Total Synthesis of Kalimantacin A

Article abstract of DOI:10.1021/acs.orglett.0c02190

The kalimantacins make up a family of hybrid polyketide-nonribosomal peptide-derived natural products that display potent and selective antibiotic activity against multidrug resistant strains of Staphylococcus aureus. Herein, we report the first total synthesis of kalimantacin A, in which three fragments are prepared and then united via Sonogashira and amide couplings. The enantioselective synthetic approach is convergent, unlocking routes to further kalimantacins and analogues for structure-activity relationship studies and clinical evaluation.

Full text of DOI:10.1021/acs.orglett.0c02190

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Letter
Total Synthesis of Kalimantacin A
Jonathan A. Davies, Freya M. Bull, Paul D. Walker, Angus N. M. Weir, Rob Lavigne, Joleen Masschelein,
Thomas J. Simpson, Paul R. Race, Matthew P. Crump, and Christine L. Willis*
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ABSTRACT: The kalimantacins make up a family of hybrid polyketide-
nonribosomal peptide-derived natural products that display potent and
selective antibiotic activity against multidrug resistant strains of Staph-
ylococcus aureus. Herein, we report the first total synthesis of kalimantacin
A, in which three fragments are prepared and then united via Sonogashira
and amide couplings. The enantioselective synthetic approach is
convergent, unlocking routes to further kalimantacins and analogues for
structure−activity relationship studies and clinical evaluation.
he kalimantacins [1−3 (Scheme 1A)] make up a family
T
of bacterial metabolites of mixed polyketide-nonriboso-
mal peptide synthase (PKS-NRPS) origin that display potent
antibiotic activity.1 Originally isolated from a soil sample
collected from the West Kalimantan region of Borneo, they are
produced by several bacteria, including Pseudomonas fluo-
rescens, and show high selectivity against multidrug resistant
Staphylococcus species, including methicillin resistant Staph-
ylococcus aureus (MRSA).2,3 The most active and abundant
member is kalimantacin A 1 (also known as batumin),3 whose
relative and absolute stereochemistry was determined in 2015
through a combination of degradation studies and fragment
synthesis.4 Preliminary clinical research has indicated that
topical application of kalimantacin A is highly effective at
disrupting and preventing the formation of S. aureus biofilms.5
Another fascinating aspect of these natural products is their
incorporation of β-branches, a structural feature present in
many polyketides with important biological activities.6
Uniquely, the kalimantacins contain three different and
sequential types of β-branches at C-3, C-5, and C-7, as well
as an additional methyl group at C-15. The biosynthetic
mechanisms that control this remarkable selectivity have
recently been investigated.6
Scheme 1. (A) Selected Kalimantacin Natural Products and
(B) Retrosynthetic Analysis of Kalimantacin Ester 4
The antistaphylococcal activity of the kalimantacins derives
from inhibition of FabI, an enoyl-acyl carrier protein reductase
enzyme that plays an essential role in fatty acid biosynthesis.7
Received: July 2, 2020
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X-ray crystallography and molecular dynamics simulations
have shown that the kalimantacin binding mode is unique,
differing significantly from those of other FabI inhibitors.8 The
stage is now set to gain further insights into the structure−
activity relationships (SARs) of the kalimantacins, which will
inspire future antistaphylococcal drug development. To realize
this potential, access to a library of analogues is now urgently
required. Herein, we describe the first total synthesis of
kalimantacin A 1 via an enantioselective, flexible, and
convergent approach.
In our retrosynthetic analysis, we anticipated that
kalimantacin A could be prepared from protected ester 4
(Scheme 1B). From here, a late-stage amide coupling of
(2R,3R)-3-hydroxybutanoic acid 5 and amine 6 was proposed.
The (E,Z)-diene was to be prepared via a Sonogashira coupling
of vinyl iodide 7 and alkyne 8, followed by stereoselective
reduction of the enyne. It was envisaged that 7 could be
assembled through lithiation of iodide 10 and reaction with
aldehyde 9. This convergent approach was designed to be
versatile and readily adaptable in terms of both chain length
and functionality to synthesize analogues for SAR studies, as
informed by X-ray crystallography and molecular dynamics
simulations with FabI. Furthermore, the route was to be
exploited for the preparation of putative biosynthetic
intermediates to further probe the mechanisms of β-branch
incorporation in polyketide biosynthesis.
alcohol 11 in 89% yield. However, treatment of 11 with LiOH
at room temperature returned only starting material and on
heating to 60 °C gave methyl ketone 12 via retro-aldol
fragmentation of the β-hydroxy ketone moiety (Scheme 2B).
This compound is of interest for SAR studies as it closely
resembles another natural product, 13, which was isolated from
a freshwater sponge and also displays activity against Gram-
positive bacteria, including S. aureus.9 Hydrolysis of methyl
ester 11 was achieved cleanly using porcine liver esterase
(PLE), giving kalimantacin A 1 in 88% yield.
Turning to the total synthesis of kalimantacin A, vinyl iodide
7 (C-12−C-20) was assembled from two building blocks,
aldehyde 9 and alkyl iodide 10, which were both prepared on a
multigram scale using previously reported procedures (see the
Supporting Information). Aldehyde 9 was synthesized in five
steps and 68% overall yield starting from the chiral epoxide
(S)-(−)-glycidol.10 Iodide 10 was prepared in three steps and
45% yield from a commercially available propionylated Evans
auxiliary.11
Lithiation of iodide 10 using tBuLi was required for the
coupling with aldehyde 9. It was found that only poor
conversion to 15 was observed at low temperatures, with
warming to 0 °C required to obtain full consumption of
aldehyde 9. However, at temperatures above approximately
−20 °C, the alkyl lithium cyclized to give cyclobutylidene 14
(which was trapped by an electrophile), meaning careful
temperature control was required (Scheme 3A).12−14 Addi-
To begin, it was important to establish if the proposed
protecting groups of 4 could be readily removed in the final
stages of the total synthesis. Thus, kalimantacin A 1 was
isolated from cultures of P. fluorescens in titers of 65 mg/L
using a procedure adapted from Mattheus et al.3 The acid was
methylated with TMSCHN2 to ester 11, and the 19-hydroxyl
was protected as the TBS ether to give 4 in 81% yield over two
steps (Scheme 2A). To ensure these protecting groups could
be removed cleanly, silyl ether 4 was treated with TBAF giving
Scheme 3. (A) Lithiation and Rearrangement of Iodide 10
and (B) Synthesis of Vinyl Iodide 7 (C-12−C-20)
Scheme 2. Semisynthetic Studies of Kalimantacin A
tionally, if an overly large excess of tBuLi was employed (>1.5
equiv with respect to iodide 10), then a secondary alcohol was
formed via addition to aldehyde 9. Following optimization,
desired alcohol 15 was isolated as a mixture of diastereomers in
83% yield and the coupling was successful on a multigram scale
(Scheme 3B). Removal of the TMS group using K2CO3 in
MeOH followed by acetylation gave ester 16. The (E)-vinyl
B
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iodide was installed through hydrostannation of the alkyne to
give 17, followed by in situ treatment with iodine to give 18.
Deprotection was undertaken at this stage to give the
corresponding alcohol, as DDQ was found to give a complex
mixture post-Sonogashira coupling. Finally, the alcohol was
transformed to mesylate 7 in 75% yield over two steps.
Preparation of alkyne 8 (C-1−C-11) was based upon our
previous work used in the structural assignment of
kalimantacin A in which iodide 19 was used as a synthetic
intermediate (Scheme 4).4 19 was subjected to lithium−
mixed cuprate species in which the trimethylsilylmethyl group
acts as an activating but nontransferable ligand.15,16 Conjugate
addition to methyl but-2-ynoate proceeded with complete
stereocontrol for the (E)-alkene, and then the TBS group was
cleaved under acidic conditions to liberate alcohol 20 in 83%
yield over two steps. Oxidation was undertaken using Dess-
Martin periodinane (DMP) to provide the aldehyde, which
was treated with Grignard reagent 21, formed from the
corresponding bromide.17 The resulting mixture of alcohols
was again oxidized using DMP to give ketone 22 as a single
enantiomer in 68% yield over three steps. The next stage was
the introduction of the exo-methylene moiety that had been
undertaken previously using Tour methylenation conditions
(Cp2ZrCl2, CH2I2, and Zn).4,18 While this was successful, the
reaction was capricious giving variable yields. Instead, it was
found that a Lombardo methylenation (TiCl4, CH2Br2, and
Zn)19 was more robust and reproducible, providing 23 in 58%
yield on a gram scale. Finally, deprotection was undertaken
using K2CO3 in MeOH to give alkyne 8.
Scheme 4. Synthesis of Alkyne 8 (C-1−C-11)
The Sonogashira coupling of vinyl iodide 7 and alkyne 8
proceeded smoothly to give enyne 24 in 88% yield, thus
completing the construction of the C-1−C-20 backbone of
kalimantacin A 1 (Scheme 5A). The next step of the synthesis
required conversion of mesylate 24 to azide 25. Maeda and co-
workers had reported that the steric bulk of a TBS group
hindered nucleophilic substitutions in similarly protected 1,2-
diols.20 However, heating mesylate 24 with NaN3 gave azide
25 in 85% yield. Reduction of azide 25 to amine 6 was
achieved using a Staudinger reaction employing PPh3 in a
mixture of THF and H2O. This reaction required very careful
degassing, as in the presence of air, rather than the required
hydrolysis of intermediate iminophosphorane 28, an aza-Wittig
halogen exchange with tBuLi and then added to a freshly
prepared solution of trimethylsilylmethylcopper to generate a
Scheme 5. (A) Completing the Total Synthesis of Kalimantacin A and (B) Formation of Urea 30
C
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reaction with carbon dioxide occurred to give isocyanate 29,
which further reacted to give dimeric urea species 30 (Scheme
5B).21,22
Paul D. Walker − School of Chemistry, University of Bristol,
Bristol BS8 1TS, United Kingdom
Angus N. M. Weir − School of Chemistry, University of Bristol,
Bristol BS8 1TS, United Kingdom
Rob Lavigne − Laboratory of Gene Technology, KU Leuven,
3001 Leuven, Belgium
Joleen Masschelein − Laboratory for Biomolecular Discovery
and Engineering, KU Leuven, 3001 Leuven, Belgium; VIB-KU
Leuven Center for Microbiology, Flanders Institute for
Biotechnology, 3001 Leuven, Belgium
The final fragment, acid 5, was prepared in two steps and
76% yield from ethyl (R)-3-hydroxybutanoate (see the
Supporting Information). Coupling of hydroxy acid 5 and
amine 6 was undertaken with no protection of the alcohol, thus
obviating the need for further protecting group manipulations.
Using COMU and iPr2NEt, hydroxy-amide 26 was isolated in
88% yield. Carbamoylation of 26 using trichloroacetyl
isocyanate was followed by concomitant hydrolysis of both
acetates with K2CO3 in MeOH. Oxidation of the resultant
alcohol with DMP provided ketone 27 in 93% yield over three
steps.
Thomas J. Simpson − School of Chemistry, University of Bristol,
Bristol BS8 1TS, United Kingdom
Paul R. Race − School of Biochemistry, University of Bristol,
Bristol BS8 1TD, United Kingdom; orcid.org/0000-0003-
0184-5630
Matthew P. Crump − School of Chemistry, University of Bristol,
Bristol BS8 1TS, United Kingdom; orcid.org/0000-0002-
7868-5818
The final key step of the total synthesis was the selective
reduction of (E)-enyne 27 to generate the required (E,Z)-
diene 4. In this case, commonly used hydrogenation with a
poisoned palladium catalyst was avoided due to concerns of
achieving the required chemoselectivity. Instead, 27 was
treated with zinc activated with copper and silver, which
gave the desired (E,Z)-diene 4 in 88% yield as a single isomer
Complete contact information is available at:
https://pubs.acs.org/10.1021/acs.orglett.0c02190
1
as determined by H NMR spectroscopy (J = 15 and 11 Hz,
Notes
respectively).23 The optical rotation of diene 4 prepared by
total synthesis was in excellent agreement with the reference
material obtained via protection of kalimantacin A 1 isolated
from cultures of P. fluorescens (Scheme 2). Finally, following
the previously established deprotection and ester hydrolysis
protocols (Scheme 2), we completed the first total synthesis of
kalimantacin A 1. The NMR spectral data and HPLC retention
time were in accord with those of an authentic sample of the
natural product (see the Supporting Information).
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
Financial support for this work was provided by the BBSRC
and EPSRC through the Bristol Centre for Synthetic Biology
(BB/L01386X/1), Bristol Chemical Synthesis Centre for
Doctoral Training for J.A.D. and P.D.W. (EP/L015366/1),
and doctoral training grants for F.M.B. and A.N.M.W.
In conclusion, herein we have reported the first total
synthesis of the PKS-NRPS-derived antibiotic natural product
kalimantacin A 1. The enantioselective and convergent
approach unites three fragments via Sonogashira and amide
couplings. This flexible synthetic strategy, combined with
recent insights into the binding of kalimantacin to FabI,8 will
enable SAR studies to be undertaken, thus paving the way for
the design of future selective antistaphylococcal drugs and their
development for clinical assessment. Additionally, this route
will be adapted for the synthesis of putative biosynthetic
intermediates to further probe the mechanisms of β-branch
incorporation in kalimantacin biosynthesis.
REFERENCES
■
(1) Tokunaga, T.; Kamigiri, K.; Orita, M.; Nishikawa, T.; Shimizu,
M.; Kaniwa, H. J. Antibiot. 1996, 49, 140.
(2) Kamigiri, K.; Suzuki, Y.; Shibazaki, M.; Morioka, M.; Suzuki, K.;
Tokunaga, T.; Setiawan, B.; Rantiatmodjo, R. M. J. Antibiot. 1996, 49,
136.
(3) Mattheus, W.; Gao, L.-J.; Herdewijn, P.; Landuyt, B.; Verhaegen,
J.; Masschelein, J.; Volckaert, G.; Lavigne, R. Chem. Biol. 2010, 17,
149.
(4) Thistlethwaite, I. R. G.; Bull, F. M.; Cui, C.; Walker, P. D.; Gao,
S.-S.; Wang, L.; Song, Z.; Masschelein, J.; Lavigne, R.; Crump, M. P.;
Race, P. R.; Simpson, T. J.; Willis, C. L. Chem. Sci. 2017, 8, 6196.
(5) Churkina, L. N.; Bidnenko, S. I.; Lopes dos Santos Santiago, G.;
Vaneechoutte, M.; Avdeeva, L. V.; Lutko, O. B.; Oserjanskaja, N. M.
BMC Res. Notes 2012, 5, 374.
ASSOCIATED CONTENT
* Supporting Information
■
sı
(6) Walker, P. D.; Williams, C.; Weir, A. N. M.; Wang, L.; Crosby, J.;
Race, P. R.; Simpson, T. J.; Willis, C. L.; Crump, M. P. Angew. Chem.,
Int. Ed. 2019, 58, 12446.
The Supporting Information is available free of charge at
https://pubs.acs.org/doi/10.1021/acs.orglett.0c02190.
(7) Mattheus, W.; Masschelein, J.; Gao, L.-J.; Herdewijn, P.;
Landuyt, B.; Volckaert, G.; Lavigne, R. Chem. Biol. 2010, 17, 1067.
(8) Fage, C. D.; Lathouwers, T.; Vanmeert, M.; Gao, L.-J.; Vrancken,
K.; Lammens, E.-M.; Weir, A. N. M.; Degroote, R.; Cuppens, H.;
Kosol, S.; Simpson, T. J.; Crump, M. P.; Willis, C. L.; Herdewijn, P.;
Experimental procedures and spectral data for all new
compounds (PDF)
AUTHOR INFORMATION
Corresponding Author
■
́
Lescrinier, E.; Lavigne, R.; Anne, J.; Masschelein, J. Angew. Chem., Int.
Ed. 2020, 59, 10549.
Christine L. Willis − School of Chemistry, University of Bristol,
Bristol BS8 1TS, United Kingdom; orcid.org/0000-0002-
3919-3642; Email: chris.willis@bristol.ac.uk
̌
(9) Rezanka, T.; Dembitsky, V. M. J. Nat. Prod. 2002, 65, 709.
́
(10) Bonini, C.; Chiummiento, L.; Videtta, V.; Colobert, F.; Solladie,
G. Synlett 2006, 2006, 2427.
(11) Forsyth, C. J.; Xu, J.; Nguyen, S. T.; Samdal, I. A.; Briggs, L. R.;
Rundberget, T.; Sandvik, M.; Miles, C. O. J. Am. Chem. Soc. 2006,
128, 15114.
(12) Baldwin, J. E. J. Chem. Soc., Chem. Commun. 1976, 734.
(13) Gilmore, K.; Alabugin, I. V. Chem. Rev. 2011, 111, 6513.
(14) Bailey, W. F.; Ovaska, T. V. J. Am. Chem. Soc. 1993, 115, 3080.
Authors
Jonathan A. Davies − School of Chemistry, University of Bristol,
Bristol BS8 1TS, United Kingdom
Freya M. Bull − School of Chemistry, University of Bristol,
Bristol BS8 1TS, United Kingdom
D
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Organic Letters
pubs.acs.org/OrgLett
Letter
(15) Bertz, S. H.; Eriksson, M.; Miao, G.; Snyder, J. P. J. Am. Chem.
Soc. 1996, 118, 10906.
(16) Dymock, B. W.; Kocienski, P. J.; Pons, J.-M. Synthesis 1998,
1998, 1655.
̌
́
́
́
(17) Kolundzic, F.; Murali, A.; Perez-Galan, P.; Bauer, J. O.;
Strohmann, C.; Kumar, K.; Waldmann, H. Angew. Chem., Int. Ed.
2014, 53, 8122.
(18) Tour, J. M.; Bedworth, P. V.; Wu, R. Tetrahedron Lett. 1989, 30,
3927.
(19) Lombardo, L. Tetrahedron Lett. 1982, 23, 4293.
(20) Maeda, K.; Yamamoto, Y.; Tomimoto, K.; Mase, T. Synlett
2001, 2001, 1808.
(21) Carnaroglio, D.; Martina, K.; Palmisano, G.; Penoni, A.;
Domini, C.; Cravotto, G. Beilstein J. Org. Chem. 2013, 9, 2378.
̈
(22) Yagodkin, A.; Loschcke, K.; Weisell, J.; Azhayev, A. Tetrahedron
2010, 66, 2210.
(23) Boland, W.; Schroer, N.; Sieler, C.; Feigel, M. Helv. Chim. Acta
1987, 70, 1025.
E
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