Synthesis of a carbohydrate-derived hydroxamic acid inhibitor of the bacterial enzyme (LpxC) involved in lipid A biosynthesis

Article abstract of DOI:10.1021/ol027458l

(Matrix presented) The enzyme LpxC (UDP-3-O-[(R)-3-hydroxymyristoyl] -GlcNAc deacetylase) catalyzes the second step of lipid A biosynthesis and is essential for bacterial growth. A GlcNAc-derived hydroxamic acid inhibitor 8 of this enzyme was synthesized

Full text of DOI:10.1021/ol027458l

ORGANIC
LETTERS
2003
Vol. 5, No. 4
539-541
Synthesis of a Carbohydrate-Derived
Hydroxamic Acid Inhibitor of the
Bacterial Enzyme (LpxC) Involved in
Lipid A Biosynthesis
,†
Xuechen Li,† Taketo Uchiyama,†,‡ Christian R. H. Raetz,§ and Ole Hindsgaul*
Department of Chemistry, UniVersity of Alberta, Edmonton, AB T6G 2G2, Canada,
College of Pharmacy, Nihon UniVersity, Chiba 274-0063, Japan, and Department of
Biochemistry, Duke UniVersity Medical Center, Durham, North Carolina 27710
ole.hindsgaul@ualberta.ca
Received December 12, 2002
ABSTRACT
The enzyme LpxC (UDP-3-O-[(R)-3-hydroxymyristoyl]-GlcNAc deacetylase) catalyzes the second step of lipid A biosynthesis and is essential
for bacterial growth. A GlcNAc-derived hydroxamic acid inhibitor 8 of this enzyme was synthesized using two different routes. Compound 8
exhibits activity toward LpxC enzymes from a wider spectrum of bacterial species than any of the previously reported hydroxamic acid
inhibitors.
The clinical efficacy of many existing antibiotics is being
threatened by the emergence of multidrug-resistant bacterial
pathogens. There is an urgent need for compounds that act
on novel molecular targets that circumvent the established
resistance mechanisms. Gram-negative bacteria, which are
responsible for a large number of infectious diseases, have
unique outer membranes that contain lipopolysaccharides
(LPS). Agents interfering with the biosynthesis of LPS are
often bactericidal or bacteriostatic.1
The hydrophobic anchor part of the LPS molecule is called
lipid A. Recent studies2 have shown that the enzymes
involved in the biosynthesis of lipid A are suitable pharma-
ceutical targets. Many of these enzymes are both unique and
essential to Gram-negative bacteria. The enzyme LpxC is
one example: it catalyzes the second step in lipid A
biosynthesis (Scheme 1). LpxC has been identified in more
than 40 Gram-negative species.3
In 1996, Merck scientists reported the discovery that
hydroxamic acids, derivatized with hydrophobic aromatic
moieties, could inhibit LpxC from E. coli. These inhibitors
were shown to bind competitively to a zinc ion of the
enzyme.4,5 We now report the synthesis of compound 8
(Scheme 2), which is a carbohydrate-derived hydroxamic
acid where the carbohydrate part resembles the natural
substrate of the LpxC enzyme: UDP-3-O-[(R)-3-hydroxy-
(3) Kline, T.; Andersen, N. H.; Harwood: E. A.; Bowman, J.; Malanda,
A.; Endsley, S.; Erwin, A. L.; Doyle, M.; Fong, S.; Harris, A. L.;
Mendelsohn, B.; Mdluli, K.; Raetz, C. R. H.; Stover, C. K.; Witte, P. R.;
Yabannavar, A.; Zhu, S. J. Med. Chem. 2002, 45, 3112.
(4) Onishi, H. R.; Pelak, B. A.; Gerchens, L. S.; Silver, L. L.; Kahan, F.
M.; Chen, M.; Patchett, A. A.; Galloway, S. M.; Hyland, S. A.; Anderson,
M. S.; Raetz, C. R. H. Science 1996, 274, 980.
† University of Alberta.
‡ Nihon University.
§ Duke University Medical Center.
(1) Ritter, T. K.; Wong, C.-H. Angew. Chem., Int. Ed. 2001, 40, 3508.
(2) (a) Raetz, C. R. H. J. Bacteriol. 1993, 175, 5745. (b) Galloway, S.
M.; Raetz, C. R. H. J. Biol. Chem. 1990, 265, 6394. (c) Kelly, T. M.;
Stachula, S. A.; Raetz, C. R. H.; Anderson, M. S. J. Biol. Chem. 1993,
268, 19866.
(5) Jackman, J. E.; Raetz, C. R. H.; Fierke, C. A. Biochemistry 1999,
38, 1902.
10.1021/ol027458l CCC: $25.00 © 2003 American Chemical Society
Published on Web 01/25/2003

from a broader range of bacterial species than the previously
reported noncarbohydrate hydroxamic acid inhibitors.
Two synthetic routes were evaluated for the preparation
of inhibitor 8. In the first (Scheme 3), the epoxide 1, available
Scheme 1
Scheme 3 a
a Reaction conditions: (a) AllylMgBr, THF; (b) SnCl4, Et3SiH,
CH2Cl2; (c) Ac2O, pyridine; (d) NaIO4, RuCl3‚H2O, CCl4/CH3CN/
H2O; (e) BnONH2‚HCl, EDAC‚HCl, TEA, CH2Cl2; (f) NaOMe,
MeOH; (g) benzaldehyde dimethylacetal, TsOH‚H2O, CH3CN; (h)
myristoyl chloride, DMAP, pyridine; (i) H2, Pd/C, AcOH
myristoyl]-GlcNAc. A study6 previously showed that com-
pound 8 exhibited inhibitory activity toward LpxC enzymes
from 1,6-anhydro-D-glucose7 or D-glucal8 in four or two steps,
respectively, was opened with allylmagnesium bromide to
give the expected trans-diaxial product 2 (79%). Reductive
opening of the 1,6-anhydro ring with SnCl4 and Et3SiH
followed by O-acetylation (Ac2O/pyridine) gave 3 (88%).
Oxidative cleavage of the double bond in 3 with ruthenium
tetroxide (generated in situ from RuCl3 and NaIO4)9 gave a
carboxylic acid derivative, where the benzyl protecting group
Scheme 2
(6) Jackman, J. E.; Fierke, C. A.; Tumey, L. N.; Pirrung, M.; Uchiyama,
T.; Tahir, S. H.; Hindsgaul, O.; Raetz, C. R. H. J. Biol. Chem. 2000, 275,
11002.
(7) Cerny, M.; Vecerkova, H.; Cerny, I.; Pacak, J. Collect. Czech. Chem.
Commun. 1980, 45, 1837 and references therein.
(8) Xue, J.; Guo, Z. Tetrahedron Lett. 2001, 42, 6487 and references
therein.
(9) Carlsen, P. H. J.; Katsuki, T.; Martin, V. S.; Sharpless, K. B. J. Org.
Chem. 1981, 46, 3936.
540
Org. Lett., Vol. 5, No. 4, 2003

problems with side reactions at the O-acylation stage.
Therefore, a second synthetic pathway to 8 was devised
(Scheme 4), starting with derivative 9 (available10 in four
steps from D-glucal). Surprisingly, both 9 and its 3,4-di-O-
acetyl derivative failed to give significant quantities of
reductive ring-opening product when treated with SnCl4 and
Et3SiH. However, selective tert-butyldimethylsilyation of 9
gave 10 (81%), which on treatment with SnCl4 and Et3SiH
afforded 11 (67%) in 10 min. Use of TiCl4 instead of SnCl4
raised the yield of 11 to 80% but required 2 h.
Scheme 4 a
Desilylation of 11 with TBAF and subsequent reaction
with benzaldehyde dimethylacetal gave 13 (85%), O-myris-
toylation of which gave 14 (98%). Oxidative cleavage of
the double bond in 14 with ruthenium tetroxide, using the
same conditions as in the first pathway, gave the carboxylic
acid derivative where hydroxamic acid function could be
introduced near the end of the synthetic route using O-
benzylhydroxylamine/EDAC to give the protected hydrox-
amic acid derivative 7 (70%). Finally, as in the first pathway,
catalytic hydrogenation of 7 gave 8 (71%). This second
synthetic pathway gave a 26.8% total yield of 8 (from 9), as
compared to 12.5% (from 1) for the first pathway.
In summary, the second synthetic pathway (Scheme 4) to
the inhibitor 8 is the more efficient of the two. Synthesis of
analogues of 8 and further biological evaluation of the
synthesized derivatives is currently ongoing in our laboratory.
a Reaction conditions: (a) tert-butyldimethylsilyl chloride, imi-
dazole, DMF; (b) TiCl4, Et3SiH, CH2Cl2; (c) TBAF, THF; (d)
benzaldehyde dimethylacetal, TsOH‚H2O, CH3CN; (e) myristoyl
chloride, pyridine; (f) NaIO4, RuCl3‚H2O, CCl4/CH3CN/H2O; (g)
BnONH2‚HCl, EDAC‚HCl, TEA, CH2Cl2; (h) H2, Pd/C, AcOH
Acknowledgment. This work is supported by the Natural
Science and Engineering Research Council of Canada (O.H.)
and the NIH (grant GM-51310 to C.R.H.R.). X.L. is the
recipient of a graduate scholarship in Carbohydrate Chem-
istry from the Alberta Research Council. The authors
acknowledge the editorial assistance of Professor Thomas
Norberg (Swedish University of Agricultural Science) in the
preparation of this manuscript.
at OH-4 had been oxidized to a benzoate group. The crude
product was reacted with O-benzylhydroxylamine and a
condensing reagent (EDAC) to give the protected hydrox-
amic acid derivative 4 (76%). Deacylation (NaOMe) of 4
and subsequent reaction with benzaldehyde dimethylacetal
gave 6 (64%). O-Acylation with myristoyl chloride then gave
7 (52%). The low yield of 7 in the O-acylation step was
attributed to concomitant N-acylation. Deprotection of 7 (H2/
Pd/C) gave the final product 8 (71%).
Supporting Information Available: Experimental pro-
cedures and spectroscopic data for compounds 2-14. This
material is available free of charge via the Internet at
http://pubs.acs.org.
OL027458L
Some drawbacks with this first synthetic scheme were
identified. The synthesis is not practical on a large scale,
and the early introduction of the -CONHOBn group creates
(10) Leteux, C.; Veyrieres, A.; Robert, F. Carbohydr. Res. 1993, 242,
119.
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