Synthesis of pyridazine-based scaffolds as α-helix mimetics

Article abstract of DOI:10.1021/ol701487g

The synthesis of several amphiphilic, nonpeptidic scaffolds that mimic the presentation of i, i + 3 or i + 4, and i + 7 residues of a peptide α-helix is described. The approach uses a pyridazine core, and the synthesis involves only a few steps and minimi

Full text of DOI:10.1021/ol701487g

ORGANIC
LETTERS
2007
Vol. 9, No. 19
3733-3736
Synthesis of Pyridazine-Based Scaffolds
as -Helix Mimetics
r
Alessandro Volonterio, Lionel Moisan, and Julius Rebek, Jr.*
The Skaggs Institute for Chemical Biology and the Department of Chemistry,
The Scripps Research Institute MB-26, 10550 North Torrey Pines Road,
La Jolla, California 92037
jrebek@scripps.edu
Received June 21, 2007
ABSTRACT
The synthesis of several amphiphilic, nonpeptidic scaffolds that mimic the presentation of i, i
+ 3 or i + 4, and i + 7 residues of a peptide
r
-helix is described. The approach uses a pyridazine core, and the synthesis involves only a few steps and minimizes the number of C−C
bond-forming reactions. The versatility of the synthesis makes it suitable for the preparation of small libraries of low molecular weight
mimetics that could be targeted to certain protein/protein interactions.
r-helix
R-Helices are the most common protein secondary structures
and play a pivotal role in many protein-protein interactions.
Frequently the critical interactions are found along a “face”
of the helix involving side chains from the i, i + 3 or i + 4,
and i + 7 residues. These project from the R-helix with well-
known distances and angular relationships.1 Molecules that
can predictably and selectively reproduce these projections
could be valuable as tools in molecular biology and,
potentially, as leads in drug discovery.2 The syntheses of
peptidomimetics having a stabilized R-helical conformation
have been achieved by introducing synthetic templates into
the peptidic chain3 by using â-hairpin mimetics,4 â-peptide
sequences,5 and unnatural oligomers with discrete folding
propensities (foldamers).6 Small synthetic molecules able to
mimic the surfaces of constrained peptides offer the advan-
tage of improved stability, lower molecular weight, and in
some cases better bioavailability. Although synthetic small
molecules that adopt various well-defined secondary struc-
tures are well-documented,7 the first useful mimetics for an
R-helix were reported only recently by Hamilton and co-
workers: the terphenyl scaffold,8 and its pyridine9 and
terephthalic acid10 analogues.
Here we describe the synthesis of small libraries of new
classes of low molecular weight R-helix mimetics having
a pyridazine ring in the central position and hydrophobic
amino acid side chains of the key i, i + 3 or i + 4, i + 7
(3) (a) Kemp, D. S.; Allen, T. J.; Oslick, S. L.; Boyd, J. G. J. Am. Chem.
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10.1021/ol701487g CCC: $37.00
© 2007 American Chemical Society
Published on Web 08/21/2007

positions. These include the pyrazole-pyridazine-piperazine
scaffold 1 and the oxadiazole-pyridazine-phenyl scaffold
2 (Figure 1).
Scheme 1. General Routes for the Synthesis of R-Helix
Mimetics Based on Pyridazine 6
Figure 1. (a) Pyrazole-pyridazine-piperazine scaffold. (b) Super-
imposition of 1 (orange) on the i, i + 3, i + 7 positions of an
R-helix. (c) Oxadiazole-pyridazine-phenyl scaffold. (d) Super-
imposition of 2 (orange) on the i, i + 3, i + 7 positions of an
R-helix.
ropyridazine.12 Accordingly, esterification of commercially
available 6-oxo-1,6-dihydropyridazine-3-carboxylic acid 5
followed by treatment with POCl3 gave 6.13 This underwent
homolytic alkylation by free isobutyl radical, generated by
silver-catalyzed oxidative decarboxylation of isovaleric acid,
and led to a mixture (ca 2:1 regioisomeric ratio) of regio-
isomers 3 and 4 that were easily separated by flash
chromatography.
The structures of regioisomers 3 and 4 were assigned on
the basis of the chemical shifts of the aromatic protons (see
the Supporting Information). Moreover, it has been reported
that similar pyridazines having a carbonitrile group instead
of the ethyl ester function reacted with pivalic acid under
the same conditions to yield a 7:3 mixture of two regioiso-
mers, the major one having the same regiochemistry (con-
firmed by X-ray analysis) of 3.14
The major regioisomer 3 underwent Sonogashira cou-
pling15 with benzyl and isobutyl alkynyl alcohols 7a,b16 and
eventually led to pyridazines 8a,b, respectively, in good
yields (Scheme 2). Oxidation of 8a,b to the corresponding
ketones 9a,b was achieved in high yields with the Dess-
Martin periodinane reagent, while oxidation with MnO2 gave
good results only with compound 8a (R2 ) isobutyl).
Acetylenic ketones such as 9 are known to undergo het-
eroannulation reactions with bis-nucleophiles like ureas,
guanidines, hydrazines, and others.17 Accordingly, com-
pounds 9a,b were reacted with hydrazine in MeOH at 0 °C
affording after 1 h the pyrazole derivatives 10a,b in high
yields. After hydrolysis of the ethyl ester function with LiOH
Inspired by the Hamilton terphenyl, we sought improved
synthetic accessibity, and an amphiphilic structure with
hydrophobic surface for recognition and a “wet edge” for
enhanced solubility.
As depicted in Scheme 1, compounds 1 and 2 could be
obtained in a few steps involving a minimum number of
C-C bond-forming reactions, starting from two regioiso-
meric 4- and 5-alkyl-3-chloro-6-carboxypyridazine ethyl
esters 3 and 4, respectively. The latter could be obtained by
nucleophilic alkylation of 3-chloro-6-carboxypyridazine ethyl
ester 611 by alkyl free radicals that are known to react with
electron-poor protonated heteroaromatics such as 3,6-dichlo-
(7) (a) Hagihara, M.; Anthony, N. J.; Stout, T. J.; Clardy, J.; Schreiber,
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Sakamuri, S.; Beck, B.; Schauer-Vukasinovic, V.; Agarwal, S.; Hess, S.;
Do¨mling, A. Bioorg. Med. Chem. Lett. 2006, 16, 1740-1743. For reviews
concerning R-helix mimetics, see: (j) Yin, H.; Hamilton, A. D. Angew.
Chem., Int. Ed. 2005, 44, 4130-4163. (k) Fletcher, S.; Hamilton, A. D. J.
R. Soc. Interface 2006, 3, 215-233. (l) Davis, J. M.; Tsou, L. K.; Hamilton,
A. D. Chem. Soc. ReV. 2007, 36, 326-334. See also: (m) Cummings, M.
D.; Schubert, C.; Parks, D. J.; Calvo, R. R.; Lafrance, L. V.; Lattanze, J.;
Milkiewicz, K. L.; Tianbao, L. Chem. Biol. Drug Des. 2006, 67, 201-205.
(n) Ahn, J.-M.; Han, S.-Y. Tetrahedron Lett. 2007, 48, 3543-3547.
(8) (a) Orner, B. P.; Ernst, J. T.; Hamilton, A. D. J. Am. Chem. Soc.
2001, 123, 5382-5383. (b) Yin, H.; Lee, G.; Sedey, K. A.; Kutzki, O.;
Park, H. S.; Orner, B. P.; Ernst, J. T.; Wang, H.-G.; Sebti, S. M.; Hamilton,
A. D. J. Am. Chem. Soc. 2005, 127, 10191-10196. (c) Yin, H.; Lee, G.;
Park, H. S.; Payne, G. A.; Rodriguez, J. M.; Sebti, S. M.; Hamilton, A. D.
Angew. Chem., Int. Ed. 2005, 44, 2704-2707.
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(15) For a very recent review on Sonogashira coupling see: Chinchilla,
R.; Na´jera, C. Chem. ReV. 2007, 107, 874-922 and references cited therein.
(16) Benzyl and isobutyl alkynyl alcohols 7a,b were obtained in excellent
yields by reacting the corresponding aldehydes with ethynylmagnesium
bromide.
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(11) Due to the electronic properties of the substituents, the electrophi-
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(17) Bagley, M. C.; Huges, D. D.; Taylor, P. H. Synlett 2003, 259-262.
3734
Org. Lett., Vol. 9, No. 19, 2007

The minor regioisomer 4 was found to be sufficiently
electron poor to undergo Suzuki coupling19 with commer-
cially available 2-alkoxyaryl boronic acids 15a,b affording
compounds 16a,b in acceptable yields (Scheme 4). Both the
Scheme 2. Synthesis of the Pyrazole-Pyridazine-Piperazine
Scaffold
Scheme 4. Synthesis of the Oxadiazole-Pyridazine-Phenyl
Scaffold
alkoxy side chains and alkyl side chains serve to mimic the
key hydrophobic residues in protein-R-helix ligand interac-
tions.9 Hydrolysis of the ethyl ester with LiOH, followed
by coupling with N-acyl hydrazides 17a,b (easily obtained
by reaction between hydrazine and the corresponding esters)
mediated by EDCI/HOBt led to the formation of intermedi-
ates 18a-d in good overall yields. Finally, N,N′-diacyl
hydrazides 18a-d were dehydrated by using POCl3 in
refluxing CH3CN to achieve the synthesis of R-helix mimetic
oxadiazole-pyridazine-phenyl scaffold 2.
followed by coupling with different commercially available
N-Boc-protected piperazines 11a,b, we obtained a small
library of compounds 12a-d. After deprotection, these were
selectively acetylated at the free amine function of the
piperazine ring leading to the target compounds 1a-d. Such
structures were recently shown to give good overlap of their
protruding functions with the side chains of R-helices.18
The versatility of alkynyl ketone 9a was further exploited
in its reaction with formamidine in refluxing EtOH leading
to the formation of the pyrimidine derivative 13 in moderate
yield (Scheme 3). Following the same strategy depicted in
Scheme 5. Synthesis of the Piperazine-Pyridazine-Phenyl
Scaffold
Scheme 3. Synthesis of the
Pyrimidine-Pyridazine-Piperazine Scaffold
Scheme 2, we obtained the synthesis of a new class of
R-helix mimetics, namely, the pyrimidine-pyridazine-
piperazine scaffold (compounds 14a-c).
Org. Lett., Vol. 9, No. 19, 2007
3735

The Suzuki coupling with 2-isopropylphenyl boronic acid
19 with use of a 2 M aqueous solution of Na2CO3 (instead
of a saturated aqueous solution of NaHCO3) gave directly
the free carboxylic acid 20, which could be used as
intermediate for the construction of other scaffolds (Scheme
5). For example, coupling 20 with N-Boc-piperazines 11b,c
gave, after the usual deprotection/acetylation sequence, the
piperazine-pyridazine-phenyl scaffold represented by com-
pounds 22b,c.
thought of as synthetic counterparts of amphiphilic R-helices
having a “wet face” along one side and a hydrophobic face
along the other side of the helix. The combinatorial synthesis
of an array of these compounds and their ability to recognize
protein surfaces are currently under investigation.
Acknowledgment. We are grateful to Novartis and the
Skaggs Institute for financial support. A.V. and L.M. are
Skaggs Postdoctoral Fellows.
In summary, the synthesis of new R-helix scaffolds
mimicking i, i + 3 or i + 4, i + 7 residues was accomplished.
The common pyridazine heterocycle originates from the
easily available building block, 6. These scaffolds may be
Supporting Information Available: Experimental pro-
cedures and full spectoscopic data for all new compounds.
This material is available free of charge via the Internet at
http://pubs.acs.org.
(18) Biros, S. M.; Moisan, L.; Mann, E.; Carella, A.; Zhai, D.; Reed, J.
C.; Rebek, J., Jr. Bioorg. Med. Chem. Lett. 2007, 17, 4641-4645.
(19) Miyaura, N.; Suzuki, A. Chem. ReV. 1995, 95, 2457-2483.
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