Synthesis and characterization of the arylomycin lipoglycopeptide antibiotics and the crystallographic analysis of their complex with signal peptidase

Article abstract of DOI:10.1021/ja207318n

Glycosylation of natural products, including antibiotics, often plays an important role in determining their physical properties and their biological activity, and thus their potential as drug candidates. The arylomycin class of antibiotics inhibits bacte

Full text of DOI:10.1021/ja207318n

ARTICLE
pubs.acs.org/JACS
Synthesis and Characterization of the Arylomycin Lipoglycopeptide
Antibiotics and the Crystallographic Analysis of Their Complex with
Signal Peptidase
Jian Liu,† Chuanyun Luo,‡ Peter A. Smith,† Jodie K. Chin,† Malcolm G. P. Page,§ Mark Paetzel,*,‡ and
Floyd E. Romesberg*,†
†Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
‡Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
§Basilea Pharmaceutica International Ltd., Grenzacherstrasse 487, CH-4058, Basel, Switzerland
S Supporting Information
b
ABSTRACT: Glycosylation of natural products, including
antibiotics, often plays an important role in determining their
physical properties and their biological activity, and thus their
potential as drug candidates. The arylomycin class of antibiotics
inhibits bacterial type I signal peptidase and is comprised of
three related series of natural products with a lipopeptide tail
attached to a core macrocycle. Previously, we reported the total
synthesis of several A series derivatives, which have unmodified
core macrocycles, as well as B series derivatives, which have a
nitrated macrocycle. We now report the synthesis and biological
evaluation of lipoglycopeptide arylomycin variants whose macrocycles are glycosylated with a deoxy-α-mannose substituent, and
also in some cases hydroxylated. The synthesis of the derivatives bearing each possible deoxy-α-mannose enantiomer allowed us to
assign the absolute stereochemistry of the sugar in the natural product and also to show that while glycosylation does not alter
antibacterial activity, it does appear to improve solubility. Crystallographic structural studies of a lipoglycopeptide arylomycin bound
to its signal peptidase target reveal the molecular interactions that underlie inhibition and also that the mannose is directed away
from the binding site into solvent which suggests that other modifications may be made at the same position to further increase
solubility and thus reduce protein binding and possibly optimize the pharmacokinetics of the scaffold.
’ INTRODUCTION
membrane. SPase acts via a unique Ser-Lys catalytic dyad with an
unusual nucleophilic attack on the si-face of the substrate, as
opposed to the re-face attack characteristic of the more common
Ser-His-Asp catalytic triad serine proteases.20 Moreover, its
position on the outer surface of the cytoplasmic membrane
should make it relatively accessible to inhibitors, although pen-
etration of the outer membrane could limit accessibility in Gram-
negative bacteria. While their novel mechanism of action origin-
ally generated much enthusiasm, excitement for developing the
arylomycins waned when it was concluded that their activity was
limited to only a few Gram-positive bacteria.16,17 However, after
reporting the first synthesis of an arylomycin, the A series
member arylomycin A2 (Figure 1), as well as several deriv-
atives,21 we demonstrated that they actually have a remarkably
broad spectrum of activity,19 including potent activity against
both Gram-positive and Gram-negative bacteria, but that activity
is limited in some cases by one of at least two resistance mech-
anisms: target mutation, specifically, the presence of a proline
residue in SPase;19 or a second as yet undefined mechanism that
The clinical and agricultural use of antibiotics imposes a relentless
selection pressure on bacteria that has driven the evolution of multi-
drug resistance in many pathogens, and novel classes of antibiotics
are needed.1,2 Bacteria produce a large assortment of antibiotics,
possibly to gain advantage over competing microorganisms for limited
resources,3À9 and these compounds have proven to be the richest
source of antimicrobials for development into therapeutics.
While most, if not all, these natural products are produced as
families of related compounds, the significance of this diversity is
debated.10À14 The arylomycins, first isolated in 2002 from a
strain of Streptomyces, consist of three related series of com-
pounds, each of which has a conserved C-terminal tripeptide
macrocycle attached to anN-terminal lipopeptide (Figure1).15À17
The macrocycle of the A series compounds is unmodified, while
those of the B series and lipoglycopeptides are nitrated and
glycosylated (and in some cases hydroxylated), respectively.15,16
The arylomycins inhibit type I signal peptidase (SPase, EC
3.4.21.89),16,18,19 which is an essential membrane-bound serine
endopeptidase with a highly conserved active site that is required
to remove the amino-terminal leader (signal) sequence during,
or shortly after, protein translocation across the cytoplasmic
Received: August 4, 2011
Published: October 14, 2011
r
2011 American Chemical Society
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region (residues 29À58), and a large carboxyl-terminal peri-
plasmic catalytic domain (residues 78À324).28,29 Proteinase K
digestion,29,30 gene-fusion,31 and disulfide cross-linking studies32,33
are all consistent with both the N- and C-termini of E. coli SPase
facing the periplasmic space. The catalytically active periplasmic
domain of E. coli SPase (SPase Δ2-76) has a molecular weight of
27 952 Da 34 and pI of 5.6.35 It has been subcloned, purified,34
characterized,35 and crystallized.36 To date, four crystal struc-
tures of E. coli SPase have been reported (all with the Δ2-76
enzyme), including the unbound protein,37 a binary complex
with a β-lactam inhibitor,20 a binary complex with an A family
arylomycin (arylomycin A2),18 and a ternary complex with arylomycin
A2 and β-sultam.38 While these structures have helped elucidate
the mechanisms of the molecular recognition underlying the
inhibition of SPase by the arylomycins, the effects of macrocycle
glycosylation remained unclear.
We now report the first synthesis of an arylomycin lipoglyco-
peptide and its biological characterization, as well as the structur-
al analysis of the binary complex with a related glycosylated and
hydroxylated derivative. Total synthesis allowed us to assign the
absolute stereochemistry of the deoxy-α-mannose substituent
and to determine that the spectrum of activity of the glycosylated
derivative is limited by the same mechanisms of resistance as are
the A series compounds. The structural analysis revealed that the
inhibitor binds in a fashion similar to that previously reported for
the A series derivative and that the sugar is oriented away from
the active site and into the aqueous environment. Consistent
with these structural studies, in addition to finding that glycosyla-
tion does not interfere with SPase binding or activity, we find that
it appears to increase aqueous solubility and reduce protein
binding on the basis of MIC values in the presence of serum
proteins. In all, the data reveal that contrary to previous con-
clusions,16 glycosylation does not interfere with the antibacterial
activity of the arylomycins, including activity against Gram-negative
bacteria, and that similar types of modifications might be used to
optimize the pharmacokinetics of this promising scaffold.
Figure 1. Structure of the arylomycin derivatives characterized in this
study. Arylomycin A-C16 and arylomycin B-C16 correspond to A and B
series arylomycins, respectively, while arylomycin C-C16 and BAL4850C
correspond to the lipoglycopeptide series of arylomycins (see text for
details).
confers Streptococcus agalactiae (S. agalactiae) with resistance to
the A series derivatives.22 Moreover, following the synthesis of a
B series arylomycin, arylomycin B-C16, we demonstrated that the
nitro group does not negatively impact activity against bacteria
that are sensitive to arylomycin C16, and importantly, that it
overcomes the resistance of S. agalactiae and imparts the scaffold
with a reasonably potent minimum inhibitory concentration
(MIC) of 8 μg/mL.22
Like the lipoglycopeptide arylomycins, many antibiotics are
glycosylated, and in some cases the sugar substituents are required
for activity.23,24 From a medicinal chemistry perspective, glycosyla-
tion can also impact an antibiotic’s potential for development as
a therapeutic by affecting its pharmacokinetic properties, including
absorption, distribution, metabolism, and excretion, at least in part
due to changes in solubility and serum binding.25 The most com-
mon sugar substituents are 6-deoxysugars, of which more than a
hundred have been identified among different secondary meta-
bolites,26 and indeed the sugar substituent of the lipoglycopeptide
arylomycins was identified as deoxy-α-mannose,16 although its abso-
lute stereochemistry was not determined.
The lipoglycopeptide arylomycins have been shown to have
moderate activity against several bacteria, inhibiting a strain of
Streptococcus pneumoniae (S. pneumoniae) with MICs ranging
from 8 to >64 μM; a strain of Staphylococcus aureus (S. aureus),
with MICs ranging from 32 to >64 μM; and a strain of
Haemophilus influenzae (H. influenzae), with an MIC of 64
μM.16 While they are not active against intact Escherichia coli
(E. coli), they were shown to have activity against permeabilized
mutant strains, leading to the suggestion that their development
as therapeutics would require the optimization of outer mem-
brane penetration.16 However, the potential role of the resistance
conferring proline has not been examined.
’ RESULTS AND DISCUSSION
Lipoglycopeptide Synthesis. To synthesize the lipoglyco-
peptide arylomycins, we modified our previously reported syn-
theses of the arylomycin A21 and B22 series compounds to increase
flexibility and material throughput. Because the absolute stereo-
chemistry of the sugar was not known, we targeted the synthesis
of both the deoxy-α-L-mannose and the deoxy-α-D-mannose
variants. The required lipopeptide 2 was prepared using the pro-
cedure of Zhu and co-workers (Scheme 1).39,40 Briefly, the
previously reported tripeptide 1 was acylated with isopalmitic acyl
chloride, generated in situ from isopalmitic acid and oxalyl chloride
in dichloromethane (DCM), yielding the fully protected fatty tail,
which was hydrolyzed under Nicolaou’s conditions (Me3SnOH/
1,2-dichloroethane (DCE)) to afford the lipopeptide 2in 51% yield.
Macrocycle synthesis commenced with the preparation of the
hydroxyphenylglycine-alanine iododipeptide 8 from commer-
cially available 4-hydroxyphenylglycine 3 (Scheme 2). Briefly,
t-butoxycarbonyl (Boc) protection of 3, followed by monoiodization,41
afforded 4 in 80% yield, which was subsequently converted into
oxazolidinone 5. After reduction by triethylsilane in trifluoro-
acetic acid (TFA), followed by reinstallation of the Boc group, the
desired N-methylamino acid 6 was obtained without racemiza-
tion. Acid 6 was then coupled to L-Ala-OMe to afford dipeptide
ester 7. Finally, hydrolysis of the methyl ester using Me3SnOH
E. coli SPase is 324 amino acids in length (molecular weight,
35960 Da; pI 6.9)27 and contains two amino-terminal transmem-
brane segments (residues 4À28 and 59À77), one smallcytoplasmic
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Scheme 1
14a in 76% yield. Similarly, 14b was obtained in 70% yield using
the same conditions.
Scheme 2
With lipopeptide tail 2 and both glycosylated macrocycles 14a
and 14b in hand, it only remained to couple and deprotect the
two halves of the molecule. Compound 2 was coupled to 14a or
14b to provide the fully protected natural products 17a and 17b
(Scheme 4). Global deprotection was carried out in three mild
reactions to avoid the possible elimination of the D-Ser hydroxyl
group. Pd/C catalyzed hydrogenation, NaOMe induced deace-
tylation, and hydrolysis with Me3SnOH provided the candidate
natural products 18a and 18b in greater than 50% yield. Com-
1
parison of the H NMR spectra of the two candidate natural
products with that of the authentic natural product (kindly pro-
vided by Dr. Sheng-Bing Peng, Eli Lilly) revealed that while
almost all of the proton resonances of the 18a spectrum are
nearly identical to the natural product, those of the sugar are
significantly different (Figure S1 of the Supporting Information).
1
In contrast, the H spectra of 18b and the natural product are
virtually identical, as are the 13C spectra. Thus, we conclude that
the lipopeptide arylomycins are glycosylated with deoxy-α-L-
mannose. Furthermore, similarities in the NMR spectra in the
region corresponding to the sugar of the different members of the
lipoglycopeptides,16 suggest that they are all glycosylated with
deoxy-α-L-mannose.
While the arylomycins, including the lipoglycopeptides, are
naturally lipidated with different fatty acids ranging in length
from 12 to 16 carbons, our analysis of the A and B series com-
pounds was performed with a straight chain C16 tail.21 Thus, for
systematic comparison of biological activity, we used the above
protocol but with the straight chain C16 lipid, to synthesize the
corresponding lipoglycopeptide derivative. As expected, this
synthesis proceeded with indistinguishable yields. For simplicity,
we refer to these derivatives as arylomycin A-C16, arylomycin
B-C16, and arylomycin C-C16, corresponding to the A, B, and
lipoglycopeptide compounds, respectively (Figure 1).
Structural Analysis of a Lipoglycopeptide Arylomycin Bound
to SPase. Structural studies focused on analysis of the glycosy-
lated and hydroxylated lipoglycopeptide antibiotic BAL4850C
and SPaseΔ2À76. BAL4850C contains the same sugar that is
characteristic of the lipoglycopeptide class of arylomycins, but is
differentiated from arylomycin C-C16 by macrocyclic hydroxyla-
tion and lipidation by an unsaturated C16 fatty acid (Figure 1). All
attempts to soak BAL4850C into preformed crystals of SPaseΔ2-76
were unsuccessful, so we instead developed a cocrystallization
method which yielded well-ordered crystals that diffracted to
beyond 2.4 Å resolution (Table 3). The initial Fo À Fc difference
map revealed a well-defined rod-shape density corresponding to
the N-terminal tripeptide, as well as a ring-shape electron den-
sity corresponding to the three residue macrocycle core of the
inhibitor with clear electron density for the mannose substituent
(Figure 2A). The modeled L-stereochemistry for the mannose
substituent is consistent with the electron density, but the resolution
provided iododipeptide 8 in quantitative yield. This sequence
produced 8 in seven steps with 40% overall yield, which required
only one column purification for product 7.
The protected tyrosine pinacol boronic ester 11 was prepared
from iodotyrosine in four steps (Scheme 3). Briefly, triply pro-
tected iodotyrosine 10 was prepared from commercially available
iodotyrosine 9 in greater than 90% yield with only one column
purification. The boronic ester of compound 11 was installed via
a Miyama reaction,42 and then deprotection, followed by HOBt/
EDC-mediated coupling to dipeptide 8 provided tripeptide 12.
To optimize macrocyclization of 12, we first employed condi-
tions that we found to be optimal for the cyclization of the bis-
methyl phenol protected A or B series macrocycle cores
(PdCl2(dppf)/NaHCO3, dimethylformamide (DMF)). How-
ever, in this case the desired product was obtained in less than
25% yield, suggesting that while the free phenol may minimize
the epimerization of 12,39 it also appears to adversely affect
the reaction. Thus, we reoptimized the cyclization conditions
(Table 1) and found that Pd(tBu3P)2 and K2CO3 provided 13 in
a satisfactory 48% yield.
The only remaining challenge was to glycosylate the free
phenol of the macrocycle without O- to C-glycoside rearrange-
ment under the required Lewis acidic reaction conditions (Table 2).43
Due to the low nucleophilicity of the phenol and the steric
hindrance of the neighboring O-benzyl group, we first attempted
to glycosylate 13 using glycosyl bromides 15 in the presence of
AgOTf and 4 Å molecular sieves in DCM, but no glycosylated
product was detected. We then investigated trichloroacetimidate
16a as a glycosyl donor. TMSOTf-promoted glycosylation,
either in catalytic or superstoichiometric quantities, yielded the
desired macrocycle in less than 40% yield. However, 10 equiv of
44
BF3ÀEt2O resulted in simultaneous glycosylation and Boc
deprotection and yielded the desired glycosylated macrocycle
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Scheme 3
Table 1. Cyclization Conditions
Table 2. Glycosylation Conditions
entrya
catalyst
base
yield, %
1
PdCl2(dppf)
K2CO3
K2CO3
K2CO3
K2CO3
K2CO3
K2CO3
K2CO3
Cs2CO3
CsF
25 c
48 c
2
Pd(0)(Pt-Bu3)2
PEPPSITM-IPrb
PdCl2(PPh3)2
Pd(OAc)2(SPhos)2
Pd2(dba)3+SPhos
Pd(PPh3)4
3
<10 d
<10 d
<10 d
<10 d
<10 d
<10 d
<10 d
<10 d
<10 d
4
5
6
7
8
Pd(0)(Pt-Bu3)2
Pd(0)(Pt-Bu3)2
Pd(0)(Pt-Bu3)2
Pd(0)(Pt-Bu3)2
9
10
NaOH
11
K3PO4
a All the reactions were carried out in dimethyl sulfoxide (DMSO) at
90 ꢀC for 24 h. b PEPPSI-IPr: (1,3-diisopropylimidazol-2-ylidene)-
(3-chloropyridyl)palladium(II) dichloride.58 c Isolated yield. d Based on
LC-MS.
a All reactions were carried out in anhydrous DCM with 4 Å molecular
sieves; details are provided in the Supporting Information. b Product
ratios determined by LC-MS. c Yields were isolated yields. d No product
detected. e Not determined.
is not high enough to independently confirm the assigned stereo-
chemistry. The electron density of the C16 fatty acid tail of the
lipoglycopeptide is weak at 1.0 σ, suggesting the fatty acid tail is
disordered. Similarly, no density was observed for the fatty acid
tail in the reported complex with arylomycin A2.18
The refined structure revealed that the arylomycin is posi-
tioned within the SPase binding site with its C-terminal macro-
cycle oriented toward the catalytic residues and both the peptide
backbone and side chains tightly packed within the substrate
binding groove (Figures 2 and 3). Similar to the complex of
SPaseΔ2-76 and arylomycin A2,18 one C-terminal carboxylate
oxygen (O45) interacts with three catalytically essential residues
of the enzyme, including the nucleophile Ser91 Oγ, the general
base Lys146 Nζ, and a component of the oxyanion hole, Ser89
Oγ. (Note that the numbering system used with previous SPase
structures18,20,37,38 is different by one residue due to an error in
the originally reported sequence of the E. coli protein.30 The
sequencing error occurred in the cytoplasmic region, between
the two N-terminal transmembrane segments, which is not
present in SPaseΔ2-76, and therefore does not affect the register
of the residues within the crystal structures, only the residue
numbering system. The numbering system used in the currently
reported structure matches that in the Swiss-Prot sequence
database (accession number, P00803).) The other C-terminal
carboxylate oxygen (O44) is hydrogen-bonded to Ile145 N and
the general base Lys146 Nζ. The peptide backbone of the
arylomycin forms 11 direct hydrogen bonds with SPase, forming
parallel β-strand interactions with the β-sheets that make up the
substrate binding groove (SPase residues 143À146 and 82À86),
seven of which are mediated by the macrocycle tripeptide and
four by the N-terminal tripeptide. Macrocycle residues N33 and
N28 form hydrogen bonds with Asp143 O and Gln86 O,
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Scheme 4
Table 3. Data Collection and Refinement Statistics
crystal parameters
space group
P43212
a, b, c (Å)
72.0, 72.0, 262.6
data collection statistics
wavelength (Å)
resolution (Å)
total reflections
unique reflections
1.5418
32.2 À 2.4 (2.5 À 2.4)a
247952 (28360)
26680 (2605)
0.105 (0.44)
10.4 (5.1)
b
Rmerge
mean I/σ(I)
completeness (%)
redundancy
99.6 (100.0)
9.3 (10.9)
refinement statistics
protein molecules (chains) in A.U.
residues
Figure 2. View of lipoglycopeptide BAL4850C within the active site
and substrate-binding groove of SPase. Due to weak electron density, the
fatty acid tail is not included. (A) Electron density for lipoglycopeptide
BAL4850C bound within the active site and substrate-binding groove of
SPase. A cross-validated 2FoÀFc electron density map contoured at 1σ
(blue) is shown with the lipoglycopeptide shown in stick representation
and colored by element (carbon, yellow; oxygen, red; nitrogen, blue).
The SPase protein is shown in cartoon representation and colored in
gray. The catalytic residues (Ser91 and Lys146) are labeled and colored
by element (carbon, gray; oxygen, red; nitrogen, blue). (B) Molecular
surface of SPase with basic residues in blue, acidic residues in red, and all
others in gray. The bound lipoglycopeptide is shown and colored as in
panel A. The S1 and S3 binding sites of SPase are labeled. Chain B within
the asymmetric unit was used to make the figure.
2
432
inhibitors
2
water molecules
57
total number of atoms
Rcryst c/Rfree d (%)
average B-factor (Å2) (all atoms)
rmsd on angles (deg)
rmsd on bonds (Å)
3617
24.5/26.5
56.5
1.098
0.007
a The data collection statistics in brackets are the values for the highest
b
resolution shell. Rmerge = ΣhklΣi |Ii(hkl) À ÆI(hkl)æ|/ΣhklΣi Ii(hkl),
where Ii(hkl) is the intensity of an individual reflection and ÆI(hkl)æ is the
c
mean intensity of that reflection. Rcryst = Σhkl ||Fobs| À |Fcalc||/Σhkl
|
F
obs| , where Fobs and Fcalc are the observed and calculated structure-
d
distance of O45. Finally, the C30 methyl group of Ala6 is directed
toward the S3 substrate-specificity pocket and is in van der Waals
contact with the side chain of SPase residue Ile145. Clearly, the
macrocycle provides the majority of the interactions involved in
SPase recognition. Interestingly, although the deoxy-α-L-mannose
factor amplitudes, respectively. Rfree is calculated using 5% of the
reflections randomly excluded from refinement.
respectively, and there is a conserved water molecule (water 14 in
chain A and water 15 in chain B) within the hydrogen-bonding
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Figure 3. Interactions between lipoglycopeptide BAL4850C and SPase. Due to weak electron density, the fatty acid tail is not included. (A) SPase is
shown in line representation and colored by element (carbon, green; oxygen, red; nitrogen, blue; residues labeled in black). The lipoglycopeptide is
shown in stick and colored by element (carbon, yellow; nitrogen, blue; oxygen, red; atoms labeled in red). Chain B within the asymmetric unit was used
to make the figure. (B) Schematic representation of lipoglycopeptide BAL4850C interactions with the active site and substrate binding groove of SPase.
Dashed lines indicate hydrogen bonds and distances are in angstroms (average value for the two molecules in the asymmetric unit). The residues
involved in van der Waals interactions are symbolized by arches.
is in van der Waals contact with SPase residue Pro88, it is
predominantly solvent exposed (Figures 2 and 3).
Also as with the A and B series compounds, arylomycin C-C16
does have significant activity against the mutant pathogens where
the arylomycin resistance-conferring proline residue is mutated
to a residue that does not confer resistance (P29S in the S. aureus
protein, and P84L in the E. coli and P. aeruginosa proteins)19
(Table 5). Moreover, the addition of polymyxin B nonapeptide,
which permeabilizes the outer membrane of Gram-negative bacter-
ia, did not significantly affect the MICs. Thus, while the spectrum of
arylomycin C-C16 is limited by the same resistance mechanisms as is
the A series compound, in contrast to previous conclusions,16 the
presence of the sugar does not impair the inhibitor’s ability to
penetrate the outer membrane of Gram-negative bacteria.
A superposition of the structures of the three SPaseÀarylomycin
complexes solved to date reveals that very little adjustment within
the protein is needed to accommodate the sugar (Figure 4). More-
over, the presence of the sugar does not appear to significantly alter
the structure of the macrocycle, which the superposition reveals is
similar, and engages the protein in a similar way, in each complex.
However, the superposition also reveals that the binding mode for
the three N-terminal residues (D-MeSer2-D-Ala3-Gly4) of the inhib-
itor is more variable, particularly at D-Ala3. These observations are
consistent with the macrocycle mediating the majority of interac-
tions between the inhibitor and the enzyme and suggest that the
N-terminal peptidic tail may be more flexible.
Biological Activity. The antibacterial activity of the lipogly-
copeptide arylomycin C-C16 was characterized by determining
the MIC required to inhibit the growth of several Gram-positive
bacteria (Table 4). Against Staphylococcus epidermidis (S. epidermidis),
Streptococcus pyogenes (S. pyogenes), S. pneumoniae, Corynebacter-
ium glutamicum (C. glutamicum), and Rhodococcus opacus
(R. opacus) arylomycin C-C16 has activity that is indistinguishable
from the analogous A series compound. Moreover, like arylomycin
A-C16, but unlike arylomycin B-C16, arylomycin C-C16 has no
activity against Streptococcus agalactiae (S. agalactiae) strain COH1,
demonstrating that the ability of the nitro substituent to impart the B
series scaffold with activity against this pathogen is unique.
Although not unprecedented among therapeutics,45À48 from a
drug development perspective, the fatty acid tails of the arylomy-
cins might prove to be a liability, for example due to decreased
solubility and increased serum binding. Thus, to begin to examine
the effects of glycosylation on aqueous solubility and serum
binding, we re-determined the MICs of arylomycin A-C16 and
arylomycin C-C16 against wild type S. epidermidis and sensitized
E. coli in the presence of pooled human serum (25À100%) or
bovine serum albumin (4À10%) in MHIIB. While the value of
MICs varied under the different conditions tested, the MIC
observed for arylomycin C-C16 was consistently 2- to 4-fold lower
than that of arylomycin A-C16 under these conditions. These small
but reproducible effects are consistent with glycosylation increasing
the concentration of the free inhibitor available for SPase binding.
We next determined the activity of arylomycin C-C16 against
Staphylococcus aureus (S. aureus), E. coli, and Pseudomonas
aeruginosa (P. aeruginosa). As with both the A and B series com-
pounds, arylomycin C-C16 has no activity against these pathogens.
’ CONCLUSIONS
Our previous demonstration that the arylomycin class of
antibiotics has a broader spectrum of antibacterial activity than
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Table 4. MICs of Arylomycin A- and C-C16 (μg/mL) a
strain
arylomycin A-C16
arylomycin CÀC16
S. epidermidis RP62A
S. epidermidis PAS9001 b
S. agalactiae COH-1
S. pyogenes MGAS-1
S. pneumoniae R800
0.25
0.25
8
8
>128
16
>128
8
8
4
2
8
C. glutamicum DSM 44475
4
R. opacus DSM 1069
1
a Arylomycin A-C16 included for comparison.19 b Evolved from S. epidermidis
RP62A to be resistant to arylomycin A-C16.19
Table 5. MICs of Arylomycin C-C16 (μg/mL) against Mu-
tants Known To Be Sensitive to Arylomycin A- and B-C16
strain
arylomycin A-C16
arylomycin CÀC16
S. aureus NCTC 8325
S. aureus P29S PAS8001 b
E. coli MG1655
>128
2
>128
4
>128
2
>128
2
E. coli P84L PAS0260b
P. aeruginosa PAO1
>128
>128
P. aeruginosa P84L PAS2008 b
8
16
Figure 4. Superposition of the active sites of SPaseÀarylomycin com-
plexes. The SPase active site residues are shown as thin lines and labeled.
The arylomycin molecules are shown in ball and stick representation.
The lipoglycopeptide BAL4850C complex (PDB ID, 3S04) is black, the
ternary complex with arylomycin A2 and a β-sultam (PDB ID, 3IIQ)38 is
red, and the arylomycin A2 complex (PDB ID, 1T7D)18 is green. Due to
weak electron density, the fatty acid tail is not included in the BAL4850C
and arylomycin A2 complexes.
a Arylomycin A-C16 included for comparison.19 b Constructed from their
respective wild type strains by mutation of the resistance-conferring
proline to either serine (S. aureus) or leucine (E. coli and P. aeruginosa).18
’ EXPERIMENTAL SECTION
General Experimental Procedures. Dry solvents were pur-
chased from Acros. Commercially available amino acids were purchased
from Bachem (Torrence, CA, USA), Chem-Impex (Wood Dale, IL,
USA), or Novabiochem (EMD Chemicals, Gibbstown, NJ, USA). Celite
545 filter aid (not acid-washed) was purchased from Fisher. Anhydrous
1-hydroxybenzotriazole (HOBt) was purchased from Chem-Impex. All
other chemicals were purchased from Fisher/Acros or Aldrich. Reac-
tions were magnetically stirred and monitored by thin layer chromatog-
raphy (TLC) with 0.25 mm Whatman precoated silica gel (with
fluorescence indicator) plates. Flash chromatography was performed with
silica gel (particle size, 40À63 μm; EMD Chemicals). 1H and 13C NMR
spectra were recorded on Bruker DRX 500 or Bruker DRX 600 spectro-
meters. Chemical shifts are reported relative to either chloroform (δ 7.26)
or methanol (δ 3.31) for 1H NMR, and either chloroform (δ 77.16) or
methanol (δ 49.00) for 13C NMR. High-resolution time-of-flight mass
spectra were measured at the Scripps Center for Mass Spectrometry.
Electrospray ionization (ESI) mass spectra were measured on either an HP
Series 1100 MSD or a PESCIEX API/Plus. For all compounds exhibiting
atropisomerism or isolated as semipure mixtures, NMR spectra are
provided in the Supporting Information. Yields refer to chromatographi-
cally and spectroscopically pure compounds unless otherwise stated.
All preparative reverse-phase chromatography was performed using
Dynamax SD-200 pumps connected to a Dynamax UV-D II detector
(monitoring at 220 nm) on a Phenomenex Jupiter C18 column (10 μm,
2.12 Â 25 cm2, 300 Å pore size). All solvents contained 0.1% TFA; solvent A,
H2O; and solvent B, 90/10 acetonitrile/H2O. All samples were loaded onto
the column at 0% B, and the column was allowed to equilibrate ∼10 min
before a linear gradient was started. Retention times are reported according to
the linear gradient used and the percent B at the time the sample eluted.
Production and Cocrystallization of SPase Δ2-76 and
Lipoglycopeptide BAL4850C and Data Collection. SPase
Δ2-76 was expressed and purified as described previously.36 Prior to
previously appreciated, and that where resistance does exist, it results
from the presence of a specific proline mutation in the target SPase
protein,19 makes the arylomycin scaffold promising for development
as a therapeutic. Toward the further exploration of this class of natural
product antibiotics, we found that the lipoglycopeptide variants can
be synthesized in reasonable yield, with the key steps being a
Pd(tBu3P)2/K2CO3-mediated macrocycle cyclization and a BF3À
Et2O-mediated trichloroacetimidate glycosylation. Characterization
of the synthetic product allowed us to unambiguously determine that
the natural products are glycosylated with deoxy-α-L-mannose, and
contrary to previous reports,16 we found that glycosylation does not
appear to interfere significantly with activity. The structural analysis
revealed that the lipoglycopeptides bind SPase in a manner analogous
to the arylomycin A series compounds with the sugar moiety oriented
away from the enzyme active site and largely solvent exposed.
Nonetheless, the structural analysis also revealed that the hydropho-
bic portion of the sugar interacts with active site residues and that
glycosylation does affect the interactions between the peptidic
position of the inhibitors tail and SPase. Thus, it remains possible
that glycosylation affects activity against bacteria that were not
examined in the current study. While the selection pressure, if any,
that favors glycosylation of the arylomycin scaffold in nature remains
unclear, it does appear that glycosylation increases the solubility of the
scaffold, an important pharmacokinetic attribute for any candidate
therapeutic. Thus, derivatization at the same position with other
substituents, e.g., other sugars, phosphates, and sulfates, etc., might
further improve the pharmacokinetic properties of the arylomycin
scaffold and aid in its potential development as a therapeutic. Experi-
ments to test this hypothesis are currently in progress.
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Journal of the American Chemical Society
ARTICLE
cocrystallization, SPase Δ2-76 (18.0 mg/mL in 20 mM Tris-HCl, pH
7.4, and 0.5% Triton-100) was combined with the lipoglycopeptide
BAL4850C (10 mM in dimethyl sulfoxide (DMSO)) in a 1:1 molar ratio
and incubated on ice for 1 h.
ISIS Draw version 2.5 (MDL Information Systems, Inc.), and PyMol.57
The atomic coordinates(accessioncode:3S04) havebeendepositedin the
Protein Data Bank, Research Collaboratory for Structural Bioinformatics,
Rutgers University, New Brunswick, NJ, USA (http://www.rcsb.org).
Determination of Antimicrobial Activity. Antimicrobial activ-
ity was examined using 13 bacterial strains, S. epidermidis RP62A,
S.aureusNCTC 8325, E. coli MG1655, P. aeruginosa PAO1, S. epidermidis
RP62A SpsIB(S29P) (PAS9001), S. aureus NCTC 8325 SpsB(P29S)
(PAS8001),19 E. coli MG1655 LepB(P84L) (PAS0260),19 P. aeruginosa
PAO1 LepB(P84L) (PAS2008),19 R. opacus DSM 1069, S. agalactiae COH-1,
S. pyogenes M1-5448, S. pneumoniae R800, and C. glutamicum ATCC
44475. Minimum inhibitory concentrations were determined from at
least three independent experiments using the CLSI broth microdilution
method. Briefly, inocula were prepared by suspending bacteria growing
on solid media into the same type of broth used in the MIC experiment
and diluting to a final concentration of 1 Â 107 colony forming units/mL.
A 5 μL aliquot of this suspension were added to the wells of a 96-well
plate containing 100 μL of media with the appropriate concentrations of
compound. The MICs of E. coli, P. aeruginosa, S. aureus, S. epidermidis,
Rhodococcus equi (R. equi), R. opacus, and C. glutamicum were determined
in cation-adjusted Mueller Hinton II broth. MICs of S. pyogenes and
S. pneumoniae were determined in Todd Hewitt broth. The MICs of
S. agalactiae were determined in cation-adjusted Mueller Hinton II broth
and in Todd Hewitt broth (MIC values differed by at most 2-fold
between these two media). In all cases MICs were defined as the lowest
concentration of compound to inhibit visible growth.
Cocrystallization trials for SPase Δ2-76 in complex with BAL4850C
(provided by Basilea Pharmaceutica International Ltd., Basel, Switzerland)
were carried out by the sitting-drop vapor diffusion method. The final
optimized reservoir condition that produced high-quality crystals for data
collection was 22% (w/v) PEG 4000 and 0.2 M KCl. The drop consisted of
2 μL of protein/inhibitor complex described above, 2 μL of reservoir
solution, and 2 μL of 0.025 M n-dodecyl-β-D-maltoside (DDM). This 6 μL
drop was equilibrated over 1 mL of reservoir solution at 20 ꢀC. The crystals
formed from a light precipitate after approximately 2 weeks and had an
average size of ∼0.2 Â 0.1 Â 0.5 mm3.
Before data collection, the crystal was transferred by a pipet from the
growth drop to a cryoprotectant composed of 24% (w/v) PEG 4000,
0.2 M KCl, 0.008 M DDM, 20% glycerol) for 30 s. The crystal was
mounted on a Hampton Research loop and flash-cryo-cooled by directly
placing it into a gaseous nitrogen stream at 100 K. The X-rays (wavelength,
1.5418 Å) were generated from Cu Kα radiation via a Rigaku MicroMax-
007 Microfocus X-ray rotating-anode generator running at 40 kV and
20 mA and equipped with Osmic Confocal VariMax High Flux optics.
The crystal-to-detector distance was set to 200 mm. All frames (280)
were recorded on a R-AXIS IV++ imaging-plate detector with a 0.5ꢀ
oscillation angle and an exposure time of 240 s/frame. The data revealed
diffraction to beyond a resolution of 2.4 Å. Data were collected, indexed,
and scaled using the program CrystalClear.49 The crystals belong to the
tetragonal space group P43212. The unit cell dimensions were deter-
mined to be a = 72.0 Å, b = 72.0 Å, and c = 262.6 Å. The Matthews
coefficient (Vm) is 3.03 Å3/Da for two molecules in the asymmetric unit.
The fraction of the crystal volume occupied by solvent was 59.3%,
calculated by the program Matthews in the CCP4i suite of programs.50,51
For crystal and data collection statistics see Table 3.
’ ASSOCIATED CONTENT
S
Supporting Information. Full characterization of synthetic
b
intermediates and compound 18a, supporting data and NMR spec-
tra, and complete ref 16 This material is available free of charge via
the Internet at http://pubs.acs.org.
Phasing, Model Building, and Refinement. A molecular
replacement solution was found using the program Phaser in the CCP4i
suite of programs.51 The atomic coordinates used for the search model
were taken from a 2.5 Å crystal structure of SPase Δ2-76 (PDB code,
1T7D; molecule A).18 The topology and parameter files for the inhibitor
were generated using the program PRODRG.52 Coordinates for the
inhibitor were manually docked into clear electron difference density
(Fo À Fc) near the active site. In addition, the main chain trace and the
side chain assignments for the dynamic regions corresponding to
residues Phe197-Asn201 and Asp305-Leu315 in chain B were built in
manually. Water molecules were added to well-defined peaks (2.0σ and
greater into the Fo À Fc maps). Model building and analysis was per-
formed with the program Coot.53,54 Refinement of the structure was
carried out using the program Refmac 5 in the CCP4i suite, as well as
CNS.51,55 The cycles of refinement were carried out for both protein
model and inhibitor model using rigid body and restrained NCS refinement
in the program Refmac 5, and simulated annealing, energy minimization,
and B-factor refinement were performed in CNS. In addition, a cycle of
TLS refinement was carried out using the TLS Motion Determination
Sever and the restrained TLS refinement protocol of Refmac 5 within
the CCP4i suite.51 In all cycles of refinement, 5% of the reflections were
set aside for cross-validation. Final refinement and analysis statistics of
the complex are provided in Table 3. The stereochemistry of the
structure model was analyzed with the program PROCHECK.56 No
stereochemical outliers were observed in the Ramachandran plot, with
96.3% of the residues in the preferred regions. An all atom superposition
of the arylomycin complexes was performed with the program Pymol57
using molecule B of the lipoglycopeptide arylomycin complex (PDB,
3S04), molecule A of the ternary complex with arylomycin A2 and a
β-sultam (PDB, 3IIQ),38 and molecule A of the arylomycin A2 complex
structure (PDB, 1T7D).18 Figures were prepared using the programs
’ AUTHOR INFORMATION
Corresponding Author
mpaetzel@sfu.ca, floyd@scripps.edu
’ ACKNOWLEDGMENT
This work was supported by the Office of Naval Research
(Awards N000140310126 and N000140810478 to F.E.R.) and
the National Institutes of Health (Grant AI081126 to F.E.R). We
also acknowledge support from the Canadian Institute of Health
research (to M.P.), the National Science and Engineering Research
Council of Canada (to M.P), the Michael Smith Foundation for
Health Research (to M.P.), and the Canadian Foundation of
Innovation (to M.P.).
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