Combinatorial Chemistry - An Online Journal 16 (2014) 41–44
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Combinatorial Chemistry - An Online Journal journal homepage: www.elsevier.com/locate/comche
Combinatorial Chemistry Online Volume 16, Issue 11, November 2014 N.K. Terrett Ensemble Therapeutics Corp., Cambridge, MA 02139, USA
1. Current literature highlights 1.1. Solution-phase parallel synthesis of acyclic nucleoside libraries Nucleic acids as found in nature and their related synthetic analogues are frequently found as components of therapeutically beneficial drug molecules. Such drugs often act by direct incorporation into nucleoside metabolic pathways, or can interfere with the general processes of DNA or RNA structure and function. Examples of drugs based on nucleosides have various uses as anticancer, antiparasitic, antiviral and antifungal agents. A recent paper describes the preparation of a library of purine, pyrimidine and 1,2,4-triazole-N-acetamide derivatives in a parallel high throughput solution-phase reaction format [1]. Amines
base
base
HATU, DIPEA, DMF
N
N Amines
COOH
2. A summary of the papers in this month’s issue
O
2.1. Polymer supported synthesis
Base = OBn
NHBn N
N
N
NHCbz N O
H2N
N H
N
HN
N
HN O
N H
N H
N O
N H
The compounds designed for this library did not contain a 50 hydroxyl group such as might be phosphorylated in naturally occurring nucleosides, and thus these analogues would not progress into nucleoside metabolic pathways. Instead the interest stemmed from the observation that acyclic nucleoside analogues with an amide bond were poorly represented in commercial compound collections. Furthermore, the intention was to prepare E-mail:
[email protected] http://dx.doi.org/10.1016/j.comche.2014.10.001
No papers this month. 2.2. Solution-phase synthesis
NH2
O N
N H
N
N
N H
N
O
SMe N
N H
N
compounds under the Pilot Scale Library Program of the NIH Roadmap Initiative to permit profiling for biological activities. The study generated a small library of 181 compounds made using an automated parallel solution phase approach. A diverse collection of amines were selected with the intention of coupling these to acetic acid derivatives of a number of bases. The seven bases selected were 6-benzylhypoxanthine, 6-benzyladenine, 6-thiomethylguanine, thymine, Cbz-cytosine, cytosine and 3-(3,4-dimethylphenylcarbamoyl)-1H-1,2,4-triazole. Following preparation of the acetic acid derivatives, several peptide coupling methods were investigated to find the best conditions to introduce the amines. Overall, the best results in terms of yield and reaction purity were obtained with HATU and DIEA in acetonitrile at room temperature. After amide coupling, solvent removal by centrifugal evaporation and automated medium pressure liquid purification gave the products. Each compound was assessed for purity by HPLC and characterised by NMR and MS analysis before submission to the Molecular Libraries Small Molecule Repository at NIH.
Isoflavonoids, a class of organic compounds that act primarily as antioxidants, are produced almost exclusively by various members of the bean family. The antioxidant characteristics that isoflavonoids exhibit help hinder the progression of certain cancers, primarily breast, prostate, and colon cancer. A three to five step synthesis for obtaining a suite of isoflavonoid derivatives has been developed. The route involves enamine formation, ring closure and halogenation, Suzuki coupling, and finally a global deprotection to obtain the respective isoflavonoid derivatives [2]. An efficient, one-pot, three-component domino strategy has been demonstrated for the synthesis of imidazo[1,2-a]pyridines using a catalytic amount of iron(III) chloride. A library of imidazo[1,2-a]pyridines was synthesised by the reaction of readily available aldehydes and 2-aminopyridines in a mixture of nitroalkane and DMF. This transformation presumably occurs by a sequential aza-Henry reaction/cyclisation/denitration [3].
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N.K. Terrett / Combinatorial Chemistry - An Online Journal 16 (2014) 41–44
Diversity-oriented synthesis of a chemical library based on a pyrrolo[1,2-a]pyrazine core has been described by using palladium-catalysed direct C6 arylation of pyrrolo[1,2-a]pyrazines with various aryl bromides. The starting materials, pyrrolo[1,2-a]pyrazines, were easily synthesised by the base-mediated N-alkylation of pyrrole-2-carboxaldehyde with several 2-bromoacetophenones followed by dehydrative cyclisation with incorporation of nitrogen by the action of ammonium acetate [4].
tures of this new catalytic methodology include its sustainability, effectiveness in the absence of solvent, a facile work-up procedure, and economic viability. PSA has been fully characterised by Fourier transform infrared spectroscopy, wide-angle X-ray scattering analysis, and scanning electron microscopy with energy dispersive X-ray spectroscopy. The catalyst can be reused several times without significant loss of activity, and in addition, no chromatographic separations are needed to obtain the desired products [10].
2.3. Scaffolds and synthons for combinatorial libraries
2.5. Novel resins, linkers and techniques
The vast majority of scaffolds found in natural products are absent from currently available compound collections used for biological screening. However, scaffolds derived from natural products may have a distinct advantage over non-natural cores in terms of providing compounds endowed with biological activities. A synthetic approach to merging a naturally occurring 1-azaadamantane core with a vicinal amino alcohol moiety that is also common in natural product chemical space has been described. The synthesis features diastereoselective epoxidation of racemic chiral 2,6-diaryl-4-methylene 1-azaadamantanes with subsequent SN2-type epoxide opening in aqueous isopropanol [5]. One pot ring synthesis of novel 4-hydrazinothiazoles through a sequential four-component route employing carbonyl compounds, aminoguanidine, isothiocyanates, and a-haloketones has been accomplished under mild reaction conditions. Base-assisted eliminative aromatisation in the [4+1] ring synthesis sheds light on some interesting leaving group propensities of amines versus hydrazines resulting in the exclusive formation of the title compounds with potential as scaffolds for drug discovery. Hydrazone deprotection was effected by acylation which subsequently provided a new set of diacylated molecular systems with a wider scope as chemical handles in the design of thiazolyl drug candidates [6]. The sulphoximine group has great potential as a substituent in drug discovery, as evidenced by two recent clinical candidates, and can be viewed as an isosteric alternative to the more commonly used sulphone. To improve accessibility of this group, a diverse range of S-alkyl and N-alkyl sulphoximine building blocks were prepared using procedures applicable on a practical scale (>10 g). In particular, synthesis of the less well exploited N-alkyl sulphoximines and the use of dimethylsulphoximine as a versatile, commercially available precursor has been proposed [7]. 2.4. Solid-phase supported reagents The synthesis of a nanopolymer-supported palladium(II) complex catalyst, [PS-tet-Pd(II)] using a simple protocol has been reported. The catalyst was characterised by X-ray diffraction, scanning electron microscopy, FT-IR, and energy dispersive X-ray spectroscopy. PS-tet-Pd(II) is a useful heterogeneous catalyst in the copper- and phosphine-free Sonogashira coupling reaction in water. It can be recovered from the reaction mixture by simple filtration and reused several times without any significant loss of catalytic activity.[8]. An ‘on-water’, efficient, high yielding, expeditious method has been developed for the synthesis of 1,4-dihydropyridine (1,4DHP) derivatives via a one-pot multi-component condensation of dimedone or 4-hydroxycoumarine, aldehydes, and ammonium acetate using Fe3O4@SiO2 nanoparticles as a recyclable heterogeneous catalyst. This method takes advantage of the use of water, a green solvent, in combination with Fe3O4@SiO2 nanoparticles as the catalyst which can be easily recovered magnetically and reused for further runs [9]. Phosphosulphonic acid (PSA) acts as a highly effective and reusable catalyst for the chemo-selective protection of aldehydes with acetic anhydride under solvent-free conditions. The desirable fea-
No papers this month. 2.6. Library applications The design and parallel solid phase synthesis of linear and oligoheterocyclic peptidomimetic analogues of Leu-enkephalin have been described. These peptidomimetics represent different unique scaffolds that distribute over space the peptidyl side chains of amino acids essential for biological activity and mimic the bioactive conformation of the Leu-enkephalin peptide. The compounds were screened in competitive radioligand binding assays to determine their affinities for l-(MOR), and j-(KOR) opioid receptors [11]. A library of stereochemically diverse and highly substituted 2,6cis piperidine derivatives have been synthesised and evaluated for their anticancer activity in cancer cells including A549 (lung cancer, CCL-185), MCF7 (breast cancer (HTB-22), DU145 (prostate cancer (HTB-81), and HeLa (cervical cancer, CCL-2). One stereoisomer emerged as a promising candidate for further design based structure–activity studies [12]. Small-molecule peptidomimetic inhibitors that already showed activity towards secreted aspartic protease 2 with potential as anti-Candida agents have been proposed as candidate HIV protease inhibitors. A library of 6,8-dioxa-3-azabicyclo[3.2.1]-octane peptidomimetic scaffolds was screened against HIV protease, resulting in the identification of hit compounds possessing IC50 values in the sub-micromolar range, and showing the bicyclic acetal portion as a potential transition state analogue in the interaction with catalytic aspartic acid residues [13]. A series of 1,2,3-triazole-coupled diaryl sulphone-containing compounds have been synthesised by copper-catalysed azidealkyne 1,3-dipolar cycloaddition (CuAAC) reaction under ultrasound irradiation. In situ formation of azides from a-bromoketones together with the CuAAC reaction in one pot has allowed safe handling and good availability of azides for the development of a small library of compounds. The sonication reduced reaction time and increased yields compared to other conditions. All synthesised compounds were evaluated for antibacterial, antifungal and antioxidant activities and some were found to be potent antifungal or antimicrobial agents [14]. Insulin exerts its metabolic actions through the insulin receptor (IR) and plays an essential role in the treatment of diabetes. In the search for bioactive insulin mimetics, a chemical library of small molecules based on an indolylkojic acid scaffold have been prepared. An in vitro screening assay was performed to stimulate glucose transport in rat L6 skeletal muscle cells, following treatment with the compounds for a time period incubation of 16 h. Several compounds have shown significant glucose uptake stimulation as compared with control compounds [15]. Virtual screening of the ChemDiversity and ChemBridge compound databases against dynamin I (dynI) GTPase activity identified a 2,5-bis-(benzylamino)-1,4-benzoquinone inhibitor. In silico lead optimisation and screening of a focused library-led synthesis resulted in the development of four discrete benzoquinone/naphthoquinone based compound libraries comprising 54 compounds in total. Sixteen analogues were more potent than the original lead
N.K. Terrett / Combinatorial Chemistry - An Online Journal 16 (2014) 41–44
and molecular modelling suggested a number of hydrogen bonding and hydrophobic interactions were involved in interactions within the dynI GTP binding site [16]. A general method for the synthesis of a library of hitherto unreported amino-1,4-naphthoquinone-appended triazoles has been accomplished via a sequential three-component reaction of substituted N-propargylaminonaphthoquinones with variously substituted alkyl bromides/2-bromonaphthalene-1,4-dione and sodium azide in the presence of Et3N/CuI in water. All the triazole hybrids were screened for their in vitro activity against Mycobacterium tuberculosis H37Rv (MTB) and one compound emerged as being more potent than the anti-TB drugs, cycloserine, pyrimethamine and equipotent with the drug ethambutol [17]. References [1] Pathak AK, Pathak V, Reynolds RC. Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides. ACS Combinatorial Sci 2014;16(9):485–93. [2] Biegasiewicz KF, Gordon IV JS, Rodriguez DA, Priefer R. Development of a general approach to the synthesis of a library of isoflavonoid derivatives. Tetrahedron Lett 2014;55(37):5210–2. [3] Santra S, Mitra S, Bagdi AK, Majee A, Hajra A. Iron(III)-catalyzed threecomponent domino strategy for the synthesis of imidazo[1,2-a]pyridines. Tetrahedron Lett 2014;55(37):5151–5. [4] Park S, Jung Y, Kim I. Diversity-oriented decoration of pyrrolo[1,2-a]pyrazines. Tetrahedron Lett 2014;70(41):7534–50. [5] Taheria A, Quinna RJ, Krasavina M. Naturally occurring scaolds for compound library design: convenient access to bis-aryl 1-azaadamantanes carrying a vicinal amino alcohol motif. Tetrahedron Lett 2014;55(39):5390–3. [6] Titus S, Sreejalekshmi KG. One-pot four-component synthesis of 4-hydrazinothiazoles: novel scaolds for drug discovery. Tetrahedron Lett 2014;55(40):5465–7. [7] Goldberg FW, Kettle JG, Xiong J, Lin D. General synthetic strategies towards Nalkyl sulfoximine building blocks for medicinal chemistry and the use of dimethylsulfoximine as a versatile precursor. Tetrahedron Lett 2014;70(37):6613–22. [8] Nasrollahzadeh M, Khalaj M, Ehsani A. A heterogeneous and reusable nanopolymer-supported palladium catalyst for the copper- and phosphine-free Sonogashira coupling reaction under aerobic conditions in water. Tetrahedron Lett 2014;55(38):5298–301. [9] Dam B, Nandi S, Pal AK. An efficient ‘on-water’ synthesis of 1,4-dihydropyridines using Fe3O4@SiO2 nanoparticles as a reusable catalyst. Tetrahedron Lett 2014;55(38):5236–40. [10] Kalla RMN, Park H, Hoang TTK, Kim I. Phospho sulfonic acid as an efficient and recyclable solid acid catalyst for the solvent-free preparation of acylals. Tetrahedron Lett 2014;55(39):5373–6. [11] Hammami S, Mighri Z, Dooley CT, Nefzi A. Synthesis and analgesic activity of alkylated, reduced and constrained oligoheterocyclic peptidomimetic analogs of Leu-enkephalin. Bioorg Med Chem Lett 2014;24(18):4482–5. [12] Kumaraswamy G, Kumar RS, Sampath B, Poornachandra Y, Kumar CG, Vemulapalli SPB, et al. A concise diastereoselective approach to enantioenriched substituted piperidines and their in vitro cytotoxicity evaluation. Bioorg Med Chem Lett 2014;24(18):4439–43. [13] Calugi C, Guarna A, Trabocchi A. Identification of constrained peptidomimetic chemotypes as HIV protease inhibitors. Eur J Med Chem 2014;84:444–53. [14] Mady MF, Awad GE, Jørgensen KB. Ultrasound-assisted synthesis of novel 1,2,3triazoles coupled diaryl sulfone moieties by the CuAAC reaction, and biological evaluation of them as antioxidant and antimicrobial agents. Eur J Med Chem 2014;84:433–43. [15] Sharma DK, Pandey J, Tamrakar AK, Mukherjee D. Synthesis of heteroaryl/aryl kojic acid conjugates as stimulators of glucose uptake by GLUT4 translocation. Eur J Med Chem 2014;85:727–36. [16] MacGregor KA, Abdel-Hamid MK, Odell LR, Chau N, Whiting A, Robinson PJ, et al. Development of quinone analogues as dynamin GTPase inhibitors. Eur J Med Chem 2014;85:191–206. [17] Bala BD, Muthusaravanan S, Choon TS, Ali MA, Perumal S. Sequential synthesis of amino-1,4-naphthoquinone-appended triazoles and triazole-chromene hybrids and their antimycobacterial evaluation. Eur J Med Chem 2014;85:737–46.
Further reading Papers on combinatorial chemistry or solid-phase synthesis from other journals [18] Berrocal JA, Nieuwenhuizen MML, Mandolini L, Meijer EW, Di Stefano S. Copper(I)-induced amplification of a [2]catenane in a virtual dynamic library of macrocyclic alkenes. Org Biomol Chem 2014;12(32):6167–74.
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[19] Broetz E, Herrmann J, Wiese J, Zinecker H, Maier A, Kelter G, et al. Synthesis and cytotoxic activity of a small naphthoquinone library: first synthesis of juglonbutin. Eur J Org Chem 2014;24:5318–30. [20] Chandra K, Roy TK, Shalev DE, Loyter A, Gilon C, Gerber RB, et al. A tandem in situ peptide cyclization through trifluoroacetic acid cleavage. Angew Chem Int Ed 2014;53(36):9450–5. [21] Chang Y-P, Chu Y-H. Mixture-based combinatorial libraries from small individual peptide libraries: a case study on a1-antitrypsin deficiency. Molecules 2014;19(5):6330–48. [22] Deiss F, Matochko WL, Govindasamy N, Lin EY, Derda R. Flow-Through synthesis on teflon-patterned paper to produce peptide arrays for cell-based assays. Angew Chem Int Ed 2014;53(25):6374–7. [23] Dell’Isola A, McLachlan MMW, Neuman BW, Al-Mullah HMN, Binks AWD, Elvidge W, et al. Synthesis and antiviral properties of spirocyclic [1,2,3]triazolooxazine nucleosides. Chem Eur J 2014;20(37):11685–9. [24] Dobi K, Hajdu I, Flachner B, Fabo G, Szaszko M, Bognar M, et al. Combination of 2D/3D ligand-based similarity search in rapid virtual screening from multimillion compound repositories. Selection and biological evaluation of potential PDE4 and PDE5 inhibitors. Molecules 2014;19(6):7008–39. [25] Douat C, Berni E, Jacquet R, Pouysegu L, Deffieux D, Quideau S. Protecting-groupfree solid-phase anchoring of polyphenolic C-glucosidic ellagitannins and synthesis of 1-alkylamino-vescalagin derivatives. Eur J Org Chem 2014;23: 4963–72. [26] Fallows AJ, Singh I, Dondi R, Cullis PM, Burley GA. Highly efficient synthesis of DNA-binding polyamides using a convergent fragment-based approach. Org Lett 2014;16(17):4654–7. [27] Feast GC, Lepitre T, Mulet X, Conn CE, Hutt OE, Savage GP, et al. The search for new amphiphiles: synthesis of a modular, high-throughput library. Beilstein J Org Chem 2014;10:1578–88. [28] Fer MJ, Doan P, Prange T, Calvet-Vitale S, Gravier-Pelletier C. A diastereoselective synthesis of 50 -substituted-uridine derivatives. J Org Chem 2014;79(16):7758–65. [29] Fulopova V, Krchnak V. Solid-phase synthesis of tri-substituted 2,5-dihydrobenzo[f][1,2,5]thiadiazepine 1,1-dioxide derivatives. ACS Comb Sci 2014;16(8):412–20. [30] Fuse S, Sugiyama S, Maitani MM, Wada Y, Ogomi Y, Hayase S, et al. Elucidating the structure-property relationships of donor-p-acceptor dyes for dye-sensitized solar cells (DSSCs) through rapid library synthesis by a one-pot procedure. Chemistry 2014;20(34):10685–94. [31] Gentry PR, Kokubo M, Bridges TM, Noetzel MJ, Cho HP, Lamsal A, et al. Development of a highly potent, novel M5 positive allosteric modulator (PAM) demonstrating CNS exposure: 1-((1H-Indazol-5-yl)sulfoneyl)-N-ethyl-N-(2-(trifluoromethyl)benzyl)piperidine-4-carboxamide (ML380). J Med Chem 2014;57(18):7804–10. [32] Han M, Song C, Jeong N, Hahn H-G. Exploration of 3-aminoazetidines as triple reuptake inhibitors by bioisosteric modification of 3-a-oxyazetidine. ACS Med Chem Lett 2014;5(9):999–1004. [33] Handore KL, Reddy DS. Total synthesis of (±)-nardoaristolone B and its analogues. Org Lett 2014;16(16):4252–5. [34] Joest C, Nitsche C, Scholz T, Roux L, Klein CD. Promiscuity and selectivity in covalent enzyme inhibition: a systematic study of electrophilic fragments. J Med Chem 2014;57(18):7590–9. [35] Joseph SC, Blackman BA, Kelly ML, Phillips M, Beaury MW, Martinez I, et al. Synthesis, characterization, and biological activity of poly(arginine)-derived cancer-targeting peptides in HepG2 liver cancer cells. J Pept Sci 2014;20 (9):736–45. [36] Kaur G, Gupta P, Harjai K, Singh V. Synthesis and antimicrobial evaluation of purine substituted N-acyl-a-carboxamides via the Ugi four-component reaction. Heterocycl Commun 2014;20(4):225–31. [37] Lee S, Lim D, Lee E, Lee N, Lee H-G, Cechetto J, et al. Discovery of carbohybridbased 2-aminopyrimidine analogues as a new class of rapid-acting antimalarial agents using image-based cytological profiling assay. J Med Chem 2014;57 (17):7425–34. [38] Li J, Wang J, Xu Z, Zhu S. Combinatorial synthesis of functionalized spirooxindole-pyrrolidine/pyrrolizidine/pyrrolothiazole derivatives via three-component 1,3-dipolar cycloaddition reactions. ACS Comb Sci 2014;16(9):506–12. [39] Liu X, Malins LR, Roche M, Sterjovski J, Duncan R, Garcia ML, et al. Site-selective solid-phase synthesis of a CCR5 sulfopeptide library to interrogate HIV binding and entry. ACS Chem Biol 2014;9(9):2074–81. [40] Lumpi D, Braunshier C, Horkel E, Hametner C, Froehlich J. Synthesis and application of monodisperse oligo(oxyethylene)-grafted polystyrene resins for solid-phase organic synthesis. ACS Comb Sci 2014;16(7):367–74. [41] Niu B, Xu L, Xie P, Wang M, Zhao W, Pittman CU, et al. Diversity-oriented syntheses: coupling reactions between electron-deficient olefins and aryl aldehydes via C(sp2)-H functionalization. ACS Comb Sci 2014;16(9):454–8. [42] Novoa A, Machida T, Barluenga S, Imberty A, Winssinger N. PNA-encoded synthesis (pes) of a 10 000-member hetero-glycoconjugate library and microarray analysis of diverse lectins. ChemBioChem 2014;15(14):2058–65. [43] Parra A, Martin-Fonseca S, Rivas F, Reyes-Zurita FJ, Medina-O’Donnell M, RufinoPalomares EE, et al. Solid-phase library synthesis of bi-functional derivatives of oleanolic and maslinic acids and their cytotoxicity on three cancer cell lines. ACS Comb Sci 2014;16(8):428–47. [44] Pathak AK, Pathak V, Reynolds RC. Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides. ACS Comb Sci 2014;16(9):485–93.
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N.K. Terrett / Combinatorial Chemistry - An Online Journal 16 (2014) 41–44
[45] Pena S, Fagundez C, Medeiros A, Comini M, Scarone L, Sellanes D, et al. Synthesis of cyclohexapeptides as antimalarial and anti-trypanosomal agents. MedChemComm 2014;5:1309–16. [46] Pinkin NK, Waters ML. Development and mechanistic studies of an optimized receptor for trimethyllysine using iterative redesign by dynamic combinatorial chemistry. Org Biomol Chem 2014;12(36):7059–67. [47] Ramos J, Potta T, Scheideler O, Rege K. Parallel synthesis of poly(amino ether)templated plasmonic nanoparticles for transgene delivery. ACS Appl Mater Interfaces 2014;6(17):14861–73. [48] Smyslova P, Kisseljova K, Krchnak V. Base-mediated intramolecular C- and Narylation of N, N-disubstituted 2-nitrobenzenesulfonamides: advanced intermediates for the synthesis of diverse nitrogenous heterocycles. ACS Comb Sci 2014;16(9):500–5. [49] Stefanucci A, Novellino E, Costante R, Mollica A. Pyroglutamic acid derivatives: building blocks for drug discovery. Heterocycles 2014;89(8):1801–25. [50] Tang Y, Cheng Q, Wang S, Zhang J. One-step liquid-phase heterogeneous synthesis of phenytoin using modified calcium oxide as a solid basic catalyst. Monatsh Chem 2014;145(9):1501–6.
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