Structurally homogeneous and heterogeneous synthetic combinatorial libraries

Summary We have designed and synthesized structurally homogeneous and heterogeneous nonpeptide libraries. Structurally homogeneous libraries are characterized by the presence of one common structural unit, a scaffold, in all library compounds (e.g. cyclopentane, cyclohexane, diketopiperazine, thiazolidine). In structurally heterogeneous libraries different organic reactions (acylation, etherification, reductive amination, nucleophilic displacement) were applied to connect bifunctional building blocks unrelated in structure (aromatic hydroxy acids, aromatic hydroxy aldehydes, amino alcohols, diamines, and amino acids). The focus of this communication is to document the use of bifunctional building blocks for the design and synthesis of structurally heterogeneous libraries ofN-(alkoxy acyl)amino acids, N,N-bis-(alkoxy acyl)diamino acids,N-acylamino ethers,N-(alkoxy acyl)amino alcohols,N-alkylamino ethers, andN-(alkoxy aryl)diamines.Abbreviations AcOH acetic acid - DCE dichloroethane - DCM dichloromethane - DEAD diethyl azodicarboxylate - DIAD diisopropyl azodicarboxylate - DIC diisopropyl carbodiimide - DIEA diisopropylethylamine - DMAP dimethylaminopyridine - DMF dimethylformamide - Fmoc fluorenylmethyloxycarbonyl - HOBt N-hydroxybenzotriazole - MeCN acetonitrile - MeOH methanol - NaOH sodium hydroxide - PEG/PS polyethylene-grafted copolystyrene - PPh₃ triphenylphosphine - t-Bu tert- butyl - TFA trifluoroacetic acid - TG TentaGel - THE tetrahydrofuran     

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     

Synthesis of C-11 modified mifepristone analog libraries

Substitution of the C-11 aniline of mifepristone can provide compounds with altered pharmacokinetic and pharmacodynamic (PK/PD) profiles that may find use for new indications. The development of new steroid intermediates and specialized library synthesis methods were required to enable the efficient preparation of structurally complex C-11 modified mifepristone analogs.     

Leadlikeness and structural diversity of synthetic screening libraries

Summary High program failure rates in the pharmaceutical industry have prompted the development of predictive software that can profile compound libraries as being ‘druglike’ (resembling existing drugs) and/or ‘leadlike’ (possessing the structural and physicochemical profile of a quality lead). In recent years, these two notions prompted pharmaceutical companies to clean up their corporate libraries of screening compounds. In order to maintain and expand the size and diversity of these corporate libraries, pharmaceutical companies still continue to add compounds to these, mainly by the acquisition of screening libraries. In this paper, we have analyzed 45 commercially available libraries, offered by suppliers of screening chemistry, for leadlikeness and diversity of the offered structures. To this end we have used a set of structural and physicochemical filters for leadlikeness that was developed in-house. These 45 supplier libraries contained a total of 5.3 million structures, of which 49% (2,592,778 structures) turned out to be unique, and only 12% (677,328 structures) were found to be both unique and leadlike. A diversity analysis revealed that big differences exist between the various offered libraries.     

Combinatorial synthesis of small-molecule libraries using 3-amino-5-hydroxybenzoic acid

Summary A non-peptide library of 2001 compounds has been prepared utilizing solid-phase techniques. The split/combine method was demonstrated to work well to form mixtures of compounds based on 3-amino-5-hydroxybenzoic acid as a core structure. The benzoic acid of the core structure served as the attachment point for the resin and the amino and hydroxy positions were variably substituted.     

Design and synthesis of two pyrazole libraries based on o-hydroxyacetophenones

Two new solid-phase syntheses of substituted pyrazoles are described. The first includes supporting an o-hydroxyacetophenone on Merrifield resin, Vilsmeier-Haack formylation on the methyl group and cyclization with a substituted hydrazine to afford a pyrazole ring with two diversity centers. The second starts from o-hydroxyacetophenone supported on Wang resin, which undergoes a Claisen condensation with a carboxylic acid ester to yield a 1,3-dicarbonyl compound that cyclizes to a pyrazole using a hydrazine. Both methods have been used to synthesize two small pyrazole libraries.     

Loading amplification of radiation grafted polymers (crowns and lanterns) and their application in the solid-phase synthesis of hydantoin libraries

Solid-phase dendrimer chemistry using a symmetrical 13C-branched isocyanate monomer was used to prepareradiation-grafted polymers with enhanced loading. Afterevaluation of the physical and chemical properties of thesenew high-loading supports, they were tested in the multipleparallel synthesis of hydantoins.     

Multiple simultaneous synthesis of phenolic libraries

Summary A series of analogous arrays of small, non-peptidyl, non-oligomeric compounds were synthesized on polystyrene resin. With the aid of a functionally differentiated phenolic scaffold, the batch preparation of unique benzamide and urea resins was accomplished, which were further derivatized in modified 96-well plates. An efficient cleavage reaction of the phenyl benzoate link enabled the isolation of more than 600 phenolic compounds in milligram quantities that were suitable for direct biological screening. The technology described herein represents a facile, economical approach to non-peptidyl chemical diversity.     

Solid phase synthesis of benzamidine-derived sulfonamide libraries

Using solid phase synthesis, a library has been constructed of benzamidine-derived sulfonamides which have strong inhibitory activity against blood coagulant thrombin. The library compounds were obtained in good yield and high purity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Solid phase synthesis of benzamidine and butylamine-derived hydantoin libraries

We have constructed a number of benzamidine- and butylamine-based hydantoin compounds by means of an efficient route using solid phase synthesis in which neat diisopropylamine was employed for a novel cyclization/traceless cleavage step. All library compounds were obtained in excellent yield and high purity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Comments on the design of chemical libraries for screening

Different representations of molecules, based ondistinct sets of properties can yield differentperspectives of the issues involved in library design.In particular, different chemical representations cangive rise to very different estimates of requiredlibrary sizes. We provide a preliminary mathematicalframework that examines the size of libraries requiredto adequately sample the spaces corresponding to somecommonly used property sets. Introduction ofconformational flexibility is also discussed as ameans of increasing coverage of chemical libraries,while at the same time considering the thermodynamicconsequences of flexibility upon detectable activity.Our theoretical analysis reveals that the propertyspaces currently in use are extremely large andunlikely to provide adequate discrimination amongcompounds.     

Solid phase synthesis of combinatorial libraries using anhydrides as templates

A simple and general approach to the synthesis of chemical libraries based on a universal anhydride template allows the preparation of large number of compounds. Various cyclic/acyclic amines, primary/secondary amines, differentially protected bifunctional amines were used as nucleophiles to react with anhydrides. The free carboxylic acid generated was then coupled with solid-bound amines. The facile and rapid generation of compounds through this multi-component assembly can be accomplished in a combinatorial parallel synthesis. This revised version was published online in August 2006 with corrections to the Cover Date.     

The use of high-throughput synthesis and purification in the preparation of a directed library of adrenergic agents

A library of potential agonists and antagonists for adrenergic receptors was prepared using high-throughput solution-phase parallel synthesis. Traditional solution-phase reductive amination reactions followed by rapid purification by ion exchange chromatography yielded products with near-analytical purity. An array of ketones and amines, arranged in an 8 × 12 matrix, were combined to form 96 individual compounds. This revised version was published online in August 2006 with corrections to the Cover Date.     

Multiplexed sorting of libraries on libraries: A novel method for empirical protein design by affinity-driven phage enrichment on synthetic peptide arrays

Chemically synthesized peptide arrays on planar cellulose carriers are proposed as libraries of ligands suitable for the multiplexed simultaneous capture of peptide-specific acceptor proteins from a large randomly mutagenized library of acceptor proteins presented on bacteriophage M13 particles. This experimental set-up can be exploited to rapidly screen for individual new, distinct binding partners from two complementary libraries (two-dimensional screening). The technical feasibility of this empirical protein design approach was demonstrated with calmodulin as an aceptor protein using an array of mastoparan variants for multiplexed phage affinity enrichment.     

Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries

Until recently, the field of diversity and library design has more or less ignored naturalproducts as a compound source. This is probably due to at least two reasons. First,combinatorial and reaction-based approaches have been major focal points in the earlydays of computational library design. In addition, a widespread view is that naturalproducts are often highly complex and not amenable to medicinal chemistry efforts. Thiscontribution introduces recent computational approaches to systematically analyzenatural molecules and bridge the gap between natural products and synthetic chemistryprograms. Large scale comparisons of natural and synthetic molecules are discussed aswell as studies designed to identify `synthetic mimics' of natural products with specificactivity. In addition, a concept for the design of natural/synthetic hybrid libraries isintroduced. Although research in this area is still in its early stages, an important lesson tobe learned from computational analyses is that there is no need to a priori `shy away'from natural products as a source for molecular design.     

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     

Solid phase organic synthesis (SPOS): A novel route to diketopiperazines and diketomorpholines

Summary The solid phase synthesis of libraries containing a 1,3,4,6-tetrasubstituted-2,5-diketo-1,4-piperazine scaffold (DKP) or a 3,4,6-trisubstituted-2,5-diketo-1,4-morpholme scaffold (DKM) from -bromocarboxylic acids and amines is described. Using a design strategy which we refer to as divergent library design, both templates were prepared from a common intermediate. The general utility of this synthetic route in creating novel, non-peptidyl chemical libraries is discussed.     

Application of an almost traceless linker in the synthesis of 2-alkylthiobenzimidazole combinatorial libraries

Resin-bound triphenylphosphine was coupledto 4-fluoro-3-nitrobenzyl bromide, and2-alkylthiobenzimidazoles were synthesized onresin in 4 steps using standard chemistries. Cleavage of the compounds from the resin wasachieved with 10% NaOH in MeOH to leave amethyl group at the attachment point. A totalof 47 amines and 40 electrophiles wereevaluated, defining the scope of the reactions,culminating in the synthesis of an 80-membertest library of high purity as determined by HPLC.     

Analysis of libraries encoded with GC tags: Compound elution,tag decode analysis,and statistical sampling analysis

Libraries encoded with electrophoric tags present a uniquechallenge with respect to library quality control and characterization. Libraries are prepared on Tentagel resin in 200-fold redundancy wherein each resin particle containsone compound per one tag set. The amount of compound presenton the bead is ca. 200–500 pmole while tag levels are estimatedat 0.5–1 pmol/bead. Several quality control protocols have been developed in order to accurately estimate bead yield andpurity for the entire library, ensure high tag fidelity, andto determine the overall performance of individual synthons. This review provides a unique, collective portrait of Pharmacopeia's approach in assessing the quality of librariesprepared using its molecular encoding technology.     

Six new photolabile linkers for solid-phase synthesis. 1. Methods of preparation

In the synthesis of combinatorial chemical libraries on solid phase, there is a need to cleave the compounds from the solid support before the library can be tested for biological activity. It is advantageous to use linkers which will release the libraries by mild photolytic cleavage. We have developed six new linkers of the photosensitive α-methyl 2-nitrobenzyl type containing amino, hydroxy, bromo and methylamino groups, and also 4-nitrophenoxycarbonyl activated OH and NH₂ groups. This revised version was published online in August 2006 with corrections to the Cover Date.