Low molecular weight amidoximes that act as potent inhibitors of lysine-specific demethylase 1

Article abstract of DOI:10.1021/jm3002845

The recently discovered enzyme lysine-specific demethylase 1 (LSD1) plays an important role in the epigenetic control of gene expression, and aberrant gene silencing secondary to LSD1 dysregulation is thought to contribute to the development of cancer. We reported that (bis)guanidines, (bis)biguanides, and their urea- and thiourea isosteres are potent inhibitors of LSD1 and induce the re-expression of aberrantly silenced tumor suppressor genes in tumor cells in vitro. We now report a series of small molecule amidoximes that are moderate inhibitors of recombinant LSD1 but that produce dramatic changes in methylation at the histone 3 lysine 4 (H3K4) chromatin mark, a specific target of LSD1, in Calu-6 lung carcinoma cells. In addition, these analogues increase cellular levels of secreted frizzle-related protein (SFRP) 2, H-cadherin (HCAD), and the transcription factor GATA4. These compounds represent leads for an important new series of drug-like epigenetic modulators with the potential for use as antitumor agents.

Full text of DOI:10.1021/jm3002845

Article
pubs.acs.org/jmc
Low Molecular Weight Amidoximes that Act as Potent Inhibitors of
Lysine-Specific Demethylase 1
Stuart Hazeldine,† Boobalan Pachaiyappan,§ Nora Steinbergs,‡ Shannon Nowotarski,‡ Allison S. Hanson,†
Robert A. Casero, Jr.,‡ and Patrick M. Woster*,§
†Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Avenue, Detroit, Michigan 48202, United States
‡Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland 21231, United States
§Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 70 President Street, Charleston,
South Carolina 29425, United States
S
* Supporting Information
ABSTRACT: The recently discovered enzyme lysine-specific demethylase 1 (LSD1) plays an important role in the epigenetic
control of gene expression, and aberrant gene silencing secondary to LSD1 dysregulation is thought to contribute to the
development of cancer. We reported that (bis)guanidines, (bis)biguanides, and their urea- and thiourea isosteres are potent
inhibitors of LSD1 and induce the re-expression of aberrantly silenced tumor suppressor genes in tumor cells in vitro. We now
report a series of small molecule amidoximes that are moderate inhibitors of recombinant LSD1 but that produce dramatic
changes in methylation at the histone 3 lysine 4 (H3K4) chromatin mark, a specific target of LSD1, in Calu-6 lung carcinoma
cells. In addition, these analogues increase cellular levels of secreted frizzle-related protein (SFRP) 2, H-cadherin (HCAD), and
the transcription factor GATA4. These compounds represent leads for an important new series of drug-like epigenetic
modulators with the potential for use as antitumor agents.
Histone lysine methylation/demethylation represents a
critical epigenetic modification cycle,5,8,9 and dysregulation of
this cycle can lead to aberrant silencing of tumor suppressor
genes. Histone lysine methylation has been shown to be a
dynamic process regulated by the addition of methyl groups by
a number of specific histone methyltransferases and removal of
methyl groups from mono-, di, and trimethyllysines by lysine
specific demethylase 1 (LSD1)8 and by specific Jumonji C
(JmjC) domain-containing demethylases.8−12 To date, 17
lysine residues and seven arginine residues on histone proteins
have been shown to undergo methylation12−16 and lysine
methylation on histones can signal transcriptional activation or
repression, depending on the specific lysine residue in-
volved.17−19
INTRODUCTION
■
Chromatin architecture is a key determinant in the regulation
of gene expression and is strongly influenced by post-
translational modification of histones.1,2 Histones, which are
the chief protein component of chromatin, are complex
macromolecules comprised of core protein subunits termed
H2a, H2b, H3, and H4. Histone tails, consisting of up to 40
amino acid residues, protrude through the DNA strand, and
lysines, arginines, serines, threonines, and tyrosines on this tail
act as sites for post-translational modification. These
modifications, including methylation, ubiquitination, sumoyla-
tion, ADP-ribosylation, and acetylation of histone lysine
residues and phosphorylation of histone serine, threonine,
and tyrosine,3 allow alteration of higher-order nucleosome
structure and thus contribute to structural changes in
chromatin.4,5 In cancer, DNA promoter CpG island hyper-
methylation in combination with other chromatin modifica-
tions, including decreased activating marks and increased
repressive marks on histone proteins 3 and 4, have been
associated with the silencing of tumor suppressor genes.6,7
A key transcription-activating chromatin mark found
associated with promoters of active genes is histone 3
dimethyllysine 4 (H3K4).20,21 The flavin adenine dinucleotide
Received: February 28, 2012
Published: August 9, 2012
© 2012 American Chemical Society
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Figure 1. Structures of previously discovered LSD1 inhibitors 1c and 2d, the monoamine oxidase inhibitors tranylcypromine 3 and pargyline 4, and
virtual screening hits 5−7.
(FAD)-dependent amine oxidase LSD1, also known as
BHC110 and KDM1,8,22 catalyzes the oxidative demethylation
of histone 3 methyllysine 4 (H3K4me1) and histone 3
dimethyllysine 4 (H3K4me2), leading to transcriptional
repression.8 Aberrant demethylation of H3K4me1 and
H3K4me2 is known to prevent expression of tumor suppressor
genes important in human cancer.23 Thus, LSD1 and other
histone demethylases have emerged as important new targets
for the development of specific inhibitors as a new class of
antitumor drugs.24
To date, only a few small molecule inhibitors of LSD1 have
been identified. The classical monoamine oxidase (MAO)
inhibitors phenelzine and tranylcypromine inhibit the recombi-
nant LSD1/CoRest complex and increase global levels of
H3K4me2.22,25 Other recently described synthetic demethylase
inhibitors include peptidic substrate mimics featuring modified
lysine residues26 and trans-2-arylcyclopropylamine ana-
logues.27−29 All of the above are based either on the peptide
substrate, making them unlikely candidates for drug develop-
ment, or on a tranylcypromine scaffold. Among the most
effective LSD1 inhibitors is the tranylcypromine-based inhibitor
(1S,2R)-NCL-1 (IC50 1.6 μM),30,31 and the (bis)-3,3-
(diphenyl)propylbiguanide known as 2d.32,33 A comprehensive
review of inhibitors of lysine demethylases has recently been
published.34
We previously reported the synthesis of a novel series of
(bis)guanidines and (bis)biguanides35 that act as potent
inhibitors of LSD1.23 The two most potent LSD1 inhibitors,
1c and 2d (Figure 1), produced significant global increases in
both H3K4me1 and H3K4me2 in HCT116 colon tumor cells
in vitro and promoted the re-expression of multiple, aberrantly
silenced genes important in the development of colon cancer,
including members of the secreted frizzle-related proteins
(SFRPs) and the GATA family of transcription factors.
Compound 2d has also been shown to produce a synergistic
effect on tumor growth when combined with 5-azacytidine in
nude mice bearing HCT116 human colon carcinoma
xenografts.33 These studies confirm that the use of histone
demethylase inhibitors in combination with a DNA methyl-
transferase inhibitor represents a highly promising and novel
approach to cancer chemotherapy.
Because of the promising antitumor effects of 1c and 2d, we
sought to find additional lead compounds for use as epigenetic
modulators. Other groups have already pursued novel
analogues related to the known monoamine oxidase inhibitors
tranylcypromine 3 and pargyline 4 (Figure 1), however, we
were interested in finding previously unknown scaffolds for use
in LSD1 inhibitor design. Thus a virtual screen strategy was
undertaken to examine the Maybridge Hitfinder 5 compound
library, with the goal of identifying potential lead compounds.
The crystal structure of LSD1 (Protein Data Bank 2V1D) was
prepared for the virtual screen using PrepWizard, and SiteMap
was then used to assess the “druggability” of the LSD1 histone-
binding pocket and to map the active site. The active site
features a hydrophilic pocket near the FAD cofactor, which
appears to be the binding area for H3K4me2. Notably, the
active site also contains a large hydrophobic pocket that could
serve as a target for the structure-based design of inhibitor
molecules. For the virtual screen, compounds in the Maybridge
database were converted from 2D to 3D, and the lowest energy
conformers were determined. These conformers were then
docked in the LSD1 active site using Glide. A total of 10 hits
were identified, each of which had a GlideScore lower than
−7.5 kcal/mol. Each of the identified molecules contained a
hydrophilic moiety that appeared to be situated near the FAD
cofactor and a hydrophobic substituent that was bound in the
hydrophobic pocket (data not shown). We examined these hits
and selected three that seemed amenable to structural
optimization, compounds 5, 6, and 7, for our initial studies
(Figure 1).
CHEMISTRY
■
Compounds 5−7 and analogues 8−33 could be readily
synthesized using the routes described in Schemes 1−3. As
was mentioned above, compounds 5−7 were among the virtual
hits identified from the Maybridge Hitfinder 5 database, as was
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Scheme 1
Scheme 2
Scheme 3
compound 12, while the remaining analogues were largely
unreported. The synthesis of carbamimidothioates 5, 8, and 9
could be completed in a single step, as shown in Scheme 1. The
appropriate bromoalkylphthalimide 34a, 34b, or 34c was
treated with thiourea 3536 to afford the desired products 5, 8,
and 9, respectively, in 62−79% yield. In each case, the product
precipitated from the reaction mixture as a white amorphous
solid.
Compounds 6, 10, and 11 were also accessible in a single
step using an adaptation of a previously published procedure,37
as shown in Scheme 2. Treatment of 1,3-dinitro-2-chloro-5-
trifluoromethylbenzene 35 with the appropriate diamine 36a−c
in the presence of triethylamine at 10 °C afforded the desired
target molecules 6, 10, and 11 in 68−87% yield.
The remaining target molecules 7 and 12−33 were
synthesized as outlined in Scheme 3. Thus substituted anilines
37−59 (see Table 1 for identities of R1, R2, and R3) were
treated with cyanoacetic acid in the presence of phosphorus
pentachloride in dichloromethane,38 resulting in the formation
of the corresponding amides 60−82. Yields for this trans-
formation were largely between 85 and 95%, although in a few
cases they were as low as 52%. These amides in turn were
reacted with hydroxylamine and sodium bicarbonate in
dichloromethane39 to yield the desired amidoximes 7 and
12−33. In this step, yields varied widely between 23 and 78%.
produced significant changes in H3K4me2 levels in the Calu-6
human lung adenocarcinoma cell line. Thus, the ability of
compounds 5−33 to produce increases in global H3K4me2
levels at both 24 and 48 h was measured as previously
described.8 Although indicative of changes in gene tran-
scription, increases in H3K4 methylation levels measured at
24 h are determined when cells are in log phase growth.
Increases in H3K4 methylation at 48 h give a more realistic
picture of changes in gene transcription because they are
measured when cells are nearing confluence. Thus, only the
results of these studies at 48 h are shown in Table 1, while
H3K4me2 levels at 24 h appear in the Supporting Information
(Table S1). Increases in H3K4me1 and H3K4me2 levels
promoted by carbamimidothioates 5, 8, and 9 and the 2,5-
dinitro-4-trifluoromethylaniline derivatives 6, 10, and 11 were
unremarkable at both 24 and 48 h. Among the fluorinated
amidoximes 12−18, compounds 16 and 17 promoted 21.4- and
12.4-fold increases at 48 h, respectively. Compounds 14 and 15
produced a 7.1- and 7.0-fold increase in H3K4me2 levels at 24
h, respectively, but this effect was not observed at 48 h.
Compounds 12, 13, and 18 had no effect on H3K4me2 at this
time point. Compound 17, which featured a 2-fluoro
substituent, produced a significant increase in H3K4me2 levels
(12.4-fold) and was easier to access synthetically, and as such a
series of 2-substituted aromatic amidoximes 19−33 was
synthesized. Among these analogues, changes in the levels of
H3K4me2 at 24 h ranged between 2.1-fold and 7658.7-fold,
with the exception of compounds 19−21, which had no
significant effect at 24 h. At the 48 h time point, significant
increases in H3K4me2 levels between 2.1- and 49-fold were
observed, with the exception of compounds 19, 20, and 25,
which did not promote increases at the 48 h time point.
The ability of the target amidoximes 5−33 to inhibit LSD1
was determined in an assay procedure utilizing the recombinant
BIOLOGICAL EVALUATION
■
For synthetic histone demethylase inhibitors to be effective at
the cellular level, any observed decreases in cellular LSD1
activity should be accompanied by an increase in global
H3K4me1 and H3K4me2 content. The fortuitous decision to
measure methylation changes prior to evaluating the analogues
as LSD1 inhibitors was made based on our preliminary findings
that suggested that fluorinated amidoximes such as 14 and 15
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Table 1. Inhibition of Purified Recombinant LSD1 Following Treatment with 10 μM 3−33, and Fold Increase in Global
H3K4me2 Levels in Calu-6 Human Lung Adenocarcinoma Cells Following Treatment with Carbamimidothioates 5, 8, and 9,
a
Aromatic Amines 6, 10, and 11, and amidoximes 7 and 12−33 at 10 μM
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Table 1. continued
a
Each data point is the average of three determinations that in each case differed by less than 5%. ND = not determined.
Figure 2. Fold increase in the expression of SFRP2 in Calu-6 anaplastic epithelial lung carcinoma cells. Cells were treated with either 1 mM
aminoguanidine (AG), 5 μM PN11144, 5 μM 2d, or 10 μM of the indicated test compound for 24 or 48 h. Each data point is the average of three
determinations that in no case differed by more than 5%.
human enzyme. Expression and purification of LSD1 were
conducted as previously reported.8,23 Enzymatic activity of
LSD1 in the presence of target compounds was determined
using luminol-dependent chemiluminescence to measure the
production of H2O2, as previously described.23,40 The results of
these experiments are summarized in Table 1. Compound 2d
inhibited purified recombinant LSD1 by 82.9% at 10 μM and
initiated a 5-fold increase in cellular H3K4me2 levels in the
Calu-6 cell model system, as previously reported.32,41 By
contrast, the monoamine oxidase inhibitors tranylcypromine 3
and pargyline 4 inhibited the enzyme by 18.4 and 68.8% at 10
μM, respectively. Carbamimidothioates 5, 8, and 9 were modest
inhibitors of LSD1, producing 24.0, 31.8, and 17.3% inhibition
at 10 μM, but this inhibition did not correlate with an increase
in H3K4me2 levels, as described above. The aminoalkylaniline
derivatives 6, 10, and 11 were essentially inactive as inhibitors
of recombinant LSD1 and also had no effect on lysine
methylation in the Calu-6 cell line. Surprisingly, despite
promoting dramatic increases in cellular H3K4me2 levels at
either 24 or 48 h, compounds 14−17, 23−27, 29, 31, and 33
were poor to modest inhibitors of LSD1. The most effective
amidoxime inhibitor, 22, exhibited a 30.1% inhibition of the
enzyme at 10 μM and an IC50 value of 16.8 μM, which
correlated with an 837.5-fold increase in H3K4me2 levels at 24
h. The parent compound 7 was a slightly better inhibitor (IC50
15.6 μM), but remarkably, it did not produce any significant
changes in H3K4 methylation. It is well established that the
specificity of LSD1 for H3K4 demethylation is observed when
the enzyme is bound to the CoREST.42,43 Thus one possible
interpretation of the lack of correlation between LSD1
inhibition and increase in methylation is that the recombinant
LSD1 used in the inhibition assay is not bound to the CoREST,
a functional corepressor required for gene expression.44 It is
possible that amidoximes related to 22 are poor inhibitors of
uncomplexed recombinant LSD1 in vitro but are more effective
inhibitors of the LSD1/CoREST complex in cultured Calu-6
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Figure 3. Fold increase in the expression of HCAD Calu-6 anaplastic epithelial lung carcinoma cells. Cells were treated with either 1 mM
aminoguanidine (AG), 5 μM PN11144, 5 μM 2d, or 10 μM of the indicated test compound for 24 or 48 h. Each data point is the average of three
determinations that in no case differed by more than 5%.
Figure 4. Fold increase in the expression of GATA4 in Calu-6 anaplastic epithelial lung carcinoma cells. Cells were treated with either 1 mM
aminoguanidine (AG), 5 μM PN11144, 5 μM 2d, or 10 μM of the indicated test compound for 24 or 48 h. Each data point is the average of three
determinations that in no case differed by more than 5%.
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cells, a hypothesis that is supported by the molecular modeling
studies described below.
methionine takes the place of the lysine corresponding to
H3K4.50 The pLys4Met H3 peptide exhibited a 30-fold greater
binding affinity (Ki = 0.05 μM) as compared to the wild-type
peptide (Ki = 1.8 μM). Because the LSD1 binding pocket and
the 21-mer cocrystal peptide ligand are relatively large, we
included only the residues that lie within 6 Å around the ligand
in our analysis. The pLys4Met H3 ligand was removed, and the
energy-minimized amidoxime 22 was substituted and docked in
the binding site of LSD1/CoREST (see the Experimental
Section). The resulting poses were scored using ChemScore.49
Visualization of the lowest energy binding mode of 22 in the
LSD1/CoREST binding site revealed that 22 binds to the same
region as that occupied by the pThr3 and pMet4 of the
pLys4Met H3 peptide, as shown in Figure 5. This result
The compounds that produced the most dramatic increases
in global H3K4me2 levels, 22−27, 29, and 31, were next
examined for their ability to promote the re-expression of
aberrantly silenced tumor suppressor genes in the Calu-6 cell
line. The soluble modulator of Wnt signaling secreted frizzle-
related protein 2 (SFRP2),45 the membrane-bound mediator of
calcium-dependent cell−cell adhesion H-cadherin (HCAD,
CDH13),46 and the zinc-finger transcription factor GATA447
were chosen because they are known to be under expressed in
human lung cancer and because their silencing is thought to
play a role in tumorigenesis.41 Cells were treated for 24 or 48 h
with a 5 μM concentration of 2d or the polyamine analogue
PN1114448 or a 10 μM concentration of each amidoxime
analogue, after which the levels of SFRP2, HCAD, and GATA4
were determined by quantitative PCR (qPCR).32,41 In the case
of each re-expressed protein, a fold increase of ≥1.5 was
considered significant. Four of the amidoxime analogues
evaluated, 25, 27, 29, and 31 produced increases in SFRP2
levels (25, 2.29-fold at 24 h, 1.45-fold at 48 h; 27, 1.69-fold at
24 h; 29, 1.55-fold at 48 h; 31, 1.89-fold at both 24 and 48 h,
Figure 2). However, none of these increases were of the same
magnitude as the increases promoted by the positive control
2d. Aminoguanidine at 1 mM (AG) and the polyamine
analogue PG1114448 had no effect on SFRP2 levels. In the case
of HCAD (Figure 3), significant increases were observed with
10 μM 23 (1.6-fold at 48 h), 26 (1.6-fold at 48 h), 27 (1.58 fold
at 48 h), 29 (1.8-fold at 48 h), and 31 (2.15-fold at 48 h). By
contrast, 2d increased HCAD expression by 1.62-fold at 24 h
and 3.83-fold at 48 h. PG11144 also had an effect at 10 μM
(1.47-fold) at 24 h. The most dramatic effects were observed in
the case of the transcription factor GATA4 (Figure 4), where
increased expression was observed following treatment with 23
(1.69-fold at 48 h), 26 (1.57-fold at 24 h, 1.77-fold at 48 h), 27
(2.06-fold at 24 h), 29 (1.66-fold at 24 h), and 31 (4.22-fold at
48 h). These effects were comparable to 2d (2.07-fold at 24 h,
1.94-fold at 48 h) for 27 (24 h) and 31, which had twice the
effect of 2d at 48 h.
Importantly, the magnitudes of the observed increases in
H3K4 methylation induced by amidoximes 22−27, 29, and 31
do not correlate well with the re-expression of the aberrantly
silenced gene products chosen for this study (SFRP2, HCAD,
and GATA4). However, the dramatic nature of the observed
increases in H3K4me2 methylation suggest that significant
changes in cellular gene expression must be taking place. As
such, we are currently undertaking a DNA microarray strategy
to determine which genes are affected in tumor cells following
treatment with amidoximes 22−27, 29, and 31.
Figure 5. Graphic representation of binding mode of amidoxime 22 in
the LSD1-CoREST complex active site. (A) Distance between the
amidoxime functionality of 22 and N-5 of the flavin ring of FAD;
distance between the MET residue of the Forneris inhibitor and N-5
of the flavin ring of FAD. (B) Hydrogen bonding distances between
22 and amino acid residues THR 335, ALA 539, and TYR 761.
supports the hypothesis that 22 and related amidoximes occupy
the active site of LSD1. The distance between the enolic
hydroxyl group of 22 and N5 of the FAD is about 6.3 Å,
whereas the distance between the sulfur of pMet4 and N5 of the
FAD is about 4.9 Å, demonstrating that the amidoxime moiety
of 22 lies in proximity to the FAD binding domain. The phenyl
group in 22 is situated in a hydrophobic cavity surrounded by
residues Phe 560, Tyr 807, and His 812. Interestingly, this is the
region that is occupied by the side chain of the p3 Thr of
pLys4Met H3 peptide. As shown in Figure 5, the phenolic
hydroxyl group of the amidoxime forms a hydrogen bond with
the side chain hydroxyl group of Thr 335, while the primary
amine group of the amidoxime moiety forms hydrogen bond
with the backbone carbonyl of Ala 539. This interaction is
IN SILICO ANALYSIS
■
To provide a rationale for the observed biological activity of the
amidoxime inhibitors, we performed an in silico docking
experiment using the GOLD software package.49 At present,
there are 27 published X-ray structures of LSD1, including
those crystallized with and without the CoREST complex and
with and without a bound ligand. For our purposes, we selected
PDB structure 2V1D because it featured the necessary
components (the LSD1 binding pocket, a cocrystallized
inhibitor as ligand, free FAD, and the associated CoREST
complex),50 and compound 22, which was the best LSD1
inhibitor in vitro (Table 1). The inhibitor in the 2 V1D
complex is a 21-mer pLys4Met H3 peptide in which a
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Figure 6. Results of in silico docking of amidoxime 22 in the active site of the LSD1/CoREST complex. The FAD cofactor is shown in red, and
distances are in angstroms.
analogous to the hydrogen bond formed between the amide
nitrogen of pAla1 in the pLys4Met H3 ligand and the backbone
carbonyl of Ala339, underscoring the importance of this
interaction. Finally, the enolic hydroxyl of the amidoxime
forms a hydrogen bond with both the backbone carbonyl of Ala
539 and the 4-hydroxyl group of Tyr 761. These docking
results suggest that 22 binds to the LSD1/CoREST active site
in exactly the same region as both H3K4 of the histone tail and
pMet4 of the pLys4Met H3 peptide. A combination of both
hydrogen bonding and hydrophobic interactions stabilize the
LSD1/CoREST complex with 22 (Figure 6), positioning it
directly in front of the FAD cofactor and blocking the access of
the substrate to the FAD. A similar docking experiment
involving 22 and native LSD1 lacking the CoREST cofactor
(PDB index 2H94) revealed that these specific interactions
between 22 and the amino acids Thr 335, Ala 539, and Tyr 761
are not present (Supporting Information, Figure S1). In this
model, the amidoxime moiety of 22 forms a hydrogen bond
with N5 of the flavin ring, but no other electrostatic
associations could be detected. Although the models shown
in Figures 6 and Supporting Information S1 are preliminary,
they support the contention that 22 acts as an inhibitor of
LSD1 only when the CoREST corepressor is present. These
data could also explain the observation that large increases in
H3K4me2 levels following treatment with 22 and its
homologues do not correlate with inhibition of LSD1 in the
assay, which does not contain CoREST. Importantly, the in
silico model shown in Figure 6 suggest modifications to 22
which could lead to more potent analogues.
expression of aberrantly silenced tumor suppressor genes.
These analogues were also shown to selectively inhibit the
growth of tumor cells with pluripotent stem cell properties.51
However, these analogues are structurally related to the
(bis)guanidine, (bis)biguanide, (bis)urea, and (bis)thiourea
analogues previously described in our laboratories,32,41,52 which
produce similar cellular effects in nonpluripotent tumor cell
lines and exhibit in vivo activity.33 Compared to the known
LSD1 inhibitors described above, compound 22 and its
homologues possess more favorable drug-like properties53
(CLogP 0.37, MW 208.21, 5 H-bond acceptors, 4 H-bond
donors) and can be readily synthesized in two steps.
Amidoximes 22−27, 29, and 31 produce dramatic increases
in global H3K4me2 levels and also promote the re-expression
of aberrantly silenced tumor suppressor genes in the Calu-6 cell
line. Thus, these compounds, and in particular 22, can be
considered lead compounds within a new structural class of
histone demethylase inhibitors. We have initiated lead
optimization studies and will report the data from these studies
in a future manuscript. Additional studies are being performed
to determine which aberrantly silenced genes are reactivated
secondary to the dramatic increases in H3K4 methylation
observed for amidoximes 22−27, 29, and 31. In addition,
amidoximes 22−27, 29, and 31 are being evaluated in other
tumor cell lines, alone and in combination with the DNA
methyltransferase inhibitor 5-azacytidine as well as in a murine
xenograft model.
EXPERIMENTAL SECTION
■
All reagents and dry solvents were purchased from Aldrich Chemical
Co. (Milwaukee, WI), Sigma Chemical Co. (St. Louis, MO), or Acros
Chemical (Chicago, IL) and were used without further purification
except as noted below. Pyridine was dried by passing it through an
aluminum oxide column and then stored over KOH. Triethylamine
was distilled from potassium hydroxide and stored in a nitrogen
atmosphere. Methanol was distilled from magnesium and iodine under
a nitrogen atmosphere and stored over molecular sieves. Methylene
chloride was distilled from phosphorus pentoxide, and chloroform was
distilled from calcium sulfate. Tetrahydrofuran was purified by
distillation from sodium and benzophenone. Dimethyl formamide
DISCUSSION
■
Our virtual screening strategy resulted in the identification of
10 potential LSD1 inhibitors that have desirable drug-like
properties and can be readily synthesized. Many of the
inhibitors of LSD1 described in the recent literature are
based either on the tranylcypromine scaffold or are
oligopeptides that are unlikely to be used as therapeutic agents.
More recently, a series of small molecules was described that
inhibit LSD1, enhance H3K4 methylation, and promote the re-
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was dried by distillation from anhydrous calcium sulfate and was
stored under nitrogen. Preparative scale chromatographic procedures
were carried out using E. Merck silica gel 60, 230−440 mesh. Thin
layer chromatography was conducted on Merck precoated silica gel 60
F-254. Ion exchange chromatography was conducted on Dowex 1 ×
8−200 anion exchange resin. Compounds 41a−c35,54 were synthesized
as previously described.
9.45 (bs, 1H), 8.41 (s, 2H), 3.10−2.95 (m, 4H), 1.27 (bs, 2H). 19F
NMR (376 MHz, CDCl3) δ −62.36 (s, 3F).
N1-(2,6-Dinitro-4-[(trifluoromethyl)phenyl]propane-1,2-diamine
Hydrochloride 10. Compound 10 was prepared from 7.41 g (100.0
mmol) of 1,3-propanediamine 36b and 0.79 g of 4-chloro-3,5-
dinitrobenzotrifluoride 35 (5.00 mmol) in 87% yield exactly as
described for the preparation of compound 6. Melting point 380−381
°C (dec.); UPLC retention time 6.69 min. 1H NMR (400 MHz,
CDCl3) δ 9.52 (bs, 1H), 8.39 (s, 2H), 3.14 (s, 2H), 2.94 (t, J = 6.0 Hz,
2H), 1.78 (quint, J = 6.0 Hz, 2H), 1.33 (bs, 2H). 19F NMR (376 MHz,
CDCl3) δ −62.36 (s, 3F).
1
All H and 13C NMR spectra were recorded on a Varian Mercury
400 mHz spectrometer, and all chemical shifts are reported as δ values
referenced to TMS or DSS. In all cases, 1H NMR, 13C NMR, and MS
spectra were consistent with assigned structures. Mass spectra were
recorded by LC/MS on a Waters autopurification liquid chromato-
graph with a 3100 mass spectrometer detector. Prior to biological
testing procedures, target molecules 5−33 were determined to be
>95% pure by UPLC chromatography (95% H2O/5% acetonitrile to
20% H2O/80% acetonitrile over 10 min) using a Waters Acquity H-
series ultrahigh-performance liquid chromatograph fitted with a C18
reversed-phase column (Acquity UPLC BEH C18 1.7 μM, 2.1 mm ×
50 mm).
Synthetic H3K4me2 peptides were purchased from Millipore
(Billerica, MA). Calu-6 cells were maintained in RPMI medium,
both supplemented with 10% fetal bovine serum (Gemini Bio-
Products, Woodland, CA) and grown at 37 °C in 5% CO2 atmosphere.
General Procedure for Preparation Carbamimidothioates 5,
8, and 9.36 2-[N-(Phthalimido)]ethyl Carbamimidothioate Hydro-
chloride 5. A 3.0 g (11.6 mmol) portion of N-(2-bromoethyl)-
phthalimide 34a and 1.77 g (12.1 mmol, 2.0 equiv) of thiourea was
dissolved in 10 mL of anhydrous ethanol, and the mixture was allowed
to reflux overnight. The reaction mixture was allowed to cool until a
white crystalline precipitate formed, and the solid was collected by
filtration, washed with acetone and ether, and dried. Recrystallization
from 1.0 M HCl/ethanol then afforded 2.05 g (62%) of pure 5 as a
white crystalline solid. Melting point 380−381 °C; UPLC retention
time 3.47 min. 1H NMR (CD3OD) δ 3.54 (t, J = 6.4 Hz, 2H), 4.05 (t,
J = 6.4 Hz, 2H), 7.90 (m, 4H).
N1-(2,6-Dinitro-4-[(trifluoromethyl)phenyl]butane-1,2-diamine
Hydrochloride 11. Compound 11 was prepared from 8.81 g (100.0
mmol) of 1,4-butanediamine 36c and 0.79 g of 4-chloro-3,5-
dinitrobenzotrifluoride 35 (5.00 mmol) in 42% yield exactly as
described for the preparation of compound 6. Melting point 374−376
°C (dec.); UPLC retention time 7.05 min. 1H NMR (400 MHz, D2O)
δ 8.48 (s, 2H), 2.94 (t, J = 6.4 Hz, 2H), 2.84 (t, J = 7.2 Hz, 2H), 1.70−
1.50 (m, 4H). 19F NMR (376 MHz, D2O) δ −62.51 (s, 3F).
General Procedure for the Preparation of Cyano-N-phenyl-
acetamides 60−82.38 2-Cyano-N-phenylacetamide 60. A 0.96 g
portion (11.1 mmol) of cyanoacetic acid was added to a mixture of
PCl5 (2.35 g, 11.1 mmol) and 200 mL of dichloromethane, and the
mixture refluxed for 30 min. After cooling, 1.03 g of aniline (11.1
mmol) was added and the solution was refluxed for 2 h. The solution
was then concentrated, H2O was added, and the solid was collected
and washed with NaHCO3 solution and H2O and dried. The
intermediate 60 was isolated in 92% yield and was of sufficient purity
to use in the subsequent reaction without further purification. 1H
NMR (400 MHz, acetone-d6) δ 9.58 (s, 1H), 7.62 (d, J = 8.4 Hz, 2H),
7.33 (t, J = 8.0 Hz, 2H), 7.11 (t, J = 7.2 Hz, 1H), 3.82 (s, 2H).
2-Cyano-N-[(2,3,4-trifluoro)phenyl]acetamide 61. Compound 61
was synthesized in 90% yield exactly as described for the preparation
of compound 60; white solid. 1H NMR (400 MHz, acetone-d6) δ 9.60
(s, 1H), 7.89−7.83 (m, 1H), 7.29−7.14 (m, 1H), 3.97 (s, 2H). 19F
NMR (376 MHz, acetone-d6) δ −141.75 (m, 1F), −147.85 (m, 1F),
−162.75 (m, 1F).
2-[N-(Phthalimido)]propyl]carbamimidothioate Hydrochloride 8.
Compound 8 was prepared from 3.0 g (11.2 mmol) of N-(3-
bromopropyl)phthalimide 34b and 1.70 g (22.4 mmol, 2.0 equiv) of
thiourea in 68% yield exactly as described for the preparation of
compound 5. Melting point 362−363 °C; UPLC retention time 4.45
min. 1H NMR (CD3OD) δ 2.11 (quint, J = 6.8 Hz, 2H), 3.22 (t, 3.22,
J = 6.8 Hz, 2H), 3.85 (t, J = 6.8 Hz, 2H), 7.87 (m, 4H).
2-Cyano-N-[(2,4-(difluoro)phenyl]acetamide 62. Compound 62
was synthesized in 76% yield exactly as described for the preparation
of compound 60; white solid. 1H NMR (400 MHz, DMSO-d6) δ 10.14
(s, 1H), 7.84−7.77 (m, 1H), 7.37−7.32 (m, 1H), 7.12−7.05 (m, 1H),
3.96 (s, 2H). 19F NMR (376 MHz, DMSO-d6) δ −114.33 (m, 1F),
−119.95 (s, 1F).
2-[N-(Phthalimido)]butyl]carbamimidothioate Hydrochloride 9.
Compound 9 was prepared from 1.5 g (5.2 mmol) of N-(4-
bromobutyl)phthalimide 34c and 0.79 g (10.4 mmol, 2.0 equiv) of
thiourea in 79% yield exactly as described for the preparation of
compound 5. Melting point 358−359 °C; UPLC retention time 5.32
2-Cyano-N-[2,3-(difluoro)phenyl]acetamide 63. Compound 63
was synthesized in 83% yield exactly as described for the preparation
1
of compound 60; yellow solid. H NMR (400 MHz, DMSO-d6) δ
10.33 (s, 1H), 7.66 (s, 1H), 7.24−7.14 (m, 2H), 3.99 (s, 2H). 19F
NMR (376 MHz, DMSO-d6) δ −138.69 (m, 1F), −149.64 (m, 1F).
2-Cyano-N-[4-(fluoro)phenyl]acetamide 64. Compound 64 was
synthesized in 83% yield exactly as described for the preparation of
1
min. H NMR (CD3OD) δ 1.82 (m, 4H), 3.22 (t, J = 7.3 Hz, 2H),
3.75 (t, J = 6.7 Hz, 2H), 7.86 (m, 4H).
General Procedure for the Preparation of Compounds 6, 10,
and 11.37 N1-(2,6-Dinitro-4-[(trifluoromethyl)phenyl]ethane-1,2-
diamine Hydrochloride 6. A solution of ethylene diamine 36a (6.0
g, 100 mmol, 6.7 mL, 20 equiv) and triethylamine (0.51 g, 0.70 mL,
5.0 mmol) in 40 mL of benzene was cooled to 10 °C, and a solution of
4-chloro-3,5-dinitrobenzotrifluoride 35 (1.36 g, 5.00 mmol) in 40 mL
of benzene was added dropwise over 2 h. The reaction was stirred
overnight and concentrated in vacuo to yield an orange liquid. This
liquid was dissolved in 200 mL of ethyl acetate, and the organic layer
was washed with two 25 mL portions of water and then 25 mL of
saturated aqueous NaCl. The ethyl acetate solution was dried over
anhydrous MgSO4, filtered, and concentrated, and the crude mixture
was purified by column chromatography on silica gel (with a gradient
of 1:1 hexanes:AcOEt to AcOEt to 3:1 AcOEt:MeOH). Fractions
containing the desired product (Rf = 0.39) were pooled and
concentrated to give an orange solid, which was dissolved in ethyl
acetate. A 1.0 M solution of HCl in ethyl acetate was added until no
more product dropped out of solution. The product was filtered and
washed with ethyl acetate to afford pure 6 as the yellow solid
dihydrochloride salt (1.55 g, 84.7% yield). Melting point 324−326 °C
(dec.); UPLC retention time 6.22 min. 1H NMR (400 MHz, CDCl3) δ
1
compound 60; white solid. H NMR (400 MHz, DMSO-d6) δ 10.34
(s, 1H), 7.55−7.53 (m, 2H), 7.20−7.13 (m, 2H), 3.88 (s, 2H). 19F
NMR (376 MHz, DMSO-d6) δ −118.87 (s, 1F).
2-Cyano-N-[3,4-(difluoro)phenyl]acetamide 65. Compound 65
was synthesized in 94% yield exactly as described for the preparation
of compound 60; white solid. 1H NMR (400 MHz, DMSO-d6) δ 10.52
(s, 1H), 7.76−7.64 (m, 1H), 7.45−7.30 (m, 1H), 7.25−7.20 (m, 1H),
3.89 (s, 2H). 19F NMR (376 MHz, DMSO-d6) δ −137.20 (m, 1F),
−144.36 (m, 1F).
2-Cyano-N-[2-(fluoro)phenyl]acetamide 66. Compound 66 was
synthesized in 85% yield exactly as described for the preparation of
1
compound 60; white solid. H NMR (400 MHz, DMSO-d6) δ 10.15
(s, 1H), 7.87 (t, J = 8.8 Hz, 1H), 7.35−7.13 (m, 3H), 3.99 (s, 2H). 19F
NMR (376 MHz, DMSO-d6) δ −126.08 (m, 1F).
2-Cyano-N-[3-(fluoro)phenyl]acetamide 67. Compound 67 was
synthesized in 68% yield exactly as described for the preparation of
1
compound 60; white solid. H NMR (400 MHz, DMSO-d6) δ 10.53
(s, 1H), 7.52 (dt, J = 11.6 Hz, 2.0 Hz, 1H), 7.41−7.34 (m, 1H), 7.28−
7.23 (m, 1H), 6.93 (td, J = 6.0 Hz, 2.4 Hz, 1H), 3.93 (s, 2H). 19F
NMR (376 MHz, DMSO-d6) δ −112.15 (m, 1F).
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1
2-Cyano-N-[2-(methoxy)phenyl]acetamide 68. Compound 68
was synthesized in 94% yield exactly as described for the preparation
of compound 60; white solid. 1H NMR (400 MHz, CDCl3) δ 8.34 (bs,
1H), 8.25 (dd, J = 8.0, 2.0 Hz, 1H), 7.12 (td, J = 8.0, 1.6 Hz, 1H), 6.97
(dt, J = 8.0, 1.2 Hz, 1H), 6.91 (dd, J = 8.0, 1.2 Hz, 1H), 3.91 (s, 3H),
3.56 (s, 2H).
2-Cyano-N-[2-(nitro)phenyl]acetamide 69. Compound 69 was
synthesized in quantitative yield exactly as described for the
preparation of compound 60; tan solid. 1H NMR (400 MHz,
CDCl3) δ 10.92 (bs, 1H), 8.68 (dd, J = 8.4, 1.2 Hz, 1H), 8.27 (dd, J =
8.4, 1.6 Hz, 1H), 7.71 (dt, J = 8.4, 1.6 Hz, 1H), 7.30 (dt, J = 8.0, 1.2
Hz, 1H), 3.67 (s, 2H).
compound 60; off-white solid. H NMR (400 MHz, CDCl3) δ 8.25
(dd, J = 8.0, 1.2 Hz, 1H), 8.24 (bs, 1H), 7.41 (dd, J = 8.0, 0.8 Hz, 1H),
7.31 (td, J = 8.0, 1.2 Hz, 1H), 7.13 (td, J = 7.6, 1.2 Hz, 1H), 3.62 (s,
2H).
2-Cyano-N-[2-(bromo)phenyl]acetamide 80. Compound 80 was
synthesized in 95% yield exactly as described for the preparation of
compound 60; white solid. 1H NMR (400 MHz, CDCl3) δ 8.24 (dd, J
= 8.0, 1.2 Hz, 1H), 8.24 (bs, 1H), 7.58 (dd, J = 8.0, 1.2 Hz, 1H), 7.35
(td, J = 8.0, 1.2 Hz, 1H), 7.07 (td, J = 7.6, 1.2 Hz, 1H), 3.62 (s, 2H).
2-(2-Cyanoacetamido)benzamide 81. Compound 81 was synthe-
sized in 97% yield exactly as described for the preparation of
1
compound 60; white solid. H NMR (400 MHz, DMSO-d6) δ 11.83
2-Cyano-N-[2-(methyl)phenyl]acetamide 70. Compound 70 was
(bs, 1H), 8.32 (d, J = 8.4 Hz, 1H), 8.31 (s, 1H), 7.80 (dd, J = 8.0, 1.2
Hz, 1H), 7.78 (s, 1H), 7.52 (td, J = 8.0, 1.2 Hz, 1H), 7.18 (td, J = 7.6,
1.2 Hz, 1H), 4.07 (s, 2H).
Ethyl 2-(2-Cyanoacetamido)benzoate 82. Compound 82 was
synthesized in 96% yield exactly as described for the preparation of
compound 60; white solid. 1H NMR (400 MHz, CDCl3) δ 11.75 (bs,
1H), 8.61 (d, J = 8.0 Hz, 1H), 8.09 (dd, J = 8.0, 1.6 Hz, 1H), 7.58 (td,
J = 8.0, 1.6 Hz, 1H), 7.17 (td, J = 7.6, 1.2 Hz, 1H), 4.42 (q, J = 7.2 Hz,
2H), 3.61 (s, 2H), 1.42 (t, J = 7.2 Hz, 3H).
General Procedure for the Preparation of Amidoximes 7
and 12−33.39 3-Amino-3-(hydroxyimino)-N-phenylpropanamide
7. A 0.9 g portion of NH2OH·HCl (12.8 mmol) was added to a
mixture of sodium carbonate (1.36 g, 12.8 mmol) in 5 mL of water,
and the solution was diluted with 50 mL of MeOH. A 1.64 g portion
(10.2 mmol) of compound 60 was then added, and the mixture
refluxed for 2 h. The mixture was cooled, the solvent was removed in
vacuo, and the resulting solid was mixed with hot 3:1 AcOEt:MeOH.
The insoluble material was then removed by filtration of the hot
mixture, and the filtrate was concentrated and purified by
chromatography on silica gel (gradient of AcOEt → 20:1
AcOEt:MeOH). Fractions containing the product were pooled and
the solvent was removed, and the resulting solid was recrystallized
from MeOH/EtOAc to afford 0.67 g (34%) of pure 7 as a white
amorphous solid. An analytical sample was prepared by recrystalliza-
tion from 1.0 M HCl/ethanol. Melting point 312−313 °C (dec.);
synthesized in 94% yield exactly as described for the preparation of
1
compound 60; white solid. H NMR (400 MHz, CDCl3) δ 7.73 (bs,
1H), 7.66 (d, J = 7.6 Hz, 1H), 7.26−7.11 (m, 3H), 3.56 (s, 2H), 2.28
(s, 3H).
2-Cyano-N-[2-(hydroxyl)phenyl]acetamide 71. Compound 71
was synthesized in 52% yield exactly as described for the preparation
of compound 60; pale purple−white solid. 1H NMR (400 MHz,
acetone-d6) δ 9.09 (bs, 1H), 7.94 (dd, J = 8.0, 1.2 Hz, 1H), 6.99 (dt, J
= 8.4, 1.2 Hz, 1H), 6.92 (dd, J = 8.0, 1.2 Hz, 1H), 6.84 (dt, J = 8.0, 1.2
Hz, 1H), 3.98 (s, 2H). 13C NMR (100 MHz, acetone-d6) δ 162.1,
148.1, 126.9, 126.1, 122.4, 120.6, 116.6, 115.8, 27.1.
2-Cyano-N-[2-(mercapto)phenyl]acetamide 72. Compound 72
was synthesized in 66% yield exactly as described for the preparation
of compound 60, except that the material was further purified by
dissolving the residue in dichloromethane and filtering through silica
gel plug; light-yellow solid. 1H NMR (400 MHz, CDCl3) δ 8.04 (d, J =
8.0 Hz, 1H), 7.90 (d, J = 8.0 Hz, 1H), 7.53 (t, J = 8.0 Hz, 1H), 7.45 (t,
J = 8.0 Hz, 1H), 4.24 (s, 2H). 13C NMR (100 MHz, CDCl3) δ 158.4,
152.8, 135.5, 126.7, 126.0, 123.3, 121.8, 115.1, 23.2.
2-Cyano-N-[2-(ethyl)phenyl]acetamide 73. Compound 73 was
synthesized in 81% yield exactly as described for the preparation of
1
compound 60; off-white solid. H NMR (400 MHz, CDCl3) δ 7.74
(bs, 1H), 7.68 (dd, J = 7.6, 1.6 Hz, 1H), 7.26−7.17 (m, 3H), 3.57 (s,
2H), 2.63 (q, J = 7.6 Hz, 2H), 1.26 (t, J = 7.6 Hz, 3H).
1
2-Cyano-N-[2-(isopropyl)phenyl]acetamide 74. Compound 74
was synthesized in quantitative yield exactly as described for the
preparation of compound 60, except that the oil was dissolved in 100
mL of ethyl acetate, and the organic layer was washed with 1.0 N
sodium bicarbonate and saturated aqueous NaCl. Filtration and
evaporation of the solvent then afforded pure 74 as an orange oil that
UPLC retention time 2.29 min. H NMR (400 MHz, acetone-d6) δ
9.53 (s, 1H), 8.70 (s, 1H), 7.65−7.63 (m, 2H), 7.31−7.27 (m, 2H),
7.07−7.04 (m, 1H), 5.39 (s, 2H), 3.17 (s, 2H).
3-Amino-3-(hydroxyimino)-N-[2,3,4-(trifluoro)phenyl]-
propanamide 12. Compound 12 was synthesized from 61 in 26%
yield exactly as described for the preparation of compound 7; white
crystals; melting point 310−312 °C (dec.); UPLC retention time 6.07
1
solidified at RT. H NMR (400 MHz, CDCl3) δ 7.85 (bs, 1H), 7.52
1
(dd, J = 7.6, 1.2 Hz, 1H), 7.32 (dd, J = 7.6, 1.2 Hz, 1H), 7.29−7.17 (m,
2H), 3.54 (s, 2H), 3.02 (septet, J = 6.8 Hz, 1H), 1.24 (d, J = 6.8 Hz,
6H).
min. H NMR (400 MHz, acetone-d6) δ 9.72 (s, 1H), 8.79 (s, 1H),
7.99−7.92 (m, 1H), 7.19−7.12 (m, 1H), 5.45 (s, 2H), 3.28 (s, 2H).
19F NMR (376 MHz, acetone-d6) δ −143.11 (m, 1F), −148.97 (m,
2-Cyano-N-[2-(phenyl)phenyl]acetamide 75. Compound 75 was
synthesized in 97% yield exactly as described for the preparation of
compound 60; white solid. 1H NMR (400 MHz, CDCl3) δ 8.20 (d, J =
8.4 Hz, 1H), 7.79 (bs, 1H), 7.55−7.23 (m, 9H), 3.39 (s, 2H).
2-Cyano-N-[2-(ethoxy)phenyl]acetamide 76. Compound 76 was
synthesized in 81% yield exactly as described for the preparation of
1F), −163.25 (m, 1F).
3-Amino-3-(hydroxyimino)-N-[2,4-(difluoro)phenyl]propanamide
13. Compound 13 was synthesized from 62 in 59% yield exactly as
described for the preparation of compound 7; white solid; melting
point 314−315 °C (dec.); UPLC retention time 2.36 min. H NMR
(400 MHz, DMSO-d6) δ 9.83 (s, 1H), 9.06 (d, J = 6.8 Hz, 1H), 7.93−
7.85 (m, 1H), 7.33−7.27 (m, 1H), 7.06−7.03 (m, 1H), 5.48 (s, 2H),
3.12 (d, J = 0.64 Hz, 2H). 19F NMR (376 MHz, DMSO-d6) δ −115.49
(d, 1F), −120.73 (bs, 1F).
3-Amino-3-(hydroxyimino)-N-[2,3-(difluoro)phenyl]propanamide
14. Compound 13 was synthesized from 63 in 43% yield exactly as
described for the preparation of compound 7; white solid; melting
1
1
compound 60; white solid. H NMR (400 MHz, CDCl3) δ 8.52 (bs,
1H), 8.26 (d, J = 8.0 Hz, 1H), 7.10 (t, J = 8.0 Hz, 1H), 6.97 (t, J = 7.6
Hz, 1H), 6.90 (d, J = 8.0 Hz, 1H), 4.13 (q, J = 6.8 Hz, 2H), 3.57 (s,
2H), 1.49 (t, J = 6.8 Hz, 3H).
2-Cyano-N-[2-(phenoxy)phenyl]acetamide 77. Compound 77
was synthesized in quantitative yield exactly as described for the
1
1
preparation of compound 60; light-yellow solid. H NMR (400 MHz,
point 290−292 °C (dec.); UPLC retention time 2.67 min. H NMR
CDCl3) δ 8.32 (dd, J = 8.0, 1.6 Hz, 1H), 8.29 (bs, 1H), 7.41−7.34 (m,
2H), 7.20−7.01 (m, 5H), 6.87 (dd, J = 8.0, 1.2 Hz, 1H), 3.53 (s, 2H).
2-Cyano-N-[2-(trifluoromethyl)phenyl]acetamide 78. Compound
78 was synthesized in 89% yield exactly as described for the
preparation of compound 60; white solid. 1H NMR (400 MHz,
CDCl3) δ 8.03 (d, J = 8.4 Hz, 1H), 8.00 (bs, 1H), 7.67 (d, J = 7.6 Hz,
1H), 7.61 (t, J = 7.6 Hz, 1H), 7.35 (t, J = 7.6 Hz, 1H), 3.61 (s, 2H).
19F NMR (376 MHz, CDCl3) δ −60.98 (s).
(400 MHz, DMSO-d6) δ 10.01 (s, 1H), 9.05 (s, 1H), 7.75−7.72 (m,
1H), 7.19−7.09 (m, 2H), 5.48 (s, 2H), 3.14 (s, 2H). 19F NMR (376
MHz, DMSO-d6) δ −139.10 (m, 1F), −150.53 (m, 1F).
3-Amino-3-(hydroxyimino)-N-[4-(fluoro)phenyl]propanamide
15. Compound 15 was synthesized from 64 in 53% yield exactly as
described for the preparation of compound 7; white solid; melting
1
point 299−300 °C (dec.); UPLC retention time 2.76 min. H NMR
(400 MHz, DMSO-d6) δ 10.07 (s, 1H), 9.02 (s, 1H), 7.61−7.57 (m,
2H), 7.15−7.10 (m, 2H), 5.44 (bs, 2H), 3.03 (s, 2H). 19F NMR (376
MHz, DMSO-d6) δ −119.87 (m, 1F).
2-Cyano-N-[2-(chloro)phenyl]acetamide 79. Compound 79 was
synthesized in 90% yield exactly as described for the preparation of
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3-Amino-3-(hydroxyimino)-N-[3,4-(difluoro)phenyl]propanamide
16. Compound 16 was synthesized from 65 in 68% yield exactly as
described for the preparation of compound 7; white solid; melting
point 320−322 °C (dec.); UPLC retention time 3.87 min. H NMR
2.4 Hz, 1H), 7.30 (dd, J = 8.0, 2.8 Hz, 1H), 7.20−7.12 (m, 2H), 5.53
(s, 2H), 3.14 (septet, J = 6.8 Hz, 1H), 3.10 (s, 2H), 1.14 (d, J = 6.8 Hz,
6H).
1
3-Amino-3-(hydroxyimino)-N-[2-(phenyl)phenyl]propanamide
26. Compound 26 was synthesized from 75 in 77% yield exactly as
described for the preparation of compound 7, except that the
compound was isolated as the hydrochloride salt by dissolving it in
ethyl acetate and adding HCl in ether; off-white solid; melting point
(400 MHz, DMSO-d6) δ 10.23 (s, 1H), 9.12−9.04 (m, 1H), 7.81−
7.76 (m, 1H), 7.40−7.34 (m, 1H), 7.33−7.28 (m, 1H), 5.47 (s, 2H),
3.06−3.01 (m, 2H). 19F NMR (376 MHz, DMSO-d6) δ −137.60 (m,
1F), −145.33 (s, 1F).
1
3-Amino-3-(hydroxyimino)-N-[2-(fluoro)phenyl]propanamide
17. Compound 17 was synthesized from 66 in 51% yield exactly as
described for the preparation of compound 7; white solid; melting
284−285 °C (dec.); UPLC retention time 6.01 min. H NMR (400
MHz, DMSO-d6) δ 12.71 (bs, 1H), 11.09 (s, 1H), 9.85 (s, 1H), 9.02
(bs, 1H), 8.73 (bs, 1H), 7.53−7.30 (m, 9H), 3.48 (s, 2H).
1
point 294−297 °C (dec.); UPLC retention time 1.95 min. H NMR
3-Amino-3-(hydroxyimino)-N-[2-(ethoxy)phenyl]propanamide
27. Compound 27 was synthesized from 76 in 59% yield exactly as
described for the preparation of compound 7; off-white crystals;
melting point 372−374 °C (dec.); UPLC retention time 3.85 min. 1H
NMR (400 MHz, DMSO-d6) δ 9.28 (s, 1H), 9.14 (s, 1H), 8.11 (d, J =
8.0 Hz, 1H), 7.04−7.00 (m, 2H), 6.92−6.86 (m, 1H), 5.67 (s, 2H),
4.07 (q, J = 6.8 Hz, 2H), 3.14 (s, 2H), 1.14 (t, J = 6.8 Hz, 3H).
3-Amino-3-(hydroxyimino)-N-[2-(phenoxy)phenyl]propanamide
28. Compound 28 was synthesized from 77 in 79% yield exactly as
described for the preparation of compound 7; white crystals; melting
(400 MHz, DMSO-d6) δ 9.79 (s, 1H), 9.05 (s, 1H), 7.97−7.88 (m,
1H), 7.25−7.05 (m, 3H), 5.48 (s, 1H), 3.13 (s, 2H). 19F NMR (376
MHz, DMSO-d6) δ −126.09 (m, 1F).
3-Amino-3-(hydroxyimino)-N-[3-(fluoro)phenyl]propanamide
18. Compound 18 was synthesized from 67 in 53% yield exactly as
described for the preparation of compound 7; white solid; melting
1
point 338−340 °C (dec.); UPLC retention time 3.32 min. H NMR
(400 MHz, DMSO-d6) δ 10.23 (s, 1H), 9.04 (s, 1H), 7.58 (d, J = 13.2
Hz, 1H), 7.33−7.66 (m, 2H), 6.88−6.84 (m, 1H), 5.46 (s, 1H), 3.06
(s, 1H). 19F NMR (376 MHz, DMSO-d6) δ −112.45 (m, 1F).
3-Amino-3-(hydroxyimino)-N-[2-(methoxy)phenyl]propanamide
19. Compound 19 was synthesized from 68 in 67% yield exactly as
described for the preparation of compound 7; white crystals; melting
1
point 275−277 °C (dec.); UPLC retention time 6.40 min. H NMR
(400 MHz, DMSO-d6) δ 9.63 (s, 1H), 9.05 (s, 1H), 8.13 (dd, J = 8.0,
1.2 Hz, 1H), 7.39 (t, J = 8.0 Hz, 2H), 7.17−7.00 (m, 5H), 6.87 (dd, J =
8.0, 1.2 Hz, 1H), 5.51 (s, 2H), 3.11 (s, 2H).
1
point 277−278 °C (dec.); UPLC retention time 2.94 min. H NMR
3-Amino-3-(hydroxyimino)-N-[2-(trifluoromethyl)phenyl]-
propanamide 29. Compound 29 was synthesized from 78 in 67%
yield exactly as described for the preparation of compound 7; pale-
green crystals; melting point 280−281 °C (dec.); UPLC retention
(400 MHz, DMSO-d6) δ 9.41 (s, 1H), 9.13 (s, 1H), 8.08 (d, J = 8.0
Hz, 1H), 7.08−7.00 (m, 2H), 6.90 (dt, J = 8.0, 1.6 Hz, 1H), 5.60 (s,
2H), 3.83 (s, 3H), 3.14 (s, 2H).
3-Amino-3-(hydroxyimino)-N-[2-(nitro)phenyl]propanamide 20.
Compound 20 was synthesized from 69 in 72% yield exactly as
described for the preparation of compound 7; orange−yellow crystals;
melting point 294−295 °C (dec.); UPLC retention time 2.09 min. 1H
NMR (400 MHz, DMSO-d6) δ 10.51 (s, 1H), 9.14 (s, 1H), 8.08 (dd, J
= 8.0, 1.2 Hz, 1H), 7.91 (d, J = 8.0 Hz, 1H), 7.72 (dt, J = 8.0, 0.8 Hz,
1H), 7.36 (dt, J = 8.0, 0.8 Hz, 1H), 5.55 (s, 2H), 3.13 (s, 2H).
3-Amino-3-(hydroxyimino)-N-[2-(methyl)phenyl]propanamide
21. Compound 21 was synthesized from 70 in 78% yield exactly as
described for the preparation of compound 7; white crystals; melting
1
time 3.31 min. H NMR (400 MHz, DMSO-d6) δ 9.72 (s, 1H), 9.12
(s, 1H), 7.73 (d, J = 8.0 Hz, 1H), 7.70−7.65 (m, 2H), 7.45−7.39 (m,
1H), 5.56 (s, 2H), 3.13 (s, 2H). 19F NMR (376 MHz, DMSO-d6) δ
−59.83 (s, 3F).
3-Amino-3-(hydroxyimino)-N-[2-(chloro)phenyl]propanamide
30. Compound 30 was synthesized from 79 in 69% yield exactly as
described for the preparation of compound 7; off-white crystals;
melting point 291−293 °C (dec.); UPLC retention time 2.66 min. 1H
NMR (400 MHz, DMSO-d6) δ 9.80 (s, 1H), 9.16 (s, 1H), 7.96 (d, J =
8.4 Hz, 1H), 7.49 (d, J = 8.0 Hz, 1H), 7.33 (t, J = 8.0 Hz, 1H), 7.15 (t,
J = 7.6 Hz, 1H), 5.63 (s, 2H), 3.18 (s, 2H).
1
point 290−291 °C (dec.); UPLC retention time 2.55 min. H NMR
(400 MHz, DMSO-d6) δ 9.44 (s, 1H), 9.09 (s, 1H), 7.51 (d, J = 7.6
Hz, 1H), 7.20 (d, J = 7.2 Hz, 1H), 7.15 (t, J = 7.6 Hz, 1H), 7.06 (t, J =
7.2 Hz, 1H), 5.53 (s, 2H), 3.11 (s, 2H), 2.21 (s, 3H).
3-Amino-3-(hydroxyimino)-N-[2-(bromo)phenyl]propanamide
31. Compound 31 was synthesized from 80 in 77% yield exactly as
described for the preparation of compound 7; white crystals; melting
3-Amino-3-(hydroxyimino)-N-[2-(hydroxyl)phenyl]propanamide
22. Compound 22 was synthesized from 71 in 53% yield exactly as
described for the preparation of compound 7; off-white crystals;
melting point 308−310 °C (dec.); UPLC retention time 1.17 min. 1H
NMR (400 MHz, DMSO-d6) δ 9.85 (s, 1H), 9.29 (s, 1H), 9.12 (s,
1H), 7.88 (dd, J = 8.0, 1.6 Hz, 1H), 6.92 (dt, J = 7.6, 1.6 Hz, 1H), 6.85
(dd, J = 8.0, 1.2 Hz, 1H), 6.75 (dt, J = 8.0, 1.6 Hz, 1H), 5.60 (s, 2H),
3.12 (s, 2H).
3-Amino-3-(hydroxyimino)-N-[2-(mercapto)phenyl]propanamide
23. Compound 23 was synthesized from 72 in 65% yield exactly as
described for the preparation of compound 7; light-gray crystals;
melting point 324−325 °C (dec.); UPLC retention time 3.32 min. 1H
NMR (400 MHz, DMSO-d6) δ 9.20 (s, 1H), 8.05 (dd, J = 8.0, 0.8 Hz,
1H), 7.94 (d, J = 8.0 Hz, 1H), 7.49 (dt, J = 7.6, 1.2 Hz, 1H), 7.41 (dt, J
= 7.6, 1.2 Hz, 1H), 5.70 (s, 2H), 3.83 (s, 2H).
3-Amino-3-(hydroxyimino)-N-[2-(ethyl)phenyl]propanamide 24.
Compound 24 was synthesized from 73 in 74% yield exactly as
described for the preparation of compound 7; off-white crystals;
melting point 266−268 °C (dec.); UPLC retention time 3.89 min. 1H
NMR (400 MHz, DMSO-d6) δ 9.43 (s, 1H), 9.10 (s, 1H), 7.50 (d, J =
7.6 Hz, 1H), 7.21 (dd, J = 7.2, 1.2 Hz, 1H), 7.19−7.08 (m, 2H), 5.55
(s, 2H), 3.11 (s, 2H), 2.58 (q, J = 7.6 Hz, 2H), 1.12 (t, J = 7.6 Hz,
3H).
1
point 278−280 °C (dec.); UPLC retention time 2.87 min. H NMR
(400 MHz, DMSO-d6) δ 9.74 (s, 1H), 9.15 (s, 1H), 7.90 (d, J = 8.0
Hz, 1H), 7.65 (d, J = 8.0 Hz, 1H), 7.37 (t, J = 8.0 Hz, 1H), 7.10 (t, J =
7.6 Hz, 1H), 5.63 (s, 2H), 3.16 (s, 2H).
2-(3-Amino-3-(hydroxyimino)propanamido)benzamide 32.
Compound 32 was synthesized from 81 in 50% yield exactly as
described for the preparation of compound 7; tan crystals; melting
1
point 320−321 °C (dec.); UPLC retention time 0.94 min. H NMR
(400 MHz, DMSO-d6) δ 11.64 (s, 1H), 9.09 (s, 1H), 8.44 (d, J = 8.4
Hz, 1H), 8.23 (s, 1H), 7.77 (dd, J = 8.0, 1.2 Hz, 1H), 7.67 (s, 1H),
7.48 (dt, J = 8.0, 1.2 Hz, 1H), 7.12 (dt, J = 7.6, 0.8 Hz, 1H), 5.52 (s,
2H), 3.06 (s, 2H).
2-(3-Amino-3-(hydroxyimino)propanamido)benzoate 33. Com-
pound 33 was synthesized from 82 in 69% yield exactly as described
for the preparation of compound 7; tan crystals; melting point 282−
1
283 °C (dec.); UPLC retention time 5.45 min. H NMR (400 MHz,
DMSO-d6) δ 10.75 (s, 1H), 9.16 (s, 1H), 8.36 (d, J = 8.4 Hz, 1H),
7.94 (dd, J = 8.0, 1.6 Hz, 1H), 7.61 (dt, J = 8.0, 1.6 Hz, 1H), 7.19 (dt, J
= 7.6, 1.2 Hz, 1H), 5.59 (s, 2H), 4.33 (q, J = 7.2 Hz, 2H), 3.12 (s, 2H),
1.33 (t, J = 7.2 Hz, 3H).
Expression and Purification of Recombinant Proteins and
the Histone Demethylase Assay. Full-length human LSD1 cDNA
was subcloned into the pET15b bacterial expression vector (Novagen,
Madison, WI) in frame with an N-terminal 6× HIS-tag and
transformed into the BL21(DE3) strain of Escherichia coli. Following
selection, expression and purification of recombinant LSD1 protein
were performed as previously described.8 Briefly, expression of LSD1-
3-Amino-3-(hydroxyimino)-N-[2-(isopropyl)phenyl]propanamide
25. Compound 25 was synthesized from 74 in 64% yield exactly as
described for the preparation of compound 7; tan crystals; melting
1
point 228−230 °C (dec.); UPLC retention time 4.87 min. H NMR
(400 MHz, DMSO-d6) δ 9.46 (s, 1H), 9.08 (s, 1H), 7.38 (dd, J = 8.0,
7388
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Article
HIS protein was induced by 1 mM isopropyl β-D-1-thiogalactopyrano-
side for 6 h at 25 °C. The HIS-tagged protein was purified using Ni-
NTA affinity purification resin and column as recommended by the
manufacturer (Qiagen, Valencia, California). Bound protein was eluted
by imidazole, and the eluate was dialyzed in PBS at 4 °C. Enzymatic
activity of LSD1 was examined using luminol-dependent chemilumi-
nescence to measure the production of H2O2, as previously
described.40 In brief, LSD1 activity was assayed in 50 mM Tris, pH
8.5, 50 mM KCl, 5 mM MgCl, 5 nmol of luminol, and 20 μg/mL of
horseradish peroxidase with the indicated concentrations of H3K4me2
(1−21 aa) peptide as substrate. The integral values were calibrated
against standards containing known concentrations of H2O2, and the
activities expressed as pmols H2O2/mg protein/min. Reaction
mixtures were incubated with or without 5 μg of purified LSD1 in
50 mM Tris, pH 8.5, 50 mM KCl, 5 mM MgCl, 0.5% BSA, and 5%
glycerol for 3 h at 37 °C. This reaction mixture was analyzed by
Western blotting using antibodies (Millipore) that specifically
recognize the dimethyl group of H3K4.
Western Blotting. Cytoplasmic and nuclear fractions were
prepared for Western blot analysis using the NE-PER Nuclear and
Cytoplasmic Extraction Kit (Pierce, Rockford, IL). Primary antibodies
against H3K4me2 were from Millipore. The pCNA monoclonal
antibody was purchased from Oncogene Research Products (Cam-
bridge, MA). Dye-conjugated secondary antibodies were used for
quantification of Western blot results using the Odyssey infrared
detection system and software (LI-COR Biosciences, Lincoln, NE).
Determination of H3K4me2, SFRP2, HCAD, and GATA4 levels in the
Calu-6 cell line were determined as previously reported.32,41
ASSOCIATED CONTENT
■
S
* Supporting Information
Results of in silico docking of amidoxime 22 in the active site of
LSD1 without the bound CoREST co-repressor. Physical
properties and inhibition of purified recombinant LSD1
following treatment with 10 μM 3−33, and fold increase in
global H3K4me2 levels in Calu-6 human lung adenocarcinoma
cells following treatment with carbamimidothioates 5, 8, and 9,
aromatic amines 6, 10, and 11 and amidoximes 7 and 12−33 at
10 μM. This material is available free of charge via the Internet
at http://pubs.acs.org.
AUTHOR INFORMATION
■
Corresponding Author
*Phone: 843-876-2453. Fax: 843-876-2353. E-mail: woster@
musc.edu. Address: Medical University of South Carolina, 70
President Street, Drug Discovery Building Room 405,
Charleston, South Carolina 29425.
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
The research described in this manuscript was supported by
NIH grant 1R01CA149095 (P.M.W.), 1RO1CA98454
(R.A.C.), and 1RO1CA51085 (R.A.C.) and by grants from
the Samuel Waxman Cancer Research Foundation (R.A.C.,
P.M.W.) and the Susan B. Komen for the Cure Foundation
(R.A.C.). In addition, a portion of this work was supported by a
grant from Progen Pharmaceuticals, Ltd., Brisbane, Queens-
land, Australia (P.M.W., R.A.C.). R.A.C. also serves as a
consultant to Progen Pharmaceuticals.
RNA Isolation and qPCR. RNA was extracted using TRIzol
reagents (Invitrogen, Carlsbad, CA). First-strand cDNA was
synthesized using SuperScript III reverse transcriptase with an
oligo(dT) primer (Invitrogen). qPCR was performed using the
following primers: SFRP2 sense, 5′AAG CCT GCA AAA ATA AAA
ATG ATG; SFRP2 antisense, 5′TGT AAA TGG TCT TGC TCT
TGG TCT (annealing at 57.4 °C); GATA4 sense, 5′GGC CGC CCG
ACA CCC CAA TCT; GATA4 antisense, 5′ ATA GTG ACC CGT
CCC ATC TCG (annealing at 64 °C). qPCR was performed in a
MyiQ single color real-time PCR machine (Bio-Rad, Hercules, CA)
with GAPDH as an internal control.
ABBREVIATIONS USED
■
Determination of Cell Viability. Calu-6 human anaplastic
nonsmall cell lung carcinoma cells were maintained in culture using
RPMI medium plus 10% fetal bovine serum. For the (3-(4,5-
dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-
2H-tetrazolium) (MTS) reduction assay, 4000 cells/well were seeded
in 100 μL of medium in a 96-well plate and the cells were allowed to
attach at 37 °C in 5% CO2 for one day. The medium was aspirated,
and cells were treated with 100 μL of fresh medium containing
appropriate concentrations of each test compound. The cells were
incubated for 4 days at 37 °C in 5% CO2. After 4 days, 20 μL of the
MTS reagent solution (Promega CellTiter 96 Aqueous One Solution
Cell Proliferation Assay) was added to the medium. The cells were
incubated for another 2 h at 37 °C under 5% CO2 environment.
Absorbance was measured at 490 nm on a microplate reader equipped
with SOFTmax PRO 4.0 software to determine the cell viability.
Molecular Modeling Studies. All molecular modeling studies
were performed using the GOLD software package, version 5.1
(Cambridge Crytallographic Data Centre, Cambridge, UK). The X-ray
coordinates of LSD1 (PDB code 2V1D) were downloaded from the
Protein Data Bank,50 and the active site was defined as a sphere
enclosing residues within 6 Å around the substrate-like peptide
inhibitor cocrystal. The 3D structure of 22 was built using Chem 3D
Pro software (version 12.0) and was energy minimized using MM2
force field for 1000 iterations and a convergence value of 0.001 kcal/
mol/Å as the termination criterion. The energy minimized amidoxime
22 was docked in the binding site of LSD1 and scored using
ChemScore.49 All poses generated by the program were visualized;
however, the pose with the highest fitness score was used for
elucidating the binding characteristics of 22 in the LSD1 active site.
The numbering sequence of amino acid residues in 2V1D is preserved
throughout this paper.
LSD1, lysine-specific demethylase 1; H3K4me1, histone 3
methyllysine 4; H3K4me2, histone 3 dimethyllysine 4; JmjC,
Jumonji C domain-containing demethylase; FAD, flavin
adenine dinucleotide; MAO, monoamine oxidase; CoREST,
RE1 silencing factor/neural restrictive silencing factor cor-
epressor protein; SFRP, secreted frizzle-related protein; HCAD,
h-cadherin; qPCR, quantitative polymerase chain reaction;
PCNA, proliferating cell nuclear antigen
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