Sirtuins are a family of NAD(+)-dependent protein deacetylases that play critical roles in epigenetic regulation, stress responses, and cellular aging in eukaryotic cells. In an effort to identify small molecule inhibitors of sirtuins for potential use as chemotherapeutics as well as tools to modulate sirtuin activity, we previously identified a nonselective sirtuin inhibitor called cambinol (IC50 ≈ 50 μM for SIRT1 and SIRT2) with in vitro and in vivo antilymphoma activity. In the current study, we used saturation transfer difference (STD) NMR experiments with recombinant SIRT1 and 20 to map parts of the inhibitor that interacted with the protein. Our ongoing efforts to optimize cambinol analogues for potency and selectivity have resulted in the identification of isoform selective analogues: 17 with >7.8-fold selectivity for SIRT1, 24 with >15.4-fold selectivity for SIRT2, and 8 with 6.8- and 5.3-fold selectivity for SIRT3 versus SIRT1 and SIRT2, respectively. In vitro cytotoxicity studies with these compounds as well as EX527, a potent and selective SIRT1 inhibitor, suggest that antilymphoma activity of this compound class may be predominantly due to SIRT2 inhibition.
Sirtuins are a family of NAD(+)-dependent protein deacetylases that play critical roles in epigenetic regulation, stress responses, and cellular aging in eukaryotic cells. In an effort to identify small molecule inhibitors of sirtuins for potential use as chemotherapeutics as well as tools to modulate sirtuin activity, we previously identified a nonselective sirtuin inhibitor called cambinol (IC50 ≈ 50 μM for SIRT1 and SIRT2) with in vitro and in vivo antilymphoma activity. In the current study, we used saturation transfer difference (STD) NMR experiments with recombinant SIRT1 and 20 to map parts of the inhibitor that interacted with the protein. Our ongoing efforts to optimize cambinol analogues for potency and selectivity have resulted in the identification of isoform selective analogues: 17 with >7.8-fold selectivity for SIRT1, 24 with >15.4-fold selectivity for SIRT2, and 8 with 6.8- and 5.3-fold selectivity for SIRT3 versus SIRT1 and SIRT2, respectively. In vitro cytotoxicity studies with these compounds as well as EX527, a potent and selective SIRT1 inhibitor, suggest that antilymphoma activity of this compound class may be predominantly due to SIRT2 inhibition.
Identification of new therapeutic compound
classes and validation
of new therapeutic targets remain major hurdles in drug discovery.
In the past decade, human sirtuins (homologues of yeast Silent Information Regulator Two or Sir-2) have emerged as targets for cancer chemotherapy as well
as for neurodegenerative and aging-related disorders such as Huntington’s
disease, Alzheimer’s disease, and diabetes.[2] Although strong evidence exists for sirtuins having a central
role in these debilitating diseases, their validation as targets for
therapeutic intervention using small molecule modulators has been
controversial.[3−5] The most publicized efforts at modulation of sirtuin
activity have been with the plant polyphenol resveratrol.[6] This purported sirtuin activator was shown to
have highly beneficial effects in animal models of metabolic disorders
(e.g., diabetes) and lifespan extension using experimental models
that have since been largely shown to be flawed.[7−9] EX-527, a potent
and selective SIRT1 inhibitor (SIRT1: human sirtuin isoform 1), was
found to be devoid of chemotherapeutic effect; however, cambinol,
tenovin-1, tenovin-6, and salermide, nonselective SIRT1/SIRT2 inhibitors,
were found to have significant antitumor activity.[1,10−12] Combined use of a nonselective sirtuin inhibitor
niacinamide (nicotinamide) and a pan-type I/II HDAC (i.e., zinc-dependent
histone deacetylases) inhibitor vorinostat yielded encouraging results
in a recent diffuse large B-cell lymphoma phase I clinical trial further
validating sirtuins as antilymphoma drug targets.[13] Additionally, SRT1720, a potent direct SIRT1 activator
that was originally developed for its potential in lifespan extension
or antiaging activity, was later found to be beneficial in a ratdiabetes
model employing a mechanism which may involve indirect activation
of SIRT1.[14] The recent functional characterization
of other sirtuin isoforms such as SIRT3, SIRT5, SIRT6, and SIRT7 has
further complicated the field as it is becoming increasingly clear
that in addition to SIRT1 and 2, these isoforms may also play major
roles in aging (SIRT3, SIRT6) as well as in cell-proliferation disorders
(SIRT7).[15] Additional controversies regarding
artifacts of popular in vitro assays to identify novel small molecule
modulators of sirtuin activity have also hampered the validation of
these enzymes for pharmacological intervention.[16]Previously, in an attempt to identify isoform selective
sirtuin
inhibitors, we carried out a phenotypic screen using an NCI chemical
library that resulted in discovery of cambinol(5-[(2-hydroxy-1-naphthyl)methyl]-6-phenyl-2-thioxo-2,3-dihydro-4(1H)-pyrimidinone) 1.[1] Titration experiments using SIRT2 and an acetyl-peptide substrate
showed that cambinol was competitive with the peptide substrate but
noncompetitive with NAD+ suggesting that its binding site
partially overlaps with that of the substrate. Cambinol inhibits SIRT1
and SIRT2 with mid-micromolar IC50 and induces hyperacetylation
of p53, a known SIRT1 target, and α-tubulin, a SIRT2 target,
in cell-based deacetylation assays.[17,18] In addition,
cambinol was found to be an effective chemosensitizer for the DNA
damaging agent etoposide both in p53-proficient and p53-deficient
cancer cell lines. As a single agent, cambinol was found to be selectively
toxic to BCL6 expressing B-cell lymphoma cells suggesting that it
could be used as a lead compound for antilymphoma drug development.[1] Cambinol however suffers from major drawbacks
including (1) moderate potency, as it did not induce tumor regression,
but a decrease in tumor growth rate, and (2) poor solubility. Since
the discovery of cambinol, we have focused on optimization of cambinol’s
potency and validation of specific sirtuin isoforms (e.g., SIRT1 and
SIRT2) as targets for B-cell lymphoma chemotherapy. The cambinol pharmacophore
has been well studied (Figure 1). The β-naphthol
nucleus is absolutely essential for activity, and the aryl ring is
also important as replacing it with five-membered or a heterocyclic
ring results in significant loss of potency.[1,19−22] The pyrimidinedione (thiouracil) heteroaryl ring requires a balance
of hydrogen bond donor and acceptor groups to maintain potency.
Figure 1
Cambinol analogues.
(a) cambinol; (b) schematic; (c) pyrazolone
analogues (e.g., 8 and 17); and (d) isoxazolone
analogues (e.g., 24).
Cambinol analogues.
(a) cambinol; (b) schematic; (c) pyrazolone
analogues (e.g., 8 and 17); and (d) isoxazolone
analogues (e.g., 24).To further develop the structure activity relationship (SAR),
we
investigated substituting the pyrimidinedione ring (heteroaryl group,
Figure 1b) with five-membered heterocycles
(pyrazolone 1c and isoxazolone 1d) as well
as altering the functional groups on the naphthyl and aryl rings.
To guide us with the specific positioning of the functional group
to observe increased potency, we conducted saturation transfer difference
(STD) NMR experiments using 20 (Figure 2). The data obtained from STD NMR experiments identified portions
of the ligand that interact with the receptor and suggest sites available
for additional elaboration. Cell-based toxicity assays show a significant
correlation between SIRT2 inhibition and cytotoxicity in the Namalwa
Burkitt’s lymphoma cell line.
Figure 2
1H NMR spectrum and STD spectrum
of (20) and SIRT1. The chemical structure of (20) using naphthalene
numbering for clarity. Relative saturation transfer (C-7 proton =100%).
1H NMR spectrum and STD spectrum
of (20) and SIRT1. The chemical structure of (20) using naphthalene
numbering for clarity. Relative saturation transfer (C-7 proton =100%).
Results
Syntheses on new cambinol
analogues closely parallel that of the
parent compound, cambinol (Scheme 1). Target
compounds are prepared by a three-step sequence from 2-hydroxy-1-naphthaldehyde
starting materials. For cambinol, base-catalyzed Knoevenagel condensation
with ethyl-benzoylacetate with 2-hydroxy-1-naphthaldehyde affords
the α,β-unsaturated β-ketoester (Scheme 1). Sodium borohydride reduction of the α,β-unsaturated
olefin followed by base-promoted 2-thiouracil formation with thiourea
yields cambinol. For naphthyl and quinolyl derivatives of cambinol,
hydroxy-naphthaldehyde and hydroxy-quinaldehyde starting materials
were prepared by titanium-catalyzed Reiche formylation reaction (1-carbaldehyde-2-hydroxynaphthalene
derivatives) from the corresponding phenols, and the Duff reaction
of hexamethylenetetramine (HMTA) with 6-hydroxy-2-quinolones in the
presence of trifluoroacetic acid (TFA) afforded the corresponding
5-carbaldehyde-6-hydroxy-2-quinolones, respectively (Schemes 1 and 2). The pyrazolone analogues
were prepared by reacting the appropriate β-ketoester with hydrazine,
while syntheses of the isoxazolone analogues used corresponding hydroxylamine
compounds as nucleophiles (Scheme 1).
Scheme 1
Synthesis
of Naphthyl Pyrimidinedione, Pyrazolone, and 5-Isoxazolone
Sirtuin Inhibitors (1–18, 24–26)
Reagents and conditions:
(a)
Cl2CHOMe, TiCl4, CH2Cl2, 0–20 °C, 24 h; (b) aryloyl ethyl acetoacetate, piperidine,
EtOH, reflux, 2 h; (c) NaBH4, pyridine, 20 °C, 2 h;
(d) thiourea, NaOEt, EtOH, reflux, 18 h; (e) hydrazine, DMF, 20 °C,
1.5 h; (f) hydroxylamine, DMF, 60 °C, 18 h;
Scheme 2
Synthesis of Quinolyl Pyrazolone Sirtuin Inhibitors (19–23)
Reagents and conditions:
(a)
HMTA, TFA, 100 °C, 2 h; (b) POX3, DMF, temp, time
X = Cl, Br; (c) aryloyl ethyl acetoacetate, piperidine, EtOH, reflux,
2 h; (d) NaBH4, pyridine, 20 °C, 24 h; (e) hydrazine,
DMF, 20 °C, 1.5 h.
Synthesis
of Naphthyl Pyrimidinedione, Pyrazolone, and 5-Isoxazolone
Sirtuin Inhibitors (1–18, 24–26)
Reagents and conditions:
(a)
Cl2CHOMe, TiCl4, CH2Cl2, 0–20 °C, 24 h; (b) aryloyl ethyl acetoacetate, piperidine,
EtOH, reflux, 2 h; (c) NaBH4, pyridine, 20 °C, 2 h;
(d) thiourea, NaOEt, EtOH, reflux, 18 h; (e) hydrazine, DMF, 20 °C,
1.5 h; (f) hydroxylamine, DMF, 60 °C, 18 h;
Synthesis of Quinolyl Pyrazolone Sirtuin Inhibitors (19–23)
Reagents and conditions:
(a)
HMTA, TFA, 100 °C, 2 h; (b) POX3, DMF, temp, time
X = Cl, Br; (c) aryloyl ethyl acetoacetate, piperidine, EtOH, reflux,
2 h; (d) NaBH4, pyridine, 20 °C, 24 h; (e) hydrazine,
DMF, 20 °C, 1.5 h.SIRT1, SIRT2, and
SIRT3 enzyme inhibition studies, carried out
using the SIRT-Glo assay (Promega Corp., Madison, WI) at a single
inhibitor concentration (50 μM), revealed a range of activities
against each target (Tables 1, 2, and 3). Cambinol, the parent of this
class of agents, was found to be an nonselective SIRT1, SIRT2 inhibitor
with 54% SIRT1 inhibition, 46% SIRT2 and 16% SIRT3 inhibition at a
single 50 μM concentration (Table 1),
and dose response titration against these enzymes with cambinol gave
IC50 values very similar to published values (SIRT1 IC50 = 56 μM, SIRT2 IC50 = 51 μM) and
>200 μM SIRT3 IC50.[1,19]
Table 1
Naphthyl Pyrimidinedione (1) and Pyrazolone (2–18) Sirtuin
Inhibitorsa
compound
R
R′
SIRT1 (% inh)
SIRT2 (% inh)
SIRT3 (% inh)
cambinol (1)
cambinol
cambinol
54
46
16
2
H
H
48
18
9
3
H
3-Br
8
25
n.d.
4
H
4-Br
36
33
22
5
H
4-CH3
58
27
21
6
H
4-F
24
29
9
7
H
4-CF3
48
29
14
8
6-phenyl
4-CH3
66
73
82
9
6-CH3O
4-CH3
64
53
35
10
6-CN
4-CH3
25
21
n.d.
11
6-CH3
4-CH3
39
19
12
12
6-C2H5
4-CH3
45
23
7
13
6-Br
H
59
47
8
14
6-Br
4-CH3
62
9
21
15
7-Br
4-CH3
42
38
13
16
3-Br
4-CH3
49
20
14
17
3-CH3O
4-CH3
78
19
14
18
6-Br
4-CH3O
40
30
18
Percentage sirtuin inhibition at
50 μM compound; n.d. = not determined.
Table 2
Quinolyl Pyrazolone Sirtuin Inhibitorsa
compound
no.
R
R1
R′
SIRT1 (% inh)
SIRT2 (% inh)
SIRT3 (% inh)
19
H
H
CH3
39
23
16
20
Cl
H
CH3
45
17
20
21
Br
H
CH3
51
38
42
22
Cl
CH3
H
27
24
32
23
Cl
H
isopropyl
85
37
32
Percentage sirtuin inhibition at
50 μM compound.
Table 3
Naphthyl 5-Isoxazolone Sirtuin Inhibitorsa
compound
no.
R2
SIRT1 (% inh)
SIRT2 (% inh)
SIRT3 (% inh)
24
H
5
87
18
25
CH3
11
48
17
26
benzyl
2
45
24
Percentage sirtuin inhibition at
50 μM compound.
Percentage sirtuin inhibition at
50 μM compound; n.d. = not determined.Percentage sirtuin inhibition at
50 μM compound.Percentage sirtuin inhibition at
50 μM compound.We
carried out an STD NMR experiment using recombinant SIRT1 and
compound 20 (Figure 2).[23] The relative saturation transfer enhancement
at positions we were able to evaluate is shown in Figure 2. The results show that C-7 proton (naphthalene
numbering is used for clarity since most of the compounds discussed
in this section are naphthalene derivatives) gives the strongest STD
signal (100% relative intensity) and forms a close contact with the
protein. The aryl C-4′ methyl protons (66% signal intensity)
and C-8 proton (74% signal intensity) form contacts with the protein,
but these may be suboptimal. Consistent with this, compounds 1 (cambinol), 2, 6, 13, and 22 that contain a small substituent at C-4′
(i.e., hydrogen or fluorine) are relatively poor and nonselective
sirtuin inhibitors. The most selective compounds 17 and 24 have methyl groups at C-4′ suggesting that SIRT1
and SIRT2 residues that interact with this group are well conserved.
Likewise, compounds that contain larger than hydrogen (i.e., methyl
or isopropyl) substituents at the C-4′ position of the aryl
moiety tend to favor SIRT1 inhibition with the bulkiest substituent
(i.e., isopropyl, compound 23) having the highest selectivity
(>3-fold, Table 4). The STD values for the
-methylene protons and the NHs of the pyrazolone moiety could not
be determined because of the overlap with the water signal and the
fast exchange with solvent deuterons, respectively. STD values for
the C-3hydrogen and for protons in the phenyl ring (C-2′,
C-3′, C-5′, C-6′) could not be accurately determined
due to overlapping signals. The most significant determinant of the
selectivity between SIRT1 and SIRT2 in the present compound series
is the H-bond donor or acceptor at the 2 position of the heteroaryl
unit (i.e., N–H or oxygen) in 17 and 24. The reversal of hydrogen bond directionality results in a reversal
of selectivity with the hydrogen-bond donor compounds 17 displaying up to a 7.8-fold SIRT1 selectivity and the hydrogen bond
acceptor 24 a 15.4-fold SIRT2 selectivity with approximately
similar overall inhibitory activity against the preferred isoform:
26 μM IC50 for 17 against SIRT1 and
13 μM IC50 for 24 against SIRT2. Substitution
of a hydrophobic aromatic group at C-6 of the naphthalene group gave
the most potent SIRT3 inhibitor (compound 8, SIRT3 IC50 6 μM). This compound however was relatively nonselective
with SIRT1 and SIRT2 IC50 of 41 and 32 μM, respectively.
The potency of C-6 phenyl substituted naphthalene across the SIRT
isoforms suggests a conserved hydrophobic pocket present in all three
proteins.
Table 4
Isoform-Selective SIRT Inhibitorsa
compound
no.
SIRT1 IC50 (μM)a
SIRT2 IC50 (μM)a
SIRT3 IC50 (μM)a
1
56
51
>200
8
41
32
6
14
37
>200
>200
17
26
>200
>200
23
21
68
122
24
>200
13
>200
Concentration giving 50% inhibition
of sirtuin activity.
Concentration giving 50% inhibition
of sirtuin activity.Our
previous studies with cambinol demonstrated that SIRT1 inhibition
could be quantified in cells by determining the level of p53 acetylation
following induction of DNA damage by the cytotoxic topoisomerase II
poison etoposide.[1] We treated NCI-H460
cells with 1 μM etoposide in the presence or absence of cambinol 1 or 14, a SIRT1-selective inhibitor (Tables 1 and 4). As expected, the
more potent SIRT1 inhibitor 14 shows a significantly
higher level of p53 acetylation at a given concentration (Figure 3). Likewise, SIRT2 inhibition results in hyper-acetylation
of α-tubulin. The SIRT2-selective inhibitor 24 induced
a rapid and robust dose-dependent increase in α-tubulin acetylation
in NCI-H460 cells (Figure 4).
Figure 3
Inhibition of SIRT1-mediated
deacetylation of p53 in the presence
of DNA damage. Determination of p53 acetylation in NCI-H460 cells
by Western blot following 24 h drug treatment.
Figure 4
Inhibition of SIRT2-mediated deacetylation of α-tubulin.
Determination of α-tubulin acetylation in NCI-H460 cells by
Western blot following 4 h treatment with trichostatin A (TsA) and
(24).
Inhibition of SIRT1-mediated
deacetylation of p53 in the presence
of DNA damage. Determination of p53 acetylation in NCI-H460 cells
by Western blot following 24 h drug treatment.Inhibition of SIRT2-mediated deacetylation of α-tubulin.
Determination of α-tubulin acetylation in NCI-H460 cells by
Western blot following 4 h treatment with trichostatin A (TsA) and
(24).Part of the motivation
behind these studies was to determine whether
SIRT1, SIRT2 or SIRT3 inhibition, or possibly a subset of these enzymes,
was responsible for cambinol’s antilymphoma activity. Cell-based
sirtuin activity assays were carried out by determining the acetylation
status of well established SIRT1 (p53) and SIRT2 (α-tubulin)
in the presence of isoform selective inhibitors. Cytotoxicity assays
were carried out with the human Burkitt’s lymphoma cell line
Namalwa grown under standard conditions.[1] Cells were plated in 96-well plates, treated with the test compound
or DMSO control for 72 h, and viable cells were quantified by luminescence
using CellTiterGlo (Promega Corp., Madison, WI). Cell viability assays
showed that both SIRT1- and SIRT2-selective series exhibit antiproliferative,
cytotoxic activity against the Namalwa Burkitt’s lymphoma cell
line, while the SIRT3-selective compound was less toxic. In the Namalwa
cell line, cell death occurs by induction of apoptosis as evidenced
by dose-dependent appearance of annexin V-positive cells as indication
of early stage apoptosis (Figure 5). In addition,
while there is a strong correlation between SIRT2 inhibition and Namalwa
cytotoxicity (r = 0.56, p = 0.0014)
(Figure 6), neither SIRT1 (r = −0.11) nor SIRT3 (r = 0.21) (data not
shown) inhibition correlates with Namalwa cytotoxicity. Three compounds,
the SIRT1-selective 17, SIRT2-selective 24 and SIRT3-selective 8, were tested against an expanded
panel of Burkitt’s lymphoma (Dakiki, Daudi, Mutu, Oku, Ramos
and Namalwa), diffuse large B-cell lymphoma (SU-DHL4 and OCI-Ly8-LAM53),
nontransformed Epstein–Barr virus (EBV) immortalized B-cell
lines (B1 and B2), and epithelial cancer cell lines (HCT116-colon,
MCF7-breast, NCI-H460-nonsmall cell lung cancer and OVCAR3-ovarian)
(Table 5). The SIRT2-selective inhibitor 24 exhibited potent cytotoxicity in both lymphoma and epithelial
cancer cell lines with IC50 ranging from 3 to 7 μM
relative to the nontransformed B-cell lines (IC50 22–28
μM).
Figure 5
Induction of apoptosis in Namalwa cells treated with 24. FACS analysis of Namalwa cells treated with DMSO (left), 10 μM
(24) (center) and 25 μM (24) (right)
for 16 h. Cells were stained with annexin V-PE (y-axis) and DAPI (x-axis). Cells entering an early
phase of apoptosis are present in the upper left panel.
Figure 6
Correlation between sirtuin inhibition and Namalwa Burkitt’s
lymphoma cell line growth inhibition. SIRT1 (red circles) and SIRT2
(blue triangles) inhibition (y-axis) versus Namalwa
growth inhibition (x-axis).
Table 5
Cell Line Growth Inhibitiona
compound
no.
Dakiki
Daudi
Mutu
Oku
Ramos
Namalwa
SU-DHL4
LAM53
8
68
n.d.
33
51
28
40
27
34
17
29
21
15
11
15
15
77
32
24
7
5
3
5
7
4
5
7
Concentration giving
50% growth
inhibition following 72 h drug treatment. Dakiki, Daudi, Mutu, Oku,
Ramos, Namalwa are Burkitt’s lymphoma cell lines. SU-DHL4 and
LAM53(OCI-Ly8-LAM53) are diffuse large B-cell lymphoma lines. B1 and
B2 are EBV-immortalized nontransformed B-cell lines. HCT116 (colon),
MCF7 (breast), NCI-H460 (lung), and OVCAR3 (ovarian) are epithelial
cancer cell lines.
Induction of apoptosis in Namalwa cells treated with 24. FACS analysis of Namalwa cells treated with DMSO (left), 10 μM
(24) (center) and 25 μM (24) (right)
for 16 h. Cells were stained with annexin V-PE (y-axis) and DAPI (x-axis). Cells entering an early
phase of apoptosis are present in the upper left panel.Correlation between sirtuin inhibition and Namalwa Burkitt’s
lymphoma cell line growth inhibition. SIRT1 (red circles) and SIRT2
(blue triangles) inhibition (y-axis) versus Namalwa
growth inhibition (x-axis).Concentration giving
50% growth
inhibition following 72 h drug treatment. Dakiki, Daudi, Mutu, Oku,
Ramos, Namalwa are Burkitt’s lymphoma cell lines. SU-DHL4 and
LAM53(OCI-Ly8-LAM53) are diffuse large B-cell lymphoma lines. B1 and
B2 are EBV-immortalized nontransformed B-cell lines. HCT116 (colon),
MCF7 (breast), NCI-H460 (lung), and OVCAR3 (ovarian) are epithelial
cancer cell lines.
Discussion and
Conclusions
Cambinol, (5-[(2-hydroxy-1-naphthyl)methyl]-6-phenyl-2-thioxo-2,3-dihydro-4(1H)-pyrimidinone) 1, is a nonselective sirtuin
inhibitor with equivalent inhibitory activity against SIRT1 and SIRT2.
It also is a reasonably potent antitumor agent in vitro and in vivo with particular activity against Burkitt’s
lymphoma cell lines.[1] In an effort to delineate
the contribution of SIRT1 and SIRT2 inhibition in this antitumor activity,
we sought to develop cambinol analogues with improved potency and
selectivity. Studies by Medda et al. and Rotili et al. have partly
addressed the structure activity relationships of six-membered pyrimidinedione-containing
(i.e., cambinol-like) compounds.[19,24] In an effort
to investigate an alternative chemical space, we prepared a series
of five-membered pyrazolone- and 5-isoxaolone-containing compounds.
The five-membered ring pyrazolone compounds (i.e., 2–23) exhibit a range of specificities but generally favor SIRT1
inhibition. The most selective of these compounds, 14 and 17, exhibit a greater than 5-fold and 7-fold, respectively,
preference for SIRT1 over SIRT2. The 5-isoxazolone compounds (i.e., 24–26) favor SIRT2 inhibition with a greater
than 15-fold preference shown by 24.In order to
gain a molecular understanding of the observed selectivity,
we sought to identify portions of the ligand involved in the interaction
with SIRT1 protein. The STD NMR experiment with recombinant SIRT1
and 20, a relatively nonselective but highly soluble
ligand, has identified positions of the ligand as potential sites
for improving selectivity and potency (Figure 2). The efficiency of saturation transfer was lowest at C-8 of the
quinolone ring system (naphthalene numbering) and at the 4-methyl
group of the aryl substituent suggesting that these portions of the
ligand interact with the protein surface but in a suboptimal manner.
Consistent with this finding, compounds with large substituents at
the C-4 position yielded more potent inhibitors (e.g., 20 versus 23, Table 2) in agreement
with the structural model proposed by Medda et al.[19] Saturation transfer was most efficient at C-4 and C-7 of
the quinoline ring suggesting close ligand/protein interactions; however,
the C-8 proton showed a weaker interaction. Examination of the structural
variation at these positions suggests a reasonable explanation of
the observed selectivities. The binding site for the C-4 phenyl position
appears to tolerate medium-sized substituents equally well in SIRT1
and SIRT2, with bulkier groups such as isopropyl showing an improved
preference for SIRT1. The strongest determinant of selectivity in
the current compound series is the hydrogen bond donor (i.e., N–H
at the pyrazolone 2 position in 17) or hydrogen bond
acceptor (i.e., O at the dihydro 1,2-oxazol-5-one 1 position in 24). Remarkably, the reversal of directionality of the hydrogen
bond donor/acceptor pair leads to a 7.8-fold SIRT1 selectivity in
the case of the former 24 and a 15.4-fold SIRT2 selectivity
for the latter, with approximately equipotent overall inhibitory activity
against the preferred isoform: 26 μM IC50 for 17 against SIRT1 and 13 μM IC50 for 24 against SIRT2. Future studies will attempt to optimize
interactions at C-4′ and C-8. Placement of a bulky hydrophobic
phenyl group at the naphthaleneC-6 position yielded 8, a potent although relatively nonselective SIRT3 inhibitor. Elaboration
of the C-6 substituent provides a means to increase overall potency.
The SAR trends observed in the current compound series provide a strong
starting point for development of potent isoform-selective as well
as pan-sirtuin inhibitors.While both SIRT1 and SIRT2-selective
compounds exhibit some degree
of cytotoxicity, a strong correlation between SIRT2 inhibition and
Namalwa cytotoxicity (r = 0.56, p = 0.0014) suggests that SIRT2 inhibition may be primarily responsible
for the observed antilymphoma activity. Lack of correlation between
SIRT1 inhibition and cytotoxicity observed in our study is consistent
with the findings that EX-527, a potent and selective SIRT1 inhibitor,
does not exhibit activity against B-cell lymphoma cell lines, as reported
previously by others for epithelial tumor cells.[25] It is possible, however, that inhibition of SIRT1 may play
a role in other tumor contexts, as suggested by the findings by Rotili
et al.[24,26] In addition to Burkitt’s lymphoma
cell lines, we tested 8, 17, and 24 against normal immortalized lymphoblastic lines (B1 and B2), diffuse
large B-cell lymphoma lines as well as a panel of solid tumor cell
lines (Table 5). Interestingly, colon (HCT116)
breast (MCF7) and nonsmall cell lung carcinoma (NCI-H460) also showed
significant sensitivity to SIRT2 inhibition. The data presented in
this manuscript make a strong case for further development of sirtuin
inhibitors as anticancer agents.
Experimental
Section
Protein Expression
HumanSIRT1 cDNA was cloned into
the pET-4a vector and transformed into BL21-DE3 Escherichia
coli cells. Expression of SIRT1 protein fusion with hexa-histidine
tag (C-terminal) was induced with IPTG (5 mM). Recombinant protein
was purified from bacterial lysates using the Ni-NTA column (Clontech
Laboratories Inc. Mountain View, CA) according to manufacturer’s
protocols.
Enzyme Inhibition Assays
SIRT1 was
expressed and purified
as described above. SIRT2 and SIRT3 were purchased from Cayman Chemical
(Ann Arbor, MI). Enzyme inhibition assays were performed in 96-well
plates using the SIRT-Glo Assay (Promega Corp., Madison WI) according
to the manufacturer’s instructions. Compounds were dissolved
in 100% DMSO and were tested over a five 3-fold dilution concentration
range (final DMSO concentration 0.25%). IC50 values were
determined in triplicate and reported values are averages of two independent
experiments.
Cell Viability Assays
Cell lines
were obtained from
ATCC (Manasas, VA) and were grown under standard conditions. For viability
assays, cells were dispensed into 96-well plates and treated with
test compounds in 100% DMSO (final DMSO concentration 0.25%). Cells
were incubated with test compounds (or DMSO controls) for 72 h, and
viability was determined using the CellTiterGlo Assay (Promega Corp.,
Madison WI) according to manufacturer’s instructions. Assays
were carried out in triplicate reported values are averages of two
independent experiments.
Western Blot
NCI-H460human lung
carcinoma cells (ATCC)
were grown under standard conditions. Drug treatment and Western blots
were carried out as previously described.[1] Antibodies for acetylated α-tubulin (clone 6-11B-1, Sigma,
St. Louis, MO), α-tubulin (clone DM1A, Calbiochem, San Diego,
CA), actin (Roche, Indianapolis, IN), acetylated p53 (Cell Signaling,
Danvers, MA), p53 (Cell Signaling, Danvers, MA) and acetylated lysine
(polyclonal antibody; Cell Signaling, Danvers, MA) were used at dilutions
recommended by the manufacturer.
Flow Cytometry
Namalwa cells were treated with 10 and
25 μM (24) or solvent (DMSO) for 16 h, washed in
phosphate buffered saline, and suspended at approximately 200 000
cells in 200 μL of binding buffer containing 5 μL of annexin
V-PE (BD Biosciences, San Jose, CA) for measuring phosphatidylserine,
and 4′,6-diamidino-2-phenylindole (DAPI) at a concentration
of 2.5 μg/mL, for nucleic acids. After 15 min incubation at
room temperature, cell fluorescence was analyzed on a FACScanR (Becton
Dickinson, Franklin Lakes, NJ).
General Chemistry
Unless specified otherwise, reagents
were obtained from Sigma-Aldrich and used without additional purification.
6-Hydroxy-2(1H)-quinolinone and 4-methylquinoline-2,6-diol
were obtained from Bioblocks Inc. 3-(4-isopropyl-phenyl)-3-oxo-propionic
acid ethyl ester was obtained from Vitas M Laboratories. Thin layer
chromatography was carried out using Merck 60 F254 silica gel plates
using appropriate solvent mixtures. Solvents were ACS reagent grade
and anhydrous solvents (Aldrich and Acros) were used as received.
Medium pressure chromatography was carried out using Biotage Isolera
with Silicycle HP cartridges. LCMS was performed using an Agilent
1100 HPLC system equipped with a Waters XTerra MS C18 5 um, 4.6 ×
50 mm column, an Agilent photodiode array detector and an in-line
Agilent 6130 single quadrupole mass spectrometer. The LC method involved
gradient elution from 0 to 95% acetonitrile in water (0.1% formic
acid) over 6 min. Final purity of compounds was determined using ACE
3, C8–300, 150 × 3.0 mm column with the above-mentioned
gradient over 15 min. Agilent ChemStation software was used to develop
methods and calculate percentage purity. All compounds reported are
at least 95% pure.
NMR Experiments
All NMR experiments
were performed
at 25 °C on a Varian Unity Plus 300 spectrometer or Varian Unity-Inova
500 MHz spectrometer equipped with a 5 mm triple-resonance 1H(13C/15N), z-axis pulsed-field
gradient probe head. For characterization purposes, samples consisted
of a ∼5 mM solution of each compound in chloroform-d (99.8% D, Cambridge Isotopes), dimethyl sulfoxide-d6 (99.9% D, Cambridge Isotopes), benzene-d6 (99.5%
D, Cambridge Isotopes) or acetone-d6 (99.9%
D, Cambridge Isotopes), and the spectra were referenced to residual
solvent peaks at 7.27, 2.50, 7.16, and 2.05 ppm, respectively. 1H-1D spectra were acquired at a resolution of 16k complex
points in the time domain with 32 accumulations each (sw = 6000 Hz,
d1 = 3 s).
Saturation Transfer Difference (STD) NMR
All STD experiments
were performed in D2O solution to eliminate the influence
of exchangeable protein protons. The purified SIRT1 stock solution
(12 μM) was dialyzed against deuterated phosphate buffered saline
(PBS). The exchange buffer was prepared by lyophilizing a PBS solution
at pH 7.4 and redissolving it in D2O (99.9% D, Cambridge
Isotopes). NMR samples contained 1.5 μM SIRT1 and 200 μM
compound 20 in PBS in D2O pH 7.4 (uncorrected
for D2O) with 1% dimethyl sulfoxide-d6 as a cosolvent. STD NMR experiments were performed at 25
°C as previously described.[27] Briefly,
two free induction decay (FID) data sets were collected in an interleaved
manner to minimize temporal fluctuations with the protein irradiation
frequency set on-resonance (−0.5 ppm) and off-resonance (40
ppm), respectively (sw =6000 Hz, 16 steady state scans, 2048 transients,
4k complex points, d1 = 3 s). Protein saturation was obtained using
a train of individual 50 ms long, frequency selective Gaussian radio
frequency (rf) pulses separated by an interpulse delay of 1 ms. The
number of selective pulses was set to 50, leading to a total saturation
time (τsat) of 2.5 s. Gradient Tailored Excitation
(WATERGATE) scheme was employed to suppress the residual water signal.[28] Suppression of the background signals arising
from the protein was not required. The FID acquired with off-resonance
irradiation generated the reference spectrum (Ioff) whereas the difference FID (off-resonance–on-resonance)
yielded the STD spectrum (ISTD = Ioff – Ion). Spectra were processed with an exponential apodization function
(1 Hz line-broadening) and zero-filling to 8k complex points before
Fourier transformation and baseline correction with a third order
Bernstein polynomial fit. The STD measurements were done in duplicate,
and all data were processed and analyzed using MNova 8.1 processing
software (Mestrelab Research, Santiago de Compostela, Spain).
Chemistry
General
Procedure I for Preparation of Substituted 2-Hydroxy-1-Naphthalene
Carbaldehydes
The procedure was adapted from the protocol
for formylation of electron rich phenols reported by Garcia et al.[29] A solution of TiCl4 (18 mmol) and
dichloromethyl ether (9 mmol) in anhydrous dichloromethane (10 mL)
was stirred at 0 °C for 15 min. A solution of the corresponding
substituted naphthol (9 mmol) in either CH2Cl2 or 1,2-dichloroethane (30 mL) was added dropwise, and the reaction
was warmed to room temperature. The reaction was allowed to stir overnight
after which it was quenched by adding 1 N HCl (10 mL). The aqueous
layer was extracted with CH2Cl2 (3 × 10
mL), and the organic layers were then combined, dried with Na2SO4, and reduced to dryness to afford a residue
which was further purified using medium pressure chromatography to
yield the pure aldehyde.
6-Bromo-2-hydroxynaphthalene-1-carbaldehyde
(51)
A reddish brown residue initially obtained
was further purified by medium pressure chromatography using a gradient
EtOAc/hexane solvent system (1–10% EtOAc) yielding 1.5 g (6
mmol, 67%) as a white powder. 1H NMR (500 MHz, chloroform-d) δ 13.12 (s, 1H), 10.79 (s, 1H), 8.24 (d, J = 8.8 Hz, 1H), 7.97 (d, J = 2.4 Hz, 1H),
7.91 (d, J = 9.3 Hz, 1H), 7.70 (dd, J = 8.8, 2.4 Hz, 1H), 7.19 (d, J = 9.3 Hz, 1H). LRMS: m/z = 249.1 (M – H)−.
2-Hydroxy-6-phenylnaphthalene-1-carbaldehyde
(52)
6-Bromo-2-hydroxynaphthalene-1-carbaldehyde
(1.39 mmol), phenyl boronic acid (2.09 mmol), bis(dibenzylideneacetone)palladium(0)
(0.0139 mmol), and tricyclohexylphosphine (0.033 mmol) were suspended
in dioxane (7 mL). To this mixture was added potassium phosphate tribasic
(1.27 M), and the solution was heated at 100 °C for 6 h. The
reaction was cooled, loaded onto a small silica column, and eluted
with EtOAc (20 mL), and the filtrate was collected. The extracts were
washed with water, dried using Na2SO4, and reduced
to dryness to afford a dark brown residue. The residue was then purified
by medium pressure chromatography using gradient EtOAc/hexane solvent
system (1–10% EtOAc) yielding 140 mg (0.56 mmol, 40%) as a
white powder. 1H NMR (500 MHz, chloroform-d) δ 13.16 (s, 1H), 10.85 (s, 1H), 8.42 (d, J = 8.8 Hz, 1H), 8.05 (d, J = 8.8 Hz, 1H), 8.00 (d, J = 2.4 Hz, 1H), 7.90 (d, J = 8.8 Hz, 1H),
7.71 (d, J = 7.3 Hz, 2H), 7.51 (t, J = 7.8 Hz, 2H), 7.42 (t, J = 7.8 Hz, 1H), 7.19 (d, J = 8.8 Hz, 1H), LRMS [ES]+: m/z = 249.1 (M + H)+.
A reddish brown residue was initially obtained
which further purified by medium pressure chromatography using a gradient
EtOAc/hexane solvent system (1–10% EtOAc) yielding 75 mg (0.37
mmol, 36%) as a white powder. 1H NMR (500 MHz, chloroform-d) δ 13.46 (s, 1H), 10.74 (s, 1H), 8.23 (d, J = 8.3 Hz, 1H), 7.69 (d, J = 7.8 Hz, 1H),
7.48 (ddd, J = 8.3, 7.6, 1.2 Hz, 1H), 7.41 (ddd, J = 8.3, 7.6, 1.2 Hz, 1H), 7.30 (s, 1H), 4.01 (s, 3H). LRMS
[ES]+: m/z = 203.1 (M
+ H)+.
General Procedure (II) for Preparation of
2-Benzoyl-3H-benzo[f]chromen-3-ones
The
compounds were synthesized
using the established synthetic route for cambinol and its analogues
reported earlier.[19] To a solution of substituted
hydroxyl naphthaldehydes (5 mmol) in ethanol (5 mL) were added the
corresponding ethyl benzoyl acetates (5 mmol). Piperidine (5 drops)
was added, and the reaction was heated under reflux for 2 h. The reaction
was allowed to cool, and the yellowish precipitate obtained was collected
by filtration and washed with ethanol several times to get the condensation
product. Synthesis of 2-benzoyl-3H-benzo[f]chromen-3-one
(29) has been previously reported.[19]
General Procedure
(III) for Preparation of Pyrazolone-Based
Analogues
The corresponding 2-benzoyl ketocoumarin (0.5 mmol)
was dissolved in dry pyridine (3 mL). To this solution was added NaBH4 (0.625 mmol), and the reaction was stirred at room temp for
2 h. The mixture was then poured in cold 2 M hydrochloric acid (10
mL), which resulted in a white precipitate. The precipitate was washed
several times with water, dried under a vacuum to yield the corresponding
2-benzoyl-1,2-dihydrocoumarin which was taken to the next step without
purification. To a stirring solution of 2-benzoyl-1,2 dihydrocoumarin
(0.1 mmol) in DMF (0.2 mL) was added hydrazine (0.125 mmol), and the
mixture was stirred for 1.5 h at room temperature. Water (5 mL) was
then added, and the aqueous layer was extracted with EtOAc (15 mL).
The organic layer was separated, dried with Na2SO4, and reduced to dryness to afford a yellowish brown crude product,
which was further purified using medium pressure chromatography.
General Procedure
(IV) for Preparation of 2-Halogenated 6-Hydroxy-Quinoline
Carbaldehydes
The corresponding 6-hydroxy-2(1H)-quinolinone (0.6 mmol) was taken up in trifluoroacetic acid (1
mL). To this solution was added hexamethylenetetramine (1.2 mmol),
and the resulting mixture was then heated at 100 °C for 2 h.
The reaction was allowed to cool, methanol (10 mL) was added, and
the solvent was evaporated to afford a dark residue. Water (15 mL)
was added, and the resulting precipitate was filtered and dried. The
precipitate was dissolved in DMF (0.8 mL), the solution cooled to
0 °C, and phosphorus oxyhalide (POCl3 or POBr3) (1.8 mmol) was added dropwise. The light gray colored suspension
was then stirred at room temp overnight. Ice-cold water (15 mL) was
added, and the precipitate was filtered and dried under a vacuum to
yield the corresponding aldehyde as a pure product. Synthesis of 6-hydroxyquinoline-5-carbaldehyde
(60) has been reported previously by using Reimer-Teimann
conditions.[31]
POBr3 (3 mmol) was added dropwise
to 2,6-dihydroxy-quinaldehyde. The suspension was heated to 50 °C
and stirred for 18 h. Ice-cold water (15 mL) was then added, and resulting
light brown precipitate was filtered and dried under a vacuum to afford
the pure product. Yield 60 mg (0.23 mmol, 45%). 1H NMR
(500 MHz, DMSO-d6) δ 11.16 (s, 1H),
8.70 (d, J = 8.8 Hz, 1H), 7.82 (d, J = 8.8 Hz, 1H), 7.42 (d, J = 9.3, 1H), 7.39 (d, J = 9.3, 1H). LRMS [ES]+: M + H+ 253.1 (M + H)+.
General Procedure (V) for Preparation of Quinoline-Based Pyrazolones
General procedure (III) for naphthalene pyrazolones was followed.
The compounds were obtained as white precipitates, which were purified
by medium pressure chromatography using a gradient MeOH/DCM solvent
system (1–10% MeOH) unless otherwise noted.
General Procedure (IV) for Preparation of
Isoxazolone Derivatives
2-(4-Methylbenzoyl)-3H-benzo[f]chromen-3-one (0.06
mmol) was taken in DMF (0.2 mL) to which was added the corresponding
hydroxylamine (0.12 mmol), and the reaction mixture was stirred at
60 °C for 18 h. The solvent was evaporated, and the residue was
dissolved in EtOAc (5 mL). The organic layer was then washed with
water, dried with Na2SO4, and reduced to dryness
to yield an oily product. The oil was further purified by medium pressure
chromatography using gradient EtOAc/hexanes solvent system (0–50%
EtOAc) to afford the pure product.
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