Synthesis of a second-generation pseudopeptide platform

Article abstract of DOI:10.1016/S0040-4039(00)00796-6

A synthetic pathway is presented to a functionalized pseudopeptide molecular platform for use in supramolecular and solution-phase combinatorial chemistry. The platform contains amino acids with quaternary asymmetric centers, the configurations of which are determined by the method of synthesis. (C) 2000 Elsevier Science Ltd.

Full text of DOI:10.1016/S0040-4039(00)00796-6

Tetrahedron Letters 41 (2000) 5013±5016
Synthesis of a second-generation pseudopeptide platform
Gebhard Haberhauer, Laszlo Somogyi and Julius Rebek Jr.*
The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037, USA
Received 1 May 2000; accepted 15 May 2000
Abstract
A synthetic pathway is presented to a functionalized pseudopeptide molecular platform for use in
supramolecular and solution-phase combinatorial chemistry. The platform contains amino acids with
quaternary asymmetric centers, the con®gurations of which are determined by the method of synthesis.
# 2000 Elsevier Science Ltd. All rights reserved.
Keywords: platform; amino acids and derivatives; macrocycles; oxazoles; combinatorial chemistry.
Rigid molecular platforms presenting three functional groups on the same face can serve as
core molecules for solution phase combinatorial chemistry as well as templates for synthetic
receptors.1 In the former application, molecular diversity is provided by the well-de®ned posi-
tioning of functionality on a large surface; in the latter application, combinations with rigid
spacers give cleft-like structures with convergent functional groups useful for selective molecular
recognition.
Earlier, we introduced platform 2 (see Fig. 1) based on the structure of naturally occurring
dolastatins (e.g. Dolastatin E (1)3 in Fig. 1) for these purposes.2 Macrocycle 2 features oxazole
rings linked by trans-amide bonds. The most favored conformation of 2 features all lone pairs
of the oxazole nitrogens and the hydrogens of the secondary amides directed to the center of the
macrocycle. This self-satisfying H-bonded pattern largely contributes to the close planarity of the
structure. The amino acid residues that connect the heterocycles are all of the same con®guration,
and the side chains are all presented on the same face of the molecule. However, the electronic
environment at the asymmetric centers caused problems with racemization during the synthesis of
platform 2, and decreased the yield of the desired all-syn compound. Consequently, the use of
platform 2 is limited to non-basic conditions.
This behavior led us to a structure resistant to racemization, with methyl groups replacing the
hydrogens at the three asymmetric centers. This modi®cation also allows for the functional
groups to be connected directly to the macrocyclic ring where their presentation and orientation
are better de®ned in space. The result is the racemization-free macrocycle 3.
* Corresponding author. Tel: +1-858-784-2250; fax: +1-858-784-2876; e-mail: jrebek@scripps.edu
0040-4039/00/$ - see front matter # 2000 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(00)00796-6

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Figure 1. Dolastatin E (1), racemization sensitive platform 2 and racemization stable platform 3
For the synthesis of platform 3 the appropriate amino acids are the natural l-threonine and the
synthetic malonic monoester derivative 6 (see Scheme 1).
Scheme 1. Synthetic route to chiral non-natural malonic monoester 6
The enantiomerically pure acid 6 is readily available from dimethylamino malonic ester 4 by
Boc-protection then alkylation to give compound 5 (Scheme 1). Enzymatic hydrolysis with porcine
liver esterase4Ðunder optimized conditions using a mixture of CH3CN and phosphate bu€er
(pH=7) as solventÐa€orded the enantiomerically pure compound 6. The preparation can be
performed on a 100 g scale.
The synthesis of oxazole building block 10 proceeds from the acid 6 by coupling to H-Thr-OBn
(7) using diphenylphosphoryl azide (DPPA). The resulting dipeptide 85 is conveniently converted
to the corresponding oxazole 10 by sequential treatment with the Dess±Martin periodinane then
cyclodehydration with triphenylphosphine in the presence of iodine and triethylamine6 (Scheme 2).
The overall yield of oxazole 10 starting from acid 6 is 60%.
Scheme 2. Synthesis of oxazole building block 10

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The desired platform 3 was synthesized according to Scheme 3. Hydrogenolysis of the Bn ester
of 10 with Pearlman's catalyst in a 3:1 mixture of ethanol and acetic acid gave the free acid
building block 11. Acid cleavage of the Boc group of 10 with TFA in CH2Cl2 provided the tri-
¯ouroacetate salt 12. Coupling to 11 with PyBOP7 gave oxazole dimer 13 in 95% yield. Cleavage
of the Boc group and PyBOP activation were repeated to give protected linear trimer 14.
Deprotection of the carboxyl by hydrogenolysis and removal of the Boc group with TFA in
CH2Cl2 a€orded the linear trimer. The macrolactamization was carried out by PyBOP activation
and addition of Hunig's base in DMF, and yielded the triester platform 15 in 86%. The yield for
the macrocyclization is much higher than that obtained during the synthesis of 2 and deserves
some comment. We can only opine that the extra methyl of the threonine-derived oxazole helps
organizeÐor preorganizeÐthe conformation to the sickle shape appropriate for cyclization and
prevents nucleophiles from approaching on a trajectory that leads to intermolecular, rather than
intramolecular products. In any case, the protected platform 15 was synthesized on a gram scale
Scheme 3. Stepwise synthesis of triacid platform 3

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and is conveniently transformed into the desired triacid platform 38 by saponi®cation using aqueous
NaOH. Fortunately, the triacid platform 3 does not tend to decarboxylation at ambient tempera-
tures; it can be coupled to primary amines leading to the elaboration of combinatorial libraries.
Application of 3 in molecular recognition is in progress and will be reported in due course.
Acknowledgements
Financial support from the Skaggs Foundation is greatly acknowledged. Gebhard Haberhauer
thanks the Deutche Forshungsgemeinschaft for a postdoctoral fellowship. The authors would
also like to express their special thanks to Professors Takeharu Haino of Hiroshima University
and Peter Wipf of the University of Pittsburgh for advice and encouragement.
References
1. Kocis, P.; Issakova, O.; Sepetov, N. F.; Lebl, M. Tetrahedron Lett. 1995, 36, 6623±6626.
2. Mink, D.; Mecozzi, S.; Rebek Jr., J. Tetrahedron Lett. 1998, 39, 5709±5712.
3. Nakamura, M.; Shibata, T.; Nakane, K.; Nemoto, T.; Ojika, M.; Yamada, K. Tetrahedron Lett. 1995, 36, 5059±
5062.
4. Fukuyama, T.; Xu, L. J. Am. Chem. Soc. 1993, 115, 8449±8450.
5. General procedure for DPPA activated peptide coupling: To a stirred solution of the N-Boc-protected amino acid
(1 equiv.), the methyl ester (1.5 equiv.) and N,N-diisopropylethylamine (1.5 equiv.) in DMF (0.3 M) was added 1.5
equiv. DPPA at 0ꢀC followed by slow addition of 3.8 equiv. N,N-diisopropylethylamine. Stirring was continued
for 20 hours while slowly allowing the reaction mixture to warm to room temperature. The DMF was evaporated,
the residue was dissolved in AcOEt and washed with water, saturated NaHCO3 solution, 1 M HCl and brine, then
dried over MgSO4 and concentrated in vacuo. Puri®cation was accomplished by chromatography on silica gel with
AcOEt:hexane (1:2).
6. Wipf, P.; Venkatraman, S. Synlett 1997, 1, 1±10.
7. General procedure for PyBOP activated coupling: To a stirred solution of the amino building block (1 equiv.), the
acid building block (1 equiv.) and N,N-diisopropylethylamine (1 equiv.) in DMF (0.06 M) was added 1.2 equiv.
PyBOP at room temperature followed by slow addition of 2.8 equiv. N,N-diisopropylethylamine. Stirring was
continued for 24 hours. The workup was as described above.
1
8. Spectroscopic data for platform 3: H NMR (methanol-d4): 9.07 (s, 3H), 2.65 (s, 9H), 2.03 (s, 9H). 13C NMR
(methanol-d4): 170.5, 161.9, 161.1, 157.1, 129.7, 60.5, 22.8, 11.7. MALDI±FTMS [M+Na]+: calculated: 611.1344;
observed: 611.1342.