Solution-phase Library Research Articles

Discovery of a Covalent Kinase Inhibitor from a DNA-Encoded Small-Molecule Library × Protein Library Selection.

We previously reported interaction determination using unpurified proteins (IDUP), a method to selectively amplify DNA sequences encoding ligand:target pairs from a mixture of DNA-linked small molecules and unpurified protein targets in cell lysates. In this study, we applied IDUP to libraries of DNA-encoded bioactive compounds and DNA-tagged human kinases to identify ligand:protein binding partners out of 32 096 possible combinations in a single solution-phase library × library experiment. The results recapitulated known small molecule:protein interactions and also revealed that ethacrynic acid is a novel ligand and inhibitor of MAP2K6 kinase. Ethacrynic acid inhibits MAP2K6 in part through alkylation of a nonconserved cysteine residue. This work validates the ability of IDUP to discover ligands for proteins of biomedical relevance.

Acyl Guanidine Inhibitors of β-Secretase (BACE-1): Optimization of a Micromolar Hit to a Nanomolar Lead via Iterative Solid- and Solution-Phase Library Synthesis

This report describes the discovery and optimization of a BACE-1 inhibitor series containing an unusual acyl guanidine chemotype that was originally synthesized as part of a 6041-membered solid-phase library. The synthesis of multiple follow-up solid- and solution-phase libraries facilitated the optimization of the original micromolar hit into a single-digit nanomolar BACE-1 inhibitor in both radioligand binding and cell-based functional assay formats. The X-ray structure of representative inhibitors bound to BACE-1 revealed a number of key ligand:protein interactions, including a hydrogen bond between the side chain amide of flap residue Gln73 and the acyl guanidine carbonyl group, and a cation-π interaction between Arg235 and the isothiazole 4-methoxyphenyl substituent. Following subcutaneous administration in rats, an acyl guanidine inhibitor with single-digit nanomolar activity in cells afforded good plasma exposures and a dose-dependent reduction in plasma Aβ levels, but poor brain exposure was observed (likely due to Pgp-mediated efflux), and significant reductions in brain Aβ levels were not obtained.

Molecular Characteristics of CTA056, a Novel Interleukin-2-Inducible T-Cell Kinase Inhibitor that Selectively Targets Malignant T Cells and Modulates Oncomirs

Interleukin-2-inducible T-cell kinase (Itk) is a member of the Btk (Bruton's tyrosine kinase) family of tyrosine kinases. Itk plays an important role in normal T-cell functions and in the pathophysiology of both autoimmune diseases and T-cell malignancies. Here, we describe the initial characterization of a selective inhibitor, 7-benzyl-1-(3-(piperidin-1-yl)propyl)-2-(4-(pyridin-4-yl)phenyl)-1H-imidazo[4,5-g]quinoxalin-6(5H)-one (CTA056), that was developed through screening a 9600-compound combinatorial solution phase library, followed by molecular modeling, and extensive structure-activity relationship studies. CTA056 exhibits the highest inhibitory effects toward Itk, followed by Btk and endothelial and epithelial tyrosine kinase. Among the 41 cancer cell lines analyzed, CTA056 selectively targets acute lymphoblastic T-cell leukemia and cutaneous T-cell lymphoma. Normal T cells are minimally affected. Incubation of Jurkat and MOLT-4 cells with CTA056 resulted in the inhibition of the phosphorylation of Itk and its effectors including PLC-γ, Akt, and extracellular signal-regulated kinase, as well as the decreased secretion of targeted genes such as interleukin-2 and interferon-γ. Jurkat cells also underwent apoptosis in a dose-dependent manner when incubated with CTA056. The potent apoptosis-inducing potential of CTA056 is reflected by the significant modulation of microRNAs involved in survival pathways and oncogenesis. The in vitro cytotoxic effect on malignant T cells is further validated in a xenograft model. The selective expression and activation of Itk in malignant T cells, as well as the specificity of CTA056 for Itk, make this molecule a potential therapeutic agent for the treatment of T-cell leukemia and lymphoma.

ChemInform Abstract: Recent Developments and Applications of Liquid-Phase Strategies in Organic Synthesis

Chemistry on soluble polymer supports, termed liquid-phase organic synthesis, is developing into an increasingly viable alternative or adjunct to the classical solid-phase approach across the broad spectrum of polymer-supported organic chemistry. Recent advances in the field include the use of soluble polymers in the combinatorial synthesis of peptide and small-molecule libraries, as catalyst and reagent supports, and as functionalized polymer-quench reagents for purifying solution-phase combinatorial libraries.

ChemInform Abstract: Mitsunobu Reaction Modifications Allowing Product Isolation Without Chromatography: Application to a Small Parallel Library.

Abstract Readily available reagents, triphenylphosphine resin and di-t-butylazodicarboxylate, were used in Mitsunobu reactions and the byproducts were removed without chromatography. The new modification was utilized to prepare a small, parallel, solution phase library.

Syntheses of Quaternary Carbon-Containing Oxazatricycle and Spiropyran Libraries via Multicomponent Reactions and Their Molecular Switching Properties

A practical protocol for the preparation of parallel solution-phase libraries of the quaternary carbon-containing oxazatricycles and spiropyrans is reported. Target compounds were obtained in moderate to excellent yields by an Et(3)N-mediated multicomponent reaction from various N-methylisoquinolium or flavylium salts and 4-hydroxycoumarins or dimedone in acetone. Purification of the final products by recrystallization in ethyl acetate/methylene chloride or by column chromatography allowed easy isolation of nine compounds of each array. Preliminary studies indicated that some of the prepared compounds exhibit redox switching, photochromic, and thermochromic properties.

Solution-Phase Parallel Synthesis of Hsp90 Inhibitors

As part of an oncology chemistry program directed toward discovery of orally bioavailable inhibitors of the 90 kDa heat shock protein (Hsp90), several solution-phase libraries were designed and prepared. A 2 x 89 library of racemic resorcinol amides was prepared affording 131 purified compounds. After evaluation in a binding assay, followed by an AKT-Luminex cellular assay, three potent analogs had functional activity between 0.1 and 0.3 microM. Resolution by preparative chiral SFC chromatography led to (+)-15, (+)-16, and (+)-17 having functional IC(50) = 27, 43, and 190 nM, respectively. (+)-15 exhibited high clearance in human hepatocytes driven primarily by glucuronidation as confirmed by metabolite identification. A second 8 x 14 exploratory library was designed to investigate heterocyclic replacements of the resorcinol ring. The second library highlights the use of the (-)-sparteine-mediated enantioselective Pd-catalyzed alpha-arylation of N-Boc-pyrrolidine to prepare chiral 2-arylpyrrolidines in parallel.

Parallel medicinal chemistry approaches to selective HDAC1/HDAC2 inhibitor (SHI-1:2) optimization

The successful application of both solid and solution phase library synthesis, combined with tight integration into the medicinal chemistry effort, resulted in the efficient optimization of a novel structural series of selective HDAC1/HDAC2 inhibitors by the MRL-Boston Parallel Medicinal Chemistry group. An initial lead from a small parallel library was found to be potent and selective in biochemical assays. Advanced compounds were the culmination of iterative library design and possess excellent biochemical and cellular potency, as well as acceptable PK and efficacy in animal models.

Two-Vial, LC−MS Identification of Ephedrine Receptors from a Solution-Phase Dynamic Combinatorial Library of over 9000 Components

Reports on dynamic combinatorial chemistry have almost exclusively involved small libraries of 10-100 compounds. We now show how more than 9000 compounds can be screened in a single LC-MS analysis to reveal a series of new receptors that bind ephedrine in water. These results demonstrate the feasibility of screening DCLs that are substantially larger than the solution-phase libraries reported thus far.

Syntheses of Oxazabicycle Library via One-Pot Tandem Reactions

A practical protocol for the preparation of a parallel solution-phase library of oxazabicycle is reported. Target compounds were obtained in moderate to good yields by a Yb(OTf)3-catalyzed one-pot tandem reaction from various anisidines, aromatic aldehydes, isobutyraldehyde, and 4-hydroxycoumarins/dimedone. Purification of the final products by either recrystallization in ethyl acetate/methylene chloride or column chromatography allowed easy isolation of the 18 components of the array.

Meso-Tetra(pentafluorophenyl)porphyrin as an efficient platform for combinatorial synthesis and the selection of new photodynamic therapeutics using a cancer cell line.

The four para fluoro groups on 5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorophenyl)-porphyrin (TPPF20) are known to react with a variety of nucleophiles, but the reaction conditions for this substitution reaction depend on the nature of the nucleophiles, e.g. primary amines versus thiols. Glycosylated derivatives of this core porphyrin have been shown to be effective photodynamic agents in the induction of necrosis or apoptosis in several cancer cell lines. The present report demonstrates that TPPF20 can be used as a core platform to efficiently generate a variety of solution-phase combinatorial libraries. The focused combinatorial libraries have substituents that are chosen from a set of motifs known to bind biopolymers such as DNA, be taken up by cancer cells, or to render the compounds amphipathic. Incubation of a breast cancer cell line with these solution-phase libraries, followed by cell lyses and extraction, affords a selection assay. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the extracts allows identification of the molecules taken up by the cells. Cell binding assays of the winning compounds synthesized directly indicate that both glycosylation and amphipathicity are key properties since neither tetraglycosylated porphyrins nor those with four polar groups are selected to the same extent. In addition, photodynamic efficacy was evaluated.

Parallel Solution-Phase Synthesis of 2-Alkylthio-5-arylidene-3,5-dihydro-4H-imidazol-4-one by One-Pot Three-Component Domino Reaction

A practical protocol for the preparation of a parallel solution-phase library of 5-arylidene imidazolone is reported. Target compounds were obtained in good yield, stereoselectively, and purity by one-pot domino reaction from various thiohydantoines, arylaldimines, and halogenoalkanes. Purification of the final products by recrystallization with a mixture of pentane/ethanol allowed simple isolation of the 17 components of the array.

Synthesis of Solution-Phase Phosphoramidite and Phosphite Ligand Libraries and Their In Situ Screening in the Rhodium-Catalyzed Asymmetric Addition of Arylboronic Acids

Herein, we report the automated parallel synthesis of solution-phase libraries of phosphoramidite ligands for the development of enantioselective catalysts. The ligand libraries are screened in situ in the asymmetric rhodium-catalyzed addition of arylboronic acids to aldehydes and imines. It is shown that the described methodology results in the straightforward discovery of leads for highly efficient enantioselective catalysts.

Discovery of tertiary aminoacids as dual PPARα/γ agonists-I

A novel series of potent dual agonists of PPARα and PPARγ, the alkoxybenzylglycines, was identified and explored using a solution-phase library approach. The synthesis and structure–activity relationships of this series of dual PPARα/γ agonists are described.

Discovery and initial development of a novel class of antibacterials: Inhibitors of Staphylococcus aureus transcription/translation

The novel bacterial transcription/translation (TT) inhibitor 1 was identified through a combination of high throughput screening and exploratory medicinal chemistry. Initial optimization of the anthranilic acid moiety and sulfonamide amine diversity was accomplished via 1- and two-dimensional solution phase libraries, resulting in an improvement in the MIC of the lead from 64 to 8 μg/mL (compound 4l). Subsequent modification of the central aromatic ring and further refinement of the sulfonamide amines required the development of a solid phase route on Wang resin. The resulting libraries generated a number of potent antibacterials with MICs of ⩽1 μg/mL (e.g., 10b, 12, and 13). During the course of this work, it became apparent that the antibacterial activity of the series is not fully correlated with TT inhibition, suggesting that at least one additional mechanism of action is operative.

Direct screening of solution phase combinatorial libraries encoded with externally sensitized photolabile tags

Solution phase combinatorial chemistry holds an enormous promise for modern drug discovery. Much needed are direct methods to assay such libraries for binding of biological targets. An approach to encoding and screening of solution phase libraries has been developed based on the conditional photorelease of externally sensitized photolabile tags. The encoding tags are released into solution only when a sought-for binding event occurs between the ligand and the receptor, outfitted with an electron-transfer sensitizer. The released tags are analyzed in solution revealing the identity of the lead ligand or narrowing the range of potential leads.

Parallel Solution-Phase Synthesis of Acrylonitrile Scaffolds Carrying l-α-Amino Acidic or d-Glycosyl Residues

A practical and straightforward protocol for the preparation of a solution-phase library of acrylonitrile scaffolds is reported. Target compounds were obtained in high yield, stereoselectivity, and purity by two simple and practical steps from cyanoacetic acid. Moreover, our study proposes a synthetic approach starting from the constructed library to obtain three-membered heterocycles.

Carbamates from Alcohol Diversity: A Simple Solution Phase Library Method.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Carbamates from alcohol diversity: a simple solution phase library method

A simple one-pot, solution phase method for the parallel synthesis of carbamates from amines and alcohols is described. The high-yielding method does not require support-bound reagents, extractions or resin washing steps and should be broadly applicable to the manual or automated generation of carbamate libraries.

Prospects for Combinatorial Chemistry in the Agrosciences

The recent progress and future prospects for the successful application of combinatorial chemistry and high throughput screening within the agrochemical lead discovery process are outlined and discussed. Solid and solution phase library synthesis technologies are reviewed and compared, and the role and importance of bioavailability, diversity and virtual screening in rational library design are detailed.