Bicyclic amino acid-carbohydrate-conjugates as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres

Article abstract of DOI:10.1039/c1ob06215h

This communication describes a general synthetic route to bicyclic amino acid-carbohydrate-conjugates, which would be useful as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres. The synthesis was achieved in 12 steps starting

Full text of DOI:10.1039/c1ob06215h

View Article Online / Journal Homepage / Table of Contents for this issue
Organic &
Biomolecular
Chemistry
Dynamic Article Links
Cite this: Org. Biomol. Chem., 2011, 9, 7300
www.rsc.org/obc
COMMUNICATION
Bicyclic amino acid-carbohydrate-conjugates as conformationally restricted
hydroxyethylamine (HEA) transition-state isosteres†‡
Sangram S. Kale,a Sanjay T. Chavan,b Sushma G. Sabharwal,b Vedavati G. Puranikc and
Gangadhar J. Sanjayan*a
Received 20th July 2011, Accepted 31st August 2011
DOI: 10.1039/c1ob06215h
This communication describes a general synthetic route to
bicyclic amino acid-carbohydrate-conjugates, which would
be useful as conformationally restricted hydroxyethylamine
(HEA) transition-state isosteres. The synthesis was achieved
in 12 steps starting from D-glucose. The striking features of
this system are the bicyclic rigid core displaying an a-amino
acid side chain and hydroxyethylamine moiety – both of which
would be potentially important for receptor interactions,
leading to various biomedical responses, as described in the
literature. Crystal structure investigation suggested extensive
intermolecular hydrogen-bonding interactions in this system,
involving the backbone amide and hydroxyl groups.
Proteases, a class of peptide-bond-cleaving enzymes that control
protein synthesis and function, offer a highly promising target for
therapeutic intervention, in several severe pathological conditions
such as AIDS, cancer, Alzheimer’s disease, malaria etc.1–3 Reac-
Fig. 1 Transition-state mimics of scissile peptide bond.
tions mediated by proteases proceed via a tetrahedral transition-
carrying an amino acid side chain as evident from a myriad of
state,4 which results from nucleophilic attack by a water molecule
on the scissile peptide bond carbonyl group. Among the transition-
state isosteres that have been successfully used in the design of
protease inhibitors, hydroxy-based isosteres, in particular HEA
isosteres,5 assumes special importance (Fig. 1). A transition-
state isostere is defined as a functional group that can mimic
the tetrahedral transition-state of amide bond hydrolysis, but
is stable and non hydrolyzable. Phosphinates,6 hydroxyethylcar-
bonyls (statins),7 hydroxyethylamines,5 hydroxymethylcarbonyls
(norstatins),8 hydroxyethylenes,9 and dihydroxyethylenes10 have
proven to be potent inhibitors of various proteases.
examples reported in the recent literature.11
The peptide backbone that carries amino acid side chains
or their surrogates facilitates receptor recognition, leading to
efficient reversible binding of the ligand with the receptor (Fig.
2).12 However, one issue that still remains to be addressed is
the conformational flexibility of the ligand that may adversely
affects receptor selectivity. In order to address this intriguing
problem, conformationally constrained peptide/mimetics carry-
ing transition-state isosteres have been designed, with varying
success.13 It is noteworthy that conformational restriction has
been proven to be an effective and simple tool to improve the
A strategy that has proved very successful for the design of
efficient protease inhibitors is based on the incorporation of a
transition-state analog into a peptide/peptidomimetic structure,
aDivision of Organic Chemistry, National Chemical Laboratory, Dr Homi
Bhabha Road, Pune, 411 008, India. E-mail: gj.sanjayan@ncl.res.in;
Fax: +91-020-2590-2629; Tel: +91-020-2590-2082
bBiochemistry Division, University of Pune, Pune-, 411007
cCenter for Materials Characterization, National Chemical Laboratory, Dr
Homi Bhabha Road, Pune, 411 008, India
† Dedicated to Prof. George W. J. Fleet, University of Oxford, UK, in
recognition of his exemplary contribution in the area of carbohydrates.
‡ Electronic supplementary information (ESI) available: General experi-
mental procedures, 1H, 13C, DEPT-135 NMR spectra and ESI mass spectra
of all new compounds are included. See DOI: 10.1039/c1ob06215h
Fig. 2 Proposed conformationally constrained carbohydrate-derived
bicyclic HEA isosteres featuring amino acid side chain.
7300 | Org. Biomol. Chem., 2011, 9, 7300–7302
This journal is
The Royal Society of Chemistry 2011
©

View Article Online
druggability, particularly the receptor selectivity, of acyclic/
flexible counterparts.13e Restricting conformational freedom of
flexible molecules can lead to substantial changes in assay
performance, as was demonstrated in a recent study using multi-
dimensional screening.13e
It is noteworthy that several bioactive natural products and
their synthetic analogs feature the bicyclic core of varying sizes,
although without amino acid side chains, as in the present case.
Some of the prominent examples would be castanospermine,
swainsonine, their ring expanded derivatives14 and a glycine-
tethered deoxynojirimycin analogue.15 Intriguingly, many of these
natural products and their synthetic analogues mentioned above
share a common bioactivity profile as glycosidase inhibitors.
The synthetic methodology disclosed herein is a short and
straightforward one starting from the readily available glucose as
the starting material. The synthetic route (Scheme 1) was initially
planned such that the amino acid-furanose-conjugated interme-
diate 4 could be subjected to a two-step acetonide deprotection-
cum-reductive amination protocol to straight away furnish the
required target bicyclic system 7. However, this strategy did not
yield a tangible result, despite best efforts. Therefore, we opted
to isolate the partially reduced advanced intermediate 6, followed
by successive acetonide deprotection and reductive amination to
yield 7. To begin with the synthesis, we started from D-glucose
and converted it to the acetonide protected azide derivative 2, in
five steps, following literature protocols.16 The known furanoside
derivative 2 was subjected to selective azide reduction followed by
coupling with N-terminal protected (as benzyloxy carbonyl, Cbz)
L-alanine to yield 3. The secondary alcohol in 3 could be efficiently
oxidized to the ketone 4 using PCC in DCM, which was ready for
the first reductive amination sequence aided by Pd(OH)2/H2 to
yield 5. It is noteworthy that this reductive amination proved
to be troublesome when Pd/C/H2, a standard condition, was
attempted. The free amine 5 was isolated and characterized as its
Cbz protected derivative 6. Next, 6 was subjected to acetonide
deprotection followed by reductive amination to successfully
furnish 7.
Fig. 3 Different views of the crystal structure of 7, clearly revealing
the relative stereochemistry. Stick PyMOL rendering (left) and ball and
stick (right). H-atoms have been deleted for clarity in the ball and stick
representation.
good quality could be obtained by slow evaporation of an aq.
methanolic solution of 7. Analysis of the crystal structure of 7
clearly reveals the relative stereochemistry of the backbone at
C4, C7, C8, and C9, as S, S, R, and R, respectively, and the
newly formed stereo junction at C9A as S. The amide group is
locked in cis-conformation, as found in the biologically important
diketopiperazines.17
It is noteworthy that 7 has been found to undergo extensive H-
bond-mediated self-assembly, as evident from its crystal structure
(Fig. 4). Three molecules of 7 self-assemble using a collection
of hydrogen bonding interactions primarily using the cis-amide
group of one molecule, and hydroxyl groups of two other molecules
forming a 14-membered H-bonded network. Intriguingly, two
hydroxyl groups of one molecule in the H-bonded network act
as hydrogen bonding donors, and two hydroxyl groups (OH) of
another molecule act as hydrogen bonding acceptors.18
Fig. 4 Self-assembled H-bonded network involving three molecules of 7,
as revealed from its crystal structure.
A preliminary investigation of the biological activity of the
constrained bicyclic amino acid-carbohydrate-conjugated HEA
isostere 7 showed 15% trypsin inhibitory activity, while no
inhibition was observed against chymotrypsin. Intriguingly, the
compound 7 did not show any inhibitory activity against any of the
glycosidases tested, under the assay conditions (ESI, S15–S16‡).
In conclusion, the present work details an efficient protocol
for the synthesis of bicyclic amino acid-carbohydrate-conjugates,
which would be of use as conformationally restricted hydroxyethy-
lamine (HEA) transition-state isosteres. The synthetic methodol-
ogy disclosed herein is noteworthy since it is a straightforward one
utilizing the readily available glucose as the starting material and
delivering the target conformationally constrained bicyclic HEA
isostere in high yielding synthetic sequences. The salient features
of this reported system are the bicyclic rigid core displaying an
Scheme 1 Regent and conditions: (i) a. TPP, THF-H2O, rt, 3 h; b.
Z–Ala–OH, EDC.HCl, CH3CN, rt, 12 h, 73%; (ii) PCC, NaOAc, MS,
DCM, rt, 5 h, 72%; (iii) Pd(OH)2/H2, MeOH, 120 psi, 24 h; (iv)
Cbz–Cl, NaHCO3, MeOH–H2O, rt, 4 h, 60%; (v) a. TFA–H2O (3 : 1);
b. Pd(OH)2/H2, MeOH, 120 psi, 24 h, 79%.
The relative stereochemistry in 7 could be unambiguously
assigned from its crystal structure (Fig. 3). Single crystals of
This journal is
The Royal Society of Chemistry 2011
Org. Biomol. Chem., 2011, 9, 7300–7302 | 7301
©

View Article Online
˚
a-amino acid side chain and hydroxyethylamine moiety – both of
which would be potentially important for receptor interactions,
leading to various biomedical responses, as described in the
literature.5,11
4 (a) F. WAngsell, P. Nordeman, J. Sa¨vmarker, R. Emanuelsson, K.
Jansson, J. Lindberg, A. Rosenquist, B. Samuelsson and M. Larhed,
Bioorg. Med. Chem., 2011, 19, 145–155; (b) A. Brik and C. Wong, Org.
Biomol. Chem., 2003, 1, 5–14.
5 (a) Marcin, Bioorg. Med. Chem. Lett., 2011, 21, 537–541; (b) M. Sova,
G. Cadez, S. Turk, V. Majce, S. Polanc, S. Batson, A. J. Lloyd, D. I.
Roper, C. W. G. Fishwick and S. Gobec, Bioorg. Med. Chem. Lett., 2009,
19, 1376–1379; (c) A. Gautier, D. Pitrat and J. Hasserodt, Bioorg. Med.
Chem., 2006, 14, 3835–3847; (d) K. Akaji, K. Teruya and S. Aimoto, J.
Org. Chem., 2003, 68, 4755–4763.
Experimental section
Single crystal X-ray crystallographic studies of 7
6 (a) T. Yamagishi, H. Ichikawa, T. Haruki and T. Yokomatsu, Org.
Lett., 2008, 10, 4347–4350; (b) R. Grzywa and J. Oleksyszyn, Bioorg.
Med. Chem. Lett., 2008, 18, 3734–3736; (c) M. Drag, R. Grzywa and
J. Oleksyszyn, Bioorg. Med. Chem. Lett., 2007, 17, 1516–1519.
7 (a) D. Gupta, R. S. Yedidi, S. Varghese, L. C. Kovari and P. M. Woster,
J. Med. Chem., 2010, 53, 4234–4247; (b) M. Muller, Angew. Chem., Int.
Ed., 2005, 44, 362–365.
8 (a) S. Nakatani, K. Hidaka, E. Ami, K. Nakahara, A. Sato, J. Nguyen,
Y. Hamada, Y. Hori, N. Ohnishi, A. Nagai, T. Kimura, Y. Hayashi and
Y. K i s o , J. Med. Chem., 2008, 51, 2992–3004; (b) A. Stoeckel-Maschek,
B. Stiebitz, R. Koelsch and K. Neubert, Bioorg. Med. Chem., 2005, 13,
4806–4820; (c) S. Weik, T. Luksch, A. Evers, J. Bc¸ttcher, C. A. Sotriffer,
A. Hasilik, H. Lc¸ffler, G. Klebe and J. Rademann, Chem. Med. Chem.,
2006, 1, 445–457.
9 (a) C. Bjo¨rklund, H. Adolfsson, K. Jansson, J. Lindberg, L. Vrang, A.
Hallberg, A. Rosenquist and B. Samuelsson, Bioorg. Med. Chem., 2010,
18, 1711–1723; (b) Y. Yamaguchi, K. Menear, N. Cohen, R. Maha, F.
Cumin, C. Schnell, J. M. Wood and J. Maibaum, Bioorg. Med. Chem.
Lett., 2009, 19, 4863–4867; (c) S. Hanessian, G. Yang, J. Rondeau, U.
Neumann, C. Betschart and M. Tintelnot-Blomley, J. Med. Chem.,
2006, 49, 4544–4567.
10 (a) J. Wannberg, Y. A. Sabnis, L. Vrang, B. Samuelsson, A. Karlen, A.
Hallberga and M. Larhed, Bioorg. Med. Chem., 2006, 14, 5303–5315;
(b) M. S. Plummer, A. Shahripour, J. S. Kaltenbronn, E. A. Lunney,
B. A. Steinbaugh, J. M. Hamby, H. W. Hamilton, T. K. Sawyer, C.
Humblet, A. M. Doherty, M. D. Taylor, G. Hingorani, B. L. Batley
and S. T. Rapundalo, J. Med. Chem., 1995, 38, 2893–2905; (c) T. I.
Oprea, C. L. Waller and G. R. Marshall, J. Med. Chem., 1994, 37,
2206–2215.
Colorless crystals of approximately 0.43 ¥ 0.09 ¥ 0.02 mm dimen-
sions, were used for data collection. Crystal to detector distance
6.05 cm, 512 ¥ 512 pixels/frame, quadrant data acquisition. Total
frames = 2424, Oscillation/frame -0.3◦, exposure/frame = 5.0
s/frame, maximum detector swing angle = -30.0◦, beam center =
(260.2, 252.5), in plane spot width = 1.24, SAINT integration,
q range = 2.66 to 25.00◦, completeness to q of 25.0◦ is 99.8%.
SADABS correction applied C9H16N2O4, M = 216.24. Crystals
belong tomonoclinic, space group P21, a = 7.8831(7), b = 8.2422(7),
◦
3
˚
˚
c = 7.9473(7) A, b = 105.506(1) , V = 497.57(8) A , Z = 2, Dc =
1.443 g/cc, m(Mo-Ka) = 0.114 mm-1, T = 296(2)K, 4835 reflections
measured, 1742 unique [I > 2s(I)], R value 0.0302, wR2 = 0.0673.
(4S,7S,8R,9R,9aS)-7,8,9-Trihydroxy-4-methylhexahydro-1H-
pyrido[1,2-a]pyrazin-3(2H)-one 7. A solution of 6 (0.19 g, 0.47
mmol) in TFA–H2O (6 mL, 3 : 1) was stirred at r.t for 4 h.
The reaction mixture was stripped of TFA completely by co-
evaporation with toluene to furnish a thick liquid, which was taken
up in methanol (20 mL) and hydrogenated with 20% Pd(OH)2
(0.07 g) at 120 psi for 24 h. The catalyst was filtered through celite,
washed with methanol, and the filtrate was concentrated to furnish
thick liquid which was purified by column chromatography to
afford◦7 (0.10 g, 79%); Rf 0.35 (MeOH/CHCl3: 30/70); mp: 233.2–
235.8 C; [a]2D2 -12.0 (c 0.5, CHCl3); IR (n) CHCl3, (cm-1) 3385,
3275, 1659, 1460; 1H NMR (400 MHz, DMSO-d6) d: 7.58 (s, 1H),
4.99–4.95 (m, 2H), 4.76–4.74 (d, J = 6.0 Hz, 1H), 3.47–3.44 (m,
4H), 3.01–2.93 (m, 3H), 2.60–2.55 (m, 2H), 1.20–1.18 (d, J = 6.8
Hz, 3H); 13C NMR (50 MHz, DMSO-d6) d: 171.5, 71.3, 71.0, 70.2,
59.6, 56.1, 49.6, 39.9; HRMS calcd. for C9H16N2O4Na, 239.1008;
Found, 239.1008. Elemental analysis calcd. for C9H16N2O4: Anal.
C, 49.99; H, 7.46; N, 12.96; Found: C, 49.57, H, 7.69, N, 13.21.
11 (a) C. Sund, O. Belda, D. Wiktelius, C. Sahlberg, L. Vrang, S. Sedig,
E. Hamelink, I. Henderson, T. Agback, K. Jansson, N. Borkakoti,
D. Derbyshire, A. Eneroth and B. Samuelsson, Bioorg. Med. Chem.
Lett., 2011, 21, 358–362; (b) Maillard, J. Med. Chem., 2007, 50, 776–
781.
12 (a) R. E. Dolle, C. V. C. Prasad, C. P. Prouty, J. M. Salvino, M. M. A.
Awad, S. J. Schmidt, D. Hoyer, T. M. Ross, T. L. Graybill, G. J. Speier,
J. Uhl, B. E. Miller, C. T. Helaszek and M. A. Ator, J. Med. Chem.,
1997, 40, 1941–1946; (b) Olson, J. Med. Chem., 1993, 36, 3039–3049.
13 (a) A. Guarna, A. Guidi, F. Machetti, G. Menchi, E. G. Occhiato, D.
Scarpi, S. Sisi and A. Trabocchi, J. Org. Chem., 1999, 64, 7347–7364;
(b) D. Scholz, P. Hecht, H. Schmidt and A. Billich, Monatshefte fur
Chemie, 1999, 130, 1283–1300; (c) J. A. Robl, M. P. Cimarusti, L. M.
Simpkins, B. Brown, D. E. Ryono, J. E. Bird, M. M. Asaad, T. R.
Schaeffer and N. C. Trippodo, J. Med. Chem., 1996, 39, 494–502; (d) E.
Marsault and M. L. Peterson, J. Med. Chem., 2011, 54, 1961–2004;
(e) Y.-K. Kim, M. A. Arai, T. Arai, J. O. Lamenzo, E. F. Dean, N.
Patterson, N. Patterson, P. A. Clemons and S. L. Schreiber, J. Am.
Chem. Soc., 2004, 126, 14740–14745.
Acknowledgements
SSK thanks CSIR, New Delhi, for a senior research fellowship.
This work was funded by International Foundation for Science
(IFS), Sweden; Grant No. No. F/4193-1.
14 (a) N. Wang, L. Zhang and X. Ye, Org. Biomol. Chem., 2010, 8, 2639–
2649; (b) N. Kumari and Y. D. Vankar, Org. Biomol. Chem., 2009, 7,
2104–2109; (c) K. S. Ajish Kumar, V. D. Chaudhari and D. D. Dhavale,
Org. Biomol. Chem., 2008, 6, 703–711; (d) C. Schaller and P. Vogel, Helv.
Chim. Acta, 2000, 83, 193–232; (e) W. H. Pearson and E. J. Hembre,
J. Org. Chem., 1996, 61, 5537–5545; (f) D. D. Dhavale, S. M. Jachak,
N. P. Karchea and C. Trombini, Tetrahedron, 2004, 60, 3009–3016;
(g) G. W. J. Fleet, N. M. Carpenter, S. Petursson and N. G. Ramsdena,
Tetrahedron Lett., 1990, 31, 409–412.
15 A. Kilonda, F. Compernolle, K. Peeters, G. J. Joly, S. Toppet and G. J.
Hoornaert, Tetrahedron, 2000, 56, 1005–1012.
16 J. Wang, J. Li, D. Tuttle, J. Y. Takemoto and C. T. Chang, Org. Lett.,
2002, 4, 3997–4000.
17 Gondry, Nat. Chem. Biol., 2009, 5, 414–420.
Notes and references
1 (a) B. E. Maryanoff and M. J. Costanzo, Bioorg. Med. Chem., 2008,
16, 1562–1595; (b) G. Fear, S. Komarnytsky and I. Raskin, Pharmacol.
Ther., 2007, 113, 354–368; (c) C. J. Scott and C. C. Taggart, Biochimie,
2010, 92, 1681–1688.
2 (a) G. Abbenante and D. P. Fairlie, Med. Chem., 2005, 1, 71–104; (b) G.
Ruiz-Go’mez, J. D. A. Tyndall, B. Pfeiffer, G. Abbenante and D. P.
Fairlie, Chem. Rev., 2010, 110, PR1–PR41.
3 (a) D. L. Buckley, T. W. Corson, N. Aberle and C. M. Crews, J. Am.
Chem. Soc., 2011, 133, 698–700; (b) A. K. Ghosh, B. D. Chapsal, A.
Baldridge, M. P. Steffey, D. E. Walters, Y. Koh, M. Amano and H.
Mitsuya, J. Med. Chem., 2011, 54, 622–634; (c) J. Nguyen, K. Kato,
K. Hidaka, H. Kumada, T. Kimura and Y. Kiso, Bioorg. Med. Chem.
Lett., 2011, 21, 2425–2429.
18 Crystallographic data of 7 has been deposited with the Cambridge
Crystallographic Data Centre: CCDC - 826859.
7302 | Org. Biomol. Chem., 2011, 9, 7300–7302
This journal is
The Royal Society of Chemistry 2011
©