Anti-MRSA agent discovery using diversity-oriented synthesis

Article abstract of DOI:10.1002/anie.200705415

Beating the superbugs: Diversity-oriented synthesis using a solid-supported phosphonate unit to synthesize 242 drug-like compounds based on 18 natural-productlike scaffolds led to the discovery of gemmacin (see scheme). This new structural class of antibiotic is active towards methicillin-resistant Staphylococcus aureus (MRSA). (Chemical Equation Presented).

Full text of DOI:10.1002/anie.200705415

Communications
DOI: 10.1002/anie.200705415
Combinatorial Chemistry
Anti-MRSA Agent Discovery Using Diversity-Oriented Synthesis**
Gemma L. Thomas, Richard J. Spandl, Freija G. Glansdorp, Martin Welch, Andreas Bender,
Joshua Cockfield, Jodi A. Lindsay, Clare Bryant, Derek F. J. Brown, Olivier Loiseleur,
HØl›ne Rudyk, Mark Ladlow, and David R. Spring*
Antibacterial drugs have played an essential role in the global
increase in quality of life and life expectancy. However, these
gains are at serious risk owing to bacterial drug resistance by
so-called “superbugs”, such as methicillin-resistant Staph-
ylococcus aureus (MRSA).[1,2] The discovery of new anti-
biotics with novel modes of action is vital to tackle the threat
of multidrug-resistant bacteria. Traditionally, antibiotics have
been discovered from natural sources;[3–7] however, there are
many disadvantages to using extracts (e.g. limited availability,
bioactive constituent identification, and complex analogue
synthesis). These problems have led to a complementary
approach of synthesizing structurally diverse, natural-prod-
uct-like small molecules directly and efficiently,[8] an
approach known as diversity-oriented synthesis (DOS).[9–15]
Whereas compound collections of a common scaffold deco-
rated with diverse building blocks have been synthesized
efficiently,[16] there are limited examples of the synthesis of
small molecules with a high degree of skeletal diversity
(usually by a build–couple–pair strategy).[17–24] Previously, we
have used a diazoacetate starting unit to mimic natureꢀs
divergent synthetic strategy with acetyl CoA (by a pluripotent
functional-group strategy) to synthesize compounds with
natural-product scaffolds (e.g. cocaine and warfarin).[24]
Herein, we report the use of a solid-supported phosphonate
unit to synthesize 242 drug-like compounds based on 18
natural-product-like scaffolds in two to five steps and their
use in discovering a new structural class of antibiotic with
anti-MRSA activity.
The solid-supported phosphonate 1 (Scheme 1) was
identified as an attractive DOS starting unit for three key
reasons. First, the reactive phosphonate functionality permits
the stereoselective formation of a,b-unsaturated acyl imida-
zolidinones (2) that could be used to generate enantioselec-
tively a wide range of scaffolds that can be diversified further.
Second, the imidazolidinone linker not only enables two-
point binding of chiral catalysts but also permits divergent
cleavage of the exocyclic acyl group (hydrolysis, reduction,
esterification, and amide formation). Thirdly, immobilization
of 1 on a silyl polystyrene support[25] simplified reaction
optimization and work-up procedures in the multistep
parallel synthesis (total of over 1000 individual steps), thereby
allowing the efficient production of milligram quantities of
242 compounds without the requirement for automation
equipment.
In the first step of the diversity-oriented synthesis, 1 was
treated with aldehyde building blocks (aryl, heteroaryl, and
alkyl; see the Supporting Information) to deliver twelve a,b-
unsaturated acyl imidazolidinones (2).[26] The second steps of
the solid-supported synthesis exploited three catalytic, enan-
tioselective, divergent reaction pathways (Scheme 1):
1) [2+3] cycloaddition (reaction b, ee 60–65%, de 78-
99%),[27] 2) dihydroxylation (reaction c, ee 88–91%),[28] and
3) [4+2] cycloaddition (reaction d, ee 89–98%, de 74–
74%).[29] Similar selectivities were observed when repeating
the reactions in solution with a triisopropylsilyl-protected
linker (as opposed to the diisopropylpolystyrene group; see
the Supporting Information). The reactions were also con-
ducted with achiral catalysts to give racemic products, which
were used for the later steps of the synthesis. This procedure
enabled the diversity-oriented synthesis to be streamlined to
half the size, yet permitted the enantioselective synthesis of
hits during the structure–activity relationship stages of this
[*] Dr. G. L. Thomas, R. J. Spandl, F. G. Glansdorp, Dr. M. Ladlow,
Dr. D. R. Spring
Department of Chemistry, University of Cambridge
Lensfield Road, Cambridge, CB2 1EW (UK)
Fax: (+44) 1223-336362
E-mail: drspring@ch.cam.ac.uk
Homepage: http://www-spring.ch.cam.ac.uk/
Dr. M. Welch
Department of Biochemistry, University of Cambridge
Tennis Court Road, Cambridge CB2 1QW (UK)
Dr. A. Bender
Leiden/Amsterdam Center for Drug Research
Leiden University, 2300 Leiden (The Netherlands)
J. Cockfield, Dr. J. A. Lindsay
Department of Cellular and Molecular Medicine
St. George’s Hospital, University of London,
Cranmer Terrace, London, SW17 0RE (UK)
Dr. C. Bryant
Department of Biochemistry, University of Cambridge
Tennis Court Road, Cambridge CB2 1QW (UK)
Dr. D. F. J. Brown
Health Protection Agency
Clinical Microbiology and Public Health Laboratory
Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QW (UK)
Dr. O. Loiseleur
Syngenta CropProtection AG
Schwarzwaldallee 215, 4002 Basel (Switzerland)
Dr. H. Rudyk
Lilly UK, Erl Wood Manor
Windlesham, Surrey, GU20 6PH (UK)
[**] This work was supported by grants from the EPSRC, BBSRC, Royal
Society, and Augustus and Harry Newman Foundation to D.R.S. and
M.W., and by generous support from GlaxoSmithKline, Lilly, and
Syngenta. We also acknowledge the EPSRC National Mass Spec-
trometry Service Centre, Swansea, for providing mass spectrometric
data. MRSA=methicillin-resistant Staphylococcus aureus.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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oriented synthesis are 1) the tandem
ring closing–opening–closing metathesis
reaction[30] (reaction o, step 3) to give
skeletally diverse tricyclic products (7-5-
7, 7-5-8) and 2) the formation of cis-
fused [3.2.1] bicyclic amines by oxidative
cleavage and tandem reductive amina-
tion with primary amines (reaction p,
step 4). In order to discover a new
antibiotic with a novel mode of action,
the diversity-oriented synthesis was
designed to populate new areas of
chemical space so that several of the
scaffolds generated are either rare or
have no known representation in nature
(e.g. the cis–trans-fused 7-5-7 tricycle
resulting from reaction o). Using the
chemistry shown in Scheme 1 and a
limited number of structurally diverse
building blocks, the diversity-oriented
synthesis was achieved of 242 small
molecules that have 18 molecular frame-
works among other unique structural
features. The library was made using
parallel synthetic techniques leading to
1–20 mg of each final product (molec-
ular-weight range 153–857, mean value
379 gmolꢀ1). All library members were
assessed for their identity and quality
and purified if necessary by recrystalli-
zation, chromatography, or extraction to
ensure greater than 90% purity of final
products (as determined by 1H NMR
spectroscopy, HPLC, and LCMS). Full
characterization of the majority (63%)
of the final compounds was undertaken;
1H NMR spectroscopy and LCMS char-
acterized the rest.
Scheme 1. Diversity-oriented synthesis of 242 compounds based on 18 discrete molecular
frameworks. Reagents and conditions: a) LiBr, 1,8-diazabicyclo[5.4.0]undec-7-ene, R1CHO,
MeCN; b) (R)-QUINAP, AgOAc, iPr2NEt, THF, ꢀ788C!258C; c) AD-mix, (DHQD)PHAL, THF/
H2O (1:1); d) chiral bis(oxazoline), Cu(OTf)2, 3 Š M.S., CH2Cl2, C5H6; e) R2COCl, DMAP,
pyridine, CH2Cl2; f) R3CHO, BH3·pyridine, MeOH; g) SOCl2, pyridine, CH2Cl2, 408C; h) R4Br,
Ag2O, CH2Cl2, 408C; i) R5C(O)R5, TsOH, DMF, 658C; j) R6CHO, TsOH, DMF, 658C; k) NaN3,
DMF, 1008C then dimethyl acetylenedicarboxylate, PhMe, 658C; l) mCPBA, CH2Cl2 then MeOH,
=
=
658C; m) CH2 CHCO2Bn, PhMe, 1208C, Grubbs II, CH2 CH2; n) OsO4, NMO, CH3C(O)CH3/
H2O (10:1); o) RNH2, Me2AlCl, PhMe 1208C; then NaH, R11X, DMF, THF; then PhMe, 1208C,
To assess the degree of overall
diversity obtained in this diversity-ori-
ented synthesis, we compared[24] the
structural diversity of our library to the
chemical space spanned by “benchmark
collections”: 1) known pharmacologi-
cally active small molecules (MDL
Drug Data Report database with a
molecular-weight cutoff of 650 gmolꢀ1
to compare size-independent diver-
7
=
Grubbs II, CH2 CH2; p) NaIO4, THF/H2O (1:1); then R NH2, NaB(OAc)3H, CH2Cl2; q) NaIO4,
THF/H2O (1:1); then R8NHR8, NaB(OAc)3H, CH2Cl2; r) R9CHO, DMF, TsOH, 608C;
s) R10C(O)R10, DMF, TsOH, 608C. DMF=N,N-dimethylformamide, THF=tetrahydrofuran,
DMAP=N,N-dimethylaminopyridine, (DHQD)PHAL=hydroquinidine 1,4-phthalazinediyl
diether, mCPBA=meta-chloroperbenzoic acid, Ts=para-toluenesulfonyl, Grubbs II=1,3-(bis-
(mesityl)-2-imidazolidinyl-idene) dichloro (phenylmethylene) (tricyclohexylphosphine) ruthe-
nium, NMO=4-methylmorpholine-N-oxide, OTf=CF3SO3, Bn=benzyl, QUINAP=1-(2-diphe-
nylphosphino-1-naphthyl)isoquinoline.
work. Later steps involved complexity-generating reactions to
diversify the molecular frameworks further and to release
divergently the compounds from the solid support. For
example, reaction b (step 2) involved the enantioselective
1,3-dipolar cycloaddition of 2 with a wide range of azome-
thine ylides complexed to Ag+ and (R)- or (S)-QUINAP and
subsequent acylation or alkylation of the resultant pyrrolidine
(reactions e and f, respectively),[27] and cleavage (step 4).
Norbornenes could be synthesized using Evansꢀs asym-
metric Diels–Alder methodology (reaction d)[29] and used in
divergent reactions l–o. Two highlights in the diversity-
sity),[31] 2) 3762 compounds marked as “antibacterials” in
the MDDR database,[32] and 3) a focused library (conven-
tional combinatorial chemistry).[33] A visual representation of
the diversity of the collections in “chemical space” is depicted
in Figure 1, and corresponding data are given in Table 1.
Describing each compound by a series of physicochemical
properties, followed by principal component analysis (PCA),
enables quantitative estimation of the diversity achieved on a
per-compound basis. Using this dataset, the DOS library,
numerically, is even more diverse than the MDDR com-
pounds, that is, 22 (relative) units for the DOS library, 19 for
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Table 2: Structure and activity (MIC50) of the three compounds identified
from the diversity-oriented synthesis with growth inhibitory activity
against three strains of S. aureus. ND=not determined.
MIC50 [mgmLꢀ1
]
MSSA
EMRSA 15
EMRSA 16
(ꢁ)gemmacin
(ꢀ)gemmacin
(+)gemmacin
(ꢁ)-3
2
ND
ND
16
32
0.5
0.5
16
8
16
16
32
32
16
32
>64
>64
>64
>32
(ꢁ)-4
Figure 1. Visual representation of the diversity of different chemical
erythromycin
oxacillin
>64
>32
collections in physicochemical and topological space using 184
molecular operating environment (MOE) descriptors followed by
principal component analysis (PCA). The DOS library synthesized in
this work is depicted by red squares. For comparison, a focused library
(blue squares), the MDL Drug Data Repository (MDDR, black dots),
and antibacterial drugs (gray dots) are depicted.
made; see the Supporting Information, section 15). Gemma-
cin showed broad-spectrum Gram-positive antibacterial
activity in vitro, including inhibition of growth of vancomy-
cin-intermediate S. aureus and vancomycin-resistant enter-
ococci (VRE; see the Supporting Information, section 17).
Gemmacin was not generally active against Gram-negative
organisms, although it showed activity against two strains of
Moraxella catarrhalis (MIC = 16 mgmLꢀ1, where MIC is the
minimum inhibitory concentration). The compound is a
selective antibacterial agent, as it showed low antifungal
activity (MIC > 64 mgmLꢀ1 for seven Candida species) and
low mammalian cell toxicity (IC50 > 64 mgmLꢀ1 in human
epithelial cells).
Table 1: Diversity of different chemical collections.
Library
(MW<650)
s[a]
s
s
Average chemical space
occupied per compound
(PC1)
(PC2)
(PC3)
MDDR
1472.11 122.53 104.56
91.92
1176.97 135.69 139.78
473.57 43.91 31.00
18.86
12.79
22.32
0.64
antibacterials 1276.50 109.01
DOS
focused
[a] Standard deviation of each representative molecular dataset in
descriptor space.
Target identification of (ꢀ)-gemmacin was attempted
with assays used to identify common antimicrobial modes of
action (such as dihydrofolate reductase inhibition, protein
synthesis, and ATP synthesis uncoupling; gemmacin was
inactive in all of these assays). Gemmacin did show activity in
an assay used to detect the generation of reactive oxygen
species (IC50 = 0.35 mgmLꢀ1 in Spodoptera frugiperda cell line
21), which suggested to us that gemmacin may be a cell-
membrane disrupter. This mode of action is consistent with
the assay shown in Figure 2.
EMRSA 16 samples were inoculated with sub-lethal and
lethal doses of gemmacin. Controls, containing dimethylsulf-
oxide (DMSO) and only the bacteria, were used for a direct
comparison. Cells incubated with gemmacin did not show
lysis of S. aureus, owing to the thick cell wall. The cells were
then treated with lysostaphin,[36] an enzyme that cleaves the
cross-linking pentaglycine bridges in the cell wall of staph-
ylococci. This procedure leaves the cell membranes intact but
reduces the optical density of the samples, as the “wall-less”
cells are less turbid. However, in the presence of lethal doses
of gemmacin, the membranes appear to have been disrupted
partially, and without the protection of the cell wall many cells
lyse, as detected by a more pronounced reduction in optical
density. When the samples are treated with the detergent
sarkosyl, membranes are disrupted, the cells lyse, and
turbidity is lost completely. While selective membrane
the MDDR, 13 for the antibacterials, and 0.6 for the focused
library (Table 1). The DOS library spans a large part of
biologically relevant chemical space and within this context is
more diverse than the MDDR library, thus illustrating the
value of our approach to deliver distinct products within the
molecular diversity spectrum.[15]
The library compounds were screened for their effect on
the growth of three strains of S. aureus: a methicillin-
susceptible S. aureus (MSSA) and two UK epidemic methi-
cillin-resistant strains (EMRSA 15 and EMRSA 16).[34] Both
MRSA strains are resistant to penicillins and erythromycin
and are responsible for the majority of infections with MRSA
in the UK.[35] Three compounds reproducibly prevented the
growth of these S. aureus strains and were rescreened to
establish the lowest concentration at which they prevented
growth (Table 2). The most potent compound, which we have
called gemmacin, was investigated further. Structure–activity
relationship (SAR) analyses demonstrated that both enan-
tiomers had similar potency (Table 2). The enantiomers do
not map onto the same pharmacophore, suggesting that their
mode of action may not involve a protein active site or
receptor. However, it was also notable that most structural
changes to gemmacin (e.g. ethyl ester or remove NO2)
resulted in significant loss of activity (13 analogues were
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Keywords: antibiotics · combinatorial chemistry ·
.
diversity-oriented synthesis · synthesis design
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disruption of bacterial cells may not be the only mechanism of
action of gemmacin, it is interesting to note that this is the
primary mode of action of antimicrobial peptides such as
magainins, defensins, gramicidin S, type A lantibiotics, and
telavancin,[1] which all have molecular weights greater than
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In summary, we have described a divergent synthetic
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aim of diversity-oriented synthesis is to achieve efficiently
high levels of skeletal diversity to explore biologically
relevant regions of chemical space. A collection of 242
natural-product-like and drug-like small molecules was
synthesized, which was more physicochemically and topolog-
ically diverse than databases of known drugs. Antibacterial
screening with pathogenic strains of MRSA uncovered
several hits, including gemmacin, which is likely to be a
selective bacterial membrane disrupter. The unusual molec-
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positive in vitro results against MRSA strains and other
bacterial pathogens, highlight that gemmacin provides a new
structure for the discovery of critically needed antibiotics.
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diversity-oriented synthetic approach as a way to discover
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