Design,synthesis and use of binary encoded synthetic chemical libraries

Summary With the advent of combinatorial chemistry a new paradigm is evolving in the field of drug discovery. The approach is based on an integration of chemistry, high-throughput screening and automation engineering. The chemistry arm is usually based on solid-phase synthesis technology as the preferred approach to library construction. One of the most powerful of the solid-phase methods is encoded split synthesis, in which the reaction history experience by each polymeric bead is unambiguously recorded. This split-and-pool approach, employing chemically robust tags, was used to construct a 85 000-membered dihydrobenzopyran library.     

Xanthines as a scaffold for molecular diversity

Summary Xanthines represent a new, versatile scaffold for combinatorial chemistry. A five-step solid-phase synthesis of xanthine derivatives is described which includes alkylations, a nucleophilic displacement reaction at a heterocycle and a ring closure reaction by condensation of a nitroso function with an activated methylene group. The selected reaction sequence allows the production of a highly diverse small-molecule combinatorial compound library.     

Solid-phase synthesis of 2-substituted 4-amino-7-oxo-5,6,7,8-tetrahydropyrido[2,3-d]pyrimidines: An example of cyclization-assisted cleavage

An efficient solid-phase synthesis of 2-substituted 4-aminopyrido[2,3-d]pyrimidines 12 by cyclization-assisted cleavage from resin is reported. The procedure starts by solid supporting an ,-unsaturated acid 8 to the Wang resin 13 by using DCC and 4-DMAP in THF. The resulting ,-unsaturated ester 14 is converted to the Michael adduct by treatment with malononitrile in NaOMe/THF. Such Michael addition constitutes the first example of a Michael reaction with malononitrile in solid-phase. Finally, the Michael adducts 15 are treated with an amidine system in MeOH to yield the corresponding pyridopyrimidines 12. Compounds 12 present three diversity centers R1, R2 and G. Having validated the chemistry on solid support, a 40-membered combinatorial library was obtained using this protocol.     

Regioselective alkylation at the N4 positionof a 3-oxo-1,4-benzodiazepine on solid support

An efficient solid phase regioselective alkylation at the N4 positionof a 3-oxo-1,4-benzodiazepine template exemplified by 4-H-2,3,4,5-tetrahydro-7-iodo-3-oxo-1H-1,4-benzodiazepine-2-acetate-polymerester is described. Further chemical elaboration atposition 7, utilizing a modified Heck reaction, allows the incorporationof amides from primary or secondary amines. The two diversity points atpositions 4 and 7 were utilized tosynthesize a 28-membered, combinatorial array on Sasrin® resin in moderate yields and >80% purity. Having validated the chemistry on solid support, acombine and splitapproach to prepare a bead-bound combinatorial library is achievableutilizing similar experimental practices and procedures as in thearray synthesis.     

Solid-supported syntheses of 3-thio-1,2,4-triazoles

Two solid-supported synthesis strategies for the preparation of 3-thio-1,2,4-triazoles are described. In the first, Rink amide resin is combined with Fmoc-protected ω-amino acids, acid hydrazides, and alkyl halides to provide diverse sets of starting materials from which numerous triazoles may be prepared. The second employs t-alkylcarbamateresin (Boc resin) which permits the use of additional pools of starting materials, including isothiocyanates and α- and ω-amino esters, resulting in triazoles with patterns of functional groups that are not possible from the initial route. The combination of multiple resins and resin attachment sites allows the preparation of a diverse library based upon the3-thio-1,2,4-triazole scaffold and avoids the pitfallof having a single linker functionality present at the same position in all library members. General synthetic procedures and representative products from each route are presented. A similarity analysis of representative sublibraries from each synthesis strategy concludes that variation of the solid-phase linker chemistry and attachment site can enhance molecular diversity of the combined triazole library. This revised version was published online in August 2006 with corrections to the Cover Date.     

Selection of peptomeric inhibitors of bovine α-chymotrypsin and cathepsin G based on trypsin inhibitor SFTI-1 using a combinatorial chemistry approach

A peptomeric library consisting of 360 monocyclic analogues of trypsin inhibitor SFTI-1 isolated from sunflower seeds was designed and synthesized by a solid-phase approach in order to select chymotrypsin and cathepsin G inhibitors. All peptomers contained a proteinogenic-Phe-mimicking N-benzylglycine (Nphe) at positions 5 and 12. Into the synthesized library, different peptoid monomers were introduced in the 7–10 segment. Deconvolution of the library against both proteinases through an iterative method in solution revealed that the strongest chymotrypsin inhibitory activity was displayed by two analogues, [Nphe^5,12]SFTI-1 (1) and [Nphe^5,12, Naem⁸]SFTI-1 (2), where Naem stands for N-(2-morpholinoethyl)glycine. After deconvolution against a cathepsin G analogue, [Nphe^5,12, Npip^8,9, Nnle¹⁰] SFTI-1 (3) (Npip = N-(3,4-methylenedioxybenzyl)glycine) appeared to be the most potent inhibitor with a high serum stability. It is worth noting that the analogues obtained by a combinatorial approach display high specificity towards one of the experimental enzymes. Another interesting feature is the lack of Pro8 in analogues 2 and 3, the amino acid residue absolutely conserved in the family of Bownan–Birk inhibitors.     

Synthetic methods for polyamine linkers and their application to combinatorial chemistry

Summary Polyamines and polyamine conjugates display a diverse range of important biological functions, ranging from antibiotics to immunosuppressants and glutamate receptor antagonists. For these reasons, polyamines provide an excellent template/scaffold for combinatorial chemistry. In this paper we present methods for the solid-phase immobilisation of polyamines for use in synthetic and combinatorial chemistry and describe how they have been employed in the preparation of a number of important polyamine conjugates and polyamine libraries. Thus, we have designed, synthesised and utilised a number of polyamine linkers for both solution and resin screening combinatorial application.     

Solid-phase synthesis of 2-substituted 4-amino-7-oxo-5,6,7,8-tetrahydropyrido[2,3-d]pyrimidines

An efficient solid-phase synthesis of 2-substituted 4-aminopyrido[2,3-d]pyrimidines 15 is reported. The procedure started by solid supporting a p-hydroxybenzaldehyde 8 to the Wang resin by using the Mitsunobu protocol. The resulting aldehyde 17 was treated with a substituted acid methyl malonate 10 to afford the corresponding alpha, beta-unsaturated ester 18, which was converted to the Michael adduct 21 by reaction with malononitrile. Cyclization of 21 with an amidine system 13 yielded the solid supported pyridopyrimidine 22, which afforded the corresponding 2-substituted 4-aminopyrido[2,3-d]pyrimidine 15 upon treatment with TFA:DCM. Compounds 15 present three diversity centers R1, R2 and R3. Having validated the chemistry on solid support, a 32-membered combinatorial library was obtained using this protocol.     

Solid-phase total synthesis of (–)-Phenylhistine and (–)-Aurantiamine. Synthesis of a diverse dehydro-2,5-diketopiperazine library. Part II

The preparation of solid supported glycine phosphonate and its utilization for the total synthesis of two natural products is presented. The proposed protocol combines diversity with accessibility and speed, which makes this scaffold suitable for automated parallel synthesis and combinatorial chemistry. The preparation of a small library of dehydro-2,5-diketopiperazines, combining several natural amino acids with diverse heterocycles (including thiazoles, pyridines, indoles and imidazoles), is also demonstrated.     

Bifunctional scaffolds as templates for synthetic combinatorial libraries

Summary A small-molecule synthetic combinatorial library was designed and synthesized that features potential pharmacophores attached to a variety of small cyclic scaffolds. The synthesis of the library involved randomization of three types of building blocks: 20 amino acids, 10 aromatic hydroxy acids and 21 alcohols, totaling a library complexity of 4200 compounds. Mitsunobu polymer-supported etherification was used in the last randomization. The library compounds were attached to beads via an ester-bond linkage enabling both on-bead as well as in-solution screening. When the library was tested against a model target, streptavidin, specific binders were found. The structures of the most active compounds were determined from the fragmentation pattern in MS/MS experiments.Abbreviations DCM dichloromethane - DEAD diethyl azodicarboxylate - DIAD diisopropyl azodicarboxylate - DIC diisopropyl carbodiimide - DMF dimethylformamide - Fmoc fluorenylmethyloxycarbonyl - HOBt N-hydroxybenzotriazole - MeOH methanol - PPh₃ triphenylphosphine - t-Bu tert-butyl - TFA trifluoroacetic acid - TG TentaGel-S-OH 130-m resin - THF tetrahydrofuran     

Parallel and automated library synthesis of 2-long alkyl chain benzoazoles and azole[4,5-<Emphasis Type="BoldItalic">b</Emphasis>]pyridines under microwave irradiation

Summary A versatile route to 40-membered library of 2-long alkyl chain substituted benzoazoles (1 and 2) and azole[4,5-b]pyridines (3 and 4) via microwave-assisted combinatorial synthesis was developed. The reactions were carried out in both monomode and multimode microwave oven. With the latter, all reactions were performed in high-throughput experimental settings consisting of an 8×5 combinatorial library designed to synthesize 40 compounds. Each step, from the addition of reagents to the recovery of final products, was automated. The microwave-assisted N-long chain alkylation reactions of 2-alkyl-1H-benzimidazole (1) and 2-alkyl-1H-benzimidazole[4,5-b] pyridines (3) were also studied.     

Solution-phase combinatorial chemistry

The use of solution phase techniques has been explored as an alternative to solid-phase chemistry approaches for the preparation of arrays of compounds in the drug discovery process. Solution-phase work is free from some of the constraints of solid-phase approaches but has disadvantages with respect to purification. This article will also illustrate some of the advances made in recent years in solution phase array chemistry including using supported reagents and simple extractive protocols for the effective preparation of high quality samples.     

Application of computer assisted combinatorial chemistry in antivirial,antimalarial and anticancer agents design

Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of Compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anti-cancer drugs. These illustrate library focusing strategies.     

Sequence-selective nonmacrocyclic two-armed receptors for peptides

Summary Tweezer-like receptor molecules have proven their potential for molecular recognition on several occasions. We decided to make twofold use of this receptor design: firstly to learn whether simple molecular forceps consisting of two peptide chains linked by a spacer are able to selectively bind to small peptides, and secondly to investigate the importance of structural preorganization for the characteristics of the receptors. We prepared two encoded combinatorial libraries based on this design, featuring two combinatorial tripeptide chains held by different scaffolds: the use of chenodeoxycholic acid as spacer provided a rigid scaffold for the forceps, whereas linking the peptide chains by a pentamethylene chain yielded a very flexible forceps structure. Molecules from the cholic acid library recognize and discriminate various enkephalins with micromolar affinities. Molecules from the flexible library show distinct interactions with the enkephalins as well, but the specificity and affinity are clearly diminished. Thus, although the interactions of molecular forceps with peptides are not crucially dependent on structural preorganization, receptors with a rigid design are clearly superior to flexible molecular forceps. Supplementary Material comprising procedures for the preparation and spectroscopical data of compounds5 through8, as well as a listing of the 104 decoded sequences from the assay of the flexible library with⁵Leu-enkephalin/Disperse Red, can be obtained from the author on request.     

Gas‐phase studies of copper catalyzed aerobic cross coupling of thiol esters and arylboronic acids

Electrospray ionization/mass spectrometry (ESI‐MS) is used to monitor a Cu‐catalyzed aerobic cross‐coupling reaction between thiol esters and arylboronic acids. The ESI spectra show the formation of Cu‐complexes with the starting thiol ester 1 and the coupling product. The formation of an ionic complex at m/z 305 is observed, most likely occurring upon the elimination of a mixed anhydride from [(1)CuOAc]⁺. An online monitoring of the reaction using ESI‐MS was carried out allowing calculation of rate constants and thermodynamic parameters (ΔH^?, ΔS^?, and ?G^?) for the title reaction.     

Ring opening cross-metathesis on solid support: a combinatorial library synthesis of highly functionalized cyclopentanes

Ruthenium catalyzed ring opening cross-metathesis of resin-bound bicyclic alkenes with terminal aryl olefins was utilized for the construction of a combinatorial library containing highly functionalized cyclopentane derivatives. The technology described herein represents a convergent method for the diastereospecific synthesis of unique cyclopentane molecular scaffolds useful for exploratory medicinal chemistry. This revised version was published online in August 2006 with corrections to the Cover Date.     

Sensitive electrospray mass spectrometry analysis of one-bead-one-compound peptide libraries labeled by quaternary ammonium salts

A rapid and straightforward method for high-throughput analysis of single resin beads from one-bead-one-compound combinatorial libraries with high resolution electrospray ionization tandem mass spectrometry (HR ESI-MS/MS) is presented. The application of an efficient method of peptide derivatization by quaternary ammonium salts (QAS) formation increases ionization efficiency and reduces the detection limit, allowing analysis of trace amounts of compounds by ESI-MS. Peptides, synthesized on solid support, contain a new cleavable linker composed of a Peg spacer (9-aza-3,6,12,15-tetraoxa-10-on-heptadecanoic acid), lysine with ?-amino group marked by the N,N,N-triethylglycine salt, and methionine, which makes possible the selective cleavage by cyanogen bromide. Even a small portion of peptides derivatized by QAS cleaved from a single resin bead is sufficient for sequencing by HR ESI-MS/MS experiments. The developed strategy was applied to a small training library of α chymotrypsin substrates. The obtained results confirm the applicability of the proposed method in combinatorial chemistry.     

Library generation through successive substitution of trichlorotriazine

Summary The decreasing reactivity of tri-, di- and monochlorotriazine was utilized for the solid-phase construction of a combinatorial library with three randomized positions, using 20 amino acids and 50 amines as building blocks. The first chlorine atom was selectively substituted by coupling a large excess of trichlorotriazine to the support-bound amino acid, thus avoiding simultaneous substitution of the second chlorine. The second and third diversity positions were selectively introduced by coupling amines at different temperatures. Mixtures of model compounds were synthesized and analyzed, showing the correct representation of all expected components. A library composed of 12 000 compounds was generated using this method.     

A new combination of protecting groups and links for encoded synthetic libraries suited for consecutive tests on the solid phase and in solution

Summary A strategy for high-throughput evaluation of combinatorial compound libraries is reported, which circumvents the necessity to test complex mixtures. The method is based on a new combination of protecting groups, solid-phase linker and tags. The bulk of the library first undergoes a binding assay with the components grafted on beads. A selection of beads carrying strong ligands is stripped from the labelled target and distributed into microvessels. The ligands are cleaved and rinsed into microeluates. Subsequently, a more detailed characterization with a functional assay in solution determines the best performers, which are identified through the peptidic tag left behind on the corresponding mother bead.Abbreviations Boc tert-butyloxycarbonyl - CCL combinatorial compound libraries - Ddz ,-dimethyl-3,5-dimethoxybenzyloxycarbonyl - DICD N,N-diisopropylcarbodiimide - DIPEA diisopropylethylamine - DMA dimethylacetamide - ESL encoded synthetic libraries - FITC fluoresceinisothiocyanate - GABA -aminobutyric acid - HOBT N-hydroxybenzotriazole - MALDI matrix-assisted laser desorption ionization - Pbf 2,2,4,6,7-pentamethyldihydrobenzofuran-5-sulfonyl - Pmc 2,2,5,7,8-pentamethylchroman-6-sulfonyl - TFA trifluoroacetic acid - Trt trityl     

In silico design of chiral dimers to direct the synthesis of a chiral zeolite

ABSTRACT

We have applied in silico materials design in an effort to design chiral organic structure directing agents (OSDAs) for the synthesis of enantiomerically enriched STW zeolite. To do so, we have used both exhaustive virtual screening of a limited set of symmetrical imidazolium dimers and a multi-objective genetic algorithm to effectively search a larger virtual combinatorial chemistry space that is too vast for an exhaustive approach.