Synthetic analogues of SB-219383. Novel C-glycosyl peptides as inhibitors of tyrosyl tRNA synthetase

Article abstract of DOI:10.1016/S0960-894X(01)00039-7

Novel inhibitors of bacterial tyrosyl tRNA synthetase have been synthesised in which the cyclic hydroxylamine moiety of SB-219383 is replaced by C-pyranosyl derivatives. Potent and selective inhibition of bacterial tyrosyl tRNA synthetase was obtained.

Full text of DOI:10.1016/S0960-894X(01)00039-7

Bioorganic & Medicinal Chemistry Letters 11 (2001) 711±714
Synthetic Analogues of SB-219383. Novel C-Glycosyl Peptides
as Inhibitors of Tyrosyl tRNA Synthetase
Pamela Brown,a,* Drake S. Eggleston,a R. Curtis Haltiwanger,b Richard L. Jarvest,a
Lucy Mensah,a Peter J. O'Hanlona and Andrew J. Popea
aGlaxoSmithKline, New Frontiers Science Park, Third Avenue, Harlow, Essex, CM19 5AW, UK
bGlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA
Received 29 November 2000; accepted 12 January 2001
AbstractÐNovel inhibitors of bacterial tyrosyl tRNA synthetase have been synthesised in which the cyclic hydroxylamine moiety of
SB-219383 is replaced by C-pyranosyl derivatives. Potent and selective inhibition of bacterial tyrosyl tRNA synthetase was
obtained. # 2001 Elsevier Science Ltd. All rights reserved.
Aminoacyl tRNA synthetases perform a crucial role in
protein biosynthesis, catalysing the attachment of an
amino acid onto its cognate tRNA. Selective inhibition
of bacterial isoleucyl tRNA synthetase can be achieved
with pseudomonic acid and synthetic analogues, and
this gives rise to potent antibacterial activity.1 In our
search for novel inhibitors of bacterial tRNA synthe-
tases as potential antibacterial agents, the natural pro-
duct, SB-219383 1,2,3 was discovered as a potent,
selective inhibitor of bacterial tyrosyl tRNA synthetase
(YRS). We have also shown that the bicyclic sca€old is
not an essential feature for enzyme inhibition. For
example, the monocyclic compound 2, derived from SB-
2193834 and the synthetic counterpart 35 show equal
potency to SB-219383. In addition, the synthesis of 3
has also enabled us to infer the absolute stereochemistry
of the natural product and its derivatives. These
compounds, however, show only weak antibacterial
activity, probably attributable to their high polarity
preventing penetration into the bacterial cell. The
hydroxylamine moiety is also a potential liability in the
structure. We sought to identify a simpli®ed carbohy-
drate based sca€old that could replace the cyclic
hydroxylamine and maintain inhibition of YRS. Here
we describe the synthesis of arabinose-derived analogues,
one of which exhibits nanomolar levels of inhibition of
YRS.
A pyranose template was selected for the initial mimic
of the hydroxylamine-containing ring. The few reported
syntheses of natural products containing C-glycosyl
a-amino acids mainly utilise multi-step introduction and
unmasking of the amino acid functionality. We wished
to use a short synthesis applicable to a variety of
*Corresponding author. Tel.: +44-1279-627633; fax: +44-1279-627628; e-mail: pam_brown-1@sbphrd.com
0960-894X/01/$ - see front matter # 2001 Elsevier Science Ltd. All rights reserved.
PII: S0960-894X(01)00039-7

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P. Brown et al. / Bioorg. Med. Chem. Lett. 11 (2001) 711±714
Scheme 1. (i) HBr, HOAc; (ii)
, ZnBr2, 1,2-dichloroethane, re¯ux, 18 h; (iii) NaBH4, MeOH, 0 ꢀC±rt, 1.5 h; (iv) BOCTyr,
1-hydroxybenzotriazole, EDAC, DMF, N(iPr)2Et, 18 h; (v) NaOMe, MeOH, 16 h; (vi) TFA.
templates, and decided to adopt a C-glycosylation
strategy in order to introduce the glycine unit in one
step. Lewis-acid promoted nucleophilic addition has
been a fruitful source of C-glycosylated sugars.6 In one
example,7 the silyl ketene acetal 4 derived from glycine,8
has been reported to react with a glucopyranoside sys-
tem, although the protected amino-acid moiety was not
elaborated further. Our development and extension of
this methodology as applied to l(+)-arabinose is
shown in Scheme 1.
tant to sodium borohydride reduction, consistent with
the steric crowding seen in the X-ray structure (Fig. 1)
preventing access of the reducing agent. The amine 8
was then coupled to l-BOC-tyrosine. Removal of the
pivaloyl groups with sodium methoxide caused hydro-
lysis of the methyl ester as well as epimerisation of one
of the amino acid stereocentres. After deprotection, the
diastereomers 9a and 9b were separated by reverse-
phase preparative HPLC. Amino acid analysis showed
that both diastereomers contained l-tyrosine, thus indi-
cating that the epimerisation had occurred at the a-ste-
reocentre of the C-glycosyl amino acid.10
l(+)-Arabinose was converted to the tetrapivaloyl
derivative 5 in 34% yield, and the structure con®rmed
by X-ray crystallography. Compound 5 was converted
into the anomeric bromide 6, and allowed to react with
the silyl ketene acetal 4 derived from N-tri¯uoroacetyl
glycine methyl ester using zinc bromide as Lewis acid
catalyst to a€ord the C-glycosylated product 7 as a 1:1
mixture of diastereomers at the glycine centre. The dia-
stereomers were separable by column chromatography.
X-ray crystallography of 7b9 con®rmed this to be the
a-l-anomer with the (S) stereochemistry at the amino
acid centre, based on the known absolute con®guration
of the sugar starting material (Fig. 1). The X-ray of
7a (unpublished results) also showed the a-l-anomer
with the opposite stereochemistry at the amino acid
centre.
The entire synthetic sequence was repeated using d-ara-
binose as the starting material, to give the diastereomers
Selective removal of the N-tri¯uoroacetate proved di-
cult as the amide was resistant to mild base hydrolysis
(potassium carbonate, methanol) whereas under
strongly basic conditions (sodium hydroxide or sodium
methoxide) partial removal of the pivaloyl groups was
seen. Successful deprotection was achieved by sodium
borohydride reduction of the (R) diastereomer 7a to 8.
However, the corresponding (S) diastereomer was resis-
Figure 1. A view of the glycoside 7b created with PLATON and
POVRAY. Disordered atoms with lower site occupancies are omitted
for clarity.

P. Brown et al. / Bioorg. Med. Chem. Lett. 11 (2001) 711±714
713
Table 1. Inhibition of S. aureus YRS
Compound
Stereochemistry at C10
(S)
Sugar ring
IC50 (nM)
2.0
1
3
(S)
1.2
9a
9b
(R)
(S)
a-l-Arabinose
a-l-Arabinose
260
100
10a
10b
(R)
(S)
b-d-Arabinose
b-d-Arabinose
NIa
NI
aNI=no inhibition at 3 mM.
Acknowledgements
10a and 10b. The pyranosyl analogues 9a, 9b, 10a and
10b were evaluated as inhibitors of Staphylococcus
aureus tyrosyl tRNA synthetase (YRS), in an amino-
acylation assay.11 As can be seen from Table 1, the l-
arabinose-derived diastereomer 9b was a potent inhi-
bitor of bacterial YRS with an IC50 value of 100 nM.
The epimer 9a was less potent, with an IC50 of 260 nM.
In contrast, no inhibition was observed for either of the
diastereomers 10a or 10b derived from d-arabinose. The
pyran 9b, is thus an inhibitor of YRS with the preferred
stereochemistry around the sugar ring, corresponding to
3 in which the hydroxylamine is directly replaced by
oxygen. By comparison to compound 3, the more active
diastereomer 9b was inferred to have the (S) stereo-
chemistry at C10. Compound 9b was also tested against
mammalian YRS and showed no inhibition up to 3 mM
indicating that the bacterioselectivity seen in the hydrox-
ylamine series has been retained.
The authors would like to thank D. O'Brien and
C. Seaman for 2D-NMR experiments.
References and Notes
1. Walker, G.; Brown, P.; Forrest, A. K.; O'Hanlon, P.; Pons,
J. E. In Recent Advances in the Chemistry of Anti-Infective
Agents; Royal Society of Chemistry: London, 1993; p 106.
2. Stefanska, A. L.; Coates, N. J.; Mensah, L. M.; Pope, A. J.;
Ready, S. J.; Warr, S. R. J. Antibiot. 2000, 53, 345.
3. Houge-Frydrych, C. S. V.; Readshaw, S. A.; Bell, D. J. J.
Antibiot. 2000, 53, 351.
4. Berge, J. M.; Broom, N. J. P.; Houge-Frydrych, C. S. V.;
Jarvest, R. L.; Mensah, L.; McNair, D. J.; O'Hanlon, P. J.;
Pope, A. J.; Rittenhouse, S. J. Antibiot. 2000, 53, 1282.
5. Berge, J. M.; Copley, R. C. B.; Eggleston, D. S.; Ham-
precht, D. W.; Jarvest, R. L.; Mensah, L. M.; O'Hanlon, P. J.;
Pope, A. J. Bioorg. Med. Chem. Lett. 2000, 10, 1811.
6. Postema, M. H. D. In C-Glycoside Synthesis; Rees, C. W.,
Ed.; CRC Press Inc.: Boca Raton, 1995; pp 1±63.
In conclusion, we have shown that a synthetic analogue
of SB-219383 in which the hydroxylamine-containing
ring is replaced by a pyranose sugar is a stereoselective
and bacterioselective inhibitor of tyrosyl tRNA synthe-
tase. These results facilitate the further development of
SARs of this series by allowing more ready synthetic
access to postulated inhibitory analogues.
7. Simchen, G.; Purkner, E. Synthesis 1990, 525.
8. Oesterle, T.; Simchen, G. Liebigs Ann. Chem. 1987, 687.
9. X-ray crystal structure determination of 7b. Crystals were
grown via the evaporation of an ethanol solution at reduced
pressure. Crystal data: colourless prism, 0.59Â0.38Â0.28 mm;

714
P. Brown et al. / Bioorg. Med. Chem. Lett. 11 (2001) 711±714
C25H38 F3NO10, Mr=506.28, orthorhombic, P212121 (no. 19),
a=11.879(5), b=16.504(7), c=32.737(13) A, V=6418(5) A3,
Z=8, Dx=1.179 Mg mÀ3, m(Mo Ka, l=0.71073 A)= 0.101
mmÀ1. Data collection: Nonius CAD4 di€ractometer, FR591
rotating anode generator, graphite monochromator, 223 K,
which were an appropriate multiple of Ueq for the bonded atom;
ref=4541, Npar=704, R1 [3162 data with I>2s(I)]=0.074,
N
wR2 (all data)=0.133, S=1.071; Ármin=0.17 e AÀ3, Ármax
=
0.28 e AÀ3; extinction coecient=0.0020(7). Crystallographic
data for this structure has been deposited with the Cambridge
Crystallographic Data Centre. Copies of the data can be
obtained, free of charge, on application to the Director, CCDC,
12 Union Road, Cambridge, CB2 1EZ, UK (Fax: +44-(0)1223-
336033 or e-mail: deposit@ccdc.cam.ac.uk).
y
max=39.98ꢀ, o/2y scans, Nref=5058, Nuniq=4696. Data
reduction: corrections for Lorentz and polarization e€ects;
decay correction, 4 standard re¯ections, maximum varia-
tion=6.4%; Rint=0.088. Solution and re®nement: SHELXTL
V5.10 IRIX package; direct methods; full-matrix least-squares
re®nement on F2; disordered tri¯uoro and t-butyl groups
modelled with partial occcupancy sites, coordinates and
anisotropic displacement parameters re®ned for the non-
hydrogen atoms (lower occupancy disordered atoms isotropic);
hydrogen atoms in idealised positions, riding or as rigid rotat-
ing groups, with isotropic atomic displacement parameters
10. All compounds were characterised by 400 MHz 1H NMR,
using 2D techniques where necessary. Comparison of 1H
NMR (D2O) chemical shifts (ppm) and coupling constants
(Hz) between compounds 3,5 9a and 9b is shown below.
11. Brown, P.; Mensah, L. M.; O'Hanlon, P. J.; Osborne,
N. F.; Pope, A. J.; Richardson, C. M.; Walker, G. Bioorg.
Med. Chem. 1999, 7, 2473.
Examples of chemical shifts (ppm) and coupling constants (Hz) for compounds 3, 9b and 9a
H
3
9b
9a
1
2
3
4
5ax
5eq
10
3.18 (dd, J=10.1, 1.1)
3.4 (bt, J=9.8)
3.87 (dd, J=10.0, 2.0)
3.62 (br.t, J=9.7)
3.77 (dd, J=9.5, 3.3)
4.05, br.t (J ca. 3)
3.70 (br d, J=12.7)
3.97 (dd, J=12.8, 2.0)
4.91 (d, J=1.9)
2.68, (dd, J=9.9, 1.5)
3.0 (bt, J=9.5)
3.55 (dd, J=9.7, 3.5)
4.01 (ddd, J ca. 4.9, 1.5, 1.5)
2.83 (dd, J=11.8, 1.2)
3.34 (dd, J=11.7, ca.3)
4.82 (d, J=1.0)
4.65 (d, J=1.5)