Synthesis of the quorum sensing molecule Diffusible Signal Factor using the alkyne zipper reaction

Article abstract of DOI:10.1016/j.tetlet.2018.04.071

The development of a concise synthesis of the quorum sensing molecule Diffusible Signal Factor is described. This route exploits an alkyne zipper reaction to form a key terminal alkyne intermediate. The chemistry outlined here may also be applied to the preparation of cis-unsaturated analogues of Diffusible Signal Factor.

Full text of DOI:10.1016/j.tetlet.2018.04.071

Tetrahedron Letters xxx (2018) xxx–xxx
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Synthesis of the quorum sensing molecule Diffusible Signal Factor using
the alkyne zipper reaction
Vydyula P. Kumar a,b, Manoj K. Gupta a,b,d, Conor Horgan a,b, Timothy P. O’Sullivan a,b,c,
⇑
a School of Chemistry, University College Cork, Cork, Ireland
b Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
c School of Pharmacy, University College Cork, Cork, Ireland
a r t i c l e i n f o
a b s t r a c t
Article history:
The development of a concise synthesis of the quorum sensing molecule Diffusible Signal Factor is
described. This route exploits an alkyne zipper reaction to form a key terminal alkyne intermediate.
The chemistry outlined here may also be applied to the preparation of cis-unsaturated analogues of
Diffusible Signal Factor.
Received 16 February 2018
Revised 13 April 2018
Accepted 26 April 2018
Available online xxxx
Ó 2018 Published by Elsevier Ltd.
Keywords:
Alkyne zipper reaction
Diffusible Signal Factor
Partial hydrogenation
Introduction
tolerance.14 The cis-unsaturated double bond is known to be criti-
cal for biological activity with the saturated derivative displaying
Although bacterial infections have traditionally been treated
with antibiotics, many organisms have developed or acquired
mechanisms that render these drugs ineffective.1,2 This increased
resistance, compounded by the limited development of new
antimicrobial agents, poses a considerable threat to public health
and has spurred researchers to investigate alternative strategies
for disease control.3,4 These strategies include targeting the signal-
ing pathways that control the synthesis of microbial virulence fac-
tors and approaches that improve the efficacy of existing
antibiotics.5,6 For bacteria, cell-cell communication or quorum
sensing (QS) has been proposed as one possible target for inhib-
tion.7,8 Among the many families of QS molecules discovered to
date, several strains of bacteria utilise Diffusible Signal Factor
(DSF, 1) for cell to cell communication (Fig. 1).9 DSF is a cis-unsat-
urated long chain carboxylic acid, namely cis-11-methyl-2-dode-
cenoic acid. DSF was first identified in the X. camprestris,10 and
was subsequently discovered in other plant and human pathogens
such as Xanthomonas oryzae pv. oryzae11 and S. maltophilia.12,13
The presence of DSF is associated with multiple effects includ-
ing increased biofilm production, greater virulence and antibiotics
significantly lower activity, while trans-DSF has little or no activ-
ity.15 This cis-unsaturated motif in also found in related QS mole-
cules e.g. Burkholderia Diffusible Signal Factor (BDSF, 2).16
DSF constitutes a useful probe in biological studies for under-
standing the role of QS in certain bacteria. Furthermore, derivatives
of DSF could form the basis of future therapies for managing resis-
tant bacterial infections. Herein we describe our efforts to find a
concise synthesis of DSF. We outline our early approaches before
discovering an efficient route which exploits the alkyne zipper
reaction. Finally, we demonstrate the utility of this approach to
the preparation of cis-unsaturated derivatives of DSF.
Results and discussion
The starting point for the synthesis of DSF involved a dilithium
tetrachlorocuprate-mediated coupling of isopentyl magnesium
bromide with 6-bromohexan-1-ol (3) to afford 9-methyldecan-1-
ol (4) in 79% yield (Scheme 1). Dilithium tetrachlorocuprate is a
copper catalyst which is soluble in organic solvents and improves
the efficiency of halide substitutions with Grignard reagents.17
Subsequent Swern oxidation of 4 furnished aldehyde 5 in 88%
yield. The next step involved a Horner-Emmons reaction to install
the cis-unsaturated ester. Stabilised Horner-Emmons reagents typ-
ically furnish the trans-isomer as the major product. However, the
fluorinated phosphonates developed by Still and Gennari bearing
electron-withdrawing groups are cis-selective.18 Accordingly,
⇑
Corresponding author at: School of Chemistry, University College Cork, Cork,
Ireland.
E-mail address: tim.osullivan@ucc.ie (T.P. O’Sullivan).
Current address: Department of Chemistry, Central University of Haryana
d
Mahendergarh, Haryana, India.
https://doi.org/10.1016/j.tetlet.2018.04.071
0040-4039/Ó 2018 Published by Elsevier Ltd.
Please cite this article in press as: Kumar V.P., et al. Tetrahedron Lett. (2018), https://doi.org/10.1016/j.tetlet.2018.04.071

2
V.P. Kumar et al. / Tetrahedron Letters xxx (2018) xxx–xxx
Fig. 1. Quorum sensing molecules DSF and BDSF.
Scheme 2. (i) isoPentyl bromide/Mg then Li2CuCl4 (cat.), 0 °C to r.t., 15 h; (ii) CBr4,
PPh3, CH2Cl2, 0–10 °C, 2 h; (iii) 11, n-BuLi (2.7 M), THF then 10, DMSO, À50 °C to r.t.,
16 h; (iv) TFA, CH2Cl2, À10 °C, 3 h then NaOCl2, 30% H2O2, Na2HPO4, CH3CN, 0 °C to
r.t., 3 h; (v). H2 (60 PSI), Pd-Pb, CH2Cl2, r.t., 48 h.
Scheme 1. (i) isoPentyl bromide/Mg then Li2CuCl4 (cat.), THF, 0 °C, 2 h; (ii) Oxalyl
chloride, DMSO, Et3N, CH2Cl2, À78 °C, 2 h; (iii) NaH, THF, 0 °C to À78 °C, 1.5 h; (iv)
LiOH, THF, MeOH, H2O, 0 °C to r.t., 16 h.
ii
i
addition of aldehyde 5 to a solution of 6 and sodium hydride in THF
at 0 °C furnished
a,b-unsaturated ester 7 in 84% overall yield as a
96%
98%
4
4
mixture of isomers. The cis-unsaturated ester was predominant,
formed in a ratio of 85:15. Careful separation of the products by
column chromatography afforded Z-7 exclusively, as confirmed
by the smaller coupling of 11.5 Hz in its 1H NMR spectrum as com-
pared to 15.7 Hz for the trans-isomer. Finally, hydrolysis of ethyl
ester Z-7 with lithium hydroxide in THF-MeOH-H2O (2:1:1) at 0
°C for 16 h provided DSF (1) in 58% yield.
14
15
iii
iv
89%
1
6
6
87%
H
CO2
13
16
While this route did provide access to DSF, it is not without its
drawbacks. Chief among these is the limited selectivity of the Hor-
ner-Emmons reaction which produces both the cis- and trans-
unsaturated esters. This is further aggravated by the difficulty in
separating these isomers. Additionally, Horner-Emmons reagent
6 is relatively expensive. For these reasons, we sought out an alter-
native route to DSF which avoided these obstacles.
This alternative approach is outlined in Scheme 2. Branched
alcohol 9 was prepared via a copper-mediated coupling as before.
An Appel reaction with 9 furnished bromide 10 in 60% yield. Lithi-
ation of 3,3-diethoxy-1-propyne (11), followed by addition of 10,
afforded acetal 12. Acidic hydrolysis of 12 revealed an unstable
aldehyde which was oxidised in situ under Pinnick conditions to
produce propargyl acid 13 in 51% overall yield. Partial hydrogena-
tion of the acetylenic bond required careful optimisation so as to
avoid over-reduction to the alkane or isomerisation. Conjugation
with the carbonyl group reduces the reactivity of the triple bond.
Use of Lindlar’s catalyst in a 60 PSI hydrogen atmosphere furnished
DSF (1) in 89% yield exclusively as the Z-isomer. While this
approach was much improved compared to the original route,
some issues remained. Chief among these was the hydrolysis/oxi-
dation step, which proved capricious and was not amenable to
scale up.
Scheme 3. (i) n-BuLi, NaI, HMPA, THF then 1-bromo-3-methylbutane À20 °C to 0
°C; (ii) n-BuLi, KOtBu, 1,3-diaminopropane, THF; (iii) n-BuLi, then CO2(g), THF; (iv)
H2 (60 PSI), Pd-Pb, CH2Cl2, r.t, 48 h.
butane at 0 °C. The next step required the isomerisation of internal
alkyne 15 using the alkyne zipper reaction. Fortuitously, our initial
choice of n-butyllithium, potassium tert-butoxide and 1,3-
diaminopropane in tetrahydrofuran proved highly effective for this
transformation. Accordingly, 15 was converted to terminal alkyne
16 in 96% yield. Evidence for the successful isomerisation to the
target compound was found in the 1H NMR spectrum with the
appearance of a 1H triplet at 1.93 ppm. Homologation of the alkyne
to the corresponding carboxylic acid was achieved by deprotona-
tion of 16 followed by addition of gaseous carbon dioxide which
gave 13 in 87% yield. Finally, partial hydrogenation of 13 produced
DSF (1).
In an effort to generate analogues of DSF, we investigated the
coupling of 1 with a suitable sulfonamide. While a large number
of examples exist for the coupling of trans-unsaturated carboxylic
acids, similar examples of successful couplings of cis-unsaturated
carboxylic acids are limited. When we attempted the EDCI-medi-
ated coupling of 1 with benzenesulfonamide, the reaction was
accompanied by isomerisation of the double bond (Scheme 4). This
tendency of cis-unsaturated carboxylic acids to readily isomerise
has previously been noted.27 Separation of these isomers is often
difficult due to their tendency to co-elute.
Key to our revised route was an alkyne zipper reaction
(Scheme 3).19 This reaction results in the isomerisation of an inter-
nal alkyne to the corresponding terminal alkyne.20–23 Other groups
have successfully adopted a similar approach in their syntheses of
natural products.24,25 The alkyne zipper reaction works best with a
strong base, such as 1,3-diaminopropanide, which is typically gen-
erated in situ from 1,3-diaminopropane.26
An alternative approach which avoids these issues is to start
with carboxylic acid 13 which undergoes EDCI coupling with ben-
zenesulfonamide to afford 15 in 39% yield (Scheme 5). Partial
hydrogenation with Lindlar’s catalyst afforded sulfonamide 14 in
64% yield exclusively as the cis-isomer.
Treatment of 1-hexyne (14) with n-butyllithium in HMPA gen-
erated an acetylide which was alkylated with 4-bromo-2-methyl
Please cite this article in press as: Kumar V.P., et al. Tetrahedron Lett. (2018), https://doi.org/10.1016/j.tetlet.2018.04.071

V.P. Kumar et al. / Tetrahedron Letters xxx (2018) xxx–xxx
3
by the Irish Research Council. The research leading to these results
has received funding from the People Programme (Marie Sklo-
dowska Curie Actions) under REA grant agreements 272194
(MKG) and 655508 (VPK).
Scheme 4. (i) PhSO2NH2, EDCI, DMAP, CH2Cl2, 25 °C, 16 h.
A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at https://doi.org/10.1016/j.tetlet.2018.04.071.
References
1. Levy SB, Marshall B. Nat Med. 2004;10:S122.
2. Taubes G. Science. 2008;321:356.
3. Sleator RD, Hill C. Science. 2008;321:1294.
4. Laxminarayan R, Duse A, Wattal C, et al. Lancet Infect Dis. 2013;1057:13.
5. Clatworthy AE, Pierson E, Hung DT. Nat Chem Biol. 2007;3:541.
6. Sperandio V. Expert Rev Anti Infect Ther. 2007;5:271.
7. Catherine Grandclément C, Tannieres M, Moréra S, Dessaux Y, Faure D. D. FEMS
Microbiol Rev. 2016;40:86.
8. Galloway WR, Hodgkinson JT, Bowden SD, Welch M, Spring DR. Chem Rev.
2011;111:28.
Scheme 5. (i) PhSO2NH2, EDCI, DMAP, CH2Cl2, 25 °C, 16 h; (ii) H2 (60 PSI), Pd-Pb,
CH2Cl2, r.t., 16 h.
9. Deng Y, Wu J, Tao F, Zhang LH. Chem Rev. 2011;111:160.
10. Barber CE, Tang JL, Feng JX, Pan MQ, Wilson TJG. Mol Microbiol. 1997;24:555.
11. He Y-W, Wu J, Cha J-S, Zhang L-H. BMC Microbiol. 2010;10:1.
12. Huedo P, Yero D, Martinez-Servat S, et al. Front Microbiol. 2015;761.
13. Huang TP, Lee Wong AC. Res Microbiol. 2007;158:702.
14. Dow JM. J Appl Microbiol. 2017;122:2.
Conclusion
15. Wang LH, He Y, Gao Y, et al. Mol Microbiol. 2004;51:903.
16. Deng Y, Wu J, Eberl L, Zhang LH. Appl Environ Microbiol. 2010;76:4675.
17. Johnson DK, Donohoe J, Kang J. Synth Commun. 1994;24:1557.
18. Still WC, Gennari C. Tetrahedron Lett. 1983;24:4405.
19. Brown CA, Yamashita A. J Am Chem Soc. 1975;97:891.
20. Hoye RC, Anderson GL, Brown SG, Schultz EE. J Org Chem. 2010;75:7400.
21. Hoye RC, Baigorria AS, Danielson ME, Pragman AA, Rajapakse HA. J Org Chem.
1999;64:2450.
DSF plays an important role in cell-to-cell communication
among various strains of bacteria and is an attractive synthetic tar-
get. We have outlined the development of a concise synthetic route
to this molecule which exploits the alkyne zipper reaction followed
by a partial hydrogenation to furnish DSF as a single isomer. This
route also provides ready access to cis-unsaturated derivatives of
DSF.
22. Xing Y, Penn JH, O’Doherty GA. Synthesis. 2009;17:2847.
23. Xing Y, O’Doherty GA. Org Lett. 2009;11:1107.
24. Mulzer M, Tiegs BJ, Wang Y, Coates GW, O’Doherty GA.
2014;136:10814.
J Am Chem Soc.
Acknowledgements
25. Sharif EU, Wang H-YL, Akhmedov NG, O’Doherty GA. Org Lett. 2014;16:492.
26. Avocetien K, Li Y, O’Doherty GA. The alkyne zipper reaction in asymmetric
synthesis. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA; 2014.
27. Snyder JM, Scholfield CR. J Am Oil Chem Soc. 1982;59:469.
CH is grateful for funding by way of a Government of Ireland
Postgraduate Research Scholarship (GOIPG/2017/1111) provided
Please cite this article in press as: Kumar V.P., et al. Tetrahedron Lett. (2018), https://doi.org/10.1016/j.tetlet.2018.04.071