Combinatorial Chemistry - An Online Journal 6 (2004) 13–16

Combinatorial Chemistry OnlineVolume 6, Issue 4, April 2004

N. K. Terrett

Pfizer Global R&D, Cambridge, MA 02139, USA

N OHNH2

OHOH

HN

NH

OHOH

R

OOH

H

RCO2H +

Scheme 1.

1. Current literature highlights

1.1. a-Fucosidase inhibitors

Iminocyclitols (also known aza-sugars) have attractedattention due to their inhibitory activity against variousglycosidases. The glucose-type iminocyclitol, deoxynoj-irimycin, has been used for the treatment of non-insulindependent diabetes, and recent studies with deoxynoj-irimycin and its derivatives indicate they are effectiveagainst hepatitis B and C, as well as glycosphingolipidstorage disorders such as Gaucher disease.

The efficacy of iminocyclitols is attributed to theirmimicry of the transition state of enzymatic glycosidiccleavage. Of the members of the glycosidase family, a-fucosidase is involved in the hydrolytic degradation ofnumerous fucose-containing glycoconjugates. This en-zyme is associated with a number of essential functions,and the abnormal accumulation of fuco-conjugates,resulting from the absence or deficiency of a-fucosidase,leads to the genetic neurovisceral storage disease fuco-sidosis. An aberrant distribution of intracellular andextracellular a-fucosidase is also found in cystic fibrosis.

Though the physiological functions of a-fucosidase arenot completely understood, potent fucosidase inhibitorsmay be used as probes for the study of fucosidases invarious disease states, and for the development ofpotential therapeutic agents. To facilitate the discoveryof new glycosidase inhibitors, a recent publicationdescribes the development of a new method for rapidderivatisation of an iminocyclitol core designed fora specific glycosidase family––in this case, particularfuconojirimycin derivatives for fucosidases.1 In thisapproach, the compounds are synthesised without pro-tecting group manipulation and under such conditions

E-mail: nick_terrett@cambridge.pfizer.com

doi:10.1016/j.comche.2004.04.001

that the product could be used directly for screeningin situ without isolation.

A solution phase library of 60 fuconojirimycin deriva-tives was synthesised as singletons according to generalScheme 1. The a-fucosidase from bovine kidney wasused for inhibition studies and a number of activecompounds were identified. One of the most potent was(i) which possessed a Ki of 0.6 nM, and selectivityagainst related glycosidases studied was high. This workhas produced the most potent and selective inhibitorsreported to date against the glycosyltransfer enzymea-fucosidase.

NNH

OHOH

OOH

HNH F

(i)

1.2. Human betaine inhibitors

The challenge for functional genomics and proteomics isto translate sequencing data into a precise understand-ing of how proteins function in cells, tissues or wholeorganisms. Small ligands that are able to specificallyinteract with proteins can be effective tools in the searchfor proteome function. Classically, new protein ligandshave been identified by SAR studies, molecular model-ling or combinatorial chemistry techniques. However,

14 N. K. Terrett / Combinatorial Chemistry - An Online Journal 6 (2004) 13–16

these approaches generally use only one protein target,and given the high number of proteins in mammalianorganisms, high-throughput screening procedures havebeen developed to handle this task. A potential draw-back with such methods is that the full range of proteinsthe chosen ligand may interact with are not discovered ifthe screening is performed with only one or a few pro-teins. This lack of information precludes our ability tocompletely understand the full spectrum of effects that aligand may have in a complex environment such as aliving cell.

Approaches that study the effects of ligands in wholecells are becoming increasingly important. Screeninglibraries using biosensor chips or arrays grafted withproteins allows real time recording of ligand-proteininteractions. Subsequent elution of these complexes canbe used for protein identification by mass spectrometry.A method to discover novel protein-ligand interactionshas been developed based on affinity capture principlescoupled to combinatorial chemistry.2

Affinity columns were prepared containing 361 differentphosphinic peptides and used to isolate all interactingproteins from crude rat liver homogenates. By applyinga deconvolution process, the most specific ligand havingthe highest affinity towards one newly discovered pro-tein target, betaine:homocysteine S-methyltransferase(BHMT), was identified from the library. The phosphi-nic peptides, which served as immobilised ligands for theisolation of rat BHMT, were then tested for their abilityto inhibit human recombinant BHMT in solution. Themost potent inhibitor also behaved as a selective ligandfor the affinity purification of BHMT from a complexmedia. Further optimisation led to (ii)––a potent BHMTinhibitor that possessed an IC50 of about 1 lM. Thiswork has demonstrated the successful application of anew and simple method for the discovery of new proteintargets for artificial ligands of interest. This methodol-ogy, in combination with 2D electrophoresis andMALDI mass spectrometry holds promise as an addi-tional method for the discovery of new specific protein-ligand interactions.

Val-Phe-W½PO2�–CH2�Leu-His-NH2

ðiiÞ

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

2.1. Solid-phase synthesis

A general procedure to prepare peptide thioacids bysolid-phase peptide synthesis has been presented.3 Themethod involves the synthesis of 4-[a-(S-acetyl)merca-ptobenzyl]phenoxyacetic acid, which once attached to asolid support is derivatised with the Boc-amino acid ofchoice after deprotection of the thiol.

The first example of a dynamic kinetic resolution (DKR)using immobilized amine nucleophiles attached to a solid

phase resin via an organic spacer has been described.4

The optical purities of the N-substituted-amino esterproducts are superior to the solution phase DKR.

Utilizing alkylation at a benzylic nitrogen-atom as a keystep, a solid-phase route for synthesis of 15N-labeledacylpolyamines has been reported.5 The derivatives wereused as reference compounds for the investigation of theMS/MS behaviour of spider toxins.

2.2. Solution-phase synthesis

A new synthesis of N-aryl- and N-heteroaryl-N 0-(aryl-alkyl)piperazines using palladium-catalysed aminationof aryl bromides and heteroaryl chlorides with mono N-benzyl- or N-(arylethyl)piperazines has been reported.6

Applying an automated parallel synthesizer the prepa-ration of a small library of potentially bioactive com-pounds can be easily achieved.

The palladium-catalysed regioselective a-monoarylationof deoxybenzoins and, a,a-diarylation of acetophenonesprovides general, efficient access to 1,2,2-triaryletha-nones and have been conducted by means of eithercommercially available polymer-anchored catalysts or avery simple homogeneous catalytic system.7

A recent review evaluates the advantages, disadvantages,and effectiveness of newly developed peptide couplingreagents used in organic synthesis.8 Each reagent wasclassified into one of eight types including phospho-nium, uronium, immonium, carbodiimide, imidazolium,organophosphorous, acid halogenating and other cou-pling reagents, according to the structural similarity.

2.3. Scaffolds for combinatorial libraries

No papers this month.

2.4. Solid-phase supported reagents

A novel polymer-supported N-heterocyclic carbene wasprepared from chloromethyl polystyrene (CM PS) resinusing a simple procedure, and has been used as a ligandfor palladium (Pd) Suzuki cross-coupling under aqueousconditions.9

A simple and efficient method has been developed forthe synthesis of a-bromoesters and ketones from b-ketoesters and diketones in one pot using a supportedreagents system.10

The novel 3-N,N-(dimethylamino)isocyanoacrylate-Wang-resin has been used for the synthesis of imidazole-4-carboxylic acids. The syntheses are performed in amicrowave reactor with reaction times of only 15 min at220 �C in the solvent dimethoxyethane.11

A new type of polymeric dehydrating reagent, readilyprepared by the treatment of polymer-supported tri-

N. K. Terrett / Combinatorial Chemistry - An Online Journal 6 (2004) 13–16 15

phenylphosphine oxide with triflic anhydride, was foundto be effective in a variety of dehydration reactions suchas ester and amide formation.12

A new cross-linked polystyrene-supported thioanisolereagent has been reported. This reagent can be treatedwith methyl trifluoromethanesulphonate to form thecorresponding sulphonium salt, and then deprotonatedto form a polymer-supported sulphur ylide that is ableto react with aldehydes and ketones to form epoxides.The thioanisole reagent can also be oxidized to form aninsoluble sulphoxide reagent useful for Swern oxidationreactions.13

2.5. Novel resins, linkers and techniques

A phenylmenthyl derivative, previously shown to be avery effective chiral auxiliary in diastereoselective [2+2]photocycloadditions of cyclic enones with ethylene, wasattached to poly(ethylene glycol)-grafted Wang resin.14

This was used for the first example of the photochemicalproduction of a bicyclo[4.2.0]octane derivative on solidsupport.

The synthesis of an ionic support and its application inthe preparation of a set of amides and sulphonamideshas been described.15 The potential was further exem-plified by the use in a one-pot multistep ionic liquidphase assisted synthesis of a tirofiban analogue.

A new oxidatively activatable safety-catch linker hasbeen developed for combinatorial solid-phase chemistryusing a two-step process starting from Merrifield resin.16

A polymer-bound iminium participates in an aza Diels–Alder cycloaddition, which leads to a supported dihy-droquinoline (DHQ resin).

A straightforward synthesis of trityl alcohols in whichone of the aryl rings is substituted with a vinyl group hasbeen presented.17 These compounds were used toincorporate trityl linker groups into polystyrene-basedorganic synthesis supports.

2.6. Library applications

A new noncovalent glycoarray assembly method formicroplates created by simply mixing together an iso-cyanate-containing C14-hydrocarbon and an amine-containing carbohydrate has been described.18 This newarray, together with the efficient methods available forsynthesis of complex oligosaccharides, could becomeuseful for the high-throughput biological evaluation ofcarbohydrate–protein and carbohydrate–carbohydrateinteractions.

A series of novel benzimidazole derivatives have beensynthesized via parallel solution-phase chemistry, andmany found to inhibit the growth of Staphylococcusaureus and Escherichia coli.19 Several analogues exhib-ited low micromolar minimal inhibitory concentrations(MIC) against both Gram-positive and Gram-negative

bacteria of clinical relevance and could serve as leads forfurther optimisations for antibacterial research.

A readily automated solid-phase approach to the syn-thesis of diverse N-(phenylalkyl)cinnamide analogues ofan NR2B antagonist, has been described.20 A 225-member focused library was synthesized using a TecanCombitec synthesizer.

Inspired by structure-based design and tailored forcombinatorial preparation, a series of novel cyclic pep-tides has been developed to yield binding ligands for thethird PDZ domain (PDZ3) of PSD-95. the postsynapticdensity-95 kDa protein.21

Solid-phase synthetic methods for biaryl-based com-pounds have been developed resulting in the construc-tion of two 1000-member libraries.22 Numerouscompounds were identified by high-throughput screen-ing using whole cell screens to exhibit anti-microbialactivity against Gram-positive bacteria.

The binding of the prokaryotic tubulin analogue, FtsZ,and the membrane-anchored protein, ZipA, presents apotential target for antibacterial therapy. Based ona small molecule inhibitor of the ZipA–FtsZ interaction,a parallel synthesis of small molecules was initiatedwhich targeted a key region of ZipA involved in FtsZbinding.23

A small library of pentapeptides containing two regionsof variability was synthesized and evaluated for lectinbinding.24 Specificity was observed and galectin inhibi-tion measured with selected sequences was 2–3 timesstronger than galactose.

The influence of aromatic substitution on a newly dis-covered class of inhibitors of dipeptidyl peptidase IV hasbeen investigated.25 A 105-fold increase in potency wasachieved by the optimisation of aromatic substituents ina parallel chemistry program.

A robust method for the solid phase synthesis of a seriesof selective caspase-3 peptide inhibitors has beendescribed.26 The inhibitors were obtained after cleavagefrom the solid support without further purification.

A small focused library of 20 3,5-substituted phenylga-lactosides based on two previous lead structures wasprepared with the aim of developing high-affinity monoand multivalent antagonists of cholera toxin (CT) andEscherichia coli heat-labile enterotoxin (LT).27 Thecrystal structures of the most promising compoundsbound to either CTB5 or LTB5 were also determined.

A library containing 29 peptides has been prepared viacatalysis by a unique ribozyme and the products anal-ysed by mass spectrometry.28 The results implicate thatthis ribozyme may have potential application in peptidesynthesis.

In order to characterise enzymes with unknown func-tion, a novel systems-based inhibitor design strategy,

16 N. K. Terrett / Combinatorial Chemistry - An Online Journal 6 (2004) 13–16

enabled by bioinformatic and NMR structural devel-opments has been developed.29 This strategy employs acombinatorial library that yielded specific inhibitors formultiple oxidoreductases.

References

1. Wu, C-Y.; et al. Angew. Chem., Int. Ed. Engl. 2003, 42(38), 4661–4664.

2. Collinsov�a, M.; et al. Chem. Biol. 2003, 10 (2), 113–122.3. Gaertner, H.; et al. Tetrahedron Lett. 2004, 45 (10), 2239–

2241.4. Valenrod, Y.; et al. Tetrahedron Lett. 2004, 45 (12), 2545–

2549.5. Manov, N.; et al. Tetrahedron 2004, 60 (10), 2387–2391.6. Michalik, D.; et al. Tetrahedron Lett. 2004, 45 (10), 2057–

2061.7. Churruca, F.; et al. Tetrahedron 2004, 60 (10), 2393–2408.8. Han, S.-Y.; Kim, Y.-A. Tetrahedron 2004, 60 (11), 2447–

2467.9. Byun, J.-W.; Lee, Y.-S. Tetrahedron Lett. 2004, 45 (9),

1837–1840.10. Aoyama, T.; et al. Tetrahedron Lett. 2004, 45 (9), 1873–

1876.11. Henkel, B. Tetrahedron Lett. 2004, 45 (10), 2219–2221.12. Elson, K. E.; et al. Tetrahedron Lett. 2004, 45 (12), 2491–

2493.13. Kwok Wai Choi, M.; Toy, P. H. Tetrahedron 2004, 60

(12), 2875–2879.14. Shintani, T.; et al. Tetrahedron Lett. 2004, 45 (9), 1849–

1851.15. de Kort, M.; et al. Tetrahedron Lett. 2004, 45 (10), 2171–

2175.16. Arseniyadis, S.; et al. Tetrahedron Lett. 2004, 45 (10),

2251–2253.17. Kwok Wai Choi, M.; Toy, P. H. Tetrahedron 2004, 60

(12), 2903–2907.18. Fazio, F.; et al. Tetrahedron Lett. 2004, 45 (12), 2689–

2692.19. He, Y.; et al. Bioorg. Med. Chem. Lett. 2004, 14 (5), 1217–

1220.20. W�eber, C.; et al. Bioorg. Med. Chem. Lett. 2004, 14 (5),

1279–1281.21. Li, T.; et al. Bioorg. Med. Chem. Lett. 2004, 14 (6), 1385–

1388.22. Look, G. C.; et al. Bioorg. Med. Chem. Lett. 2004, 14 (6),

1423–1426.23. Jennings, L. D.; et al. Bioorg. Med. Chem. Lett. 2004, 14

(6), 1427–1431.24. Arnusch, C. J.; et al. Bioorg. Med. Chem. Lett. 2004, 14

(6), 1437–1440.25. Peters, J.-U.; et al. Bioorg. Med. Chem. Lett. 2004, 14 (6),

1491–1493.

26. Grimm, E. L.; et al. Bioorg. Med. Chem. 2004, 12 (5), 845–851.

27. Mitchell, D. D.; et al. Bioorg. Med. Chem. 2004, 12 (5),907–920.

28. Cui, Z.; et al. Bioorg. Med. Chem. 2004, 12 (5), 927–933.29. Sem, D. S.; et al. Chem. Biol. 2004, 11 (2), 185–194.

Further Reading

Papers on combinatorial chemistry or solid-phase synthesis fromother journals

Ohno, H.; Tanaka, H.; Takahashi, T. Solid-phase synthesis ofN-alkylated naltrindoles using a 3-nitrobenzyl safety-catchlinker. Synlett 2004, (3), 508–511.

Amaya, T.; Tanaka, H.; Takahashi, T. Solid-phase synthesisof carbohydrate cluster on tree-type linker with three typesof orthogonally cleavable part. Synlett 2004, (3), 503–507.

Amaya, T.; Tanaka, H.; Takahashi, T. Combinatorial synthe-sis of carbohydrate cluster on tree-type linker with orthog-onally cleavable parts. Synlett 2004, (3), 497–502.

Olsen, C. A.; Witt, M.; Jaroszewski, J. W.; Franzyk, H. Diolsas building blocks in solid-phase synthesis of polyaminetoxins by fukuyama-mitsunobu alkylation. Synlett 2004,(3), 473–476.

Oliver, M.; Jorgensen, M. R.; Miller, A. D. Solid-phaseassisted N-1 functionalization of azamacrocycles. Synlett2004, (3), 453–456.

Mei, Y.; Beers, K. L.; Byrd, H. C. M.; VanderHart, D. L.;Washburn, N. R. Solid-phase ATRP synthesis of peptide-polymer hybrids. Journal of the American Chemical Society2004, 126 (11), 3472–3476.

Lee, J. H.; Nandy, S. K.; Lawrence, D. S. A highly potent andselective PKCa inhibitor generated via combinatorialmodification of a peptide scaffold. Journal of the AmericanChemical Society 2004, 126 (11), 3394–3395.

de Koning, M. C.; Filippov, D. V.; van der Marel, G. A.; vanBoom, J. H.; Overhand, M. Synthesis of peptide-PNA-peptide conjugates by semi-solid-phase chemical ligationcombined with deactivation/capture of excess reactants.European Journal of Organic Chemistry 2004, (4), 850–857.

Parr, N. J.; McKeown, S. C.; Lindvall, M. K.; Lorthioir, O. E.;Congreve, M. S.; Watson, S. P. The application ofquantitative analytical constructs for chemistry optimiza-tion, monomer rehearsal and reactivity prediction in solidphase library synthesis. Letters in Organic Chemistry 2004,1 (1), 87–92.

Juskowiak, G. L.; Stachel, S. J.; Tivitmahaisoon, P.; VanVranken, D. L. Fluorogenic peptide sequences-transforma-tion of short peptides into fluorophores under ambientphotooxidative conditions. Journal of the American Chem-ical Society 2004, 126 (2), 550–556.