Combinatorial Chemistry Online Volume 17, Issue 6, June 2015

Combinatorial Chemistry - An Online Journal 17 (2015) 21–24

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Combinatorial Chemistry - An Online Journal journal homepage: www.elsevier.com/locate/comche

Combinatorial Chemistry Online Volume 17, Issue 6, June 2015 N.K. Terrett Ensemble Therapeutics Corp., Cambridge, MA 02139, USA

1. Current literature highlights 1.1. Macrocyclic XIAP antagonists from a DNA-programmed chemistry library X-Chromosome-linked Inhibitor of Apoptosis Protein (XIAP) is an endogenous protein that binds and inhibits the activation of caspases responsible for programmed cell death or apoptosis. Increased XIAP expression often correlates with poor clinical outcomes in cancer treatment, as XIAP prevents the natural apoptosis of tumor cells. Small molecule antagonists of XIAP have been recognized as agents that have the potential to accelerate apoptosis and can result in tumor shrinkage. A recent paper describes the discovery of novel XIAP antagonists from a library of macrocycles generated using DNA-programmed chemistry [1]. DNA-programmed chemistry is a compound library technology in which small molecules being synthesized have their preparation dictated by specific DNA base sequences. As the small molecule is built up from individual building blocks, they are selectively introduced by specific double-stranded DNA duplex formation, bringing the reacting components into close proximity, ensuring high fidelity between the DNA base sequence and final product structure. After completion of the library, affinity selection assays can reveal active compounds and their associated SAR by reading the attached DNA base sequences. From a library of 160,000 macrocyclic peptidomimetics based on the N-terminal tetrapeptide sequence AVPI, of the endogenous XIAP inhibitor known as Smac, a number of compounds were discovered that had weak affinity for the BIR3 domain of XIAP – the part of the protein that sequesters caspase-9. For example, compound 1 was found to have an IC50 value for BIR3 of 1.3 lM, but this and other compounds from the library had no measurable affinity for the BIR2 domain of XIAP responsible for sequestering caspases-3 and -7. Consequently a follow-up library of 1,800 compounds was designed, synthesized and screened to exploit the SAR so far discovered, and in the hope that combined inhibitors of both BIR domains might be discovered. This subsidiary library was successful in finding such combination antagonists including compound 2 (BIR2 IC50 = 4.9 lM; BIR3 IC50 = 0.39 lM).

E-mail: [email protected] http://dx.doi.org/10.1016/j.comche.2015.04.002

O

H N

O

O

Me

H N

N

NHMe O

HN

N N

HOOC

N 1

O HOOC

O

H N

N H

N

O O

O

Me

H N O

NHMe

O N N N

2

Subsequent optimization of compounds through medicinal chemistry discovered superior XIAP antagonists in which the peptide sequence was cyclized from the P3 proline group to the P5 position (e.g. compound 3, BIR2 IC50 = 140 nM; BIR3 IC50 = 160 nM). Ultimately, by preparing dimeric macrocycles that contained two binding epitopes, XIAP antagonists were discovered with superior affinity and the ability to bind to both BIR domains simultaneously (e.g. compound 4). These macrocycles also had potent functional activity in a caspase rescue assay. Incubation of the compounds in a tumor cell lysate in the presence of recombinant XIAP BIR2-3 protein resulted in appreciable increase in pro-apoptotic caspase concentrations. Compound 4 also exhibited significant anti-proliferative activity in cancer cell apoptosis models against human breast cancer (MDA-MB-231) and melanoma (A875) cell-lines. Having demonstrated that this compound exhibited satisfactory exposure in mice following intravenous administration, it was progressed to a human melanoma tumor xenograft mouse model. A 30 mg/kg dose was administered intraperitoneally every three days resulting in tumor regression that lasted 12 days following the fifth and final dose.

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Me

Me O

O NH HN

NHMe

N H

N

Me

O O

HOOC

N

3

N N

O HOOC NH

O

Me

O NHMe

O

HN

NHMe

NH

O

N N N

O O

O

HN

O

Me

2.3. Scaffolds and synthons for combinatorial libraries

Me NH

N

N

HN Me

O O

N N N

Me Me

discovery, a library of fluorine-substituted bicyclic pyridines has been rapidly constructed [5]. Chondroitin sulfate (CS), which belongs to the glycosaminoglycan superfamily, is a linear sulfated polysaccharide involved in various biological processes. The CS structure is very heterogeneous and contains various sulfation patterns owing to the multiple and random enzymatic modifications that occur during its biosynthesis. In a recent study, a common intermediate possessing an orthogonally removable protective group was designed and a library of all 16 types of CS disaccharide structure generated by sulfation was systematically synthesized [6].

Me Me

4

COOH

In addition to inhibition of the XIAP BIR2 and 3 domains, the key compounds in this publication also have affinity for the related cIAP1 protein. There are currently a number of small molecules, that are potent antagonists of both XIAP and cIAP, in development for cancer therapy, and this new series of dimeric macrocycle offers an alternative structural class of potent IAP inhibitor. 2. A summary of the papers in this month’s issue 2.1. Polymer supported synthesis No papers this month. 2.2. Solution-phase synthesis An efficient and general protocol has been described for the synthesis of bisindolylmethanes by the reaction of indole with aldehydes in the presence of BF3OEt2. The method is rapid and applicable for aromatic, heteroaromatic, and aliphatic aldehydes [2]. A one-pot, sulfuric acid-promoted, dehydro-aromatization reaction to rapidly convert pseudopterosins into 14,15-dihydroelisabatin B has been reported. A mechanism invoking redox cycling between the substrate catechol and ortho-quinone moieties is proposed. This method opens up a unique route to rapidly provide libraries of novel marine natural product derivatives for drug discovery [3]. An efficient and environment-friendly method for the synthesis of benzopyranopyrimidines has been developed using the ultrasound-mediated condensation of salicylic aldehydes, malononitrile and secondary amines under solvent-free conditions. The reaction proceeds at room temperature in the presence of polystyrene supported p-toluenesulfonic acid to give the desired products in good to excellent yield [4]. A concise and efficient three-component synthesis of diverse fluorine-substituted bicyclic pyridines has been achieved by refluxing a mixture of different types of heterocyclic ketene aminals, triethoxymethane, and fluorine-containing methylene compounds under solvent-free and catalyst-free conditions. As these bicyclic pyridines provide new opportunities for drug

A new bis-cationic cyclic amino acid, 9-amino-3,7-diazabicyclo[3.3.1]nonane-9-carboxylic acid (9-amino-bispidine-9-carboxylic acid; Abp), which is available for both solution phase and solid phase peptide synthesis, has been designed and synthesized. A heterotripeptide Cbz-Leu-Abp-Ala-OMe containing Abp has also been prepared, and its dominant conformation analyzed by examining NMR and IR spectra and performing molecular modeling. This tripeptide formed a b-turn structure as its preferred conformation in solution [7]. 2.4. Solid-phase supported reagents A fluorous Grubbs–Hoveyda metathesis catalyst supported on TeflonÒ powder, has been prepared. By modulating the hydrophobicity of the reaction medium at the end of a reaction, the supported catalyst could be recovered by simple filtration even though the catalyst existed in a homogeneous state during the reaction. In RCM reactions, the catalyst could be reused up to three times with only a slight loss in reactivity with each subsequent cycle [8]. Copper nanoparticles have been supported and modified by carbon nitride, used as a support and investigated as an immobilized N-donor ligand. The modified nanoparticle catalyst was evaluated with the oxidation of propargylic alcohols and showed catalytic efficiency as well as a significant ligand or support effect in the reaction [9]. A simple and efficient method for the synthesis of pharmaceutically relevant propargylamines through a one-pot three-component coupling reaction using nano Au/CeO2 as a heterogeneous catalyst has been reported. The reactions were carried out using a mixture of amines, CH2Cl2, and terminal alkynes [10]. Two convenient green protocols for the synthesis of b-amino ketones have been developed. The approaches involve one-pot aza-Michael-type and Mannich-type reactions of a series of aldehydes, ketones, and amines in the presence of a catalytic amount of the magnetic solid sulfonic acid catalyst, Fe3O4@SiO2@Me&EtPhSO3H, at room temperature. The catalyst can be reused four times without loss of activity [11]. 2.5. Novel resins, linkers and techniques No papers this month. 2.6. Library applications A series of structurally diverse 4-bromo spiro-isoxazolines possessing a variety of aromatic and aliphatic substituents at the 3 position, have been synthesized through a 1,3-dipolar cycloaddition followed by intramolecular cyclization. Antiproliferative activity of the compounds was evaluated in vitro by using two breast cancer cell lines (MCF-7 and MDA-MB-231) and two prostate

N.K. Terrett / Combinatorial Chemistry - An Online Journal 17 (2015) 21–24

cancer cell lines (PC-3 and DU-145) using the MTT viability assay, and IC50 values were obtained [12]. A catalyst-free synthesis of 6,9-dihydro-[1,3]dioxolo[4,5-g] thieno[3,4-b]quinolin-8(5H)-ones as novel analogs of podophyllotoxins has been developed by a three-component reaction of aldehydes, ethyl 2,4-dioxotetrahydrothiophene-3-carboxylate and 3,4-(methylenedioxy)aniline. This methodology not only provided a new chemical library for the screening of anticancer activity, but also features excellent isolated yields, short reaction time, simple work up procedure and little environmental impact [13]. The b-OG pocket is a cavity in the flavivirus envelope (E) protein that has been identified as a promising site for the design of antiviral agents that interfere with virus entry into the host cell. A recent study explored the generation of a novel class of molecules that are hybrids between two hit compounds reported previously. First, a library of twenty hybrid molecules were designed and synthesized, and antiviral evaluation in a virus-cell-based assay for dengue virus E carried out [14]. A library of potent inhibitors of polyphenol oxidase and their structure activity relationships have been described. Azachalcone derivatives were synthesized and tested for their tyrosinase inhibitory activity, and two compounds strongly inhibited and were more potent than the positive control kojic acid [15]. The sex peptide receptor in Drosophila melanogaster (DrmSPR) is an interesting G protein-coupled receptor that is involved in postmating responses such as increased egg-laying and decreased receptivity of the female. To discover small molecule agonists for DrmSPR, a compound library based on a pyrazolodiazepine scaffold, previously reported as a potential privileged structure, was screened. Structure–activity relationship studies of the hit compounds, were explored through analog synthesis resulting in 6-benzyl pyrazolodiazepine derivatives found to be small molecule agonists for DrmSPR [16]. Current FDA-approved chemotherapeutic antimetabolites elicit severe side effects that warrant their improvement. A recent publication describes the design of compounds with mechanisms of action focusing on inhibiting DNA replication rather than targeting multiple pathways. As 5-(a-substituted-2-nitrobenzyloxy)methyluridine-50 -triphosphates had previously been revealed as synthesis terminators, a library of 35 thymidine analogs was synthesized and evaluated in an MTT cell viability assay of MCF-7 breast cancer cells [17]. Rapid and efficient synthesis of a phenyl-1H-1,2,3-triazole library has enabled cost-effective biological testing of a range of novel non-steroidal anti-inflammatory drugs with potential for improved drug efficacy and toxicity profiles. Anti-inflammatory activities of the phenyl-1H-1,2,3-triazole analogs synthesized were assessed using the xylene-induced ear edema mouse model. At least four analogs showed more potent effects than the reference anti-inflammatory drug diclofenac at the same dose of 25 mg/kg [18].

References [1] Seigal BA, Connors WH, Fraley A, Borzilleri RM, Carter PH, Emanuel SL, et al. The discovery of macrocyclic XIAP antagonists from a DNA programmed chemistry library, and their optimization to give lead compounds with in vivo antitumor activity. J Med Chem 2015;58(6):2855–61. [2] Swetha A, Madhu Babu B, Meshram HM. An efficient and rapid protocol for the synthesis of diversely functionalized bisindolylmethanes. Tetrahedron Letts 2015;56(14):1775–9. [3] McCulloch MWB, Kerr RG. Rapid structural diversification of pseudopterosins: sulfuric acid promoted dehydro-aromatization yielding 14,15-dihydro-elisabatin B. Tetrahedron Letts 2015;56(15):2030–3. [4] Thirupathaiah B, Reddy MV, Jeong YT. Solvent-free sonochemical multi-component synthesis of benzopyranopyrimidines catalyzed by polystyrene supported p-toluenesulfonic acid. Tetrahedron 2015;71(14):2168–76.

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[5] Zhu D-D, Chen X-B, Huang R, Yan S-J, Lin J. Three-component solvent-free synthesis of fluorine substituted bicyclic pyridines. Tetrahedron 2015;71(16): 2363–8. [6] Wakao M, Obata R, Miyachi K, Kaitsubata Y, Kondo T, Sakami C, et al. Synthesis of a chondroitin sulfate disaccharide library and a GAG-binding protein interaction analysis. Bioorg Med Chem Lett 2015;25(7):1407–11. [7] Yamashita H, Demizu Y, Misawa T, Shoda T, Kurihara M. Synthesis of a biscationic a, a-disubstituted amino acid (9-amino-bispidine-9-carboxylic acid) and its eects on the conformational properties of peptides. Tetrahedron 2015; 71(15):2241–5. [8] Kobayashi Y, Inukai S, Kondo N, Watanabe T, Sugiyama Y, Hamamoto H, et al. A medium fluorous Grubbs-Hoveyda 2nd generation catalyst for phase transfer catalysis of ring closing metathesis reactions. Tetrahedron Letts 2015;56(11): 1363–6. [9] Lv W, Tian J, Deng N, Wang Y, Zhu X, Yao X. Dual-immobilized copper catalyst: carbon nitride-supported copper nanoparticles catalyzed oxidation of propargylic alcohols. Tetrahedron Letts 2015;56(11):1312–6. [10] Berrichi A, Bachir R, Benabdallah M, Choukchou-Braham N. Supported nano gold catalyzed three-component coupling reactions of amines, dichloromethane and terminal alkynes (AHA). Tetrahedron Letts 2015;56(11):1302–6. [11] Movassagh B, Tahershamsi L, Mobaraki A. A magnetic solid sulfonic acid modified with hydrophobic regulators: an efficient recyclable heterogeneous catalyst for one-pot aza-Michael-type and Mannich-type reactions of aldehydes, ketones, and amines. Tetrahedron Letts 2015;56(14):1851–4. [12] Das P, Omollo AO, Sitole LJ, McClendon E, Valente EJ, Raucher D, et al. Synthesis and investigation of novel spiro-isoxazolines as anti-cancer agents. Tetrahedron Letts 2015;56(14):1794–7. [13] Li T, Lu T, Yu C, Yao C. An efficient synthesis of [1,3]dioxolo[4,5-g]thieno[3,4b]quinolin-8(5H)-ones as novel thiazapodophyllotoxin analogues with potential anticancer activity. Bioorg Med Chem Lett 2015;25(7):1417–9. [14] Jadav SS, Kaptein S, Timiri A, De Burghgraeve T, Badavath VN, Ganesan R, et al. Design, synthesis, optimization and antiviral activity of a class of hybrid dengue virus E protein inhibitors. Bioorg Med Chem Lett 2015;25(8):1747–52. [15] Radhakrishnan SK, Shimmon RG, Conn C, Baker AT. Azachalcones: a new class of potent polyphenol oxidase inhibitors. Bioorg Med Chem Lett 2015;25(8): 1753–6. [16] Kim J-h, Jeong P-h, Lee J-Y, Lee J-h, Kim Y-J, Kim Y-C. Discovery and structure– activity relationships of pyrazolodiazepine derivatives as the first small molecule agonists of the Drosophila sex peptide receptor. Bioorg Med Chem 2015;23(8):1808–16. [17] Borland KM, AbdulSalam SF, Solivio MJ, Burke MP, Wolfkiel PR, Lawson SM, et al. Base-modified thymidines capable of terminating DNA synthesis are novel bioactive compounds with activity in cancer cells. Bioorg Med Chem 2015; 23(8):1869–81. [18] Kim TW, Yong Y, Shin SY, Jung H, Park KH, Lee YH, et al. Synthesis and biological evaluation of phenyl-1H-1,2,3-triazole derivatives as anti-inflammatory agents. Biorg Chem 2015;59:1–11.

Further reading Papers with relevance to combinatorial chemistry or solid-phase synthesis from other journals Aboye T, Kuang Y, Neamati N, Camarero JA. Rapid parallel synthesis of bioactive folded cyclotides by using a tea-bag approach. ChemBioChem 2015;16(5): 827–33. Alizadeh A, Bayat F, Sadeghi V. Tandem One-pot synthesis of indoles having a structural moiety of propellane. Lett Org Chem 2015;12(3):153–8. Arndt H-D, Rizzo S, Noecker C, Wakchaure VN, Milroy L-G, Bieker V, et al. Divergent solid-phase synthesis of natural product-inspired bipartite cyclodepsipeptides: total synthesis of seragamide A. Chem - Eur J. 2015;21(14):5311–6. Beaver E. J, C. Peacor B, V. Bain J, James LI, L. Waters M. Contributions of pocket depth and electrostatic interactions to affinity and selectivity of receptors for methylated lysine in water. Org Biomol Chem 2015;13(11):3220–6. Fair RJ, Hahm HS, Seeberger PH. Combination of automated solid-phase and enzymatic oligosaccharide synthesis provides access to a(2,3)-sialylated glycans. Chem Commun 2015;51(28):6183–5. Fang L, Yao G, Pan Z, Wu C, Wang H-S, Burley GA, et al. Fully automated synthesis of DNA-binding Py-Im polyamides using a triphosgene coupling strategy. Org Lett 2015;17(1):158–61. Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, et al. Identification of structure-activity relationships from screening a structurally compact DNAencoded chemical library. Angew Chem Int Ed 2015;54(13): 3927–31. He QQ, Wimmer N, Verquin G, Meutermans W, Ferro V. Investigations into the decomposition of aminoacyl-substituted monosaccharide scaolds from a drug discovery library. Org Biomol Chem 2015;13(13):4070–9. Isidro-Llobet A, Hadje GK, Galloway WRJD, Giacomini E, Hansen MR, Mendez-Abt G, et al. A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaolds. Org Biomol Chem 2015;13(15): 4570–80. Jadhav KB, Lichtenecker RJ, Bullach A, Mandal B, Arndt H-D. Dynamic combinatorial enrichment of polyconformational D-/L-peptide dimers. Chemistry 2015;21(15): 5898–908.

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Jimenez-Moreno E, Gomez AM, Bastida A, Corzana F, Jimenez-Oses G, JimenezBarbero J, et al. Modulating weak interactions for molecular recognition: a dynamic combinatorial analysis for assessing the contribution of electrostatics to the stability of CH-p bonds in water. Angew Chem Int Ed 2015;54(14): 4344–8. Kushwaha RN, Srivastava R, Mishra A, Rawat AK, Srivastava AK, Haq W, et al. Design, synthesis, biological screening, and molecular docking studies of piperazinederived constrained inhibitors of DPP-IV for the treatment of type 2 diabetes. Chem Biol Drug Des 2015;85(4):439–46. Kwak S-h, Kim Mj, Lee S-D, You H, Kim Y-C, Ko H. Solid-phase synthesis of quinolinone library. ACS Comb Sci 2015;17(1):60–9. Lampkowski JS, Maza JC, Verma S, Young DD. Optimization of solid-supported GlaserHay reactions in the microwave. Molecules. 2015;20(4):5276–85. Li J, Nowak P, Otto S. An allosteric receptor by simultaneous ‘‘casting’’ and ‘‘molding’’ in a dynamic combinatorial library. Angew Chem Int Ed 2015;54(3): 833–7. Mitrovic S, Soedarmadji E, Newhouse PF, Suram SK, Haber JA, Jin J, et al. Colorimetric screening for high-throughput discovery of light absorbers. ACS Comb Sci 2015;17(3):176–81. Mouradzadegun A, Elahi S, Abadast F. Synthesis of a functionalized polymer based on a calix[4]resorcinarene via covalently anchored cationic moieties: a reactive solid support for ring transformation and expansion of thiopyrylium salts. Synthesis 2015;47(05):630–40. Neres J, Hartkoorn RC, Chiarelli LR, Gadupudi R, Pasca MR, Mori G, et al. 2Carboxyquinoxalines kill Mycobacterium tuberculosis through non-covalent inhibition of DprE1. ACS Chem Biol 2015;10(3):705–14. Nowak P, Saggiomo V, Salehian F, Colomb-Delsuc M, Han Y, Otto S. Localized template-driven functionalization of nanoparticles by dynamic combinatorial chemistry. Angew Chem Int Ed 2015;54(14):4192–7. Pauli D, Bienz S. Regioselective solid-phase synthesis of N-mono-hydroxylated and Nmono-methylated acylpolyamine spider toxins using an 2-(ortho-nitrophenyl)ethanal-modified resin. Org Biomol Chem 2015;13(15):4473–85.

Qian W-J, Burke Jr TR. Mitsunobu mischief: neighbor-directed histidine N(s)alkylation provides access to peptides containing selectively functionalized imidazolium heterocycles. Org Biomol Chem 2015;13(14):4221–5. Ratni H, Rogers-Evans M, Bissantz C, Grundschober C, Moreau J-L, Schuler F, et al. Discovery of highly selective brain-penetrant vasopressin 1a antagonists for the potential treatment of autism via a chemogenomic and scaold hopping approach. J Med Chem 2015;58(5):2275–89. Schmidt D, Schuhmacher F, Geissner A, Seeberger PH, Pfrengle F. Automated synthesis of arabinoxylan-oligosaccharides enables characterization of antibodies that recognize plant cell wall glycans. Chem - Eur J 2015;21(15):5709–13. Schutznerova E, Krchnak V. Solid-phase synthesis of 2-Aryl-3-alkylamino-1H-indoles from 2-Nitro-N-(2-oxo-2-arylethyl)benzenesulfonamides via base-mediated Carylation. ACS Comb Sci 2015;17(2):137–46. Sherborne GJ, Chapman MR, Blacker AJ, Bourne RA, Chamberlain TW, Crossley BD, et al. Activation and deactivation of a robust immobilized Cp⁄Ir-transfer hydrogenation catalyst: a multielement in situ X-ray absorption spectroscopy study. J Am Chem Soc 2015;137(12):4151–7. Song A, Tom J, Yu Z, Pham V, Tan D, Zhang D, et al. Development of orthogonally protected hypusine for solid-phase peptide synthesis. J Org Chem 2015;80(7): 3677–81. Thillier Y, Sallamand C, Baraguey C, Vasseur J-J, Debart F. Solid-phase synthesis of oligonucleotide 5’-(a-P-thio)triphosphates and 5’-(a-P-thio)(b, c-methylene) triphosphates. Eur J Org Chem 2015;2:302–8. Woodring JL, Patel G, Erath J, Behera R, Lee PJ, Leed SE, et al. Evaluation of aromatic 6substituted thienopyrimidines as scaolds against parasites that cause trypanosomiasis, leishmaniasis, and malaria. MedChemComm 2015;6:339–46.