduced
pressure and the residue purified by column chromatography (1:1 EtOAc–hexane, Rf 0.35) to give the product 13 as
a colorless oil (186 mg, 55%) as a mixture of diastereoisomers and
as a mixture of amide rotamers by 1H NMR at room temperature. 1H NMR (400 MHz, CDCl3) δ 7.38–7.24
(m, 4H), 7.23–7.08 (m, 4H), 5.68 (br s, 1H), 4.18–3.97
(m, 2H), 3.85–3.42 (m, 6H), 3.27–3.10 (m, 1H), 3.10–3.00
(m, 1H), 2.97–2.85 (m, 1H), 2.50–2.40 (m, 2H), 1.45–1.38
(m, 9H).
LiBH4 (3 mg, 0.13 mmol) was
added to a solution of 13 (18 mg, 0.04 mmol) in dry THF
(1 mL). The solution was stirred for 3 h (rt). Water was added (2
mL), followed by DCM (2 mL), and the phases were separated. The organic
layer was dried over MgSO4 and the solvent removed under
reduced pressure to give the product 14 as a colorless
oil (12 mg, 71%) as a mixture of diastereoisomers and as a mixture
of amide rotamers by 1H NMR at room temperature. 1H NMR (400 MHz, CDCl3) δ 7.36–7.24 (m, 4H),
7.17 (m, 4H), 5.89–5.59 (br s, 1H), 4.18–3.86 (m, 2H),
3.77–3.63 (m, 2H), 3.61–3.09 (m, 4H), 3.04 (m, 1H),
2.95–2.84 (m, 1H), 2.54–2.38 (m, 2H), 1.46–1.36
(m, 9H).
TFA (11 μL, 0.11 mmol) was added to
a solution of 14 (12 mg, 0.02 mmol) in DCM (1 mL), and
the reaction was stirred at for 2 h (rt). The solvent was removed
under reduced pressure, and the crude residue was purified by preparative
LCMS (method B) to give the product 2 as a colorless
oil (3 mg, 31%) as a mixture of diastereoisomers. 1H NMR
(400 MHz, MeOD) δ 7.43–7.24 (m, 8H), 4.06–3.76
(m, 2H), 3.72 (s, 1H), 3.61–3.55 (m, 1H), 3.52–3.37
(m, 3H), 3.29–3.14 (m, 1H), 2.99–2.85 (m, 2H), 2.72–2.39
(m, 3H). m/z 407 ([M + H]+). HRMS found 407.1313, C21H25N2O2Cl2 requires 407.1293. LCMS Rt = 12.44 min. Complete experimental details including
LCMS methods are provided in the Supporting Information.
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