From bead to flask: Synthesis of a complex β-amido-amide for probe-development studies

Article abstract of DOI:10.3762/bjoc.9.31

A concise synthesis of benzimidazole-substituted β-amido-amide LLW62 is presented. The original synthesis of compounds related to LLW62 was developed on Rink resin as part of a "one-bead, one-compound" combinatorial approach for on-bead screening purposes. The current synthesis is carried out in solution and is amenable to scale-up for follow-up studies on LLW62 and investigations of related structures. The key step involves the use of a β-amino acid-forming three-component reaction (3CR), the scope of which defines its role in the synthetic strategy.

Full text of DOI:10.3762/bjoc.9.31

From bead to flask: Synthesis of a complex
β-amido-amide for probe-development studies
Kevin S. Martin1,2, Cristian Soldi1, Kellan N. Candee1,
Hiromi I. Wettersten2,3, Robert H. Weiss2,3,4 and Jared T. Shaw*1,2,4
Full Research Paper
Open Access
Address:
Beilstein J. Org. Chem. 2013, 9, 260–264.
1Department of Chemistry, University of California, Davis, CA 95616,
USA, 2Comparative Pathology Graduate Group, University of
California, Davis, CA 95616, USA, 3Division of Nephrology, Dept. of
Internal Medicine, University of California, Davis, Medical Center,
Sacramento, CA 95817, USA and 4UC Davis Comprehensive Cancer
Center, 2279 45th Street Sacramento, CA 95817, USA
doi:10.3762/bjoc.9.31
Received: 09 October 2012
Accepted: 07 January 2013
Published: 06 February 2013
This article is part of the Thematic Series "Synthetic probes for the study
of biological function".
Email:
Jared T. Shaw* - jtshaw@ucdavis.edu
Guest Editor: J. Aubé
* Corresponding author
© 2013 Martin et al; licensee Beilstein-Institut.
License and terms: see end of document.
Keywords:
β-amino acid; benzimidazole; multicomponent reaction
Abstract
A concise synthesis of benzimidazole-substituted β-amido-amide LLW62 is presented. The original synthesis of compounds related
to LLW62 was developed on Rink resin as part of a “one-bead, one-compound” combinatorial approach for on-bead screening
purposes. The current synthesis is carried out in solution and is amenable to scale-up for follow-up studies on LLW62 and investi-
gations of related structures. The key step involves the use of a β-amino acid-forming three-component reaction (3CR), the scope of
which defines its role in the synthetic strategy.
Introduction
Library syntheses and high-throughput screening can often be lates the activity of cyclin kinases [13-15]. One function of p21
combined to enable the discovery of new small-molecule probes is that it acts downstream of p53 to repair DNA-damaged cells
that modulate biological phenomena [1]. Although the use of and may function to convey anti-apoptotic activity to cancer
solid-phase, split-pool combinatorial synthesis for the prepar- cells (Figure 1) [13]. As such, an inhibitor of p21 could sensi-
ation of solutions of small-molecule libraries has declined, the tize malignant cells to DNA-damaging chemical and radiation
use of these compounds for on-bead screening has resulted in therapy by subverting this p21-mediated DNA repair process
recent screening innovations [1,2]. The Lam and Kurth groups [14-17]. In this study, we developed a synthesis of LLW62 (1,
have published several “one-bead, one-compound” (OBOC) Figure 2), which is a complex benzimidazole-substituted
library syntheses of heterocyclic structures for a variety of β-amido-amide similar in structure to inhibitors of p21 that
screening endeavors [3-12]. Some of these compounds were were reported previously to support studies of this compound as
identified as inhibitors of p21, which is a protein that modu- a biological probe [14,15].
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Beilstein J. Org. Chem. 2013, 9, 260–264.
raphy and partially characterized by matrix-assisted laser
desorption/ionization mass spectrometry [14]. In the current
synthesis, we set out to develop a concise and scalable solution-
phase route to 1 and provide characterization data for 1 and all
intermediate compounds.
In our retrosynthetic analysis, we envisioned 1 coming from
acylation of benzimidazole 3 with isocyanate 2 (Figure 2). We
initially sought to avoid nitration, protection and deprotection
steps and access this intermediate by performing a late-stage
3CR with benzimidazole 4, which would be available from
nitrile 6 or acid 7 (Figure 2, A). Although synthesis of 4
proceeded without difficulty from acid 7, this route was unsuc-
cessful at a late stage for a reason that we describe below. We
next envisioned benzimidazole 3 emanating from β-amino ester
10, which could be accessed in a few steps starting with an
early stage 3CR of aldehyde 11, malonic acid (5), and ammoni-
um acetate (Figure 2, B). Gratifyingly, 10 was converted to the
requisite benzimidizole 3 in three steps and carried through to 1.
Figure 1: p21 determines the fate of DNA-damaged [13] cells.
Results and Discussion
Our initial target was benzimidazole 4, which we envisioned
The synthesis of 1 emanates from a one-pot, three-component originating from nitrile 6 or acid 7, each of which is commer-
reaction (3CR) of an arylaldehyde, malonic acid (5), and ammo- cially available (Figure 2). We first attempted to synthesize 4
nium acetate, which assembles the β-amino acid core (Figure 2) from 6, which would lead to the shortest possible synthesis of 1.
[14,15,18]. In the reported synthesis of 1, a protected β-amino Nitrile 6 was treated with N-(3-aminopropyl)pyrrolidine (8) to
acid core was attached to Rink-amide resin and carried through produce aniline 12 in 81% yield (Scheme 1) [19]. This com-
to 1 by a series of elaboration and tagging steps [14,15]. Syn- pound was reduced to aniline 13 in 79% yield and converted to
thetic intermediates in this route were not characterized, and 1 the benzimidizole 14 in 63% yield with aldehyde 9 under oxida-
was ultimately purified by high-performance liquid chromatog- tive conditions. The resultant nitrile proved to be extremely
Figure 2: Retrosynthetic analysis of LLW62 (1) from acid 7 (A) or aldehyde 11 (B).
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Beilstein J. Org. Chem. 2013, 9, 260–264.
insoluble and difficult to handle. Several reduction conditions
were attempted to produce benzimidazole 4 with no success. In
addition, attempts to use the nitrile in a Blaise-type reaction or
similar nucleophilic addition were also unsuccessful (not
shown). Although nitrile 6 would have provided the shortest,
most direct entry into the requisite β-amino core structure, we
turned our attention to another route to 4.
Scheme 1: Attempted synthesis of aldehyde 4 from nitrile 6.
Acid 7 was immediately more promising as a starting material
for benzimidazole 4. Commercially available 7 was converted
to methyl ester 15 in 90% yield, due to its ease of handling
(Scheme 2) [20]. Next, SNAr displacement of the fluoride of 15
by N-(3-aminopropyl)pyrrolidine (8) proceeded in high yield,
99%, to give aniline 16 [20]. Reduction of the nitro group was
nearly quantitative and subsequent benzimidazole formation
with Oxone furnished benzimidazole 17 in 47% yield over two
steps [20,21]. The ester of 17 was smoothly reduced to the
alcohol 18, in 74% yield, and immediately oxidized to the alde-
Scheme 2: (A) Synthesis of 4 from acid 7 and (B) attempted β-amino
acid-forming 3CRs.
hyde 4, in 87% yield. Unfortunately, 4 produced none of the (63%) provided aniline 26 as our key intermediate for forming
desired β-amino acid 3 under several different variants of the the benzimidazole core of 1. We next attempted to produce 27
3CR with malonic acid (5) and ammonium acetate. Tan and under the higher yielding oxidative conditions described for the
Weaver demonstrated previously that the β-amino acid forming formation of nitrile containing benzimidazole 14. The yield for
3CR works best for electron-rich aldehydes and poorly for elec- this reaction was significantly lower, less than 50%, compared
tron-deficient aldehydes [18]. Thus, we suspected that aldehyde to the reaction to produce 14, and we observed some transesteri-
4 may be too electron poor for the 3CR to work efficiently. Our fication of the methyl ester with butanol to produce a mixture of
suspicions were supported by attempting 3CRs on aldehydes 19 27 and the butyl ester of 27 as the major products (not shown).
and 20, each of which has a single nitro group, and neither was We thus turned to using Oxone, and benzimidazole formation
successful in this transformation.
proceeded in acceptable yield (44%) from aniline 26 to furnish
27. Benzimidazole 27 was then saponified under basic condi-
An early-stage 3CR enabled the use of the least electron-poor tions to give acid 28 (86%) [21]. Installation of the primary
aldehyde in this key step (Scheme 3). Heating of 4-fluorobenz- amide of 1 was then achieved in a single pot by treatment of 28
aldehyde (11), malonic acid and ammonium acetate under with ethyl chloroformate to make the mixed anhydride fol-
reflux proceeded smoothly, as previously described, to furnish lowed by displacement with ammonia gas to produce 29 in 65%
β-amino acid 21 in 73% yield [18]. Methylation of 21 (80%) yield [22]. Final Boc deprotection of 29 with TFA (87%) and
followed by nitration of 22 (67%), boc protection of 23 and subsequent acylation of the free amine of 30 with isocyanate 2
SNAr displacement of the fluoride in 24 with amine 8 (71% (75%) provided the desired compound 1 in 11 total steps and
over two steps), and finally reduction of the nitro group of 25 3% overall yield.
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Scheme 3: Synthesis of LLW62 by using an early stage 3CR.
Conclusion
RHW acknowledges research support from the NIH (NCI/
We have completed a solution-phase synthesis of 1 and thus 1R01CA135401; NIDDK/1R01DK082690) and the Medical
provided a common route to related compounds that may Service of the US Department of Veterans’ Affairs. The authors
emerge from future on-bead screening experiments. The key thank Dr. Ruiwu Liu and Professor Kit S. Lam (Division of
step was the 3CR to form the β-amino acid core structure. Hematology and Oncology, Department of Internal Medicine,
Although the electronic requirements of this reaction limit it to University of California Davis Comprehensive Cancer Center)
electron-rich, or at least not excessively electron poor, aromatic for helpful discussions.
aldehydes, application of this transformation early in the syn-
References
1. Dolle, R. E.; Le Bourdonnec, B.; Worm, K.; Morales, G. A.;
thesis ultimately proved successful. Although this route is not
suitable for large-scale production of 1, multigram quantities of
Thomas, C. J.; Zhang, W. J. Comb. Chem. 2010, 12, 765–806.
this compound and benzimidazoles of comparable complexity
doi:10.1021/cc100128w
are easily accessible for early stage studies of these compounds
2. Kodadek, T. Chem. Commun. 2011, 47, 9757–9763.
in vitro and in vivo using model organisms.
doi:10.1039/c1cc12102b
3. Aina, O. H.; Marik, J.; Liu, R.; Lau, D. H.; Lam, K. S. Mol. Cancer Ther.
2005, 4, 806–813. doi:10.1158/1535-7163.MCT-05-0029
Supporting Information
4. Dixon, S.; Ziebart, K. T.; He, Z.; Jeddeloh, M.; Yoo, C. L.; Wang, X.;
Lehman, A.; Lam, K. S.; Toney, M. D.; Kurth, M. J. J. Med. Chem.
Supporting Information File 1
2006, 49, 7413–7426. doi:10.1021/jm0609869
Experimental procedures and compound characterization.
5. Zhang, H.; Aina, O. H.; Lam, K. S.; de Vere White, R.; Evans, C.;
[http://www.beilstein-journals.org/bjoc/content/
supplementary/1860-5397-9-31-S1.pdf]
Henderson, P.; Lara, P. N.; Wang, X.; Bassuk, J. A.; Pan, C.-x.
Urol. Oncol.: Semin. Orig. Invest. 2012, 30, 635–645.
doi:10.1016/j.urolonc.2010.06.011
6. Lam, K. S.; Lehman, A. L.; Song, A.; Doan, N.; Enstrom, A. M.;
Maxwell, J.; Liu, R. Methods Enzymol. 2003, 369, 298–322.
doi:10.1016/S0076-6879(03)69017-8
Acknowledgements
This work was supported by the National Science Foundation
(CAREER award to JTS) and the National Institutes of Health
(NIGMS/P41GM089153). CS thanks CAPES (Coordenação de
Aperfeiçoamento de Pessoal de Nível Superior) and the
Brazilian Ministry of Education for a postdoctoral fellowship.
7. Lam, K. S.; Salmon, S. E.; Hersh, E. M.; Hruby, V. J.;
Kazmierski, W. M.; Knapp, R. J. Nature 1991, 354, 82–84.
doi:10.1038/354082a0
8. Liu, G.; Fan, Y.; Zhao, Z.; Lam, K. S. Zhongguo Yaowu Huaxue Zazhi
2002, 12, 311–318.
263

Beilstein J. Org. Chem. 2013, 9, 260–264.
9. Miyamoto, S.; Liu, R.; Hung, S.; Wang, X.; Lam, K. S. Anal. Biochem.
2008, 374, 112–120. doi:10.1016/j.ab.2007.10.028
10.Park, S. I.; Renil, M.; Vikstrom, B.; Amro, N.; Song, L.-w.; Xu, B.-l.;
Lam, K. S. Lett. Pept. Sci. 2001, 8, 171–178.
doi:10.1023/A:1016297601361
11.Xiao, W.; Wang, Y.; Lau, E. Y.; Luo, J.; Yao, N.; Shi, C.; Meza, L.;
Tseng, H.; Maeda, Y.; Kumaresan, P.; Liu, R.; Lightstone, F. C.;
Takada, Y.; Lam, K. S. Mol. Cancer Ther. 2010, 9, 2714–2723.
doi:10.1158/1535-7163.MCT-10-0308
12.Dixon, S. M.; Milinkevich, K. A.; Fujii, J.; Liu, R.; Yao, N.; Lam, K. S.;
Kurth, M. J. J. Comb. Chem. 2007, 9, 143–157.
doi:10.1021/cc060090p
13.Weiss, R. H. Cancer Cell 2003, 4, 425–429.
doi:10.1016/S1535-6108(03)00308-8
14.Weiss, R.; Park, S.-H.; Lam, K. S.; Liu, R. Inhibitors of Cyclin Kinase
Inhibitor p21. WO Patent WO2010039668A2, April 8, 2010.
15.Park, S. H.; Wang, X.; Liu, R.; Lam, K. S.; Weiss, R. H.
Cancer Biol. Ther. 2008, 7, 2015–2022. doi:10.4161/cbt.7.12.7069
16.Park, S.-H.; Park, J.-Y.; Weiss, R. H. J. Urol. 2008, 180, 352–360.
doi:10.1016/j.juro.2008.02.038
17.Weiss, R. H.; Borowsky, A. D.; Seligson, D.; Lin, P.-Y.; Dillard-Telm, L.;
Belldegrun, A. S.; Figlin, R. A.; Pantuck, A. D. J. Urol. 2007, 177,
63–69. doi:10.1016/j.juro.2006.08.073
18.Tan, C. Y. K.; Weaver, D. F. Tetrahedron 2002, 58, 7449–7461.
doi:10.1016/S0040-4020(02)00824-4
19.Göker, H.; Kuş, C.; Boykin, D. W.; Yildiz, S.; Altanlar, N.
Bioorg. Med. Chem. 2002, 10, 2589–2596.
doi:10.1016/S0968-0896(02)00103-7
20.Dietrich, S. A.; Lindauer, R.; Stierlin, C.; Gertsch, J.; Matesanz, R.;
Notararigo, S.; Diaz, J. F.; Altmann, K.-H. Chem.–Eur. J. 2009, 15,
10144–10157. doi:10.1002/chem.200901376
21.Cellier, M.; Fabrega, O. J.; Fazackerley, E.; James, A. L.; Orenga, S.;
Perry, J. D.; Salwatura, V. L.; Stanforth, S. P. Bioorg. Med. Chem.
2011, 19, 2903–2910. doi:10.1016/j.bmc.2011.03.043
22.Yan, S.; Larson, G.; Wu, J. Z.; Appleby, T.; Ding, Y.; Hamatake, R.;
Hong, Z.; Yao, N. Bioorg. Med. Chem. Lett. 2007, 17, 63–67.
doi:10.1016/j.bmcl.2006.09.095
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