Parallel microwave-assisted library of imidazothiazol-3-ones and imidazothiazin-4-ones

A methodology for the generation of a microwave-assisted parallel library and its conversion into a second library is described. A 24-membered library of substituted 4(5)-sulfanyl-1H-imidazoles was generated and subsequently converted into a second library of bicyclic imidazo[5,1-b]thiazol-3-ones and imidazo[5,1-b]thiazin-4-ones. The first library was generated using a three-component reaction and transformed into a daughter library with a polymer-supported coupling agent. The procedure involved the use of an array of expandable reaction vessels, which can accommodate pressure buildup due to microwave heating without loss of volatile solvents or reagents. Library generation time for each library was 16 min.     

A solid-phase, library synthesis of natural-product-like derivatives from an enantiomerically pure tetrahydroquinoline scaffold

With the goal of developing a library synthesis of tetrahydroquinoline-derived natural-product-like small molecules, a practical synthesis of enantiomerically pure tetrahydroquinoline scaffold was achieved. An asymmetric aminohydroxylation reaction was the key step in this strategy. This scaffold was further immobilized onto the solid support for the library generation. The library was obtained from three diversity sites: (i) acylation of the hydroxyl group (R(1)), (ii) coupling of the Fmoc-protected amino acid to the amino group (R(2)), and (iii) amidation of the N-terminal amine group (R(3)).     

Design,synthesis and spectroscopic characterisation of a focused library based on the polyandrocarpamine natural product scaffold

A focused library based on the marine natural products polyandrocarpamines A ( 1 ) and B ( 2 ) has been designed and synthesised using parallel solution‐phase chemistry. In silico physicochemical property calculations were performed on synthetic candidates in order to optimise the library for drug discovery and chemical biology. A library of ten 2‐aminoimidazolone products ( 3–12 ) was prepared by coupling glycocyamidine and a variety of aldehydes using a one‐step stereoselective aldol condensation reaction under microwave conditions. All analogues were characterised by NMR, UV, IR and MS. The library was evaluated for cytotoxicity towards the prostate cancer cell lines, LNCaP, PC‐3 and 22Rv1. Copyright © 2013 John Wiley & Sons, Ltd.     

Combinatorial synthesis of a small-molecule library based on the vinyl sulfone scaffold

[reaction: see text] A 30-member library of small molecules based on the vinyl sulfone scaffold was prepared on rink amide resin, using solid phase-based reactions such as oxidation and Horner-Wadsworth-Emmons reaction. The library was designed such that three points of diversity were readily introduced in the library to accommodate the S(1)', S(1), and S(2) binding pockets of different cysteine proteases, making the strategy suitable for high-throughput generation of potential cysteine protease inhibitors.     

Two- and three dimensional combinatorial chemistry from multicomponent Grignard reagents

The conjugate addition of five component Grignard reagents to methyl ecgonidine was used to create libraries of 3-substituted tropanes. By variation in the reagent combination in 10 such 5-membered sublibraries, a library of 25 compounds was made in a two-dimensional format. Screening of this library led to identification of two new potent monoamine transporter ligands that were subsequently synthesized. The most potent compound in this library was (1R,2S,3S,5S)-3-(3,4-dimethylphenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid methyl ester, which inhibited dopamine transporter (hDAT) binding and reuptake with a K(i) of 26 and 20 nM, respectively. The conjugate addition to a 5-membered library of methyl ecgonidine analogues with variation of nitrogen substituent was also carried out and used to create 15 sublibraries of 25 compounds, which displayed 125 compounds in a three-dimensional format. From this 3D library, several potent dopamine transport inhibitors were likewise identified and synthesized. The most potent hDAT inhibitor discovered was (1R,2S,3S,5S)-3-(3,4-dimethylphenyl)-8-pentyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid methyl ester. The study also showed that 3-alkyltropanes were poor inhibitors of monoamine transporters.     

Development of a library of 6-arylcoumarins as candidate fluorescent sensors

[structure: see text]. A bromocoumarin scaffold (1) was reacted with various boronic acid derivatives (2a-l) to afford a library of 6-arylcoumarins (3a-l). This library was found to contain candidate fluorescent sensors for peptidase activity and for nitric oxide.     

Synthesis and screening of a molecularly imprinted polymer library targeted for penicillin G

A library of molecularly imprinted polymers (MIPs) was synthesized by radical bulk polymerization using the beta-lactam antibiotic penicillin G as the template. Diversity of the library was obtained by combining various functionalized monomers and cross-linkers and by varying the stoichiometry and the concentration of the components in the prepolymerization mixtures. The library was screened for selectivity to penicillin G by a radioligand binding assay and was compared to a corresponding control library. The best MIP candidate, showing the highest selectivity for penicillin G, was prepared from methacrylic acid and trimethylolpropane trimethacrylate as the functionalized monomer and cross-linker, respectively. Cross-reactivity studies with other beta-lactam antibiotics showed a low cross-reactivity of penicillin V (15%), ampicillin (16%), and amoxicillin (19%). Nafcillin and oxacillin showed less cross-reactivity (<1%). Cross-reaction with a cephalosporin antibiotic (cephapirin) and structurally nonrelated antibiotics (chloramphenicol, tetracycline, dapsone, and erythromycin) was less than 0.01%.     

Design and synthesis of a diverse morpholine template library

Efficient and general procedures have been developed for the solution-phase preparation of substituted morpholine derivatives, and a library has been produced around generic structure 1. This library was designed with proprietary modeling software for use as a general screening library. The 30 R1 reagents were phenols, and the 275 R2 reagents were taken from five different reagent classes, giving a variety of product classes in the final library of 8250 potential products. All of the library members were generated from a common intermediate, mesylate (5), which was synthesized efficiently, in bulk, in three steps from N-benzylethanolamine (2). High-throughput chemistry using robotics was carried out to produce the 7907 library members, which were individually characterized by reversed-phase LC/MS analysis.     

Glycopeptides as oligosaccharide mimics: high affinity sialopeptide ligands for sialoadhesin from combinatorial libraries

Two different sialic acid containing glycopeptide (sialopeptide) libraries were synthesized using the portion mixing method and ladder synthesis. The libraries were attached via an IMP spacer and a photolabile linker to PEGA(1900) resin in order to facilitate rapid and unambiguous structural analysis of hits by MALDI-TOFMS. One library contained a lactamized sialic acid moiety at the N terminus of a pentapeptide, while a second library displayed a sialic acid residue at the center of a heptapeptide. The sialopeptide libraries were screened against the recombinant binding domain (SnD1) of a sialic acid binding Ig-like protein, sialoadhesin (Siglec-1). No ligands were identified from the lactamized sialic acid library, underscoring the importance of the carboxylic acid moiety for binding. Screening of the second gave few distinct hits (approximately 0.03% of library) with a high consensus. The high-affinity ligands contained, in most cases, a WG motif following the sialylated Thr. The strength of binding of selected ligands was determined by surface plasmon resonance. The best sialopeptide ligand, WLLT(Sa)WGT, exhibited micromolar affinity of SnD1; >10 times the affinity of SnD1 to 3'-sialyl lactose.     

Solid-phase synthesis of a 6-phenylquinolin-2(1H)-one library directed toward nuclear hormone receptors

A library of 6-phenylquinolin-2(1H)-ones with diversity at position 1 and the ortho, meta, and para positions of the pendant phenyl ring has been synthesized using solid-phase parallel synthetic techniques. A key step in the synthesis of the library is a tandem alkylation cleavage in which diversity can be introduced at position 1 simultaneously to the cleavage from the resin. The yields of this step were significantly improved over what has previously been reported by addition of cesium carbonate to scavenge the acid that is formed during the reaction. Furthermore, we have shown that the solid support linkage is tolerant to Suzuki coupling and etherification reaction conditions and that selective cleavage of the linkage can take place in the presence of esters. The resulting 6-phenylquinolin-2(1H)-one library was screened against a panel of nuclear hormone receptors (androgen, estrogen alpha and beta isoforms, glucocorticoid, mineralocorticoid, and progesterone). Certain members of this library display moderate affinity for several of these receptors, and consequently, the 6-phenylquinolin-2(1H)-one core of the library may be considered a privileged structure for nuclear hormone receptors. In contrast, other members of the library display high selectivity for a particular receptor. The highest affinity ligand (9{2,1,1}) possesses an affinity of 330 nM for the androgen receptor, whereas the most selective ligand (9{2,4,1}) displays an affinity of 900 nM for the androgen receptor and a selectivity of 140-fold over the next highest affinity receptor.     

Combinatorial synthesis of benztropine libraries and their evaluation as monoamine transporter inhibitors

A combinatorial synthesis of benztropine analogues is presented. Radical azidonation of 3-benzyloxy-8-azabicyclo[3.2.1]octane-8-carboxylic acid tert-butyl ester 3 to 3-(1-azidobenzyloxy)-8-azabicyclo[3.2.1]octane-8-carboxylic acid tert-butyl ester 4 was used as a key step in the synthesis. This step was optimized by adding 10% DMF to the reaction. Reaction of 4 with phenyl magnesium bromide followed by Boc removal and N-methylation gave benztropine 1. Reaction of five-component Grignard reagents with 4 was used to create a two-dimensional library of 25 N-normethylbenztropine analogues. Further reaction of this library with five alkyl bromides was carried out to create a three-dimensional library containing 125 compounds. Screening of the libraries towards binding and inhibition of uptake of the human dopamine (hDAT), serotonin (hSERT) and norepinephrine transporters (hNET) was carried out. None of the synthesized compounds were found to be stronger than benztropine, and none were selective for inhibition of binding over monoamine uptake.     

Parallel solid-phase synthesis and structural characterization of a library of highly substituted chiral 1,3-oxazolidines

The rapid parallel synthesis and characterization of diverse chirally defined 1,3-oxazolidines is reported. Three diversity elements were incorporated in a 6 x 4 x 4 block approach to generate a 96-member 1,3-oxazolidine library. The synthetic route involved initial attachment of six nonracemic phenylglycidols, (2S,3S)1A-C and (2R,3R)-2A-C, to 2% cross-linked polystyrene resin via a chlorodiethylsilane linker (PS-DES), followed by regio- and stereoselective oxirane ring opening with four primary amines (3a-d). The key condensation reaction between the resulting polymer-bound beta-amino alcohols and four aldehydes (4a-d) was found to occur optimally in warm benzene (60 degrees C) in the presence of anhydrous magnesium sulfate. Cleavage of the oxazolidines from the resin support was achieved with TBAF to give the individual members (2R,4R,5R)-5Aaa-Cdd and (2S,4S,5S)-6Aaa-Cdd in good to excellent yields (51-99%) based on mass recovery. Purities of all these crude products was generally >85% (as measured by LCMS). 1H, 13C NMR, and 1D difference nOe of the library members confirmed the structural and stereochemical integrity of the substituents around the 1,3-oxazolidine core. The asymmetric induction at C-2 (cis or trans to the C-4 substituent) ratio ranged from 4 to I to 49 to 1 across the library. This report highlights the versatility of the 1,3-oxazolidine heterocycle as a scaffold for concise parallel library construction and opens the way for high-throughput screening of such compounds in the biological sphere.     

Solution-phase parallel synthesis of hexahydro-1H-isoindolone libraries via tactical combination of Cu-catalyzed three-component coupling and Diels-Alder reactions

Parallel solution-phase synthesis of combinatorial libraries of hexahydro-1 H-isoindolones exploiting a novel "tactical combination" of Cu-catalyzed three-component coupling and Diels-Alder reactions was accomplished. Three distinct libraries consisting of 24 members (library I), 60 members (library II), and 32 members (library III) were constructed. Variation of three substituents on the isoindolone scaffold in library I was exclusively achieved by the choice of the building blocks. In the syntheses of libraries II and III, sublibraries of isoindolone scaffolds were prepared initially in a one-pot/two-step process and were further diversified via Pd-catalyzed Suzuki cross-coupling reaction with boronic acids at two different diversification points. The Lipinski profiles and calculated ADME properties of the compounds are also reported.     

Expedient Lewis acid catalyzed synthesis of a 3-substituted 5-arylidene-1-methyl-2-thiohydantoin Library

An efficient and rapid solution phase combinatorial synthesis of a 3-substituted 5-arylidene-1-methyl-2-thiohydantoin library was developed. The salient feature for this library production procedure is the addition of the Lewis acid catalyst, indium(III) trifluoromethanesulfonate, which serves to facilitate the direct condensation of aldehydes with 3-substituted 1-methyl-2-thiohydantoins. Use of this Lewis acid catalyst has resulted in faster reaction times, higher conversions and better purity profiles for these condensation reactions as compared to traditional uncatalyzed reactions. The resulting 315 member library of 3-substituted 5-arylidene-1-methyl-2-thiohydantoin is described.     

A spiroisoxazolinoproline-based amino acid scaffold for solid phase and one-bead-one-compound library synthesis

An efficient, multigram synthesis of a spiroisoxazolinoproline-based amino acid, 7, requiring minimal purification, delivering good cis:trans diastereoselectivity (approximately 1:4), and providing good yields is reported. Surface-bound studies of the reduction of an arylnitro group in the presence of an isoxazoline ring with tin(II) dichloride dihydrate were undertaken to confirm the stability of the isoxazoline ring. Full derivitization of this spiroisoxazolinoproline-based amino acid scaffold was performed during the synthesis of a sample library with high yields and high purity that validated the efficiency of the chemistry that was employed in resin-bound library synthesis. A 129,600 member one-bead-one-compound (OBOC) library based on the scaffold 7 was synthesized utilizing a dual amino acid encoding method and bifunctionalization of TentaGel resin.     

Vergleich von Bibliothekssuchverfahren für Steroidmassenspektren

Zusammenfassung 29 Bibliothekssuchverfahren wurden mit einer Bibliothek von 524 Steroidmassenspektren geprüft. Mit einer Stichprobe von 100 Spektren wurde die Wiedererkennung verrauschter Spektren in der Bibliothek abgeschätzt. Besonders rasche und erfolgreiche Verfahren sind mit binär codierten Spektren (konstante Intensitätsschwelle von 1–5% des Basispeaks) und mit reduzierten Spektren (1 oder 2 Peaks in Massenintervallen der Länge 7 oder 14) möglich. Mit diesen Verfahren wurden 93–100% der unbekannten Spektren durch das 1. Nachbarspektrum der Bibliothek richtig identifiziert. Die Wiedererkennungsrate verrauschter Spektren steht in engem Zusammenhang mit dem Informationsgehalt (Entropie) der codierten Bilbliothek.

---

Comparison of library search methods for steroid mass spectraRecognition of noisy spectra in a library

29 library search methods have been tested with a library of 524 steroid mass spectra. A random sample of 100 spectra was used as unknown to estimate recognition of noisy spectra in the library. Binary encoded spectra with constant thresholds of 1–5% of base peak or reduced spectra with 1 (or 2) peaks in mass ranges of 7 (or 14) mass units enable quick and successful searches. 93–100% of the unknowns were identified correctly by the first neighbour spectra of the library. Recognition of noisy spectra is closely related to information content (entropy) of coded libraries.

     

Parallel Synthesis of Novel 3-Substituted 1-Ethyl-6-methylpyrimido[4,5-c]pyridazine-5,7(1H,6H)-dione Analogs

A library of novel 1H-pyrimido[4,5-c]pyridazine-5,7-dione analogs was prepared in a parallel fashion via the cyclization of 6-(1-ethylhydrazinyl)-3-methylpyrimidine-2,4(1H,3H)-dione (4) with α-bromoketones and was then isolated by a two-step purification method with >90% purity. Both the library synthesis and purification method proved suitable for analogs with a high diversity of substitution at the 3-position including various alkyl, aryl, and heteroaryl groups.     

Highly enantioselective ruthenium-catalyzed reduction of ketones employing readily available Peptide ligands

Highly efficient and selective catalysts for the asymmetric reduction of aryl alkyl ketones under hydrogen-transfer conditions (2-propanol) were obtained by combining a novel class of pseudo-dipeptide ligands with [[RuCl(2)(p-cymene)](2)]. A library of 36 dipeptide-like ligands was prepared from N-Boc-protected alpha-amino acids and the enantiomers of 2-amino-1-phenylethanol and 1-amino-2-propanol. The catalyst library was evaluated with the reduction of acetophenone and excellent enantioselectivity of 1-phenylethanol was obtained with several of the novel catalysts. A ligand based on the combination of N-Boc-L-alanine and (S)-1-amino-2-propanol (ligand A-(S)-4) was found to be particular effective. When the situ formed ruthenium complex of this ligand was employed as the catalyst in the hydrogen-transfer reaction of various aryl alkyl ketones, the corresponding alcohol products were achieved in excellent enantioselectivity (up to 98 % ee).     

Application of comprehensive two-dimensional gas chromatography to sterols analysis

The applicability of comprehensive two-dimensional gas chromatography (GCxGC) for sterol analysis was investigated by separation and identification of endogenous sterols in standards, and spiked in human urine. The modulation temperature was optimized to achieve the best separation and signal enhancement. The separation pattern of trimethylsilyl (TMS) derivatives of sterols was compared on two complementary column sets. Whilst the BPX5/BPX50 column set offers better overall separation, BPX50/BPX5 provides better peak shape and sensitivity. Comparison of the identification power of GCxGC-TOFMS against both the NIST05 MS library and a laboratory created (in-house) TOFMS library was carried out on a free sterols extract of urine, derivatised and spiked at the World Anti-Doping Agency (WADA) limit of 2 ng mL(-1). The average match quality for 19 analysed sterols on the BPX50/BPX5 column set was 950/1000 when searched against the in-house library; only four were identified against the NIST05 library, at a match threshold of 800. The match quality of GCxGC-TOFMS spectra was superior to that for analysis using 1D GC-TOFMS for sterols spiked in urine at 10 ng mL(-1). An r(2)>0.997 was obtained for the concentration range between 0.25 ng mL(-1) and 10 ng mL(-1) for three selected sterols. The lowest limit of detection (LOD) was obtained for estrone (0.1 ng mL(-1)) and the highest LOD was for 5alpha-androstan-3alpha,11beta-diol-17-one, epitestosterone and cholesteryl butyrate (1 ng mL(-1)), using a match threshold of at least 800 and signal-to-noise ratio of at least 10. TOFMS coupled to GCxGC enabled satisfactory identification of sterols in urine at their LOD. A minimum acceptable match (MAM) criterion for urinary sterols using 2D retention times and TOF mass spectra is introduced. This study shows that GCxGC-TOFMS yields high specificity for steroids derived from urine, with detection limits appropriate for use in doping control.     

Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using self-organizing maps

A virtual screening procedure based on a topological pharmacophore similarity metric and self-organizing maps (SOM) was developed and applied to optimizing combinatorial products functioning as P(1) purinergic receptor antagonists. The target was the human A(2A) receptor. A SOM was developed using a set of biologically tested molecules to establish a preliminary structure-activity relationship. A combinatorial library design was performed by projecting virtually assembled new molecules onto the SOM. A small focused library of 17 selected combinatorial products was synthesized and tested. On average, the designed structures yielded a 3-fold smaller binding constant ( approximately 33 vs approximately 100 nM) and 3.5-fold higher selectivity (50 vs 14) than the initial library. The most selective compound obtained revealed a 121-fold relative selectivity for A(2A) with K(i) (A(2A)) = 2.4 nM, and K(i) (A(1)) = 292 nM. This result demonstrates that it was possible to design a small, activity-enriched focused library with an improved property profile using the SOM virtual screening approach. The strategy might be particularly useful in projects in which structure-based design cannot be applied because of a lack of receptor structure information, for example, in the many projects aiming at finding new GPCR modulators.