Towards an asymmetric synthesis of the bacterial peptide deformylase (PDF) inhibitor fumimycin

Article abstract of DOI:10.1039/b916372g

Studies towards the synthesis of the bacterial peptide deformylase (PDF) inhibitor fumimycin are reported. The synthetic approach features an organocatalytic access to the α,α-disubstituted amino acid unit and results in the synthesis of an advanced inter

Full text of DOI:10.1039/b916372g

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Towards an asymmetric synthesis of the bacterial peptide deformylase (PDF)
inhibitor fumimycin†‡
Caroline E. Hartmann,a Patrick J. Gross,a Martin Niegerb and Stefan Bra¨se*a
Received 10th August 2009, Accepted 5th October 2009
First published as an Advance Article on the web 19th October 2009
DOI: 10.1039/b916372g
Studies towards the synthesis of the bacterial peptide de-
formylase (PDF) inhibitor fumimycin are reported. The
synthetic approach features an organocatalytic access to the
a,a-disubstituted amino acid unit and results in the synthesis
of an advanced intermediate which already contains all
functionalities of fumimycin.
In the course of screening for new bacterial peptide deformylase
(PDF) inhibitor lead structures, fumimycin (1)1 was isolated from
the fermentation broth of Aspergillus fumisynnematus F746.2
Fig. 1 Fumimycin (1) and sorbillactone A/B (2) (unsaturated/saturated).
Structurally it is related to sorbicillactones A and B (2) from
Penicillium chrysogenum.3 These also possess a skeleton with a six-
membered ring fused with the similar five-membered lactone and
an a,a-disubstituted amino acid moiety linked to a fumaric acid
residue. Besides exhibiting antibacterial activity against S. aureus,
MRSA (methicillin resistant S. aureus) and QRSA (quinolone-
resistant S. aureus), compound 1 (Fig. 1) shows promising in-
hibitory activity towards S. aureus PDF with an IC50 of 4.1 mM. As
the emergence of bacterial resistance to all known classes of
antibiotics is a serious hazard to humans, the search for new
antibiotics with novel modes of action is of utmost urgency.
A field that has attracted more and more attention lately is
the bacterial PDF (EC 3.5.1.31) as a potential target.4 Peptide
deformylase is an enzyme that catalyzes the removal of the formyl
group at the N-terminus of bacterial proteins and is on the
other hand not required in the mammalian cells. Although PDF
inhibitors offer access to a new area of antibacterial agents,3a,5
few PDF inhibitors have been reported so far.6 Hence, from this
starting point, 1 could be an interesting lead structure for future
structural optimizations.7,8
We became interested in fumimycin through the a,a-
disubstituted amino acid precursor unit,9 as such building blocks
have been the focus of our research for quite some time. Therefore
we turned our attention to the application of different method-
ologies to forming this crucial stereogenic centre since fumimycin
was isolated as a non racemic mixture with unknown absolute
configuration.
Considering a strategy for the construction of the key structure,
we envisioned an organocatalytic approach to the stereogenic
centre (Scheme 1).
Claisen-rearrangement of the allylic substituent and exchange
of the amide side group followed by a ring opening of the
lactone would lead to our central product 4. Subsequently, the
N-electrophile, which can be introduced via an organocatalytic
reaction, is disconnected to afford 5 which is synthesized from 6
in a Wittig reaction.
aInstitut fu¨r Organische Chemie, Karlsruhe Institute of Technology
(KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany. E-mail: stefan.
braese@kit.edu; Fax: +49 721 608 8581; Tel: +49 721 608 2903
bLaboratory of Inorganic Chemistry, University of Helsinki, 00014, Helsinki,
Finland
† Electronic supplementary information (ESI) available: General methods,
experimental procedures and NMR and HPLC spectra. CCDC reference
number 738983. For ESI and crystallographic data in CIF or other
electronic format see DOI: 10.1039/b916372g
Our synthesis began with a Baeyer–Villiger type oxidation
(Dakin reaction)10 of commercially available 2,4-dimethoxy-
benzaldehyde (8) into the corresponding phenol 10 (Scheme 2),
which could then be etherified into 12 with a yield of 83%.11
Acylation of the aromatic ring using the mixed anhydride formed
by trifluoroacetic acid anhydride and acetic acid gave rise to the
acetophenone 14 in 74% yield.12 To overcome the drawbacks of
this route that lie in the harsh conditions necessary to deprotect
the hydroxyl groups, we also tested a protection group other
than methyl ether. Starting from 2,4-dihydroxybenzaldehyde,
the hydroxyl groups were protected with tert-butyl-diphenylsilyl-
chloride (TBDPSCl) to furnish 9 in 87% yield. Oxidation of the
aldehyde to 11 proceeded smoothly, but successive treatment with
allylbromide produced only traces of 13, which is probably due to a
migration of the protective groups throughout the molecule under
‡ Crystal structure determination
The single-crystal X-ray diffraction study was carried out on a Nonius
Kappa-CCD diffractometer at 123(2) K using Mo-Ka radiation (l =
24a
˚
0.71073 A). Direct Methods (SHELXS-97) were used for structure
solution and refinement was carried out using SHELXL-9724a (full-matrix
least-squares on F2). Hydrogen atoms were localized by difference electron
density determination and refined using a riding model (H(N) free). The
absolute structure of 21 could not be determined reliably by refinement
of Flack’s x-parameter (x = 0.2(7)),24b but using Bayesian statistics on
Bijvoet differences the absolute configuration at C2 was determined as
(C2:S) (FLEQ = 0.05(40)).24c
21: colourless, C20H28N2O8, M = 424.44, crystal size 0.40 ¥ 0.25 ¥
˚
0.15 mm, orthorhombic, space group P212121 (No. 19): a = 8.681(1) A,
3
˚
˚
˚
b = 9.784(1) A, c = 24.875(3) A, V = 2112.8(4) A , Z = 4, r(calc) =
1.334 Mg m-3, F(000) = 904, m = 0.103 mm-1, 16621 reflexes (2qmax = 55◦),
4774 unique [Rint = 0.051], 276 parameters, 1 restraint, R1 (I > 2s(I)) =
0.036, wR2 (all data) = 0.087, GOOF = 1.07, largest diff. peak and hole
-3
˚
0.212/-0.244 e A . CCDC 738983.
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Scheme 1 Retrosynthetic analysis with the planned key step highlighted.
Scheme 3 Model study starting from 12.
Scheme 2 Synthesis of the acetophenone 14.
the reaction conditions. Even under varied reaction conditions, an
improvement of the yield was not possible.
Compound 12 was used as a model system, and was submitted
to microwave irradiation and underwent a Claisen rearrangement
within 2 h to give 16 in 80% yield (Scheme 3).13 In a further step,
the isomerization of this compound was also tested. First, the free
phenol 16 was protected using dimethylsulfate in 43% yield, then
2,4-dimethoxy-6-allylanisole (17) in THF was heated to reflux for
16 h in the presence of potassium-tert-butoxide. This procedure
furnished 1,2,4-trimethoxy-6-propenylbenzene (18) in 66% yield
with the thermodynamically more stable E-isomer being the only
product. For practical reasons, though, 14 was used as a starting
point for further studies.
Scheme 4 Generation of the aldehyde 20 through four different routes.
The preparation of the starting material for our key step
began with a Wittig reaction with methoxymethyl(triphenyl)-
phosphonium chloride at -78 C (Scheme 4). Unfortunately, the
◦
Simply by changing the reaction temperature to 0 ◦C, however, 19
could be isolated in 60% as a E/Z-mixture of 1 : 1.36.
electron-rich acetophenone did not react under these conditions.
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Cleavage of the enol ether under acetic conditions14 resulted in
formation of the desired product 20 in 39% yield. Using an im-
proved procedure of Cohen and co-workers under mild conditions,
treatment of the starting material with chlorotrimethylsilane/NaI
for 5 min at rt furnished 83% of the aldehyde 20.15 Alternatively, we
performed an epoxidation of 14 and Meinwald rearrangement to
20. As a fortuitous outcome, the intermediate epoxide opened
to the designated aldehyde 20 directly without addition of
accessory Lewis acid.16 Nevertheless, with this direct method the
yields remained lower (at best 18% with diiodomethane17 and
29% with trimethylsulfonium iodide,18 no reaction at all with
trimethylsulfoxonium iodide), thus the synthesis of 20 was most
efficiently achieved when using Wittig-reaction and subsequent
cleavage rather than by use of the one-pot procedure.
We then turned our attention towards the main topic of our
study. The direct, catalytic a-amination of a-substituted carbonyl
compounds with either sulfonamides (Scheme 5, path 1 and 2) or
azodicarboxylates (path 3) as nitrogen sources represents one of
the simplest procedures for construction of the stereogenic centre
attached to a nitrogen atom. The first procedure we followed was
the addition of chloramine-T to our substrate (path 1). Following
a previously developed procedure,19 aldehyde 20 was exposed to
1.5 eq chloramine-T and 5 mol% L-proline in acetonitrile at rt for
16 h. On TLC, though, only starting material and the sulfonamide
as the byproduct of the reagent could be observed. Even when the
amount of catalyst was increased to 1.0 eq. and the temperature
was raised to 60 ◦C, the reaction mixture remained the same. This
is however probably explicable by the higher substitution pattern
with three electron-donating groups on the aromatic backbone. In
our earlier work, we found that with 2 mol% catalyst and either
an un- or fluorine-substituted phenylic backbone, the reaction
proceeded well (83%), whereas with a methoxy substituent a drop
in yield was observed (71% in 4-position and 74% in 3-position).19
Table 1 Selected data of the optimization of the addition of azodicar-
boxylates to aldehyde 20a
Entry Reagent eq. L-proline Temp./◦C Time/h Yield (%) Ee (%)
1
2
3
4
5
6
7
8
9
DEAD 0.5
DEAD 1.0
DEAD 2.0
DEAD 0.5
DEAD 0.5
DEAD 0.5
DEAD 1.0
DBAD 1.0
DBAD 2.0
DtBAD 2.0
60
60
60
80
rt
60
60
60
60
60
16
16
16
16
120
1
48
50
80
41
72b
47c
42c
45
81
71
38
35
47
44
8
33
34
26
23
60
1
16
16
16
10
a Solvent: acetonitrile. b Solvent: 1,4-dioxane. c Application of constant
microwave power of a max. of 200 W.
from electronic effects of the substrate. In an earlier work23 it had
been shown that a drop of yield from 87% to 63% was observed
when switching from one to two methoxy-substituents. In our case,
with a system bearing three electron-pushing groups, this effect
should be obviously even more distinctive. In order to overcome
this handicap, the catalyst amount was first raised to 1.0 and in the
next step to 2.0 equivalents (Table 1, Entries 2 and 3). Gratifyingly,
in the latter case, 80% of the amidated product could be obtained.
The enantioselectivity, however, remained the same for 0.5 and
1.0 equivalent of catalyst; only with 2.0 eq. of catalyst an ee of
47% was reached. Heating the reaction mixture even more to
80 ◦C with 0.5 eq of L-proline had no positive influence on the
reaction outcome as the yield remained in the same range as at a
lower temperature with just a slightly higher ee of 44% (Table 1,
Entry 4 compared to Entry 1). We also performed the reaction
at room temperature within 5 d using 1,4-dioxane as a solvent
(Entry 5). This combination gave the best results in the case of
hydratropaldehyde with 87% conversion and 67% ee. In our case,
an increased yield of 72% was observed, but the enantioselectivity
decreased significantly to 8% ee. In this case the catalyst probably
functions more as a sub-stoichiometric base rather than in a true
catalytic way.
The reaction was also tested using microwave heating, however
with disappointing results (Table 1, Entries 6 and 7). Contrary
to our previously published findings,22 neither the yield nor
enantioselectivity could be improved. The structure of 21 is
presented in Fig. 2. Besides diethyl azodicarboxylate, dibenzyl
(DBAD) and di-tert-butyl (DtBAD) azodicarboxylates could also
be utilized as nitrogen-transfer reagents (Entries 8–10). For the
dibenzyl compound, the yields display the same trend as with
the ethyl ester, the enantioselectivities on the other hand being
lower than with the ethyl residue (Table 1, Entries 8 and 9).
Surprisingly, when changing from dibenyzl- to di-tert-butylazo-
compound, stereoselectivity rose significantly to 60% with the yield
dropping only slightly to 71% (Table 1, Entry 10).
Scheme 5 Addition of N-electrophiles to aldehydes.
Employing a different N-electrophile (Scheme 5, path 2, in the
case of tosylazide same product as from path 1 was isolated),
conversion of 20 with 1.2 eq. tosylazide and 1.0 eq. L-proline in
ethanol at rt for 3 d was attempted,20 but again no reaction was
observed.
Path
3 comprises the attack of azodicarboxylates to
a-substituted aldehydes.9,21 In compliance with previously pub-
lished results, 20 was stirred with 1.5 eq diethyl azodicarboxylate
◦
and 50 mol% L-proline in acetonitrile at 60 C for 16 h as a test
reaction (Table 1, Entry 1).22 Pleasingly, 48% of the amidated
product 21 could be isolated. Most likely the low yield results
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Fig. 2 Molecular structure of 21 (displacement parameters are drawn at
50% probability level).
Oxidation of the aldehyde 21 and subsequent esterification
of the free carboxylic acid with dimethylcarbonate and DBU
furnished 24 in 21% yield over two steps (Scheme 6).
7 For a different approach to these molecules from our laboratories:
P. Gross and C. Hartmann, unpublished.
8 For a different approach to these lactones prior to the discovery of
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46–61; A. de la Hoz, A. Diaz-Ortiz, M. Victoria Gomez, J. Antonio
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Scheme 6 Mild oxidation and esterification of 21.
Conclusions
In conclusion, we prepared an advanced arene precursor of the
fungal natural product fumimycin using a Claisen rearrangement
and an asymmetric organocatalytic amination reaction. We are
now exploring this method for the total synthesis of fumimycin.
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We gratefully acknowledge the financial support provided by the
DFG (Schwerpunktprogramm Organokatalyse), the Karlsruhe
Institute of Technology (KIT) (FYS to C.E.H., grant for inter-
disciplinary research), the Karlsruhe House of Young Scientists
(KHYS) from the Karlsruhe Institute of Technology (grant to
C.E.H.), the BMBF, the Landesgraduiertenfo¨rderung (fellowship
to C.E.H.) and the German Business Foundation (fellowship for
P. J. G. ).
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Notes and references
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©