Synthesis of pyrrolidine-based hamamelitannin analogues as quorum sensing inhibitors in staphylococcus aureus

Article abstract of DOI:10.3762/bjoc.14.260

Interfering with bacterial cell-to-cell communication is a promising strategy to combat antimicrobial resistance. The natural product hamamelitannin and several of its analogues have been identified as quorum sensing inhibitors. In this paper the synthesi

Full text of DOI:10.3762/bjoc.14.260

Synthesis of pyrrolidine-based hamamelitannin analogues as
quorum sensing inhibitors in Staphylococcus aureus
Jakob Bouton1, Kristof Van Hecke2, Reuven Rasooly3 and Serge Van Calenbergh*1
Full Research Paper
Open Access
Address:
Beilstein J. Org. Chem. 2018, 14, 2822–2828.
1Laboratory for Medicinal Chemistry, Ghent University,
Ottergemsesteenweg 460, 9000 Ghent, Belgium, 2XStruct,
Department of Chemistry, Ghent University, Krijgslaan 281 S3, 9000
Ghent, Belgium and 3Western Regional Research Center, Foodborne
Toxin Detection & Prevention Research Unit, Agricultural Research
Service, United States Department of Agriculture, Albany, CA 94710,
USA
doi:10.3762/bjoc.14.260
Received: 01 August 2018
Accepted: 01 November 2018
Published: 12 November 2018
This article is part of the thematic issue "Antibacterials, bacterial small
molecule interactions and quorum sensing".
Email:
Serge Van Calenbergh* - serge.vancalenbergh@ugent.be
Guest Editor: D. Spring
* Corresponding author
© 2018 Bouton et al.; licensee Beilstein-Institut.
License and terms: see end of document.
Keywords:
hamamelitannin; iminosugar; pyrrolidine; quorum sensing;
Staphylococcus aureus
Abstract
Interfering with bacterial cell-to-cell communication is a promising strategy to combat antimicrobial resistance. The natural prod-
uct hamamelitannin and several of its analogues have been identified as quorum sensing inhibitors. In this paper the synthesis of
pyrrolidine-based analogues of a more lead-like hamamelitannin analogue is reported. A convergent synthetic route based on a key
ring-closing metathesis reaction was developed and delivered the pyrrolidine analogue in 17 steps in high yield. Chemoselective
derivatization of the pyrrolidine nitrogen atom resulted in 6 more compounds. The synthesized compounds were evaluated in a
biofilm model, but were all inactive.
Introduction
Antimicrobial resistance is rapidly becoming a global threat [3,4]. Recently, targeting bacterial virulence has gained a lot of
[1,2]. It is estimated that worldwide, at least 700 000 people die attention [5-7]. It has been hypothesized that by “disarming” the
every year from drug-resistant strains of common bacterial pathogen, rather than inhibiting its growth, selective pressure
infections. Strategies to deal with the global antimicrobial resis- for resistance development will be much lower. Furthermore,
tance problem need to be multifactorial. Next to disease preven- reduction of bacterial virulence directly protects the host, and at
tion and the development of new antibiotics, it is essential to in- the same time renders the bacteria more susceptible towards the
vestigate innovative strategies to combat bacterial infections host defense system and antibiotics.
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Beilstein J. Org. Chem. 2018, 14, 2822–2828.
The Centers for Disease Control and Prevention (CDC) have a diverse set of analogues by chemoselective late-stage derivati-
listed a number of bacteria that present serious, urgent and con- zation of the pyrrolidine nitrogen. Previously, we used the
cerning threats [8]. One of these problematic bacteria is methi- iminosugar 5 to prepare a series of 2’-homoazanucleosides.
cillin-resistant Staphylococcus aureus (MRSA), a human This possible precursor was synthesized convergently in
pathogen that causes a wide range of clinical infections. In 12 steps [20]. The pyrrolidine ring was constructed via alkyl-
S. aureus, virulence is mainly mediated by quorum sensing, a ation of 6 and 7, followed by ring-closing metathesis. Stereose-
bacterial cell-to-cell communication system based on the secre- lective dihydroxylation of the resulting alkene then furnished
tion of signal molecules [9-11]. The natural product hamameli- the protected iminosugar 5. However, using intermediate 5 as a
tannin (1) has been identified as a non-peptide analogue of RIP starting point for the hamamelitannin analogues would render
(RNAIII-inhibiting protein), an inhibitor of the RAP/TRAP the synthetic route very linear and impractical to produce suffi-
(RNAIII-activating protein/target of RAP) quorum sensing cient amounts required to prepare a series of analogues.
system in S. aureus (Figure 1) [12-14]. Furthermore, hamameli-
tannin has been shown to inhibit biofilm formation and to Therefore, we envisioned a modification of the previously de-
potentiate the activity of antibiotics against staphylococcal veloped synthetic route, where the two fully functionalized side
biofilms in vitro and in vivo [12,15]. Structural optimization of chains are introduced prior to coupling and ring closure to
hamamelitannin by our group resulted in several more potent afford 8. This new synthetic route would be more convergent
and more druglike analogues of which compound 2 emerged as and efficient for the preparation of 3. Retrosynthetic analysis
a promising starting point for further optimization and subse- led to 9 and 10 as two key synthons, which would be assem-
quent development (Figure 1) [16-19]. Our earlier work bled via a Mitsunobu–Fukuyama reaction, and subsequently the
revealed that the optimal side chain substituents are an secondary amine converted to the pyrrolidine ring via a ring-
o-chlorobenzamide on the 5-position and a non-substituted closing metathesis reaction [21].
benzamide on the 2’-position. In absence of any structural infor-
Results and Discussion
mation of the inhibitor–target interaction, we were interested in
replacing the core tetrahydrofuran scaffold by a pyrrolidine ring Chemistry
in order to further elucidate the structure–activity relationship. The synthesis of fragment 9 is depicted in Scheme 2 and proved
The pyrrolidine nitrogen atom provides an extra point of diver- to be challenging. It was essential to introduce the nosyl group
sification, allowing further elaboration of the scaffold. Substitu- only in the last step, since several previous attempts to synthe-
ents on the ring nitrogen might lead to additional interactions size 9 failed due to side reactions caused by the strongly elec-
with the target and therefore provide more potent analogues. tron-withdrawing properties of the nosyl group. The successful
Moreover, the O-to-N replacement is expected to increase solu- synthesis starts with a Pd-catalyzed dynamic kinetic asym-
bility and possible polar interactions with the target. In this metric transformation of racemic butadiene monoepoxide to 12,
work we report the design, synthesis and biological evaluation employing phthalimide as nucleophile [22,23]. Attempts to
of a number of pyrrolidine-based hamamelitannin analogues.
substitute the alcohol functionality of 12 via displacement of the
derived mesylate with NaN3 failed, similar to previously re-
The envisioned strategy for the synthesis of the target pyrrol- ported difficulties by Trost et al. [24]. The benzamide substitu-
idine-based hamamelitannin analogues is depicted in Scheme 1. ent was therefore introduced via Mitsunobu reaction with
The synthesis of 4 as a key intermediate allows to gain access to N-Boc-protected ortho-chlorobenzamide 13. Removal of the
Figure 1: Structures of hamamelitannin (1), lead compound 2 and target compounds 3.
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Beilstein J. Org. Chem. 2018, 14, 2822–2828.
Scheme 1: Proposed strategy for the synthesis of the target analogues.
Scheme 2: Synthesis of fragment 9. Reagents and conditions: a) phthalimide, Pd2(allyl)2Cl2, ligand 15, Na2CO3, CH2Cl2, rt; b) i) 13, DEAD, PPh3,
toluene, 0 °C to rt; ii) TFA, CH2Cl2, H2O, rt; c) i) ethylenediamine, EtOH/THF 7:3, reflux; ii) p-Ns-Cl, Et3N, THF, 0 °C.
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Beilstein J. Org. Chem. 2018, 14, 2822–2828.
Boc-group with TFA resulted in 14. Next, the phthalimide was
removed via refluxing with ethylenediamine and the resulting
amine protected as para-nitrobenzenesulfonamide to obtain the
desired fragment 9.
The synthesis of 10 starts from commercially available 2-meth-
ylene-1,3-propanediol (16), which was selectively monopro-
tected in high yield as TBS ether (Scheme 3) [25]. The
remaining alcohol was then substituted for a phthalimide via
Mitsunobu reaction. Phthalimide deprotection, acylation with
benzoic acid, and removal of the silyl protecting group
furnished 10.
Fragments 9 and 10 were coupled under Mitsunobu conditions
(Scheme 4), affording 20 contaminated with Mitsunobu byprod-
ucts. Unfortunately, attempted ring-closing metathesis of 20
using the Grubbs–Hoveyda II catalyst failed to produce any
product, probably due to the insolubility of 20 in solvents suit-
able for metathesis reactions (1,2-DCE, toluene) and/or the
coordinating ability of the three (sulfon)amide functionalities
[26,27].
Scheme 3: Synthesis of fragment 10. Reagents and conditions:
a) TBSCl, NaH, THF, rt; b) phthalimide, PPh3, DEAD, THF, 0 °C to rt;
c) H2NNH2·H2O, MeOH, reflux; d) BzCl, Et3N, CH2Cl2, 0 °C; e) TBAF,
THF, rt.
To circumvent this problem, we were forced to alter the initial
synthetic strategy and used a different eastern fragment for the
ring-closing metathesis reaction. The ortho-chlorobenzamide Dihydroxylation selectively yielded the desired stereoisomer of
substituent would then be introduced in a later stage. We chose diol 26, which was subsequently protected as isopropylidene
to protect alcohol 12 as TBS ether and used the derived nosyl- acetal. In the next step, after removal of the TBS group and
protected fragment 23 as the coupling partner (Scheme 5).
mesylation, attempted substitution with NaN3 resulted only in
an elimination product. This led us to replace the electron-with-
Fragments 23 and 10 were coupled via Mitsunobu reaction, drawing nosyl protecting group with a Boc group. After
yielding 24 in 49% yield (Scheme 6). Fortunately, ring-closing removal of the TBS ether and mesylation of the resulting
metathesis of 24 now smoothly afforded 25 in high yield. alcohol, substitution with NaN3 now smoothly provided azide
Scheme 4: Coupling of 9 and 10 and attempted ring-closing metathesis. Reagents and conditions: a) PPh3, DEAD, THF/DMF 2:1, 0 °C to rt;
b) 5 mol % Grubbs–Hoveyda II, 1,2-DCE, 50 °C.
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Beilstein J. Org. Chem. 2018, 14, 2822–2828.
29. The azide was then reduced under classical Staudinger
conditions, followed by amide formation with ortho-chloroben-
zoic acid and a final acidic deprotection step to provide the
desired analogue 4. Despite the change of the initial strategy
and resulting elongation of the synthetic route, the overall syn-
thesis still proved to be very efficient, delivering 4 in 6% yield
in 17 steps from 16.
The pyrrolidine nitrogen was then further derivatized with
several small substituents (Scheme 7). Reductive amination
with several aldehydes resulted in 3a–c. The N-methyl ana-
logue 3d was synthesized via methylation with MeI. The
methanesulfonamide 3e and acetamide 3f, in which the cationic
character of the pyrrolidine nitrogen is removed, were also syn-
thesized.
The correct stereochemistry of the synthesized analogues was
unequivocally proven via X-ray structural analysis of com-
pound 3a (Figure 2).
Scheme 5: Synthesis of alternative eastern fragment 23. Reagents
and conditions: a) TBSCl, imidazole, CH2Cl2, rt; b) H2NNH2·H2O,
MeOH, reflux; c) p-Ns-Cl, Et3N, CH2Cl2, 0 °C.
Scheme 6: Synthesis of 4. Reagents and conditions: a) PPh3, DEAD, THF, 0 °C to rt; b) Grubbs–Hoveyda II (5 mol %), 1,2-DCE, 50 °C;
c) K2OsO4·2H2O, NMO, acetone/H2O 3:1, rt; d) 2-methoxypropene, CSA (cat.), THF, rt; e) PhSH, K2CO3, MeCN, 50 °C; f) Boc2O, Et3N, CH2Cl2, rt;
g) TBAF, THF, rt; h) Ms-Cl, Et3N, CH2Cl2, 0 °C; i) NaN3, DMF, 60 °C; j) PMe3, H2O, THF, rt; k) 2-chlorobenzoyl chloride, Et3N, CH2Cl2, 0 °C;
l) conc. HCl, MeOH/H2O 1:1, reflux.
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Scheme 7: Late stage functionalization of the pyrrolidine nitrogen. Reagents and conditions: A) (masked) aldehyde, NaBH3CN, AcOH, MeOH, 60 °C;
B) MeI, DIPEA, THF, 0 °C; C) Ms-Cl, Et3N, THF, 0 °C; D) AcOH, DIPEA, HATU, DMF, rt.
Conclusion
A convergent synthetic route for the synthesis of pyrrolidine-
based hamamelitannin analogues was developed. The origi-
nally envisioned strategy failed due to difficulties in the ring-
closing metathesis reaction, but modification of one of the cou-
pling partners solved this issue. The desired pyrrolidine-based
analogue was synthesized in 17 steps and chemoselective modi-
fication of the nitrogen atom provided 6 analogues. Unfortu-
nately, these analogues were inactive in inhibiting S. aureus
biofilm formation.
Supporting Information
Supporting Information File 1
Figure 2: Molecular X-ray structure of 3a, showing thermal displace-
ment ellipsoids at the 50% probability level. Positional disorder of the
chlorophenyl ring and the water solvent molecule are not shown.
Experimental details.
[https://www.beilstein-journals.org/bjoc/content/
supplementary/1860-5397-14-260-S1.pdf]
Biological evaluation
The synthesized analogues were tested in a S. aureus biofilm
model, but were all inactive (see Supporting Information
File 1).
Acknowledgements
Izet Karalic is gratefully acknowledged for technical assistance.
KVH thanks the Hercules Foundation (project AUGE/11/029
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Beilstein J. Org. Chem. 2018, 14, 2822–2828.
17.Vermote, A.; Brackman, G.; Risseeuw, M. D. P.; Coenye, T.;
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Excellence”) and the Special Research Fund (BOF) – UGent
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ORCID® iDs
Jakob Bouton - https://orcid.org/0000-0003-4193-7644
Kristof Van Hecke - https://orcid.org/0000-0002-2455-8856
Serge Van Calenbergh - https://orcid.org/0000-0002-4201-1264
19.Vermote, A.; Brackman, G.; Risseeuw, M. D. P.; Coenye, T.;
Van Calenbergh, S. Eur. J. Med. Chem. 2017, 127, 757–770.
doi:10.1016/j.ejmech.2016.10.056
20.Bouton, J.; Van Hecke, K.; Van Calenbergh, S. Tetrahedron 2017, 73,
4307–4316. doi:10.1016/j.tet.2017.05.083
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