combinatorial chemistry online volume 11 issue 1 january 2009

An ephedrine receptor from a dynamic combinatorial library Dynamic combinatorial libraries are generated from a set of building blocks using solution-phase reversible reactions.. A recen

Combinatorial Chemistry Online

Volume 11, Issue 1, January 2009

N K Terrett

Ensemble Discovery Corp., Cambridge, MA 02139, USA

1 Current literature highlights

1.1 An ephedrine receptor from a dynamic combinatorial library

Dynamic combinatorial libraries are generated from a set of

building blocks using solution-phase reversible reactions As all

po-tential compounds in the library are in equilibrium, the proportion

of compounds generated reflect the relative stability of each

Addi-tion of a guest molecule will enhance the stability of compounds

that bind the guest and will perturb the equilibrium in favour of

those library compounds A recent paper describes the formation

of a dynamic combinatorial library of over 9000 compounds, and

the successful identification of compounds that binds ephedrine.1

The library was prepared by the oligomerisation of equimolar

amounts of eight diverse disulphide building blocks in water at pH

8.0 Results indicated that cyclic products up to tetramer in size were

being generated Running the preparation for one week in both the

presence and absence of 5 mM ephedrine resulted in libraries

con-taining different proportions of product Ephedrine was chosen for

this study, as it is a member of the phenylethylamine class of

com-pound that also includes dopamine, adrenaline and amphetamine,

many of which have pharmacological activity in the CNS

To identify if any compounds were amplified in the presence of

ephedrine, HPLC analyses of the two libraries was undertaken

seeking peaks that were enhanced for the ephedrine templated

li-brary In particular, one peak corresponding to a compound with a

mass of 922.7 was highly enriched in the templated library

Through LC-MS-MS experiments, this compound was identified

as being a tetramer composed of two equivalents each of

disul-phides 1 and 2 Indeed it was observed that (1)2(2)2and the close

analogue (1)(2)3were only observed when the ephedrine template

was present

To confirm binding and identify the specific isomers that bind ephedrine, a follow-up library was prepared using only the build-ing blocks, 1 and 2 It was observed that there was little selectivity

in amplification between the isomers of (1)2(2)2 A similar lack of selectivity was observed with (1)(2)3, and thus no attempts were made to separate them Isothermal calorimetry demonstrated that the binding event was enthalpy driven with affinities amongst the highest reported to date for synthetic receptors for this class of molecule

1.2 Solid-phase synthesis of a library of FK228 analogues Histone deacetylases (HDACs) participate in the post-transla-tional modification of histones by catalysing a deacetylation These result in a change of DNA conformation, resulting in epigenetic gene regulation, a process than can play a critical role in cell pro-liferation, differentiation and thus also in cancer Consequently, there has been a search for inhibitors of HDACs, the most fully de-scribed of which is FK228 (3), a natural product isolated from Chro-mobacterium violaceum

FK228 operates as a pro-drug - reduction of the disulphide bond when the compound enters cells results in the release of a thiol group that binds to a catalytic zinc cation in the HDAC active site Total synthesis of FK228 has been achieved but is a laborious pro-cess, and access to analogues has been problematic A recent pub-lication has described a solid-phase route to the synthesis of FK228 analogues based on a modified compound (4) with isosteric substitutions.2

The modifications in the structure of 4 allowed more rapid synthesis using readily available building blocks The trans double bond in the heptenoic acid residue of FK228 was replaced with an amide bond, and the ester bond in the depsipeptide macrocyclic backbone was also converted to an amide Finally, the unusual

SH

SH

COOH

HOOC

HS

O

HN

N H

H

NH S S O

O

HN

N H

H

NH S HN S O

O

R2

O

E-mail: nterrett@ensemblediscovery.com

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(Z)-dehydrobutyrine amino acid in FK228 was replaced with a

variable amino acid substituent, permitting further structural

var-iation A solid-phase synthetic approach to compound 4 was

devel-oped, using a standard N-Fmoc/tBu peptide synthesis strategy,

preparing a linear pentapeptide prior to the macrocyclisation and

disulphide formation

From the library of analogues prepared, screening for the

inhi-bition of T24 human bladder carcinoma cell growth revealed two

compounds showing significant inhibition at 0.5lM One of the

lead compounds demonstrated significant growth inhibition

against six human cancer cell lines with IC50values between 0.18

and 0.06lM

2 A summary of the papers in this month’s issue

2.1 Solid-phase synthesis

No papers this month

2.2 Solution-phase synthesis

A library of flavonols has been made through the

Algar-Flynn-Oyamada reaction from 20-hydroxyacetophenones and

benzalde-hydes Glycosylation of these flavonols with various glycosyl

donors affords a library of glycosylated flavonols which are

poten-tially useful pharmacologically active compounds and will be

studied for biological activities.3

A fast and straightforward three-component reaction to prepare

2-amino-5-alkylidene-thiazol-4-ones suitable for parallel

synth-esis has been reported The one-pot microwave methodology

in-volves Knoevenagel condensation of aromatic aldehydes and

rhodanine, followed by displacement of the thiocarbonyl sulphur

with primary or secondary amines in the same reaction mixture.4

A practical strategy for the parallel synthesis of

diazabenz[e]a-ceanthrylene-based heterocycles has been reported The key step

in this approach was a microwave-assisted condensation and

cycli-sation reaction between an anthranilic acid derivative and a 20

-carbomethoxy substituted N-aryl lactam The scope of the reaction

has been explored as a function of both the nature and position of

substituents in both components and variations in lactam ring size.5

2.3 Scaffolds and synthons for combinatorial libraries

Novel multifunctional chemotypes based ona-tetralone,a

-in-danone, and chromanone have been synthesised by a

chemo-enzy-matic approach by applying an enzymatic irreversible

transesterification strategy The scaffolds synthesised can be

further elaborated with subsequent enzymatic as well as chemical

transformations for the generation of new sets of structurally

re-lated organic molecules.6

2.4 Solid-phase supported reagents

An efficient and operationally simple method for C3-alkylation

of 4-hydroxycoumarins has been developed under acidic medium

giving good yields of the products In the present method, a

reusa-ble AmberliteÒ IR-120 resin was used as an acid catalyst and

secondary benzyl alcohols were used as alkylating agents The

3-alkylated-4-hydroxycoumarins thus obtained offered an easy

access for the synthesis of 3,4-disubstituted coumarins by way of

Pd-catalyzed coupling reactions.7

2.5 Novel resins, linkers and techniques

A new sensitive and practical colorimetric test for

solid-sup-ported hydroxyl and thiol groups has been described The assay

is based on the direct labelling with low amounts of commercially available NF31 in the presence of DMAP at room temperature, resulting in easily detectable red beads.8

A new, fluorous-tagged chiral auxiliary has been developed for the asymmetric, samarium diioide-mediated coupling of aldehydes anda,a-unsaturated esters.a-Butyrolactones have been obtained

in moderate to good isolated yield and in high enantiomeric excess The fluorous tag allows the auxiliary to be conveniently recovered

by fluorous solid-phase extraction (FSPE) and reused.9

2.6 Library applications General, high-yielding microwave assisted organic synthesis protocols for the expedient synthesis of functionalised 3,6-disub-stituted-[1,2,4]triazolo[4,3-b]pyridazines have been described This approach was amenable to an iterative analogue library synth-esis strategy for the lead optimisation of an M1 antagonist screen-ing hit.10

The affinity of nine different saccharides to a library of solid-supported pentapeptide diboronic acids was measured using a competitive binding assay, which employed alizarin as the chro-mophoric indicator Considerable variation in carbohydrate bind-ing strengths was observed and the remarkably selective bindbind-ing characteristics of these boronic acid-peptide hybrids suggest their potential use in carbohydrate sensors and cell-specific diagnostics and therapeutics.11

3,5-Diaryl carbothioamide pyrazolines designed as mycobactin analogues have been reported to be potent antitubercular agents under iron limiting conditions These compounds were evaluated for their MAO-inhibitory activity against rat liver MAO-A and MAO-B The thirty-two compounds analysed have shown a spec-trum of activity from selective to nonselective against these two isoforms.12

Inspired by polyhydroxylated pyrrolidine alkaloid natural pro-ducts, a 18-membered library of 2-aryl polyhydroxylated pyrroli-dines has been efficiently prepared in two or three synthetic steps from known chiral cyclic nitrones The inhibitory activity of all these compounds against various glycosidase enzymes was evaluated.13

A small library of HI-236 derivatives substituted at the C-2 phe-nolic oxygen have been synthesised and evaluated as HIV non-nu-cleoside reverse transcriptase inhibitors (NNRTI) A number of them have superior antiviral activity to HI-236 as evaluated in both cell culture and in an RT inhibition assay.14

References

1 Ludlow, R F.; Otto, S J Am Chem Soc 2008, 130 (37), 12218-12219.

2 Di Maro, S et al J Med Chem 2008, 51 (21), 6639-6641.

3 Li, Z et al Tetrahedron Letters 2008, 49 (51), 7243-7245.

4 Anderluh, M et al Tetrahedron, 2009, 65 (1), 344-350.

5 Jones, A M et al Tetrahedron, 2009, 65 (2), 563-578.

6 Mahapatra, T et al Tetrahedron: Asymmetry 2008, 19 (21), 2497-2507.

7 Reddy, C R et al Tetrahedron, 2008, 64 (51), 11666-11672.

8 Caroen, J.; Van der Eycken, J Tetrahedron Lett 2009, 50 (1), 41-44.

9 Vogel, J C et al Tetrahedron, 2008, 64 (52), 11876-11883.

10 Aldrich, L N et al Tetrahedron Lett 2009, 50 (2), 212-215.

11 Duggan, P J.; Oermann, D A Tetrahedron 2009, 65 (1), 109-114.

12 Jayaprakash, V et al Bioorg Med Chem Lett 2008, 18 (24), 6362-6368.

13 Tsou, E -L et al Bioorg Med Chem 2008, 16 (24), 10198-10204.

14 Hunter, R et al Bioorg Med Chem 2008, 16 (24), 10270-10280.

Further Reading

Papers on combinatorial chemistry or solid-phase synthesis from other journals Betts, H M.; Barnard, P J.; Bayly, S R.; Dilworth, J R.; Gee, A D.; Holland, J P Controlled axial coordination: solid-phase synthesis and purification of metallo-radiopharmaceuticals Angewandte Chemie, International Edition 2008, 47 (44),

Roof, R A.; Sobczyk-Kojiro, K.; Turbiak, A J.; Roman, D L.; Pogozheva, I D.; Blazer, L L.;

Neubig, R R.; Mosberg, H I Novel peptide ligands of RGS4 from a focused one-bead,

one-compound library Chemical Biology & Drug Design 2008, 72 (2), 111–119.

Kwon, Y -U.; Kodadek, T Encoded combinatorial libraries for the construction of

cyclic peptoid microarrays Chemical Communications (Cambridge, United

King-dom) 2008, (44), 5704-5706.

Caballero, E.; Figueroa, J.; Puebla, P.; Pelaez, R.; Tome, F.; Medarde, M

Imino-Diels-Alder reactions of 1-aryl-3-(trialkylsiloxy)-1,3-butadienes in solution and the

solid phase European Journal of Organic Chemistry 2008, (23), 4004-4014.

Gareiss, P C.; Sobczak, K.; McNaughton, B R.; Palde, P B.; Thornton, C A.; Miller, B L.

Dynamic combinatorial selection of molecules capable of inhibiting the (CUG)

repeat RNA-MBNL1 interaction in vitro: discovery of lead compounds targeting

myotonic dystrophy (DM1) Journal of the American Chemical Society 2008, 130

(48), 16254-16261.

Lee, J T.; Mah, H.; Nam, K D.; Shin, D.; Ha, D -C.; Hahn, H -G Syntheses of

1,3-imidazolin-2-ones and 1,3-imidazolin-2-thiones from new building blocks,c

-aminoacetoace-tanilides Journal of Combinatorial Chemistry 2008, 10 (6), 803-806.

Lee, S S.; Lim, J.; Cha, J.; Tan, S.; Heath, J R Rapid microwave-assisted CNBr cleavage of

bead-bound peptides Journal of Combinatorial Chemistry 2008, 10 (6), 807-809.

Albada, H Bauke; Liskamp, Rob, M J TAC-scaolded tripeptides as artificial hydrolytic

receptors: a combinatorial approach toward esterase mimics Journal of

Combinatorial Chemistry 2008, 10 (6), 814-824.

Gobin, O C.; Schueth, F On the suitability of dierent representations of solid catalysts

for combinatorial library design by genetic algorithms Journal of Combinatorial

Chemistry 2008, 10 (6), 835-846.

Baxendale, I R.; Ley, S V.; Smith, C D.; Tamborini, L.; Voica, A -F A bifurcated

pathway to thiazoles and imidazoles using a modular flow microreactor Journal

of Combinatorial Chemistry 2008, 10 (6), 851-857.

Bogolubsky, A V.; Ryabukhin, S V.; Plaskon, A S.; Stetsenko, S V.; Volochnyuk, D M.;

Tolmachev, A A Dry HCl in parallel synthesis of fused pyrimidin-4-ones Journal

of Combinatorial Chemistry 2008, 10 (6), 858-862.

Verdie, P.; Subra, G.; Averland-Petit, M -C.; Amblard, M.; Martinez, J Solid-phase

synthesis of 4-methylcarboxy-1,4-benzodiazepine-2,5-diones Journal of

Combi-natorial Chemistry 2008, 10 (6), 869-874.

Chen, Y -Y.; He, W -Y.; Wu, Y.; Niu, C -Q.; Liu, G Dynamic selection of novel

vancomycin N-terminal derivatives by resin-bound reversed D-Ala-D-Ala Journal

of Combinatorial Chemistry 2008, 10 (6), 914-922.

Fraczyk, J.; Kaminski, Z J Design, synthesis, and application of a library of

supramolecular structures formed by N-lipidated peptides immobilized on

cellulose Journal of Combinatorial Chemistry 2008, 10 (6), 934-940.

Cho, C -H.; Neuenswander, B.; Lushington, G H.; Larock, R C Parallel synthesis of a multi-substituted benzo[b]furan library Journal of Combinatorial Chemistry 2008,

10 (6), 941-947.

Shortridge, M D.; Hage, D S.; Harbison, G S.; Powers, R Estimating protein-ligand binding affinity using high-throughput screening by NMR Journal of Combinator-ial Chemistry 2008, 10 (6), 948-958.

Roskov, K E.; Epps, T H., III; Berry, B C.; Hudson, S D.; Tureau, M S.; Fasolka, M J Preparation of combinatorial arrays of polymer thin films for transmission electron microscopy analysis Journal of Combinatorial Chemistry 2008, 10 (6), 966-973.

Messeguer, J.; Cortes, N.; Garcia-Sanz, N.; Navarro-Vendrell, G.; Ferrer-Montiel, A.; Messeguer, A Synthesis of a positional scanning library of pentamers of N-alkylglycines assisted by microwave activation and validation via the identifica-tion of trypsin inhibitors Journal of Combinatorial Chemistry 2008, 10 (6), 974-980 McIntee, J W.; Sundararajan, C.; Donovan, A C.; Kovacs, M S.; Capretta, A.; Valliant, J.

F A convenient method for the preparation of fluorous tin derivatives for the fluorous labeling strategy Journal of Organic Chemistry 2008, 73 (21), 8236-8243 Ziach K.; Jurczak J Controlling and measuring the equilibration of dynamic combinatorial libraries of imines Organic Letters 2008, 10 (22), 5159-5162 O’Keefe B M.; Simmons N.; Martin S F Carbonylative cross-coupling of ortho-disubstituted aryl iodides Convenient synthesis of sterically hindered aryl ketones Organic Letters 2008, 10 (22), 5301-5304.

Duschmale, J J.; Woltering, T J.; Bleicher, K H A highly efficient synthesis route for the rapid generation of 1,2,5,6-tetrasubstituted benzimidazoles Synlett 2008, (10), 1467-1470.

Jeon, M -K.; Kwon, J -J.; Kim, M -S.; Gong, Y -D A novel solid-phase synthetic method for 1,4-benzodiazepine-2,5-dione derivatives Synlett 2008, (11), 1651-1656.

Tsukamoto, H.; Suzuki, R.; Kondo, Y Traceless solid-phase synthesis of mappicine ketone library via multiple chemoselective palladium-catalyzed reactions on benzenesulfonate linker Synlett 2008, (13), 2005-2010.

Fu, G -Y.; Sheng, S -R.; Liu, X -L.; Cai, M -Z.; Huang, X Solid-phase organic synthesis

of vinyl-substituted 1,3,4-oxadiazoles using polymer-bounda-selenopropionic acid Synthetic Communications 2008, 38 (23), 4240-4249.

Liu, Z.; Mu, Y.; Lin, J.; Chen, Y Traceless solid-phase synthesis of 1,2,3-thiadiazole derivatives from resin-bound acylhydrazine Synthetic Commu-nications 2008, 38 (24), 4407-4414.

Vogel, P Combinatorial synthesis of linearly condensed polycyclic compounds, including anthracyclinones, through tandem Diels-Alder additions Topics in Current Chemistry 2008, 282(Anthracycline Chemistry and Biology I), 187-214.