Comprehensive survey of chemical libraries for drug discovery and chemical biology: 2006

Synthesis of 2-Alkoxy/Thioalkoxy Benzo[d]imidazoles and 2-Thione Benzo[d]imidazoles via a Phase-Based, Chemoselective Reaction

2-Alkoxy/thioalkoxy benzo-[d]-imidazole and 2-thione benzo-[d]-imidazole libraries were constructed in solution phase and on solid phase, respectively. The key step in this work is the phase-based chemoselective reaction of the 2-mercaptobenzo-[d]-imidazole intermediate with benzyl chloride (solution phase) and Merrifield resin (solid phase). In the solution-phase case, benzyl chloride reacted with the thiol group of 2-mercaptobenzo-[d]-imidazole, whereas in the solid-phase case, Merrifield resin was introduced at an internal amine group of benzo-[d]-imidazole. To afford the desired 2-alkoxy/thioalkoxy benzo-[d]-imidazole analogues, we used various alkyl halides, alcohols, and thiols in solution phase, and to obtain 2-thione benzo-[d]-imidazole derivatives on solid phase, we used diverse alkyl halides and boronic acids. Finally, to measure the drug potential to be orally active and the molecular diversity in three-dimensional (3D) space, we calculated physicochemical properties and displayed energy-minimized 3D structures. As a result, the libraries from solution phase and solid phase show distinct features in physicochemical properties and skeletal diversities in 3D space.

Synthesis of novel polyhydroxylated pyrrolidine–triazole/-isoxazole hybrid molecules

A straightforward synthesis of novel, 2-heterocyclyl polyhydroxylated pyrrolidines is described.

Ugi-based approaches to quinoxaline libraries

An expedient and concise Ugi-based unified approach for the rapid assembly of quinoxaline frameworks has been developed. This convergent and versatile method uses readily available commercial reagents, does not require advanced intermediates, and exhibits excellent bond-forming efficiency, thus exemplifying the operationally simple synthesis of quinoxaline libraries.

Recent progress on fluorous synthesis of biologically interesting compounds

This article highlights research papers published in 2011 and 2012 on fluorous linker-assisted synthesis of biologically interesting small molecules and biomolecules.

Diversity oriented synthesis of a vinblastine-templated library of 7-aryl-octahydroazonino[5,4-b]indoles via a three-component reaction

A vinblastine-templated library of 7-aryl-octahydroazonino[5,4-b]indoles was prepared by a three-component reaction from indolizino[8,7-b]indoles, chloroformates, and activated arenes via a chloroformate mediated fragmentation of the indolizinoindole nucleus followed by insertion of an activated arene. In addition to N3-carbamoyl-7-aryl-octahydroazonino[5,4-b]indoles prepared in one step, a wide range of N3-substituted substrates were synthesized in one pot via the derivatization of a versatile N3-H-azonino[5,4-b]indole intermediate generated in situ by application of the same strategy. A subset of 308 compounds out of a virtual library of 3216, representing 13 different chemotypes, was prepared by high throughput solution-phase synthesis and subsequently purified by mass-triggered high performance liquid chromatography (HPLC). A total of 188 compounds with a minimum purity of 80% by UV214 nm and 85% by evaporative light scattering detection (ELSD) was isolated for primary screening.

Parallel chemistry in the 21st century

The tool chest of techniques, methodologies, and equipment for conducting parallel chemistry is larger than ever before. Improvements in the laboratory and developments in computational chemistry have enabled compound library design at the desks of medicinal chemists. This unit includes a brief background in combinatorial/parallel synthesis chemistry, along with a discussion of evolving technologies for both solid- and solution-phase chemistry. In addition, there are discussions on designing compound libraries, acquisition/procurement of compounds and/or reagents, the chemistry and equipment used for chemical production, purification, sample handling, and data analysis.

Synthesis of a unique isoindoline/tetrahydroisoquinoline-based tricyclic sultam library utilizing a Heck-aza-Michael strategy

The synthesis of a unique isoindoline- and tetrahydroisoquinoline (THIQ)-containing tricyclic sultam library, utilizing a Heck-aza-Michael (HaM) strategy is reported. Both isoindoline and THIQ rings are installed through a Heck reaction on a vinylsulfonamide, followed by one-pot deprotection and intramolecular aza-Michael reaction. Subsequent cyclization with either paraformaldehyde condensation or 1,1'-carbonyldiimidazole coupling generates a variety of tricyclic sultams. Overall, a 160-member library of these sultams, together with their isoindolines/THIQ and secondary sulfonamides precursors, were constructed using this strategy.

High Throughput Chemistry in Drug Discovery

This chapter outlines the evolution of high throughput chemistry from its origins in the genome revolution of the early 1990's to its current practice as an integral tool in drug discovery, via the concept of the large “universal library” to the practice of small targeted arrays for structure–activity relationship generation. The technologies developed as part of this evolution are also outlined including early ACT peptide synthesisers and other automated and non-automated devices for both solid-supported and solution-based approaches. Finally, the chapter outlines several case studies of the application of high throughput synthesis to drug discovery.

Microwave-assisted solution-phase synthesis and DART-mass spectrometric monitoring of a combinatorial library of indolin-2,3-dione schiff bases with potential antimycobacterial activity

A combinatorial library composed of eleven hydrazides A-K and eleven indolin-1,2-dione derivatives 1-11 has been designed to formally generate sublibraries of 22 mixtures, M₁-M₂₂ comprising of 121 Schiff bases, A-K(1-11). The designed library has been synthesized by the solution-phase method and microwave-assisted synthetic techniques. The formation of individual compounds of each mixture was confirmed by Direct Analysis in Real Time (DART) as ionization technique connected to an Ion Trap as a mass detector. The synthesized mixtures were evaluated for their antimycobacterial activity against four Mycobacterium strains; M. intercellulari, M. xenopi, M. cheleneoi and M. smegmatis. Variable antimycobacterial activity was revealed with the investigated mixtures and maximum activity was shown by M₈, M₁₀, M₁₁, and M₁₅ with MIC values of 1.5, 3.1, 6.2 and 0.09 μg/mL, respectively. Application of the indexed method of analysis on these active mixtures revealed that compounds D₈, D₁₀ and D₁₁ may contribute to the activity of the tested mixtures.

Polymer supported synthesis of novel benzoxazole linked benzimidazoles under microwave conditions: in vitro evaluation of VEGFR-3 kinase inhibition activity

An efficient soluble polymer-supported method has been developed for the parallel synthesis of substituted benzimidazole linked benzoxazoles using focused microwave irradiation. The key step involves the amidation of 4-hydroxy-3-nitrobenzoic acid with polymer-immobilized o-phenylenediamine. Application of mild acidic conditions promoted the ring closure to furnish the benzimidazole ring. After hydrogenation of the nitro-group to amine, the resulted polymer conjugates underwent efficient ring closure with various alkyl, aryl and heteroaryl isothiocyanates to generate the polymer-bound benzimidazolyl benzoxazoles. The polymer-bound compounds were finally cleaved from the support to furnish benzimidazole linked benzoxazole derivatives. The efficacy of the resultant angular bis-heterocyclic library was studied against vascular endothelial growth factor receptor (VEGFR-3). The preliminary screening of these novel compounds exhibits moderate to high inhibition (IC(50) = 0.56-1.42 μM). This protocol provides an easy access to novel angular bis-heterocycles which have potential for the discovery of novel leads for targeted cancer therapeutics.

High transfection efficiency of cationic lipids with asymmetric acyl-cholesteryl hydrophobic tails

The ability of a nonviral gene delivery system to overcome extra- and intracellular barriers is a critical issue for the future clinical applications of gene therapy. In recent years much effort has been focused on the development of a variety of DNA carriers, and cationic liposomes have become the most common nonviral gene delivery system. One hundred and eighty novel cationic lipids with asymmetric acyl-cholesteryl hydrophobic tails were synthesized by parallel solid-phase chemistry. The liposomes were prepared and gel retardation assays were used to study the binding efficiency between the prepared liposome and the DNA. Transfection efficiencies of the lipids were evaluated against various mammalian cells, such as human embryonic kidney (HEK293), human cervical adenocarcinoma (HeLa), canine osteosarcoma (D17), colorectal adenocarcinoma (COLO 205), and human prostate adenocarcinoma (PC3) cells. The lipids with an acyl portion at the terminal part of the polyamine backbone exhibited higher transfection efficiency than those with the acyl portion as an internal part of the backbone. These compounds also showed higher transfection efficiency and lower cytotoxicity than the commercially available agents, Effectene, DOTAP, and DC-Chol.

Methods for combinatorial and parallel library design

Diversity has historically played a critical role in design of combinatorial libraries, screening sets and corporate collections for lead discovery. Large library design dominated the field in the 1990s with methods ranging anywhere from purely arbitrary through property based reagent selection to product based approaches. In recent years, however, there has been a downward trend in library size. This was due to increased information about the desirable targets gleaned from the genomics revolution and to the ever growing availability of target protein structures from crystallography and homology modeling. Creation of libraries directed toward families of receptors such as GPCRs, kinases, nuclear hormone receptors, proteases, etc., replaced the generation of libraries based primarily on diversity while single target focused library design has remained an important objective. Concurrently, computing grids and cpu clusters have facilitated the development of structure based tools that screen hundreds of thousands of molecules. Smaller "smarter" combinatorial and focused parallel libraries replaced those early un-focused large libraries in the twenty-first century drug design paradigm. While diversity still plays a role in lead discovery, the focus of current library design methods has shifted to receptor based methods, scaffold hopping/bio-isostere searching, and a much needed emphasis on synthetic feasibility. Methods such as "privileged substructures based design" and pharmacophore based design still are important methods for parallel and small combinatorial library design. This chapter discusses some of the possible design methods and presents examples where they are available.

Divergent solution-phase synthesis of diarylpyrimidine libraries as selective A3 adenosine receptor antagonists

A practical and divergent solution-phase synthetic strategy has been optimized to prepare a highly diverse library of 2,4-diaryl- and 2,6-diarylpyrimidines. Structural elaboration of the starting heterocyclic scaffolds was accomplished by exploiting the potential for diversity offered by the Suzuki-Miyaura cross-coupling reaction. These studies enabled the identification of structurally simple, highly potent, and selective A(3) adenosine receptor antagonists.

Solid-phase synthesis of 1,3,6-trisubstituted-1H-thiazolo[4,5-c][1,2]thiazin-4(3H)one-2,2-dioxide derivatives using traceless linker

A new solid-phase route for preparation of 1,3,6-trisubstituted-1H-thiazolo[4,5-c][1,2]thiazin-4(3H)one-2,2-dioxide derivatives is described. Our synthetic route is begun with a thiazole resin and relies on the sulfonamide formation, Mitsunobu-type N-alkylation, cyclization, and nucleophilic substitution methodology cleavage on a solid support. The strategy permits the incorporation of three points of diversity into the thiazolo[4,5-c][1,2]thiazine ring system in good overall yields.

Reagent based DOS: a "Click, Click, Cyclize" strategy to probe chemical space

The synthesis of small organic molecules as probes for discovering new therapeutic agents has been an important aspect of chemical-biology. Herein we report a reagent-based, diversity-oriented synthetic (DOS) strategy to probe chemical and biological space via a "Click, Click, Cyclize" protocol. In this DOS approach, three sulfonamide linchpins underwent cyclization protocols with a variety of reagents to yield a collection of structurally diverse S-heterocycles. In silico analysis is utilized to evaluate the diversity of the compound collection against chemical space (PC analysis), shape space (PMI) and polar surface area (PSA) calculations.

Solid-phase synthesis of thiazolo[4,5-b]pyridine derivatives using Friedländer reaction

Traceless solid-phase synthesis of 2,5,6,7-tetrasubstituted thiazolo[4,5-b]pyridine derivatives is described. Thorpe-Ziegler type cyclization of solid supported cyanocarbonimidodithioate with alpha-halo ketones afforded thiazole resin, which were converted to the desired thiazolopyridine resin by the Friedländer protocol under microwave irradiation conditions. After oxidation of sulfides to sulfones, nucleophilic desulfonative substitution with amines gave the target thiazolo[4,5-b]pyridine derivatives in good overall yields.

Scaffold-directed and traceless synthesis of tricyclic quinoxalinone imidazoles under microwave irradiation: for SCS-09 special issue-combinatorial approaches to drug discovery

Traceless synthesis of 2-aminoimidazoquinoxalinones has been performed on soluble polymer support under open-vessel microwave dielectric heating. The reaction progression is monitored directly by the conventional proton NMR which indicated no release of the substrate from the support. Fmoc-deprotected amino acid polymer conjugates react with 1,5-difluoro-2,4-dinitro benzene to yield polymer bound dinitro fluoro amines, which are further substituted by various primary amines to yield PEG-immobilized dinitrodiamines. Simultaneous reduction of aromatic meta-dinitro group leads to the traceless release of 2-quinoxalinones, followed by N-hetero cyclization with various isothiocyanates in the presence of mercury(II)chloride to furnish 2-aminoimidazoquinolinone rings with three points of diversity at rapid pace.

Synthesis of 1-(4-trifluoromethoxyphenyl)-2,5-dimethyl-3-(2-R-thiazol-4-yl)-1H-pyrroles via chain heterocyclization

The title compounds, (4-trifluoromethoxyphenyl)-2,5-dimethyl-3-(2-R-thiazol-4-yl)-1H-pyrroles, were prepared in four steps starting from commercially available 4-trifluoromethoxyaniline. The pyrrole (second ring) was added in one step using the Paal-Knorr method. The thiazole (third ring) was added in three steps using chloroacylation with chloroacetonitrile followed by heterocyclization with thioamides/thioureas.

Kinetics of resin-supported Mitsunobu esterification and etherification reactions

Solid-phase Mitsunobu reaction is very useful in organic and parallel synthesis. In this work, we optimize the solid-phase Mitsunobu esterification and etherification reactions and investigated their kinetics by single-bead FTIR microspectroscopy method. Thirteen solid-phase Mitsunobu esterification reactions proceeded at rates between 2.5 x 10(-3) and 19 x 10(-3) s(-1), while five etherification reactions at generally slower rates between 3.3 x 10(-3) and 8.9 x 10(-3) s(-1). We discovered that reaction rates, as in solution phase Mitsunobu reactions, linearly correlated to pK(a) values of acids and phenols used in the reaction. By studying side reactions and intermediates, we found that the solid-phase reaction mechanism also bears remarkable similarities to that of solution phase Mitsunobu reaction.

Bis-enaminone based parallel solution-phase synthesis of 1,4-dihydropyridine derivatives

Two variations of a parallel solution-phase synthesis of N-substituted dimethyl 4-oxo-1,4-dihydropyridine-3,5-dicarboxylates 4 and methyl 3-oxo-3,5-dihydro-2H-pyrazolo[4,3-c]pyridine-7-carboxylates 9 from dimethyl acetone-1,3-dicarboxylate (1) were developed. The first synthetic method comprises preparation of the bis-enaminone reagents 2 and 8 and their cyclization with primary amines 3 via double substitution of both dimethylamino groups to give dihydropyridines (DHPs) 4 and 9, respectively. Another variation consists of preparation of the monoenaminone reagents 5 and 10, followed by substitution of the dimethylamino group with primary amines 3, and cyclization of the so formed intermediates 6 with N,N-dimethylformamide dimethylacetal (DMFDMA). In this manner, a library of 46 analytically pure compounds, 24 intermediates 6, 11, and 13, and 22 final dihydropyridines 4 and 9 was obtained employing just a simple filtration workup.

Traceless solid-phase synthesis of 2,4,6-trisubstituted thiazolo[4,5-d]pyrimidine-5,7-dione derivatives

An expedient, traceless, solid-phase synthesis of 2,4,6-trisubstituted thiazolo[4,5-d]pyrimidine-5,7-dione derivatives has been developed. The solid-phase synthetic route utilizes urea formation by a microwave irradiation promoted reaction of a thiazole amino ester resin with an isocyanate. The resulting urea resin is converted to a thiazolopyrimidinedione resin, containing two diversity elements at N-4 and N-6, by using a one-pot cyclization/N-alkylation process. After oxidation to form a sulfone, nucleophilic C-2 substitution with amines, the third diversity element, gives the target 2,4,6-trisubstituted thiazolo[4,5-d]pyrimide-5,7-dione derivatives. This highly efficient solid-phase synthetic sequence enables the incorporation of three points of diversity into the preparation of the thiazolo[4,5-d]pyrimidine-5,7-dione ring system.

Distributed Drug Discovery, Part 2: global rehearsal of alkylating agents for the synthesis of resin-bound unnatural amino acids and virtual D(3) catalog construction

Distributed Drug Discovery (D³) proposes solving large drug discovery problems by breaking them into smaller units for processing at multiple sites. A key component of the synthetic and computational stages of D³ is the global rehearsal of prospective reagents and their subsequent use in the creation of virtual catalogs of molecules accessible by simple, inexpensive combinatorial chemistry. The first section of this article documents the feasibility of the synthetic component of Distributed Drug Discovery. Twenty-four alkylating agents were rehearsed in the United States, Poland, Russia, and Spain, for their utility in the synthesis of resin-bound unnatural amino acids 1, key intermediates in many combinatorial chemistry procedures. This global reagent rehearsal, coupled to virtual library generation, increases the likelihood that any member of that virtual library can be made. It facilitates the realistic integration of worldwide virtual D³ catalog computational analysis with synthesis. The second part of this article describes the creation of the first virtual D³ catalog. It reports the enumeration of 24 416 acylated unnatural amino acids 5, assembled from lists of either rehearsed or well-precedented alkylating and acylating reagents, and describes how the resulting catalog can be freely accessed, searched, and downloaded by the scientific community.