Design, synthesis, and evaluation of octahydropyranopyrrole-based inhibitors of mammalian ribonucleotide reductase

Article abstract of DOI:10.1016/j.bmcl.2005.08.062

Inhibitors of mammalian ribonucleotide reductase possessing a novel octahydropyranopyrrole scaffold based on a cyclic heptapeptide inhibitor have been designed, synthesized, and evaluated. Structure-function studies reveal that the bicyclic scaffold is in

Full text of DOI:10.1016/j.bmcl.2005.08.062

Bioorganic & Medicinal Chemistry Letters 15 (2005) 5146–5149
Design, synthesis, and evaluation of octahydropyranopyrrole-based
inhibitors of mammalian ribonucleotide reductase
Michael J. Fuertes, Jaskiran Kaur, Prasant Deb, Barry S. Cooperman
and Amos B. Smith, III*
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
Received 29 July 2005; revised 18 August 2005; accepted 22 August 2005
Available online 19 September 2005
Abstract—Inhibitors of mammalian ribonucleotide reductase possessing a novel octahydropyranopyrrole scaffold based on a cyclic
heptapeptide inhibitor have been designed, synthesized, and evaluated. Structure–function studies reveal that the bicyclic scaffold is
indeed necessary to maintain inhibitory activity.
ꢀ 2005 Elsevier Ltd. All rights reserved.
Ribonucleotide reductases (RR) constitute well-recog-
nized targets for cancer and antiviral intervention, given
the central role this enzyme plays in regulating DNA
replication.1 In 1990, Cooperman and co-workers
demonstrated that the mammalian ribonucleotide reduc-
tase (mRR), a class Ia RR, can be inhibited via
competitive binding at the R1 subunit by the heptapep-
tide N-AcFTLDADF (linear P7, IC50 = 20 lM), which
corresponds to the C-terminus of the R2 subunit.2 Trans-
fer-NOE NMR studies demonstrated that P7 bound to
mRR assumes a reverse b-turn structure consisting of
the amino acids TLDA.3 By exploiting a lactam bridge
to constrain the turn, we subsequently reported the de-
sign, synthesis, and evaluation of several cyclic oligopep-
tides, of which cyclic peptide 1 (Fig. 1) revealed a higher
binding affinity to mR1 by 2.5 times relative to the linear
peptide P7.4 More recently, we have focused on the
design and synthesis of inhibitors of mRR based on
non-peptidal scaffolds, which hold the promise of both
higher affinity and selectivity, as well as bio-availability
Figure 1. Top: cyclic-P7 (1); bottom: tetrahydropyran-based inhibitor 2.
employing an octahydropyranopyrrole scaffold to mimic
and stability, and hence would hold the promise of great-
the b-turn.
er therapeutic potential. To this end, we reported the use
of a tetrahydropyran scaffold to constrain the b-turn.5
The resultant inhibitor 2, however, proved to be signifi-
cantly less potent (20·) than P7. In this letter, we describe
the design, synthesis, and biological evaluation of an
inhibitor of mRR based on cyclic oligopeptide 1,
At the outset, we reasoned that the low binding affinity
of 2 to mR1 resulted from steric conflicts with either or
both of the 2-O-carboxymethyl and 4-O-isobutyl pen-
dant groups. Structure–function studies on the interac-
tion of the linear P7 peptide suggest that these groups
may not be essential for inhibitory activity; we therefore
redesigned and then constructed two pyran-based
Keywords: Mammalian; Ribonucleotide; Reductase; mRR; Peptido
mimetic; Octahydropyranopyrrole; Non-peptidal.
mimetics 3a and 3b, which (1) exclude the Asp4
*
side-chain mimic and (2) accommodate a more concise
synthetic approach (Scheme 1). The syntheses of 3a
Corresponding author. Tel.: +1 215 898 4860; fax: +1 215 898
5129; e-mail: smithab@sas.upenn.edu
0960-894X/$ - see front matter ꢀ 2005 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2005.08.062

M. J. Fuertes et al. / Bioorg. Med. Chem. Lett. 15 (2005) 5146–5149
5147
Scheme 1.
and 3b began with a Ferrier glycosidation6 involving tri-
O-acetyl-D-glucal and isobutanol. Palladium-catalyzed
allylic amination with N-benzyl methyl amine, employ-
ing the Baer and Hanna protocol,7 provided amine (+)-
5 in 75% yield for the two steps. Acetate methanolysis8
followed by sequential TBS protection of the resultant
alcohol and N-debenzylation using the Olofson reagent9
furnished amine (+)-6 in 80% yield for the three-step se-
quence. Installation of the peptidyl side chain followed in
turn by alkylation with BrAc-D-Asp-D-Phe bis-benzyl es-
ter, TBS removal, DCC-mediated esterification, and
hydrogenolysis led to prospective inhibitors (À)-3a and
(À)-3b. The extent to which (À)-3a,b bind to mR1 and
thereby inhibit enzyme activity was measured employing
an assay previously developed in our laboratory based
on an FTLDADF-Sepharose affinity column.10 Assay
results revealed that (À)-3a and (À)-3b exhibited little
or no inhibitory activity. We therefore abandoned fur-
ther efforts to exploit the tetrahydropyran as a scaffold
for the development of mRR inhibitors.
Figure 2. Top: peptidomimetic target 7; bottom: overlay of the MM2
minimized structure of 7 (gray) on the NMR-derived conformation of
cyclic peptide 1 (green).
Molecular design and modeling exploiting the MM2 force
field included with MacroModel (v3.1) suggested that the
octahydropyranopyrrole scaffold might be a more appro-
priate platform upon which to attach and thereby display
the appropriate side chains corresponding to the key ami-
no acid residues present in 1. We initially targeted pepti-
domimetic 7 for synthesis; the appendages include a
hydrocinnamate ester, an isobutyloxy group, and a free
hydroxyl to mimic the N-AcPhe1, Leu3, and Asp4 resi-
dues, respectively, and the requisite Asp6-Phe7 moiety
for the C-terminus. Illustrated in Figure 2 is an overlay
of the MM2 minimized structure of 7 (gray) on the
NMR-derived conformation of cyclic peptide 1 (green).
tion6 of commercially available (À)-tri-O-acetyl-D-glu-
cal with isobutanol. The corresponding glycoside
(7.8:1 a/b ratio) was then subjected to acetate methan-
olysis8 and monosilylation (TIPSOTf, 2,6-lutidine,
À5 ꢁC)11 to furnish allylic alcohol (+)-8 in 83% yield
for the three steps. Swern oxidation,12 followed by
Johnson iodination,13 next led to a-iodoenone (+)-9
(92%, two steps), which upon Luche reduction
(NaBH4, CeCl3Æ7H2O, MeOH)14 produced a separable
mixture (2.3:1) of alcohols, of which the major isomer
was reacted under Mitsunobu conditions15 with the
The synthesis of 7 (Scheme 2) again began with the
bismuth (III) trichloride mediated Ferrier glycosyla-

5148
M. J. Fuertes et al. / Bioorg. Med. Chem. Lett. 15 (2005) 5146–5149
Scheme 2.
Weinreb amide derived from N-Ts glycine to furnish
aminoglycolate (+)-10 in 38% (two steps). Anionic
cyclization (n-BuLi, THF, À78 ꢁC, 72%),16 followed
by a second Luche reduction (96%) of the resultant
enone, then gave allylic alcohol (+)-11 as a single
isomer. Hydroxyl-directed hydrogenation (30 mol %
Wilkinsonꢀs catalyst),17 protection of the alcohol as
the benzyl ether (92%), and reductive removal of the
tosyl group (Na, naphthalene, 90% yield)18 cleanly
furnished amine (+)-12. Installation of the C-terminal
peptidal side chain was then achieved by sequential
alkylation with ethyl bromoacetate (90% yield), basic
hydrolysis (KOH, THF/H2O), and coupling with D-
Asp-D-Phe bis-benzyl ester (pyBOP, HOBt, DIPEA,
CH2Cl2, 70% for two steps). Removal of the triisopro-
pylsilyl-protecting group (HFÆpyridine, 90%),19 acyla-
tion of the resultant alcohol with hydrocinnamoyl
chloride, and global deprotection employing transfer
hydrogenation conditions (8.8% formic acid/MeOH,
10% Pd/C)20 completed the synthesis of (À)-7.
Figure 3. Active mRR inhibitor (À)-14 and inactive compound (À)-15.

M. J. Fuertes et al. / Bioorg. Med. Chem. Lett. 15 (2005) 5146–5149
5149
J. S.; Lepine-Frenette, C.; Dansereau, N., et al. Biochem.
Cell Biol. 1991, 69, 79.
3. (a) Fisher, A.; Laub, P. B.; Cooperman, B. S. Nat. Struct.
Biol. 1995, 2, 951; (b) Pellegrini, M.; Liehr, S.; Fisher, A.
L.; Laub, P. B.; Cooperman, B. S.; Mierke, D. F.
Biochemistry 2000, 39, 12210.
4. Liehr, S.; Barbosa, J.; Smith, A. B., III; Cooperman, B. S.
Org. Lett. 1999, 1, 1201.
5. Smith, A. B., III; Sasho, S.; Barwis, B. A.; Sprengeler, P.;
Barbosa, J.; Hirschmann, R.; Cooperman, B. S. Bioorg.
Med. Chem. Lett. 1998, 22, 3133.
6. (a) Ferrier, R. J.; Prasad, N. J. J. Chem. Soc. C 1969, 1,
570; (b) Swamy, N. R.; Venkateswarlu, Y. Synthesis 2002,
5, 598.
7. Baer, H. H.; Hanna, Z. S. Can. J. Chem. 1981, 59, 889.
8. Plattner, J. J.; Gless, R. D.; Rapoport, H. J. Am. Chem.
Soc. 1972, 94, 8613.
9. Olofson, R. A.; Martz, J. T.; Senet, J. P.; Piteau, M.;
Malfroot, T. J. Org. Chem. 1984, 49, 2081.
10. Pender, B. A.; Wu, X.; Axelsen, P. H.; Cooperman, B. S.
J. Med. Chem. 2001, 44, 36.
Pleasingly, mimetic (À)-7 did indeed inhibit mRR,
although 5–6 times less potently than P7. Encouraged
by this result, we prepared two related congeners, (À)-
14 and (À)-15 (Fig. 3), wherein only the N-terminal car-
boxylate moiety was varied. Assay results revealed that
(À)-14 exhibited increased activity relative to (À)-7,
whereas (À)-15 had little or no inhibitory activity. Com-
pound (À)-14, which contains the 3-(9-fluorenyl)propa-
noyl group, proved to be our most potent compound
(IC50 = 40–50 lM), exhibiting an activity roughly half
of P7.
In summary, we have identified octahydropyranopyrrole
as a viable scaffold for the construction of b-turn mimet-
ics. Moreover, we have exploited this structural motif to
access our most potent small molecule nonpeptide pepti-
domimetic inhibitor of mRR to date. Further investiga-
tions to unveil additional structure–activity relationships
of this scaffold, and thereby to maximize inhibition of
mRR, continue in our laboratory and will be reported
in due course.
11. (a) Corey, E. J.; Cho, H.; Rucker, C.; Hua, D. H.
Tetrahedron Lett. 1981, 22, 3455; (b) Tanaka, K.; Yoda,
H.; Isobe, Y.; Kaji, A. J. Org. Chem. 1986, 51, 1856.
12. Omura, K.; Swern, D. Tetrahedron 1978, 34, 1651.
13. Johnson, C. R.; Adams, J. P.; Braun, M. P.; Senanayake,
C. B. W. Tetrahedron Lett. 1992, 33, 917.
Acknowledgments
14. Luche, J. L. J. Am. Chem. Soc. 1978, 100, 2226.
15. (a) Mitsunobu, O. Synthesis 1981, 1; (b) Henry, J. R.;
Marcin, L. R.; McIntosh, M. C.; Scola, P. M.; Harris,
G. D., Jr.; Weinreb, S. M. Tetrahedron Lett. 1989, 30,
5709.
Financial support was provided by the National Insti-
tutes of Health (National Cancer Institute) through
Grant CA58567 and the University of Pennsylvania.
16. Sha, C. K.; Huang, S. J.; Zhan, Z. P. J. Org. Chem. 2002,
67, 831.
References and notes
17. (a) Brown, J. M. Angew. Chem., Int. Ed. Engl. 1987, 26,
190; (b) Hoeger, C. A.; Okamura, W. H. J. Am. Chem.
Soc. 1985, 107, 268.
18. (a) McIntosh, J. M.; Matassa, L. C. J. Org. Chem. 1988,
53, 4452; (b) Heathcock, C. H.; Blumenkopf, T. A.; Smith,
K. M. J. Org. Chem. 1989, 54, 1548.
19. Wipf, P.; Kim, H. J. Org. Chem. 1993, 58, 5592.
20. El Amin, B.; Anantharamaiah, G. M.; Royer, G. P.;
Means, G. E. J. Org. Chem. 1979, 44, 3442.
1. (a) Cory, J. G. Adv. Enzyme Regul. 1988, 27, 437; (b)
Szekeres, T.; Fritzer-Szekeres, M.; Elford, H. L. Crit. Rev.
Clin. Lab. Sci. 1997, 34, 503; (c) Robins, M. J. Nucleosides
Nucleotides 1999, 18, 779.
2. (a) Yang, F. D.; Spanevello, R. A.; Celiker, I.; Hirsch-
mann, R.; Rubin, H.; Cooperman, B. S. FEBS Lett. 1990,
272, 61; (b) Cosentino, G.; Lavallee, P.; Rakhit, S.; Plante,
R.; Gaudette, Y.; Lawetz, C.; Whitehead, P. W.; Duceppe,