Synthesis and evaluation of vancomycin aglycon analogues that bear modifications in the N-terminal D-leucyl amino acid

Article abstract of DOI:10.1021/jm801549b

The synthesis and biological evaluation of a series of vancomycin aglycon analogues bearing alternative residue 1 N-methyl-d-amino acids are described. The analogues were prepared to define whether H-bonding d-amino acids could improve the affinity for th

Full text of DOI:10.1021/jm801549b

J. Med. Chem. 2009, 52, 1471–1476
1471
Synthesis and Evaluation of Vancomycin Aglycon Analogues That Bear Modifications in the
N-Terminal D-Leucyl Amino Acid
Christine M. Crane and Dale L. Boger*
Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La
Jolla, California 92037
ReceiVed December 8, 2008
The synthesis and biological evaluation of a series of vancomycin aglycon analogues bearing alternative
residue 1 N-methyl-D-amino acids are described. The analogues were prepared to define whether H-bonding
D-amino acids could improve the affinity for the model ligands N,N′-Ac2-L-Lys-D-Ala-D-Ala (2) and N,N′-
Ac2-L-Lys-D-Ala-D-Lac (3) and improve antimicrobial activity against vancomycin-sensitive or vancomycin-
resistant bacteria. Additionally, a series of analogues with appended nucleophiles (hydrazines and amines)
on the residue 1 D-amino acids are described that were examined for their ability to react with the C-terminal
ester of 3, forming a covalent attachment of L-Lys-D-Ala to the natural product analogues.
Introduction
Vancomycin (1) is used as the antibiotic of last resort for the
treatment of Gram-positive bacterial infections, especially those
caused by methicillin-resistant Staphylococcus aureus, and for
patients who are allergic to ꢀ-lactam antibiotics. Vancomycin
binds to the peptide terminal portion of the bacterial cell wall
peptidoglycan precursor, specifically to the sequence L-Lys-D-
Ala-D-Ala, thereby inhibiting transpeptidase-catalyzed cross-
linking and maturation of the bacterial cell wall.1 However,
Enterocococci bacterial strains, VanA and VanB,a have devel-
oped an inducible vancomycin-resistance pathway, in which the
C-terminal amino acid is modified from D-alanine to D-lactic
acid (Figure 1).1,2 This modification (NH f O) reduces the
affinity of 1 for the ligand 1000-fold and renders the antibiotic
ineffective, with a corresponding 1000-fold drop in antimicrobial
activity.1d This loss of affinity has been partitioned into the loss
of a key H-bond and lone pair repulsive interactions between
the residue 4 carbonyl of vancomycin and the ester oxygen of
the D-Lac on the C-terminus of the ligand.3,4 The former
contributes 10-fold and the latter 100-fold to the experimentally
Figure 1. Schematic representation of the interactions between
vancomycin (1), vancomycin aglycon (5), and model ligands N,N′-
observed 1000-fold loss in affinity for the ligand.3,4
Ac2-L-Lys-D-Ala-D-Ala (2) and N,N′-Ac2-L-Lys-D-Ala-D-Lac (3).
A significant amount of the lost affinity and antimicrobial
activity can be restored by simply removing the offending
residue 4 carbonyl of the natural product.4 The resulting
methylene derivative Ψ[CH2NH]Tpg4]vancomycin aglycon (4)
was recently prepared by total synthesis and was shown to
exhibit significant activity against resistant VanA bacteria and
dual binding properties for both N,N′-Ac2-L-Lys-D-Ala-D-Ala
(2) and N,N′-Ac2-L-Lys-D-Ala-D-Lac (3) (Figure 2).4 In continu-
ing efforts to improve on the properties of 4, we wished to
establish whether further modification at the N-terminus of 4
with unnatural amino acids presenting appended H-bond donat-
ing groups that H-bond to the residue 2 carbonyl of the ligand
might further enhance its affinity for the model ligand 2 or 3,
Figure 2. [Ψ[CH2NH]Tpg4]Vancomycin aglycon.
and thereby further improve the antimicrobial properties.
However, rather than embark on a total synthesis of such
analogues, the premise could be easily investigated first by
preparing the analogues on the aglycon of vancomycin 5 (Figure
3), where semisynthetic procedures are well-established.5,6 Thus,
the analogues containing N-terminal D-serine (6), O-tert-butyl-
D-serine (7), D-threonine (8), mono- or bidentate H-bond
donating analogues of 3-amino-D-phenylalanine (9-11), 3-ami-
nomethyl-D-phenylalanine (12), and their corresponding hydra-
* To whom correspondence should be addressed. Phone: 858-784-7522.
Fax: 858-784-7550. E-mail: boger@scripps.edu.
a Abbreviations: VanA, vancomycin/teicoplanin type-A resistant; VanB,
teicoplanin-senstitive and vancomycin type-B resistant; VRE, vancomycin-
resistant Enterococci; H-bond, hydrogen bond; D-Lac, D-Lactic acid; DCC,
dicyclohexylcarbodiimde; TFA, trifluoroacetic acid; Pd/C, palladium on
activated carbon; EtNCO, ethyl isocyanate; Pt/C, platinum on activated
carbon; NaBH3CN, sodium cyanoborohydride; MIC, minimum inhibition
concentration; Et3N, triethylamine.
10.1021/jm801549b CCC: $40.75
2009 American Chemical Society
Published on Web 02/11/2009

1472 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 5
Crane and Boger
Figure 4. Target molecules.
Figure 3. Proposed binding of the N-terminally modified vancomycin
analogue 11 with ligand 2 as determined by molecular modeling using
the program MOLOC.7a,b Molecular modeling was preformed starting with
the X-ray crystal structure of 5 cocrystallized with 2 determined to 1.8 Å
resolution (PDB code 1FVM):7c,d (a) schematic view; (b) ball and stick
representation. Black dashed lines represent H-bonds. Distances between
H-atom and heteroatom of H-bonding partner are given in angstroms.
Color code is as follows: ligand skeleton, dark-gray; vancomycin
skeleton, light-gray; N-terminal amino acid skeleton, orange; O, red;
N, blue; H, white. Figure was generated with the molecular graphics
program Chimera.8
Scheme 1
zine counterparts 13-15 were prepared herein for examination
(Figure 4). The modifications at the N-terminus of 5 were
expected to alter the binding pocket for the ligand (Figures 1SI
and 2SI of Supporting Information), an effect that could be
compensated for by the H-bond donating residues.
The effect of N-terminal modification on the antimicrobial
activity for a series of chlorobiphenyl vancomycin derivatives has
been explored by Kahne and co-workers.9 Chlorobiphenyl vanco-
mycin and related analogues operate with a different or additional
mode of action than vancomycin and are ∼100-fold more active
against vancomycin-sensitive bacteria and vancomycin-resistant
Enterococci (VRE). Moreover, and unlike vancomycin, this activity
is maintained when the N-terminal D-leucyl residue is modified or
completely removed.1a,10 Williams and co-workers5 probed the
charge verses nonpolar contributions of the N-methylammonium
and D-leucyl moieties of 1, and Hunt and co-workers11 have
examined the antimicrobial properties of N-demethylvancomycin
(2-fold enhancement). In addition, Preobrazhenskaya and co-
workers12 studied the effect on antimicrobial activity of N-acylation
or nitrosylation at the N-terminus of vancomycin. Most recently,
Williams and co-workers reported the effect of acylation at the
N-terminus N-methylamine of 1 on the affinity for 2.13
hydrochloride (1), which was deglycosylated to provided the
intermediate vancomycin aglycon (5).14 Subsequent removal of
the N-terminal D-leucyl residue of 5 by Edman degradation using
the sequential action of phenyl isothiocyanate and trifluoroacetic
acid provided 16 as reported (Scheme 1).6
Target molecules 6 and 7 were prepared from commercially
available N-Boc-O-tert-butyl-D-serine (17), and 8 was accessed
using N-Boc-O-tert-butyldimethylsilyloxy-D-threonine (18). Se-
lective N-methylation using the conditions of Cheung and
Benoiton15 provided the corresponding N-Boc-N-methylamino
acids 19 and 20 in 92% and 60% yields, respectively. Dicy-
clohexylcarbodiimde (DCC) mediated symmetrical anhydride
formation of 19 and 20 followed by coupling to the free amine
of 16 in the presence of sodium bicarbonate (NaHCO3) provided
the protected target molecules. Subsequent treatment of the
Chemistry
Desleucylaglucovancomycin (16) was prepared in two steps
according to literature procedures starting from vancomycin

Vancomycin Aglycon Analogues
Journal of Medicinal Chemistry, 2009, Vol. 52, No. 5 1473
Scheme 2
and UV-difference titration assays within 1 day after liberation
of the hydrazine 13 (Scheme 3). Compounds 14 and 15 were
subsequently prepared, as these analogues were envisioned to
have improved stability (Figure 4).
Target molecules 12 and 15 were prepared starting from
commercially available N-Boc-3-cyano-D-phenylalanine (33,
Scheme 4). Selective N-methylation following the conditions
of Cheung and Benoiton15 provided carboxylic acid 34 in 97%
yield, which was esterified with MeI/KHCO3, in DMF to provide
ester 35 in 99% yield. Reduction of the nitrile to the corre-
sponding methylamine with hydrogen gas (H2), Raney Ni, and
aqueous 28% ammonium hydroxide (NH4OH) in methanol
provided the amine 36 in 97% yield. Alternative hydrogenation
conditions employing H2 and 10% Pd/C at atmospheric pressure
or 50 psi in methanol, tetrahydrofuran, or acetic acid provided
only complex mixtures, and reactions performed with Raney
Ni in the absence of NH4OH cleanly provided the bis-alkylamine
byproduct. Subsequent protection of the amine 36 with di-tert-
butyl dicarbonate provided 37 (86%), and hydrolysis of the ester
with LiOH in tetrahydrofuran/water provided the desired
carboxylic acid 38 in 88%. DCC-mediated anhydride formation
of 38 followed by coupling with 16 provided the target molecule
12 as its bis-TFA salt in 47% yield (two-steps) after treatment
with 1:9 TFA in dichloromethane and purification by reverse-
phase HPLC (Scheme 4).
resulting intermediates with trifluoroacetic acid (TFA) in
dichloromethane provided the TFA salts of target molecules 6,
7, and 8 with yields for the two-step transformation of 24%,
47%, and 53%, respectively, after purification by reverse-phase
HPLC (Scheme 2).
Compounds 9-11 were obtained from intermediate 20, which
in turn was prepared from commercially available N-Boc-3-nitro-
D-phenylalanine (21, Scheme 3). Selective N-methylation of 21
using the conditions of the Cheung and Benoiton15 provided 22 in
82% yield. Subsequent esterification with methyl iodide (MeI) and
potassium carbonate (K2CO3) provided ester 23 in 94% yield,
which was reduced to amine 20 (H2, 10% Pd/C, 98%). Intermediate
20 was hydrolyzed and protected to provide 24 in 75% yield by
sequential action of LiOH and di-tert-butyl dicarbonate (Boc2O).
DCC-mediated symmetrical anhydride formation of 24 and cou-
pling with 16 in the presence of NaHCO3 provided the target
molecule 9 as its bis-TFA salt in 51% yield (two steps), after
treatment with 1:1 TFA in dichloromethane and purification by
reverse-phase HPLC (Scheme 3).
Intermediate 20 was treated with ethyl isocyanate (EtNCO)
to generate the ethylurea 25 in 97% yield. Hydrolysis of ester
25 with LiOH provided the carboxylic acid 26 (88%), which
was coupled to 16 in the presence of NaHCO3 following
preparation of its symmetrical anhydride using DCC. The target
molecule 10 was isolated by reverse-phase HPLC as its TFA
salt in a 44% yield (two steps) after treatment of the protected
intermediate with TFA in dichloromethane (Scheme 3).
The guanidine derivative 11 was also obtained from inter-
mediate 20 (Scheme 3). Treatment of 20 with commercially
available N,N′-di-Boc-1H-pyrazole-1-carboxamidine (27)16 pro-
vided the bis-protected guanidine derivative 28 in 47% yield.
Subsequent hydrolysis of ester 28 with LiOH provided the
carboxylic acid 29 (66%) and was followed by treatment of 29
with DCC to prepare the symmetrical anhydride, which was
coupled with the free amine of 16 in the presence of NaHCO3.
The target molecule 11 was isolated by reverse-phase HPLC
as its bis-TFA salt in 27% yield (two steps) after treatment of
the protected intermediate with TFA in dichloromethane (Scheme
3).
Amination of the amine on 36 with oxaziridine 3117 provided
the protected hydrazine 39 (58%) in anhydrous toluene (30 min),
and the yield was comparable conducting the reaction in
dichloromethane (52%) (Scheme 4). Extended reaction times
of 24 or 48 h in dichloromethane or toluene provided lower
yields of the desired hydrazine (22% and 30-47%, respectively),
and the bis-amination byproduct dominated. Hydrolysis of the
ester of 39 using LiOH in tetrahydrofuran/water provided the
desired carboxylic acid 40 (62%). The hydrazine was then
protected with di-tert-butyl dicarbonate in the presence of
NaHCO3 to provide 41 in 87%. DCC-mediated anhydride
formation of carboxylic acid 41 followed by coupling with 16
provided the target molecule 15 as its bis-TFA salt in 52% yield
(two steps) after treatment with TFA in dichloromethane (1:9)
and purification by reverse-phase HPLC (Scheme 4). As
observed with the derivative 13, the hydrazine function of
compound 15 proved unstable, with a lifetime of 3 days when
stored as a solid. Therefore, compound 15 was used for all
biological and UV-difference titration assays within 1 day after
liberation of the free hydrazine. For assay purposes, a crude
sample, after deprotection and without purification by reverse-
phase HPLC, was used for all assays, as purification caused
additional decomposition. However, a purified sample was
prepared for characterization purposes.
Compound 14 was prepared from commercially available
N-Boc-O-benzyl-D-homoserine (42) initiated by selective
N-methylation of 42 as described previously using the
conditions of Cheung and Benoiton15 to provide intermediate
43 (96%, Scheme 5). Subsequent debenzylation under an
atmosphere of H2 gas over 10% Pd/C provided the crude
alcohol, which was immediately oxidized to the aldehyde
using Dess-Martin periodinane and condensed with tert-butyl
carbazate to provide the hydrazone 44 (48%, three steps).
Reduction of the hydrazone was initially problematic, as bis-
alkylhydrazine was the major byproduct (not shown). The
hydrazone was cleanly reduced to the hydrazine 45 in 76%
yield under an atmosphere of H2 gas over 5% Pt/C with the
additive tert-butyl carbazate (2 equiv), which prevented bis-
alkyl hydrazine formation. Similar conditions in the absence
The phenylhydrazine amino acid precursor 30 was obtained
in two steps from intermediate 20. Amination of the aniline of
20 with oxaziridine 3117 proceeded in modest, but sufficient
yield (23%) with both standard and extended reaction times
(24-72 h) as the bis-aminated side product predominated (not
shown). Subsequent hydrolysis of the methyl ester 32 with LiOH
provided the carboxylic acid 30 in 65% yield. The acid 30 was
then transformed to its symmetrical anhydride with DCC and
coupled with 16 in the presence of NaHCO3. The protected
intermediate was treated with TFA in dichloromethane to
provide the desired target molecule 13 (49%, two steps) as its
bis-TFA salt after purification by reverse-phase HPLC. Com-
pound 13 was somewhat unstable and was used for all biological

1474 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 5
Crane and Boger
Scheme 3
Scheme 4
Scheme 5
amounts of desired product. Other conditions employing
sodium cyanoborohydride (NaBH3CN) or hydrogenation over
10% Pd/C in acetic acid, methanol, or tetrahydrofuran at
atmospheric pressure or at 50 psi of pressure provided only
complex mixtures. Mono-Boc protected hydrazine 45 was
then bis-Boc protected with di-tert-butyl dicarbonate in a
mixture of tetrahydrofuran/water to provide carboxylic acid
46 (49%). DCC-mediated anhydride formation with 46 and
coupling with 16 provided the target molecule 14 as its bis-
TFA salt in 49% yield (two steps) after treatment with 1:9
TFA in dichloromethane and purification by reverse-phase
HPLC (Scheme 5). As observed with hydrazine derivatives
13 and 15, derivative 14 was also unstable. It was therefore
used for all biological and UV-difference titration assays
within 1 day after liberation of the hydrazine and stored as
a solid. For assay purposes, a crude sample, isolated after
deprotection and without purification by reverse-phase HPLC,
was used for all assays, as additional purification caused
of tert-butyl carbazate provided a mixture of unreacted
starting material and bis-alkyl hydrazine with only trace

Vancomycin Aglycon Analogues
Journal of Medicinal Chemistry, 2009, Vol. 52, No. 5 1475
Table 1. Binding and Antimicrobial Properties
benzylamine derivative 12, despite the higher Ka of the former for
the ligand 3 and the altered binding pocket (Figure 2SI). Aniline
derivative 9, phenylhydrazine derivative 13, and alkylhydrazine
derivative 14 displayed slightly enhanced antimicrobial properties
that paralleled enhanced affinities for 3 (Table 1), again despite
the potentially altered binding pocket (Figure 2SI). As observed
in the assay against vancomycin-sensitive S. aureus, the only
analogue that showed enhanced potency against the VanA strain
was compound 15 (MIC ) 170 µg/mL, Table 1). However, this
increase (4-fold) was modest and overall the results did not reveal
a unique behavior for the hydrazine series against the vancomycin-
sensitive or vancomycin-resistant bacteria. Since the binding affinity
of 15 for 3 did not correlate directly with its antimicrobial potency,
as 15 had the same affinity as natural product for 3, it is not clear
what factors are contributing to its modestly enhanced potency.
MIC (µg/mL)
association constants
compd S. aureusa E. faecalisb 2c (×105 M-1
)
3d (×102 M-1
)
1
5
6
7
8
1.25e
2000e
640e
800
320
800
320
640
320
640
2.0f
1.7
0.3
0.9
2.6
0.3
2.0
1.1
0.8
0.3
1.1
1.7
1.8f
1.2f
2.1
2.0
0.8
2.1
4.6
3.5
0.8
1.9
1.5
1.5
0.625e
40
20
40
20
31
10
>10
10
9
10
11
12
13
14
15
320
>400
170
10
1.25
a Vancomycin-sensitive (strain ATCC 25923). b Vancomycin-resistant
(VanA,strainBM4166).c N,N′-Ac2-L-Lys-D-Ala-D-Ala.d N,N′-Ac2-L-Lys-D-Ala-D-
Lac. e Taken from ref 18b. f Taken from ref 4.
For vancomycin analogues 6-8, any observed loss in affinity
may be the result of a change in the overall nonpolar surface
area in this region of the natural product (Figure 5S1) as
observed for the N-terminal D-alanine and D-glycine analogues
of vancomycin reported by Williams and co-workers.5 These
analogues, which in contrast maintained the vancosamine sugar,
exhibited a loss in affinity for 2 (20-fold, 0.85 × 105 and 0.77
× 105 M-1, respectively).5 Further, analysis by molecular
modeling7 of the conformation of the D-serine and D-threonine
derivatives 6 and 7 revealed that the hydroxy groups may point
away from the carboxylate when the ligand is bound, adopting
a more favorable gauche conformation (Figure 5SI). Therefore,
it might be expected that the serine derivative 6 would have a
lower affinity for 2 and that the analogous gauche conformation
for 7 directs the threonine methyl substituent toward the ligand,
increasing both the nonpolar surface area in this region of the
ligand and its affinity for 2 when compared to 6 (Table 1).
However, the reverse trend is observed for the binding results
with the ester ligand 3 and the distinctions are modest enough
that definitive trends are difficult to discern.
further decomposition. However, a purified sample was
prepared for the purposes of characterization.
Results and Discussion
The antimicrobial properties of derivatives 6-15 were
determined against a vancomycin-sensitive Staphylococcus
aureus (S. aureus, strain ATCC 25923) and a vancomycin-
resistant (VanA) Enterococcus faecalis (E. faecalis, strain
BM4166) in a microtiter plate-based antimicrobial assay (Table
1).4,18 The latter VanA strain maintains an inducible resistance
pathway upon treatment with glycopeptide antibiotics, including
vancomycin (1) and teicoplanin, and is a virulent strain that is
difficult to treat compared to a VanB strain. When unchallenged,
it utilizes D-Ala-D-Ala peptidoglycan cell wall precursors, but
upon treatment with a glycopeptide it will switch to D-Ala-D-
Lac peptidoglycan cell wall precursors. The binding properties
of 6-15 for 2 and 3 were also determined and compared to 1
and 5 using a well-established UV-difference titration assay,
which gives association constants (Ka) for the complexes with
the model tripeptides 2 and 3 of the peptidoglycan cell wall
precursors (Table 1).18,19 For an exemplary saturation binding
curve with 2 or 3 and subsequent Scatchard analysis see the
Supporting Information (Figures 3SI and 4SI).
Compounds 6-14 all lost a significant amount of antimicrobial
activity against a vancomycin-sensitive S. aureus (Table 1). Only
the vancomycin derivative 15 (MIC ) 1.25 µg/mL), which arose
as the best of the series, displayed a MIC comparable to vanco-
mycin (MIC ) 1.25 µg/mL)4,18 and the vancomycin aglycon (MIC
) 0.625 µg/mL)4,18 against vancomycin-sensitive S. aureus (Table
1). The reduced in vitro antimicrobial properties were paralleled
by lower measured affinities (Ka values) of compounds 6, 7, 9,
12, and 13 for the model ligand 2, which lost anywhere from 2- to
10-fold in affinity. Interestingly, compounds 8, 10, 11, 14, and 15
displayed comparable affinities for 2, and with the exception of
15, this did not translate to comparable antimicrobial properties
(Table 1).
The D-phenylalanine derivatives 9 and 13, with the H-bond
donating groups (aniline or hydrazine) attached directly to the
aromatic ring, lost significant affinity for 2 but gained affinity
for 3. Extension of the H-bond donating system by one or two
additional atoms from the aromatic ring restores some of the
lost affinity for 2 and 3 as demonstrated by compounds 10, 11
and 14, 15, in spite of the altered binding pocket in the
N-terminal region of the natural product (Figure 2SI). However,
analogue 12 with the single methylene extension still has a
slightly lower Ka in comparison to the natural product 5 (Table
1). The most significant positive impact on binding affinity was
observed with 10 and 11 and their relative affinity for 3, which
increased 3- to 4-fold potentially reflecting the bidentate H-bond
represented in Figure 3.
A series of reaction conditions were explored to investigate
the potential of a reaction occurring between the appended
hydrazines of analogues 13-15 and the C-terminal ester of N,N′-
Ac2-L-Lys-D-Ala-D-Lac (3) (Table 1SI), the hope being that the
hydrazine would react with the ester of the bound ligand 3
generating a covalent adduct with the natural product analogue.
However, varying the solvent, temperature, concentration,
substrate, or pH did not influence the reaction outcome and the
desired adduct product was never observed. This result was
surprising, as the same intermolecular reaction between 3 and
the commercially available hydrazines phenylhydrazine and
The antimicrobial properties of 6-15 were also investigated
against a vancomycin-resistant E. faecalis (VanA), and the results
revealed that 6-14 did not display markedly different antimicrobial
properties than the natural product. The antimicrobial activities of
the N-terminal D-serine and D-threonine analogues 6 and 8 were
slightly lower than 5, even though the former had a similar affinity
for the model ligand 3 (Table 1). Analogue 7 bearing the O-tert-
butyl ether showed improved potency over its hydroxy counterpart
6 and a comparable affinity for 3; a result that may be attributed
to its enhanced hydrophobic character. There was no change in
the antimicrobial activities of ethylureido derivative 10 and

1476 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 5
Crane and Boger
123, 1862–1871. (f) Crowley, B. M.; Mori, Y.; McComas, C. C.; Tang,
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Teicoplanin, and Ramoplanin: Synthetic and Mechanistic Studies. Med.
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2-bromophenylhydrazine with triethylamine (Et3N) at 70 °C did
provide the desired acylated hydrazines (data not shown).
Conclusions
(5) Cristofaro, M. F.; Beauregard, D. A.; Yan, H.; Osborn, N. J.; Williams,
D. H. Cooperativity between Non-Polar and Ionic Forces in the
Binding of Bacterial Cell Wall Analogues by Vancomycin in Aqueous
Solution. J. Antibiot. 1995, 48, 805–810.
(6) (a) Booth, P. M.; Stone, D. J. M.; Williams, D. H. The Edman
Degradation of Vancomycin: Preparation of Vancomycin Hexapeptide.
J. Chem. Soc., Chem. Commun. 1987, 1694–1695. (b) Booth, P. M.;
Williams, D. H. Preparation and Conformational Analysis of Vanco-
mycin Hexapeptide and Aglucovancomycin Hexapeptide. J. Chem.
Soc., Perkin Trans. 1 1989, 2335–2339.
(7) (a) Gerber, P. R.; Mu¨ller, K. MAB, a Generally Applicable Molecular
Force Field for Structure Modelling in Medicinal Chemistry. J. Com-
put.-Aided Mol. Des 1995, 9, 251–268. (b) Gerber Molecular Design.
http://www.moloc.ch. (c) Protein Databank (PDB code 1FVM), 1.8
Å resolution. http://www.rcsb.org. (d) Nitanai, Y.; Kikuchi, T.; Kakoi,
K.; Hanamaki, S.; Fujisawa, I.; Aoki, K. Crystal Structures of the
Complexes between Vancomycin and Cell-Wall Precursor Analogs.
J. Mol. Biol., in press.
A series of N-terminal derivatives of the vancomycin aglycon
were prepared replacing the residue 1 N-methyl D-leucyl amino
acid with a series of N-methyl D-amino acids bearing H-bond
donor or reactive nucleophilic substituents. An examination of
their antimicrobial activity against vancomycin-sensitive and
vancomycin-resistant bacteria and their affinity for model ligands
2 and 3 incorporating D-Ala-D-Ala and D-Ala-D-Lac did not
reveal evidence of significant enhancements in activity or
affinity, including those capable of formation of covalent adducts
derived from their reaction with ligand 3 bearing an ester.
Whether this reflects the limitations of our original designs or
features of binding not yet recognized is unknown but is a topic
of our continuing studies.
Acknowledgment. We gratefully acknowledge the financial
support of the National Institutes of Health (Grant CA 41101), Dr.
G. Boldt for supplying gram quantities of vancomycin aglycon,
and Professor K. D. Janda for the use of the HF apparatus.
(8) (a) All molecular graphics images were produced using the UCSF
Chimera package from the Resource for Biocomputing, Visualization,
and Informatics at the University of California, San Francisco
(supported by Grant NIH P41 RR-01081). For details, see the
following: (b) Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch,
G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF ChimerasA
Visualization System for Exploratory Research and Analysis. J. Com-
put. Chem. 2004, 25, 1605–1612. (c) Chimera home page can be found
at http://www.cgl.ucsf.edu/chimera.
Supporting Information Available: Compounds 5 and 16 were
prepared according to published procedures.6,14 Full experimental
details and characterization for all new intermediates and final
compounds are provided in the supporting information. This material
is available free of charge via the Internet at http://pubs.acs.org.
(9) Kahne, D.; Walker, S.; Silva, D. J. Desleucyl Glycopeptide Antibiotics
and Methods of Making Same. Patent WO 2000/59528 (US
2004110665), 2000.
(10) Kim, S. J.; Matsuoka, S.; Patti, G. J.; Schaefer, J. Vancomycin
Derivative with Damaged D-Ala-D-Ala Binding Cleft Binds to Cross-
Linked Peptidoglycan in the Cell Wall of Staphylococcus aureus.
Biochemistry 2008, 47, 3822–3831.
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