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Antimicrobial Agents and Chemotherapy, February 2009, p. 496-504, Vol. 53, No. 2
0066-4804/09/$08.00+0 doi:10.1128/AAC.00633-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.
Inhibition of Inositol Phosphorylceramide Synthase by the Cyclic Peptide Aureobasidin A
Paul A. Aeed,
Casey L. Young,
Marek M. Nagiec,
and
Åke P. Elhammer*
Pharmacia Corp., 7000 Portage Rd., Kalamazoo, Michigan 49001
Received 14 May 2008/
Returned for modification 21 September 2008/
Accepted 23 November 2008

ABSTRACT
By using a detergent-washed membrane preparation, the interaction
of the fungal natural product inhibitor aureobasidin A (AbA)
with inositol phosphorylceramide synthase (IPC synthase) was
studied by kinetic analysis of wild-type and mutant enzyme-catalyzed
reactions. AbA inhibited the wild-type enzyme from both
Candida albicans and
Saccharomyces cerevisiae in an irreversible, time-dependent
manner, with apparent
Ki values of 183 and 234 pM, respectively.
Three synthetic chemistry-derived AbA derivatives, PHA-533179,
PHA-556655, and PHA-556656, had affinities 4 to 5 orders of
magnitude lower and were reversible inhibitors that competed
with the donor substrate phosphatidylinositol (PI). AbA was
a reversible, apparently noncompetitive inhibitor, with a
Ki of 1.4 µM, of the IPC synthase from an AbA-resistant
S. cerevisiae mutant. The
Km values for both substrates (ceramide
and PI) were similar when they interacted with the mutant and
the wild-type enzymes. By contrast, the
Vmax for the mutant
enzyme was less than 10% of that for the wild-type enzyme. A
comparison of the results obtained with AbA with those obtained
with two other natural products inhibitors, rustmicin and khafrefungin,
revealed that while rustmicin appeared to be a reversible, noncompetitive
inhibitor of the wild-type enzyme, with a
Ki of 16.0 nM, khafrefungin
had the kinetic properties of a time-dependent inhibitor and
an apparent
Ki of 0.43 nM. An evaluation of the efficiencies
of these compounds as inhibitors of the mutant enzyme revealed
for both a drop in the apparent affinity for the enzyme of more
than 2 orders of magnitude.

INTRODUCTION
Sphingolipids are important components of eukaryotic cell membranes
(
8). Properties like membrane dimensions and rigidity are believed
to be directly influenced by the presence of sphingolipids (
5,
11,
18). Moreover, it has been demonstrated that sphingolipids
are important signaling molecules (
8,
26), that they are involved
in the transport and targeting of membrane proteins (
4,
15,
27,
29), and that the downregulation of sphingolipid biosynthesis
impairs the pathogenicity of the human pathogen
Cryptococcus neoformans (
14,
19). Fungal cellular membranes contain significant
amounts of sphingolipids (
33). As much as 16% of the total lipid
content in the
Saccharomyces cerevisiae plasma membrane and
approximately 10% of the total lipid content in the Golgi membrane
are sphingolipids (
17,
24). The composition of fungal sphingolipids
differs from that of their mammalian counterparts, primarily
in the substituent at the 1-hydroxyl of the ceramide backbone.
While mammalian sphingolipids may be substituted at this position
with phosphocholine or, on glycosylceramides, various carbohydrates,
fungal sphingolipids mainly contain phosphoinositol and, in
some species, carbohydrates. The ceramide-linked phosphoinositol
moiety in fungi can be further derivatized with mannose, galactose,
and an additional phosphoinositol group (
8). Although the reaction
steps in the assembly of the ceramide portion of sphingolipids
are similar in mammalian and fungal cells, the fungal biosynthetic
pathway diverges at the addition of phosphoinositol. As a consequence,
the enzyme catalyzing this reaction, inositol phosphorylceramide
synthase (IPC synthase), has been pursued as a target in antifungal
drug discovery (
16,
23,
34,
36). Supporting the validity of
this concept are the facts that the IPC synthase gene (
AUR1)
has been shown to be essential in fungi and that potent antifungal
compounds that are specific inhibitors of IPC synthase have
been identified (
23).
A functional homolog of the fungal AUR1 gene was recently identified in the protozoan Leishmania major, and the activity of the corresponding enzyme, IPC synthase, was shown to be sensitive to the fungal IPC synthase inhibitor aureobasidin A (AbA) (7). IPC synthase activities have also been identified in Trypanosoma cruzii and Trypanosoma brucei (6, 25). Moreover, since unperturbed sphingolipid synthesis appears to be essential for protozoan parasite infectivity in trypanosomes as well as in Toxoplasma gondii, IPC synthase may represent a tractable target for the development of drugs for the treatment not only of fungal infections but also of protozoan infections (10, 25, 28).
The specific IPC synthase inhibitors identified to date are natural compounds isolated from the fermentation medium of microorganisms (20, 21, 31, 32, 35). The structures of three important inhibitor compounds, AbA, rustmicin, and khafrefungin, are shown in Fig. 1.
AbA is a cyclic depsipeptide isolated from the fungus
Aureobasidium pullulans (
31). It is a comparatively large molecule with a
number of side chains, several of which are believed to be important
for activity (
3,
16). Considerable efforts have been invested
in attempts to map which portions of the AbA molecule contain
the elements essential for the inhibitory activity, the so-called
pharmacophore, but no comprehensive conclusions have been reached.
Substantial efforts have also been made to create derivatives
of AbA, such as the three synthetic AbA derivatives evaluated
in the investigation described here, with structures that are
less complex but that retain the inhibitory properties of the
native molecule. Again, these efforts have largely been unsuccessful
(see reference
16 and references therein). AbA has MICs in the
low- and sub-µg/ml range for
S. cerevisiae,
Candida albicans,
and
C. neoformans. It is considerably less effective against
Aspergillus fumigatus (
37). The in vitro 50% inhibitory concentrations
(IC
50s) for IPC synthase activities in various
Saccharomyces,
Candida, and
Aspergillus strains have been reported to range
from 0.2 to 4.9 nM (
23,
37); and a
Ki value of 0.55 nM for the
IPC synthase activity in
S. cerevisiae has been reported (
36).
Although AbA is an efficient inhibitor of IPC synthase, mutants resistant to the compound can be generated by chemical mutagenesis. Sequence analysis of these mutants has identified two positions, His 157 (13) and Phe 158 (12), in the IPC synthase (AUR1) gene sequence where mutations can generate resistant enzymes. The substituting amino acid in both reported mutants is a tyrosine. Interestingly, both sites (His 157 and Phe 158) are, to a considerable extent, removed from the amino acid residues believed to be involved in the catalytic function of the enzyme (18). Data on the kinetic properties of the mutant enzymes have not been reported.
Rustmicin (galbonolide A) is a 14-membered macrolide produced by the fungi Micromonospora chalcea and Streptomyces galbus (1, 9, 30). The molecule is a potent antifungal agent with MICs in the low-µg/ml range for both C. albicans and S. cerevisiae. It has also been reported that rustmicin is a reversible IPC synthase inhibitor and has an in vitro IC50 of about 3.8 nM (21).
Khafrefungin, an agent isolated from an unidentified fungus, is composed of an aldonic acid esterified to a linear polyketide (Fig. 1). Khafrefungin is fungicidal against both C. albicans and S. cerevisiae, and the compound reportedly inhibits the C. albicans IPC synthase with an IC50 of 0.6 nM (20).
This report presents the results of an in vitro kinetic evaluation of the inhibition of C. albicans and S. cerevisiae IPC synthases by native AbA. The time-dependent nature of AbA inhibition is documented, and an apparent Ki value is presented. In addition, a comparison of the properties of AbA with those of three synthetic derivatives, as well as those of the IPC synthase inhibitors rustmicin and khafrefungin, is presented, together with data describing the altered kinetic properties of IPC synthase from an AbA-resistant (AbAr) S. cerevisiae mutant. Constraints on the possible mechanisms of AbA inhibition are discussed.

MATERIALS AND METHODS
Cells.
Candida albicans (ATCC 38247) cells were cultured as described
previously (
2)
Saccharomyces cerevisiae (SJ21R) cells were cultured,
and an AbA
r mutant was constructed as described previously (
12,
13).
Enzymes.
Detergent-washed membranes from C. albicans, S. cerevisiae, and S. cerevisiae AbAr cells were prepared as described previously (2).
Inhibitors.
AbA was from TaKaRa Biomedicals. PHA-533179, PHA-556655, and PHA-556656 (Fig. 1) were synthesized at Pharmacia. Khafrefungin was isolated from Mycelia sterilia (ATCC 74305) by previously published procedures (20, 22). Rustmicin (galbonolide A) was a gift from Hans Achenbach (University of Erlangen, Erlangen, Germany).
IPC synthase assay.
IPC synthase assays were performed essentially as described previously (2). Briefly, A 28-µl enzyme mixture containing 10 µg (protein) of detergent-washed membranes, phosphatidylinositol (PI), and potassium phosphate buffer (pH 7.0) was preincubated for 30 min in a 96-well plate. The standard enzymatic reaction was started by addition of a substrate mix containing C6-NBD (7-nitro-2-1,3-benzoxadiazol-4-yl)-ceramide (Avanti Polar Lipids) in ethanol or 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate (CHAPS) diluted to 12 µl with water to the preincubated membranes. For inhibitor studies, the substrate mix also contained 2 µl inhibitor solution in dimethyl sulfoxide (DMSO). The final assay volume was 40 µl; and the final concentrations were 50 mM potassium phosphate (pH 7.0), 0.25 mg membrane protein/ml, 100 µM PI, 5 µM C6-NBD-ceramide, 0.6 mM CHAPS, 0.3% ethanol, and 5% DMSO. Following incubation at room temperature, the reaction was stopped by addition of 200 µl of 96% methanol, and the reaction product was isolated on ion-exchange resin and quantified as outlined previously (20).
Data analysis.
The inhibition of C. albicans and S. cerevisiae wild-type enzymes by AbA was analyzed as two-step irreversible inhibition. Progress curves were consistent with first-order kinetics, and Ki and inactivation constant (kinact) values were calculated from the first-order rate constant (kobs) with the following equation:
where [
S] and [
I] denote the substrate
and the inhibitor concentrations, respectively
Kinetic parameters for both substrates were calculated by using the Michaelis-Menten equation.
Competitive, reversible inhibitors were analyzed by measuring the initial reaction velocities (v) and calculating Ki by using the following equation:
AbA inhibition of the
S. cerevisiae AbA
r enzyme was analyzed
as noncompetitive, reversible inhibition by measuring the initial
reaction velocities and calculating
Ki by using the following
equation:

RESULTS AND DISCUSSION
As a first step in the analysis of the effect of AbA on IPC
synthase, a determination was made as to whether the interaction
between the enzyme and the inhibitor was time dependent. Product
formation was plotted as a function of time at several different
inhibitor concentrations. Figure
2A and B shows that both the
C. albicans and
S. cerevisiae enzymes clearly interact with
the inhibitor in a time-dependent manner. Particularly at higher
inhibitor concentrations, the product formation reaches a plateau
10 to 15 min into the reaction, indicating that product formation
has ceased, that the substrate cannot compete with the inhibitor,
and that the inhibitor is essentially titrating the enzyme.
Figure
2C and D shows that AbA inhibited the
C. albicans and
S. cerevisiae enzymes with very similar apparent
Ki values of
183 pM and 234 pM, respectively. The apparent
kinact values
for these two enzymes were 2.5 ms
–1 and 1.8 ms
–1,
respectively, hence confirming the potency of this inhibitor
observed in the experiments described above.
To confirm the irreversible nature of the interaction between
IPC synthase and AbA, an experiment was performed in which the
C. albicans enzyme was preincubated with AbA prior to the initiation
of the reaction. Figure
3 shows that this clearly resulted in
a time-dependent inactivation of the enzyme. There was a significant
difference in the amount of product formed in the reaction with
preincubation compared to that formed in the reaction without
preincubation.
The compounds PHA-533179, PHA-556655, and PHA-556656 (Fig.
1)
are derived from the native AbA structure. The molecules are
the result of a synthetic chemistry effort to generate smaller,
less complicated molecules that retain at least a significant
portion of the inhibitory properties of native AbA. Evaluation
of the compounds with the
C. albicans enzyme revealed that although
these compounds retained significant inhibitory activity, they
were all at least 3 orders of magnitude less potent than native
AbA (Fig.
4D, inset). Figure
4A shows that, in contrast to AbA,
PHA-533179 do not inhibit IPC synthase in a time-dependent manner.
The amount of product formed increased with time at all inhibitor
concentrations tested. Moreover, determinations of the kinetic
parameters at increasing substrate concentrations in the presence
of increasing concentrations of inhibitor revealed that while
the
Km values for PI increased significantly with increasing
inhibitor concentrations, the
Vmax values remained essentially
constant (Fig.
4B). By contrast, no such increase was observed
when the ceramide concentrations were varied (Fig.
4C). These
observations suggest that PHA-533179 (as well as PHA-556655
and PHA-556656, with which similar results were obtained; data
not shown) competes with the donor substrate PI. Analysis of
the three compounds as reversible, competitive inhibitors resulted
in
Ki values of 11.8, 10.5, and 7.9 µM, respectively (Fig.
4D, inset). These values are more than 4 orders of magnitude
higher than the
Ki value of 183 pM determined for native AbA
(compare this result with those described above), suggesting
that the derivatives retain only a minor fraction of the potency
of the parent molecule. It appears likely that these molecules,
which in essence are fragments of the native AbA molecule, are
lacking several of the binding functionalities required for
high-affinity binding to the IPC synthase enzyme. Previous investigations
have shown that mere manipulations of side chains on AbA can
have drastic effects on the inhibitory effect of the compound
(
16). Conceivably, at least some of these effects may have been
caused by a loss of affinity for the enzyme. Interestingly,
all three AbA derivatives appeared to compete with the donor
substrate PI. Since the native molecule is a time-dependent
inhibitor, it was not possible to determine whether it interacts
with the substrate binding site(s) on the enzyme. Nonetheless,
given the observations discussed above and assuming that the
three AbA derivatives still inhibit IPC synthase in a manner
similar to that of native AbA, although they are less potent
than native AbA, it is possible that the inhibitory effect of
the native compound is the result of binding to or at the PI
binding site on the enzyme. Consequently, AbA may in fact be
a competitive inhibitor, albeit a very potent one. Interestingly,
however, this conclusion is not consistent with the data generated
for the AbA
r enzyme (see below).
To gain additional insight into the interaction(s) between IPC
synthase and AbA, the kinetic properties of IPC synthase from
an AbA-resistant
S. cerevisiae mutant were studied. The IPC
synthase in this strain contained the previously described F158Y
mutation (
12). As a first step in the characterization of this
enzyme, the kinetic parameters of both substrates were determined
for the wild-type
S. cerevisiae enzyme. This resulted in a
Km value of 3.0 µM for C
6-NBD-ceramide, which is quite similar
to that of the
C. albicans enzyme (3.3 µM), and a
Km value
for PI of 555 µM, which is approximately four times higher
than that of the
C. albicans enzyme (Table
1). The
Vmax values
for the
S. cerevisiae enzyme were 367 and 824 pmol min
–1 mg protein
–1 for C
6-NBD-ceramide and PI, respectively.
Both these values are a little less than 40% of the values obtained
with the
C. albicans enzyme (884 and 1864 pmol min
–1 mg
protein
–1, respectively [
2]). Taken together, the data
indicate that slight differences in the catalytic properties
of the
C. albicans and
S. cerevisiae enzymes may exist. However,
it appears more likely, given that both enzyme preparations
are made from detergent-washed membranes, that differences in
the overall protein, lipid, and/or carbohydrate compositions
of the two cell types, as well as in the amounts of the enzyme
preparations recovered (again, likely caused by structural differences
in the two cell types), are the true reasons for the observed
differences. A more accurate comparison must await purification
of the two enzymes. Nonetheless, the data generated strongly
suggest that the catalytic properties of IPC synthase are quite
similar in
C. albicans and
S. cerevisiae. This conclusion is
further supported by the very similar sensitivities of the two
enzymes to AbA (Fig.
2 and data not shown).
View this table:
[in this window]
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|
TABLE 1. Kinetic properties of C. albicans wild-type, S. cerevisiae wild-type and S. cerevisiae AbAr IPC synthasea
|
Determination of kinetic parameters (for the two substrates)
for the
S. cerevisiae AbA
r mutant enzyme (Table
1) yielded
Km values similar to those for the wild-type enzyme: approximately
2.0 and 330 µM for C
6-NBD-ceramide and PI, respectively
(compare these results with those presented above). In contrast,
the
Vmax values, at approximately 25 and 69 pmol min
–1 mg protein
–1 for C
6-NBD-ceramide and PI, respectively,
were less than 10% of those obtained for the wild-type
S. cerevisiae enzyme. Clearly, the amino acid substitution in IPC synthase
conferring AbA resistance has a considerable impact on the catalytic
performance of the enzyme. Nonetheless, the affinities for the
two substrates appeared to be essentially unaltered for the
mutant enzyme. This is in stark contrast to the affinity of
the mutant enzyme for AbA, which was reduced by more than 3
orders of magnitude. A kinetic evaluation revealed that AbA
is a reversible inhibitor of the
S. cerevisiae AbA
r mutant enzyme,
with an apparent
Ki of approximately 1.4 µM (Fig.
5).
Determinations of the values of the kinetic parameters at several
substrate concentrations in the presence of increasing concentrations
of the inhibitor showed that in assays with the mutant enzyme,
AbA does not appear to compete with the binding of either PI
(Fig.
5B) or ceramide (Fig.
5C).
Although the finding that native AbA does not compete with the
binding of PI in the mutant enzyme is in contrast to the mechanism
of action of AbA-derived compounds PHA-533179, PHA-556655, and
PHA-556656, this finding is consistent with the fact that the
mutations cause a drop in the affinity of AbA for the mutant
IPC synthase of more than 3 orders of magnitude. Since the mutations
have virtually no effect on the affinity of AbA for either substrate
(Table
1) but cause a drastic drop in the reaction velocity,
the mutations may alter the enzyme such that although the substrates
are still capable of binding to the enzyme with an affinity
similar to that of the wild-type enzyme, their orientation or
intermolecular distance(s) in the active site is compromised.
AbA may bind to a site that is related to or part of the active
site. Alternatively, the compound may bind to a site that is
removed from the near vicinity of the active site but that still
influences (by steric means or otherwise) the catalytic function
of the enzyme. It is noteworthy, in this context, that the amino
acid substitutions of the AbA
r mutants are located at positions
believed to be quite remote from the enzyme active site (
12,
13,
18).
Two other natural products, rustmicin and khafrefungin, are both specific inhibitors of IPC synthase. However, they differ significantly from AbA in their interaction with the enzyme. In contrast to AbA, rustmicin is a reversible inhibitor with an apparent Ki. almost 2 orders of magnitude higher than that of AbA (Fig. 6; Table 2). The data also suggest that this inhibitor does not compete with either of the two substrates. As discussed above, since the interaction of AbA with wild-type IPC synthase is time dependent, it is difficult to determine whether this compound interacts with the enzyme in a competitive or a noncompetitive manner. Interestingly, the IC50 of rustmicin for the AbAr enzyme shows the same increase as that of AbA of approximately 3 orders of magnitude compared to that for the wild-type enzyme (Table 2). This indicates a possible overlap between the binding sites for AbA and rustmicin. It is also consistent with the possibility (supported by the data generated with the AbAr enzyme) that AbA does not compete with the substrate binding site(s) on the wild-type enzyme. Despite significant differences in the structures of khafrefungin and AbA, khafrefungin appears to be similar to AbA in its interaction with IPC synthase. The compound is a time-dependent inhibitor with an apparent Ki of approximately 425 pM (Fig. 7; Table 2). Moreover, the binding site of this compound appears, at least to some extent, to overlap with that of AbA, since the AbAr enzyme was again about 3 orders of magnitude less sensitive to this inhibitor than the wild-type enzyme (Table 2).
Taken together, the observations presented in this report suggest
that AbA is an irreversible, time-dependent inhibitor of IPC
synthase in both
C. albicans and
S. cerevisiae. Moreover, the
entire, intact structure of the compound appears to be important
for both the affinity and the specific inhibitory mechanism
of this compound. Hence, the inhibitory activity of AbA may
not be mediated by a specific portion of the structure, a pharmacophore,
but rather, the entire structure appears to be essential for
full biological activity. All fragments of the structure evaluated
were comparatively inactive, and compounds comprising other
portions of the AbA structure have even less potency (data not
shown). The data are consistent with previously published data
that suggest that the range of structural alterations that can
be made to AbA but that result in the retention of its inhibitory
activity is quite limited (summarized in reference
16). Two
other inhibitors, rustmicin and khafrefungin, show some similarities
to AbA in their modes of action with the IPC synthase, with
the most significant difference being their lower affinity for
the enzyme (particularly for rustmicin). Evidence for a competitive
mechanism was not found for any of the three inhibitors.

ACKNOWLEDGMENTS
We thank Joyce Cialdella, Ray Zielinski, and Ming-Shang Kuo,
at Pfizer, Inc., for the preparation and purification of khafrefungin.

FOOTNOTES
* Corresponding author. Present address: AureoGen Biosciences, Inc., 6475 Technology Avenue, Suite C, Kalamazoo, MI 49009. Phone: (269) 353-3805. Fax: (269) 585-6083. E-mail:
ake.p.elhammer{at}aureogen.com 
Published ahead of print on 1 December 2008. 
Present address: Pfizer, Inc., 333 Portage Street, Kalamazoo, MI 49007. 
Present address: Replidyne Corporation, 1450 Infinite Drive, Louisville, CO 80026. 
Present address: Global Research and Development, Pfizer, Inc., 700 Chesterfield Parkway West AA4E, Chesterfield, MO 63017-1732. 

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Antimicrobial Agents and Chemotherapy, February 2009, p. 496-504, Vol. 53, No. 2
0066-4804/09/$08.00+0 doi:10.1128/AAC.00633-08
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