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Benzil Analogues as Inhibitors
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 8 2907
to 100 µM, and data were fitted to the following equation to
These analogues do not inhibit human acetylcholinest-
erase (hAcChE) or butyrylcholinesterase (hBuChE) but
are potent inhibitors of mammalian CEs, with Ki values
in the low nanomolar range.
determine the mode of enzyme inhibition:22
[I]{[s](1 - â) + Ks(R - â)}
i )
[I]{[s] + RKs} + Ki{R[s] + RKs}
Experimental Section
where i is the fractional inhibition, [I] is the inhibitor
concentration, [s] is the substrate concentration, R is the
change in affinity of substrate for enzyme, â is the change in
the rate of enzyme substrate complex decomposition, Ks is the
dissociation constant for the enzyme substrate complex, and
Ki is the inhibitor constant. Examination of the curve fits
where R ranged from 0 to ∞ and â ranged from 0 to 1 was
performed using GraphPad Prism software and Perl data
language. The curves generating the highest r2 values were
analyzed using Akaike’s information criteria23,24 to identify the
best model for enzyme inhibition. Ki values were then calcu-
lated from the equation predicted by Prism to be the best fit
for the experimental data.
Enzyme Inhibition Assays Using 4-Methylumbellifer-
one Acetate (4-MUA) as a Substrate. Metabolism of 4-MUA
was assessed by a fluorimetric assay using either a Hitachi
F2000 fluorescence spectrophotometer or a Millipore Cytofluor
2350 with an excitation wavelength of 365 nm and an emission
wavelength of 460 nm. Samples were incubated with 0.75 mM
of 4-MUA in 50 mM Hepes, pH7.4, and the release of
4-methylumbelliferone was measured over a 1 min time
interval. The rate of substrate catalysis was linear over this
time period. Enzyme inhibition by selected compounds and
determination of Ki values were performed as described above.
Inhibition of Acetylcholinesterase and Butyrylcho-
linesterase. The ability of compounds to inhibit hAcChE and
hBuChE was performed as previously described using either
1 mM acetylthiocholine (AcTCh) or 1 mM butyrylthiocholine
(BuTCh), respectively, as substrates.25-28
Chemicals. Compounds were purchased from the following
sources. Benzil (1), 3-7, 14, 19, 20, 22-26, 28, 31, 36, 38-
40, 53, 57-59, and 61 were all purchased from Sigma Aldrich
Biochemicals (St. Louis, MO). 2, 18, 21, 48, and 49 were
obtained from Pfaltz and Bauer (Waterbury, CT). 8, 11, 15,
43-47, 50-52, and 56 were purchased from Alfa Aesar (Ward
Hill, MA). 10, 41, and 60 were obtained from VWR Scientific
Products (West Chester, PA). 16 was purchased from Ryan
Scientific (Isle of Palms, SC). 17 was obtained from Toronto
Research Chemicals (Toronto, Canada). 27, 32, and 35 were
purchased from Maybridge (Tintagel, U.K.). 29, 30, 33, and
34 were obtained from Industrial Research Ltd., (Auckland,
New Zealand). 37 and 54 were purchased from TCI America
(Portland, Oregon), and 42 and 55 were obtained from ACROS
(Fisher Scientific, Pittsburgh, PA). The synthesis of compounds
9, 12, and 13 is described in this article.
CPT-11 was kindly provided by Dr. J. P. McGovren (Pfizer,
Cambridge, MA).
Synthetic Reagents. 4-Chlorobenzaldehyde, 3,5-difluoro-
benzaldehyde, 3,4,5-trifluorobenzaldehyde, thiamine, copper
acetate, and ammonium nitrate were all purchased from
Sigma Aldrich.
Enzymes. Pure rCE and hCE1 were prepared as described
previously.17 hiCE was prepared by concentration of baculo-
virus media from Sf9 cells expressing a secreted form of the
protein. While not homogeneous, the preparation was at least
60% pure. Since no CE activity is expressed or secreted from
uninfected Sf9 cells, the only CE present in the culture media
was the recombinant protein. The Genbank accession numbers
for the cDNAs used for CE production were as follows: rCE,
AF036930;18 hCE1, M73499;19 hiCE, Y09616.20
Synthesis of Benzil Analogues. Benzil analogues were
synthesized by condensation of the substituted benzaldehydes
(0.04 mol) in the presence of thiamine hydrochloride (0.002
mol) and alcoholic sodium hydroxide (0.005 mol) to yield the
benzoin,29 with subsequent oxidation using copper acetate
(0.001 mol) and ammonium nitrate (0.006 mol) in 80% acetic
acid.30 Products were purified by recrystallization, melting
points were determined using a Mel-temp (Barnstead Inter-
national, Dubuque, IA), and purity and structures were
assessed by TLC, NMR, and total C, H, N analysis.
Human AcChE and BuChE were obtained from Sigma
Aldrich.
Library of Compounds and TRAP Screening. Screening
of compounds was performed using a library of small molecules
obtained from Telik using their target-related affinity profiling
(TRAP) technology.15 Briefly, TRAP defines an “affinity finger-
print” for a particular molecule by determining its binding
affinities to a panel of proteins. In an iterative screening
process (∼70 compounds for each iteration), computational
analysis of fingerprints is performed and compared to the
biological activity obtained for each compound. The first series
of compounds to be assayed was chosen because their finger-
prints encompassed the diversity of fingerprints present within
the entire library. Subsequent analyses are based on compu-
tational analysis of the fingerprints of the compounds that
inhibited CEs. Routinely three to four iterations were per-
formed using approximately 300 compounds. The advantage
of this methodology is that molecules of multiple chemotypes
demonstrating inhibitory activity can be identified by assaying
as few as 200 compounds.14,15
Enzyme Inhibition Assays and Determination of Ki
Values Using Nitrophenyl Acetate (o-NPA) as a Sub-
strate. CE inhibition was determined using a spectrophoto-
metric multiwell plate assay with 3mM o-NPA as a sub-
strate.18,21 Briefly, test compound (100 µM) and substrate were
aliquoted into wells and enzyme was added using a multiwell
pipettor. The rate of change in absorbance at 420 nm was
measured at 15 s intervals for 5 min and compared to wells
containing no inhibitor. Compounds that demonstrated 50%
reduction in CE activity were subsequently evaluated in detail.
Routinely, assays were performed in duplicate and included
both positive (50 µM bis(4-nitrophenyl) phosphate (BNPP)) and
negative controls (DMSO, no enzyme).
4,4′-Dichlorobenzil (1,2-Bis(4-chlorophenyl)ethane-1,2-
dione, 9). 4,4′-Dichlorobenzil was synthesized from 1,2-bis-
(4-chlorophenyl)-2-hydroxyethanone to yield a yellow solid
(yield 62%). Physical and NMR parameters of 9 were as
1
follows: mp 196-198 °C; H NMR (500 MHz, CDCl3) δ 7.53
(d, 2H, J ) 8.5 Hz, Ar-H), 7.94 (d, 2H, J ) 8.5 Hz, Ar-H).
1,2-Bis(3,5-difluorophenyl)ethane-1,2-dione (12). 1,2-
Bis(3,5-difluorophenyl)ethane-1,2-dione was synthesized from
1,2-bis(3,5-difluorophenyl)-2-hydroxyethanone to yield a yellow
solid (yield 74%). Physical and NMR parameters of 12 were
as follows: mp 135-137 °C; 1H NMR (500 MHz, CDCl3) δ 7.15
(dd, 2H, J ) 2.4 Hz, Ar-H), 7.51 (dt, 4H, J ) 2.2 Hz, Ar-H).
1,2-Bis(3,4,5-trifluorophenyl)ethane-1,2-dione (13). 1,2-
Bis(3,4,5-trifluorophenyl)ethane-1,2-dione was synthesized from
2-hydroxy-1,2-bis(3,4,5-trifluorophenyl)ethanone to yield a yel-
low solid (yield 96%). Physical and NMR parameters of 13 were
as follows: mp 102-103 °C; 1H NMR (500 MHz, CDCl3) δ 7.68
(d, 4H, J ) 6.6 Hz, Ar-H).
Irreversible Enzyme Inhibition Assays. Irreversible
inhibition of CEs by the inhibitors was assessed by preincu-
bating the enzymes with the compounds at 1 µM on ice for
either 1 or 24 h. After incubation, the samples were extensively
diluted in 50 mM Hepes, pH7.4, and CE activity was deter-
mined using 3mM o-NPA as a substrate. As a positive control,
50 µM BNPP was included in these assays.
Molecular Modeling of Benzil-Based Carboxylesterase
Inhibitors. 3D-QSAR analyses were performed using Quasar
4.031,32 running on a Macintosh G4. Structures for each
analogue were initially constructed with ChemBats3D for
Further analysis of inhibitors was performed in a similar
fashion except that inhibitor concentrations ranged from 1 pM