4642
E. I. Parkinson et al. / Bioorg. Med. Chem. 19 (2011) 4635–4643
withdrawing properties of the halogen, and the fact that bromine is
a relatively good leaving group, it is possible that nucleophilic at-
pounds maybe subjected to metabolic processes that may
inactivate them, but as yet we have not identified a specific mecha-
nism for the lack of activity of this molecule. However it is clear that
compounds of this type can be used to modulate intracellular levels
of CE activity and can be used as biochemical tools to evaluate en-
zyme function.
tack by the O
c within the catalytic serine could occur either at
the carbonyl, or the methylene, carbon atom. The latter would re-
sult in covalent bond formation and irreversible inhibition of the
enzyme. However, as indicated in Table 1, no loss of enzyme activ-
ity was observed following dilution of the inhibitor from the reac-
tion. These results imply that interaction of the protein with the
inhibitor occurred at the carbonyl carbon and not at the vicinal car-
bon atom. Additionally, since the kinetic analyses indicated that
the mode of enzyme inhibition was partially competitive, this in-
fers that these inhibitors bind to the same site within the CE, and
that they structurally resemble the substrate. This would argue
that a similar mechanism of interaction likely occurs between
the enzyme and the inhibitor/substrate. Again, these data support
the hypothesis that the catalytic serine undergoes nucleophilic at-
tack of the carbonyl carbon atom. Furthermore, the halogens also
increased the hydrophobicity of the molecules (Table 1), likely
allowing for a further increase inhibitor potency. Since the active
site gorges of CE are very hydrophobic,2,21 compounds demonstrat-
ing greater c log P values would preferentially localize within this
domain. Evidence to this effect has been noticed with a series of
isatin analogues.18 Overall, these results suggest that the electro-
philicity of the carbonyl carbon atom plays a role in determining
the potency of inhibition towards CEs.
To further examine the effect of small molecule hydrophobicity
on enzyme inhibition, we synthesized a series of alkyl-1,2-diones
and evaluated their inhibitory potency against the CEs. We reasoned
that by simply increasing the size of the alkyl group, we could effect
an increase in the c log P of the compounds, without significantly
altering the electrostatic configuration of the molecule. As indicated
in Table 2, increasing the length of the alkyl side chains resulted in
dramatically reduced Ki values for the inhibitors with the CEs. This
correlated well with the increasing c log P values of the compounds
(Fig. 2). This phenomenon was observed for all three mammalian
CEs, suggesting that the environment within the active site was sim-
ilar for each protein. As indicated above, since the active sites of
these enzymes are highly hydrophobic, this increase in potency is
likely due to preferred localization of the longer chain compounds
within this domain. Indeed, since good correlation coefficients were
observed between the Ki values for enzyme inhibition and the
c log P values of these molecules (Fig. 2), this suggests that this
parameter is an important factor in determining inhibitor potency.
Based upon our observations with the 1,4-diphenylbutane-2,3-
dione analogues and the alkyl-1,2-diones, we hypothesized that
compounds containing a phenyl group and alkyl chain on either side
of the dione moiety should yield very potent CE inhibitors. As dis-
played in Table 3, we saw selective enzyme inhibition by such mol-
ecules, with inhibitory potency correlating with the hydrophobicity
of the molecule (Fig. 2). These results are in agreement with those
described for the alkyl-1,2-diones and further reinforce the impor-
tance of hydrophobicity towards enzyme inhibition.
5. Conclusions
Overall, our studies have delineated the roles of selected atoms
within the 1,2-dione CE-specific inhibitors and demonstrated that
the electrophilicity of the carbonyl group, the conformation that
the molecules adopt, and the hydrophobicity of these compounds
play major roles in determining inhibitor potency. Our data further
support the hypothesis that nucleophilic attack by the protein on
the carbonyl carbon atom represents the most likely mechanism
of enzyme inhibition. This has yielded several series of small mol-
ecules that demonstrate potency and selectivity towards CE, and
elucidated the chemical requirements for the design of further
compounds. These studies are currently underway.
Acknowledgments
The authors wish to thank Drs. Thomas Webb and Kip Guy for
helpful discussion and critical reading of the manuscript. This work
was supported in part by NIH Grants CA108775, an NIH Cancer Cen-
ter Core Grant CA21765, and by the American Lebanese Syrian Asso-
ciated Charities and St. Jude Children’s Research Hospital (SJCRH).
Supplementary data
Supplementary data associated with this article can be found, in
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Having identified the necessary properties for these molecules to
effect CE inhibition in vitro, we evaluated the ability of selected com-
pounds to modulate enzyme activity in cells and to determine
whether these inhibitors could alter CPT-11 cytotoxicity in cells
expressing hiCE. We confirmed that the majority of the alkyl and
phenylalkyl derivatives were cell permeable and were effective at
inhibitionhydrolysisof CPT-11by hiCE. Furthermore, in cell viability
studies, benzil and compound 22 were effective at modulating the
toxicity of this drug. Surprisingly, tetradecane-7,8-dione (13) was
ineffective at reducing CPT-11 toxicity in cells expressing hiCE. At-
tempts to identify a mechanism for this lack of activity (e.g. the
use of serum-free culture media to eliminate protein binding, the
use of glass culture dishes to minimize interaction with the plastic-
ware, etc) have so far been unsuccessful. Potentially, these com-