A modular synthetic approach toward exhaustively stereodiversified ligand libraries

Article abstract of DOI:10.1021/ol006560k

(Matrix presented) This report describes a modular approach to the synthesis of stereodiversified natural product-like libraries. Monomers 2 and 3 were coupled in parallel by silyl-tethered olefin metathesis to generate all 16 stereoisomers of cis-enediol

Full text of DOI:10.1021/ol006560k

ORGANIC
LETTERS
2000
Vol. 2, No. 25
3999-4002
A Modular Synthetic Approach toward
Exhaustively Stereodiversified Ligand
Libraries
Tiffany Malinky Gierasch,†,‡ Milan Chytil,†,‡ Mary T. Didiuk,‡,§ Julie Y. Park,‡,§
,‡,|
Jeffrey J. Urban,‡ Steven P. Nolan,¶ and Gregory L. Verdine*
Department of Chemistry and Chemical Biology, HarVard UniVersity, Cambridge,
Massachusetts 02138, and Department of Chemistry, UniVersity of New Orleans,
New Orleans, Louisiana 70148
Verdine@chemistry.harVard.edu
Received September 7, 2000
ABSTRACT
This report describes a modular approach to the synthesis of stereodiversified natural product-like libraries. Monomers 2 and 3 were coupled
in parallel by silyl-tethered olefin metathesis to generate all 16 stereoisomers of cis-enediols 1. All 16 stereoisomers were incorporated into
chimerae having flanking peptidic segments. These chimerae exhibited a broad range of hydrophobicities, raising the possibility that
stereochemical variation might be used to tune the pharmacologic properties of small molecules.
A major challenge of the post-genomic era will be to discover
potent and selective ligands to the large number of macro-
molecular receptors having unclear or unknown biological
function.1 The chemical genetics approach toward this
problem entails the synthesis and screening of diverse organic
molecules to identify those that have an observable pheno-
typic effect on cells.2 To date, design and synthesis of small-
molecule libraries has primarily focused on achieving
diversity through functional group variation among members
of the library.3 The alternative and complementary strategy
of varying functional group presentation through extensive
stereochemical diversification has received much less atten-
tion.4,5 Indeed, the only case of true library generation by
exhaustive stereochemical diversification is the panel of all
32 polyketide stereoisomers individually synthesized by
Patterson and co-workers.6 Although this case represents a
triumph of asymmetric synthesis, it also illustrates the
difficulties of achieving exhaustive stereochemical coverage
(3) See, for example: Tan, D. S.; Foley, M. A.; Shair, M. D.; Schreiber,
S. L. J. Am. Chem. Soc. 1998, 120, 8565-8566. Gordon, E. M.; Barrett,
R. W.; Dower, W. J.; Fodor, S. P. A.; Gallop, M. A. J. Med. Chem. 1994,
37, 1385-1401. Thompson, L. A.; Ellman, J. A. Chem. ReV. 1996, 96,
555-600. Hermkens, P. H. H.; Ottenheijm, H. C. J.; Rees, D. C.
Tetrahedron 1997, 53, 5643-5678. Bunin, B. A.; Plunkett, M. J.; Ellman,
J. A.; Bray, A. M. New. J. Chem. 1997, 21, 125-130.
(4) Reggelin, M.; Brenig, V. Tetrahedron Lett. 1996, 37, 6851-6852.
Lee, D.; Sello, J. K.; Schreiber, S. L. J. Am. Chem. Soc. 1999, 121, 10648-
10649. Annis, D. A.; Helluin, O.; Jacobsen, E. N. Angew. Chem., Int. Ed.
1998, 37, 1907-1909. Sutherlin, D. P.; Armstrong., R. W. J. Org. Chem.
1997, 62, 5267-5283. Paterson, I.; Scott, J. P. J. Chem. Soc., Perkin Trans.
1 1999, 1003-1014.
(5) Houghten, R. A.; Pinilla, C.; Blondelle, S. E.; Appel, J. R.; Dooley,
C. T.; Cuervo, J. H. Nature 1991, 354, 84-86. Gallop, M. A.; Barrett, R.
W.; Dower, W. J.; Fodor, S. P. A.; Gordon, E. M. J. Med. Chem. 1994, 37,
1233-1251. Doerner, B.; Husar, G. M.; Ostresh, J. M.; Houghten, R. A.
Bioorg. Med. Chem. 1996, 4, 709-715. Burgess, K.; Godbout, C.; Li, W.;
Payza, K. Bioorg. Med. Chem. Lett. 1996, 6, 2761-2764. Feng, Y.;
Pattarawarapan, M.; Wang, Z.; Burgess, K. J. Org. Chem. 1999, 64, 9175-
9177. Virgilio, A. A.; Bray, A. A.; Zhang, W.; Trinh, L.; Snyder, M.;
Morrissey, M. M.; Ellman, J. A. Tetrahedron 1997, 53, 6635-6644.
Wermuth, J.; Goodman, S. L.; Jonczyk, A.; Kessler, H. J. Am. Chem. Soc.
1997, 119, 1328-1335.
† These authors contributed equally to this work.
‡ Harvard University.
§ Current addresses: M.T.D., Pfizer Central Research, Groton, CT; J.Y.P.,
Caltech University, Pasadena, CA.
¶ University of New Orleans.
Institute of Chemistry and Cell Biology.
(1) Mitchison, T. J. Chem. Biol. 1994, 1, 3-6. Schreiber, S. L. Science
2000, 287, 1964-1969.
(2) Mayer, T. U.; Kapoor, T. M.; Haggarty, S. J.; King, R. W.; Schreiber,
S. L.; Mitchison, T. J. Science 1999, 286, 971-974.
(6) Paterson, I.; Channon, J. A. Tetrahedron Lett. 1992, 33, 797-800.
10.1021/ol006560k CCC: $19.00 © 2000 American Chemical Society
Published on Web 11/03/2000

while also enabling variation of functional groups. Here we
report a modular approach to the synthesis of libraries of
natural product-like molecules comprising all possible ste-
reoisomers. This approach lays the groundwork for the
generation of small molecule libraries bearing extensive
variation in both stereochemistry and functional groups.
From the standpoint of biological potency, we considered
it important for the library members to possess a semirigid
acyclic framework rich in stereogenic centers, with a
hydrocarbon framework presenting both hydrogen-bonding
functionality and variable side chain (“R”) groups. For
reasons of synthetic practicality, we sought a route that would
allow stringent stereochemical control, be broadly inclusive
of functional groups, and converge on the final products
through a late-stage carbon-carbon bond-coupling step.
Among the candidate systems considered a priori, we selected
the cis-enediol unit 1 (Scheme 1) for development in the
initial phase of this study.
modular construction approach, which takes advantage of
the chemical orthogonality and functional group tolerance
of olefin metathesis, is intended to allow expedient construc-
tion of libraries varied in both stereochemistry and side chain
functionality. Here we demonstrate this synthetic approach
for the example in which both R1 and R2 are isobutyl groups
(Schemes 2 and 3).
Scheme 2a
Scheme 1. Retrosynthetic Scheme for the Synthesis of
Stereodiversified Libraries Containing the cis-Enediol Module 1
a Key: (a) 2.0 equiv of Cx2BOTf, TEA, THF, 0 f -78 °C,
then CH2CHCHO -78 f 0 °C; (b) 0.5 M NaOH in MeOH:H2O
(4:1); (c) PhCH2SH, DCC, cat. DMAP, CH2Cl2, 0 °C; (d) 2.4 equiv
of TBDMSCl, imidazole, DMF; (e) THF:MeOH:H2O (2:1:1); (f)
(PhO)2PON3, TEA, MeCN, reflux, then cat. CuCl, 9-fluoren-
emethanol, MeCN; (g) AcOH:THF:H2O (2:1:1), 55 °C; (h) 1.1
equiv of Bu2BOTf, i-Pr2NEt, CH2Cl2, 0 f -78 °C, then
CH2CHCHO, -78 f 0 °C; (i) PhCH2SLi, AlMe3, CH2Cl2 0 °C;
(j) 1.2 equiv of TBDMSCl, imidazole, DMF; (k) LiOOH, THF:
MeOH:H2O (3:1:1), 0 f 20 °C, then aqueous 1.0 M Na2SO3; (l)
AcOH:THF:H2O (2:1:1), 45 °C.
The internal framework of 1 presents two independently
diversifiable “R” groups and two hydroxyls, which can
interact with receptors through nonpolar and hydrogen-
bonding interactions, respectively. Chemically differentiated
ends in 1 allow for the sequential attachment of two
additional “R” groups. The presence of four sp3-hybridized
stereogenic centers in 1 gives rise to an ensemble of 16
stereoisomers, each of which can be accessed individually
by stereocontrolled synthesis. Although the acyclic frame-
work allows some degree of conformational freedom,
significant restrictions are imposed by 1,3-allylic strain across
the cis-configurated olefin and by torsional strain between
adjacent tertiary carbons. This results in strong and unique
conformational preferences for each of the 16 stereoisomers;7
such preorganization lowers the entropic cost of receptor
recognition and enhances its specificity. The entire stereo-
chemical ensemble covers a broad range of conformational
space, increasing the likelihood that one or more members
will be chemically complementary to a receptor pocket.
Retrosynthetically 1 was envisioned to arise from two
modular building blocks, amino monomer 2 and carboxy
monomer 3, via ruthenium-mediated olefin metathesis.8 This
Monomers 3 were accessed in a stereocontrolled fashion
via either Evans9 (syn) or Masamune10 (anti) chiral auxiliary-
controlled aldol chemistry. Monomers 2 were obtained
stereospecifically from 3 though the Curtius rearrange-
ment,11,12 thus providing an efficient and convenient overall
process for monomer generation. Coupling monomers 2 and
3 via olefin metathesis raises the challenge of generating only
heterocoupled products while controlling the olefin geometry.
Both issues were resolved by employing a ring-closing
metathesis (RCM) strategy.13
(8) Grubbs, R. H.; Chang, S. Tetrahedron 1998, 54, 4413-4450. Fu¨rstner,
A. Angew. Chem., Int. Ed. 2000, 39, 3012-3043.
(9) Evans, D. A.; Gage, J. R.; Leighton, J. L. J. Am. Chem. Soc. 1992,
114, 9434-9453.
(10) Abiko, A.; Liu, J.-F.; Masamune, S. J. Am. Chem. Soc. 1997, 119,
2586-2587.
(11) Duggan, M. E.; Imagire, J. S. Synthesis 1989, 131-132.
(12) The isocyanate intermediate can also be trapped with lithium tert-
butoxide to yield the Boc-protected version of the amino monomer. See
the Supporting Information for further details.
(7) Karplus, M.; Zoete, V.; Michelien, O.; Verdine, G. L., unpublished
results.
4000
Org. Lett., Vol. 2, No. 25, 2000

Scheme 3a
Table 1. RCM of 9 Mediated by a Thermostable Metathesis
Catalysta
configuration
isolated
allylic
(N f C)
yield (%)
catalyst (%)
substitution
RSSR
RRRR
RRRS
RSSS
RSRS
RRSS
RRSR
RSRR
69
69
69
67
73
83
70
79
15
10
10
15
10
10
10
5
trans
trans
trans
trans
cis
cis
cis
cis
a Key: (a) Me2SiCl2 in pyridine, then anti-3 in pyridine; (b)
Cl2(IMes)(PCy3)RudCHPh, toluene, 70 °C; (c) HF/pyridine, THF,
0 f 20 °C.
a Reactions were carried out under argon for 1 h in toluene (2.5 mM
with respect to catalyst) at 75 °C.
varied somewhat from run to run, we noted a consistent
influence of substituent stereochemistry on the reaction
efficiency. Specifically, closure of rings with cis substitution
at the allylic carbons required lower catalyst loadings (5-
10%) and furnished higher yields (70-85%) than the
corresponding trans-substituted rings (10-15% and 65-
70%, respectively). A likely explanation for this effect is
that both allylic substituents on the seven-membered siloxane
ring are pseudoequatorial in the cis case, while one is
pseudoaxial and the other pseudoequatorial in the trans case.
Stereodiversified units 11 are suitably equipped for
chemoselective functionalization at the amino and carboxy
terminal ends. To explore one potentially useful elaboration,
we chose to synthesize chimerae having 11 flanked by
peptidic functionality. The 16 stereoisomeric units 11 were
activated for carboxy-terminal functionalization by conver-
sion to the corresponding 3-hydroxy-1,2,3-benzotriazin-
4(3H)-one esters.19 These activated esters were coupled under
standard conditions to the N-terminus of a tripeptide (C-
Lys-His-Ile-N) immobilized on Rink Amide AM resin.
Following capping and Fmoc deprotection, five additional
residues were coupled (C-His-Phe-Pro-His-Pro-N), the N-
terminus was acetylated, and the chimeric products were
deprotected and released from the resin under standard
conditions. HPLC analysis of the crude products revealed
in each case a single major product,20 which was shown by
electrospray ionization mass spectrometry to possess the mass
(662.0 or 662.1 AMU, M + 2H) expected of the chimerae
12. Importantly, the cis-enediol units were found to withstand
the strongly acidic conditions (95% trifluoroacetic acid, 3
h, room temperature) employed in peptide cleavage and
deprotection. These results demonstrate that unit 1 can be
cleanly functionalized at both ends, thereby producing an
ensemble of stereochemically diversified chimerae.
Monomer 3 was monosilylated14 using excess Cl2SiMe2,
separated from the excess silylating agent in vacuo, and then
reacted with 1 equiv of monomer 2 to produce the het-
erotethered product 9 in yields ranging from 60 to 90%, with
the major side products being monosilylated monomer 3 and
unreacted monomer 2. The strongest determinant of tethering
efficiency was the relative stereochemistry of the carboxy
monomer. Syn monomers 3 consistently gave lower yields
(60-65%) while the anti monomers proceeded in 85-90%
yield. Variations in the reaction conditions, including reaction
time, temperature, and order of monomer silylation, had no
effect on the reaction progress.
Although the Grubbs catalyst15 has been used to form
seven-membered siloxane rings of the type found in 10,16
this catalyst proved inefficient with our system. The conver-
sion of 9 to 10 required stoichiometric amounts of Grubbs
catalyst and gave low yields (<30%) and poor mass balances
(<60%).17 The difficulty of the present RCM operation
presumably arises from the steric crowding and high density
of heteroatom functionality in our substrates. Following
recent reports of improved product conversion by a thermo-
stable metathesis catalyst,18 we tested the ability of this new
catalyst to perform RCM on our substrates (9 f 10) and
observed dramatically improved results. On a 25-100 mg
scale, 5-15 mol % of catalyst at 75 °C gave yields in the
range of 65-85% after removal of the silyl tether to produce
the 16 stereodiversified units 11, with exclusive formation
of the Z-configurated olefin (Table 1). Although the yields
(13) Grubbs, R. H.; Miller, S. J.; Fu, G. C. Acc. Chem. Res. 1995, 28,
446-452.
(14) Myers, A. G.; Gin, D. Y.; Rogers, D. H. J. Am. Chem. Soc. 1994,
116, 4697-4718.
(15) Schwab, P.; Grubbs, R. H.; Ziller, J. W. J. Am. Chem. Soc. 1996,
118, 100-110. Schwab, P. France, M. B.; Ziller, J. W.; Grubbs, R. H.
Angew. Chem., Int. Ed. Engl. 1995, 34, 2039-2041.
The members of the ensemble 12 differ only in their
stereochemistry at the four asymmetric centers of the
(16) Evans, P. A.; Murthy, V. S. J. Org. Chem. 1998, 63, 6768-6769.
Hoye, T. R.; Promo, M. A. Terahedron Lett. 1999, 40, 1429-1432.
(17) The following parameters were varied widely: reaction time and
temperature, solvent, substrate and catalyst concentration, catalyst loading,
order of addition, rigor of oxygen exclusion, tether structure.
(18) Huang, J.; Stevens, E. D.; Nolan, S. P.; Petersen, J. L. J. Am. Chem.
Soc. 1999, 121, 2674-2678. Fu¨rstner, A.; Thiel, O.; Ackerman, L.; Schanz,
H.-J.; Nolan, S. P. J. Org Chem. 2000, 65, 2204-2207. Scholl, M.; Trnka,
T. M.; Morgan, J. P.; Grubbs, R. H. Tetrahedron Lett. 1999, 40, 2247-
2250.
(19) Atherton, E.; Holder, J. L.; Meldal, M.; Sheppard, R. C.; Valerio,
R. M. J. Chem. Soc., Perkin Trans. 1 1988, 2887-2894. Masamune, S.;
Kamata, S.; Schilling, W. J. Am. Chem. Soc. 1975, 97, 3515-3516.
(20) None of the minor products had the mass of 12, but instead had
lower masses, indicating that they arose from incomplete coupling rather
than racemization of the stereodiversified unit.
Org. Lett., Vol. 2, No. 25, 2000
4001

enantiomeric cis-enediols 11 exhibit identical retention times,
these give rise to diastereomeric pairs of chimerae 12 having
pronounced differences in their hydrophobicities (RRSR,
∼13 min f SSRS, ∼27 min). The observation that stereo-
chemistry strongly impacts hydrophobicity raises the exciting
prospect of using stereochemical variation not only to
optimize affinity but also to tune the pharmacologic proper-
ties of small molecule ligands.
Here we have described a modular synthetic approach
toward the construction of small molecule libraries having
exhaustive stereochemical variation at every sp3-hybridized
center. Nature has made exquisite use of stereochemical
variation to fine-tune the biological activity of small mol-
ecules. The present studies aim to emulate this aspect of
Nature in the creation of potent ligands for chemical genetic
studies.
Figure 1. HPLC trace of the ensemble of 16 chimerae 12, which
differ only in the stereochemistry within the cis-enediol unit
(asterisks). The stereochemical designations (e.g., RRRR) cor-
respond to their order in the structure above, reading from left to
right. The HPLC run is a linear gradient at 1 mL/min from 18 to
33% (v/v) MeCN in H2O with 0.1% (v/v) trifluoroacetic acid over
35 min using a Beckmann 5 µm C18 column (4.6 mm × 15 cm),
with UV detection at 220 nm.
Acknowledgment. M.C. is an Alfred Bader Fellow and
an Eli Lilly and Hoffmann-La Roche Scholar. T.M.G. and
M.T.D. were supported by fellowships from DOD and NSF,
respectively. The NSF and the Louisiana Board of Regents
provided partial support for catalyst development. We thank
Dr. Angelika Fretzen for advice, Natalie Bowman for
experimental assistance, Dr. Andrew Tyler for expert as-
sistance with mass spectra, and NIH (1-S10-RR04870) and
NSF (CHE 88-14019) for providing NMR facilities.
embedded cis-enediol unit. To assess the impact of this
stereochemical diversity on a pharmacologically relevant
physical property of the molecules, we compared their
hydrophobicities by measuring retention times on a reversed-
phase C18 HPLC column.
As is evident in Figure 1, the stereochemistry of 1 has a
surprisingly large effect on the overall hydrophobicity of the
chimerae 12. For example, inverting the configuration at a
single stereogenic center alters the retention time by as much
as 9 min (SRSR, ∼17 min f SRSS, ∼26 min). Even though
Supporting Information Available: Experimental details
and characterization data regarding the preparation of all
synthetic intermediates and products. This material is avail-
able free of charge via the Internet at http://pubs.acs.org
OL006560K
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Org. Lett., Vol. 2, No. 25, 2000