Combinatorial Parallel Synthesis Research Articles

Antimony salt-promoted cyclization facilitating on-DNA syntheses of dihydroquinazolinone derivatives and its applications

DNA-encoded chemical libraries technology has become a novel approach to finding hit compounds in early drug discovery. The chemical space in a DEL would be expanded to realize its full potential, especially when integrating privileged scaffold dihydroquinazoline that has demonstrated a variety of diverse bioactivities. Driven by the requirement of parallel combinatorial synthesis, we here report a facile synthesis of on-DNA dihydroquinazolinone from aldehyde and anthranilamide. This DNA-compatible reaction was promoted by antimony trichloride, which has been proven to accelerate the reaction and improve conversions. Notably, the broad substrate scope of aldehydes and anthranilamides was explored under the mild reaction condition to achieve moderate-to-excellent conversion yields. We further applied the reaction into on-DNA macrocyclization, obtaining macrocycles embedded dihydroquinazolinone scaffold in synthetically useful conversion yields.

Synthesis of Nitrone-derived Pyrrolidine Scaffolds and Their Combinatorial Libraries to Develop Selective α-l-Rhamnosidase Inhibitors.

A general and flexible approach toward the development of α-l-rhamnosidase (α-l-Rha-ase) inhibitors is described. Five enantiopure poly-substituted pyrrolidine-based scaffolds bearing the C1-aminomethyl moiety were designed and synthesized from five-membered cyclic nitrones. Each structurally diversified amide library of these scaffolds was rapidly generated via combinatorial parallel synthesis and applied for in-situ inhibition study against α-l-Rha-ase, allowing us to efficiently identify new inhibition hits. Surprisingly, all promising inhibitors are derived from the same scaffold 3. Among them, the most potent and selective inhibitor is pyrrolidine 19 with Ki =0.24 μM, approximately 24-fold more potent than the reference compound DAA (Ki =5.7 μM). It is the first study to comprehensively prepare pyrrolidine-based scaffolds and libraries for inhibition study against α-l-Rha-ase.

Construction of Response Patterns for Metal Cations by Using a Fluorescent Conjugated Polymer Sensor Array from Parallel Combinatorial Synthesis

Pattern-based strategy is an emerging field of interest for effective sensing applications. Seven different conjugated polymers from combinatorial synthesis were combined into a sensor array, and seven metal cations were selected as representative analytes. The response patterns for each cation were constructed by collecting the individual fluorescence responses from seven polymers in the array. Each ion owns a characteristic pattern. Some of them have similar modes of response with subtle differences, while some patterns are distinctively different. The family/period the metal cations belong to and the charges/electronic configurations they possess may account for such similarity/difference in the pattern.

Method to screen aromatic ligands in mixtures for quantitative affinities to target using magnetic separation of bound ligands along with HPLC and UV photometry detection

A new screening method was tested to estimate the affinity of an aromatic ligand in a mixture through competitive binding against an exogenous reference ligand. The target protein was immobilized on magnetic particles and one or several ligand(s) in each reaction mixture were prepared by parallel combinatorial-synthesis without purification. Specifically, the binding of aromatic biotin derivatives to streptavidin immobilized on magnetic particles was used as the model. An approximation equation that works under the condition of binding ratios below 0.1 for the candidate ligand and the reference ligand was developed. It was found that the relative affinity of each biotinylated aromatic candidate ligand in mixtures was consistent with that by using HPLC-MS analyses or by a homogenous method using its purified counterpart. Hence, this new screening method using HPLC-UV is considered to be highly effective.

Estimation of affinities of ligands in mixtures via magnetic recovery of target-ligand complexes and chromatographic analyses: chemometrics and an experimental model

BackgroundThe combinatorial library strategy of using multiple candidate ligands in mixtures as library members is ideal in terms of cost and efficiency, but needs special screening methods to estimate the affinities of candidate ligands in such mixtures. Herein, a new method to screen candidate ligands present in unknown molar quantities in mixtures was investigated.ResultsThe proposed method involves preparing a processed-mixture-for-screening (PMFS) with each mixture sample and an exogenous reference ligand, initiating competitive binding among ligands from the PMFS to a target immobilized on magnetic particles, recovering target-ligand complexes in equilibrium by magnetic force, extracting and concentrating bound ligands, and analyzing ligands in the PMFS and the concentrated extract by chromatography. The relative affinity of each candidate ligand to its reference ligand is estimated via an approximation equation assuming (a) the candidate ligand and its reference ligand bind to the same site(s) on the target, (b) their chromatographic peak areas are over five times their intercepts of linear response but within their linear ranges, (c) their binding ratios are below 10%. These prerequisites are met by optimizing primarily the quantity of the target used and the PMFS composition ratio.The new method was tested using the competitive binding of biotin derivatives from mixtures to streptavidin immobilized on magnetic particles as a model. Each mixture sample containing a limited number of candidate biotin derivatives with moderate differences in their molar quantities were prepared via parallel-combinatorial-synthesis (PCS) without purification, or via the pooling of individual compounds. Some purified biotin derivatives were used as reference ligands. This method showed resistance to variations in chromatographic quantification sensitivity and concentration ratios; optimized conditions to validate the approximation equation could be applied to different mixture samples. Relative affinities of candidate biotin derivatives with unknown molar quantities in each mixture sample were consistent with those estimated by a homogenous method using their purified counterparts as samples.ConclusionsThis new method is robust and effective for each mixture possessing a limited number of candidate ligands whose molar quantities have moderate differences, and its integration with PCS has promise to routinely practice the mixture-based library strategy.

Modular synthesis of heparan sulfate oligosaccharides for structure-activity relationship studies.

Although hundreds of heparan sulfate binding proteins have been identified and implicated in a myriad of physiological and pathological processes, very little information is known about the ligand requirements for binding and mediating biological activities by these proteins. This difficulty results from a lack of technology for establishing structure-activity relationships, which in turn is due to the structural complexity of natural heparan sulfate (HS) and difficulties of preparing well-defined HS oligosaccharides. To address this deficiency, we developed a modular approach for the parallel combinatorial synthesis of HS oligosaccharides that utilizes a relatively small number of selectively protected disaccharide building blocks, which can easily be converted into glycosyl donors and acceptors. The utility of the modular building blocks has been demonstrated by the preparation of a library of 12 oligosaccharides, which has been employed to probe the structural features of HS for inhibiting the protease, BACE-1. The complex variations in activity with structural changes support the view that important functional information is embedded in HS sequences. Furthermore, the most active derivative provides an attractive lead compound for the preparation of more potent compounds, which may find use as a therapeutic agent for Alzheimer's disease.

Fluorescent sensor array in a microfluidic chip

Miniaturization and automation are highly important issues for the development of high-throughput processes. The area of micro total analysis systems (muTAS) is growing rapidly and the design of new schemes which are suitable for miniaturized analytical devices is of great importance. In this paper we report the immobilization of self-assembled monolayers (SAMs) with metal ion sensing properties, on the walls of glass microchannels. The parallel combinatorial synthesis of sensing SAMs in individually addressable microchannels towards the generation of optical sensor arrays and sensing chips has been developed. [figure: see text] The advantages of microfluidic devices, surface chemistry, parallel synthesis, and combinatorial approaches have been merged to integrate a fluorescent chemical sensor array in a microfluidic chip. Specifically, five different fluorescent self-assembled monolayers have been created on the internal walls of glass microchannels confined in a microfluidic chip.

Design and synthesis of new nonpeptide caspase-3 inhibitors

Highly effective computer-aided (virtual) and real biological screening over quinoline derivatives is described, which has led to the discovery of a new structural class of caspase-3 inhibitors. This enzyme (belonging to the group of cysteine proteases) is a promising therapeutically-significant biological target that is involved in the development of various pathological states in the human organism. The virtual screening method is based upon evaluation of a target-specific profile of compounds by means of a special algorithm intended for the analysis of multiparametric data arrays (self-organizing Kohonen maps). Using this approach, it is possible to carry out directed selection of compounds for a targeted synthesis. The biological screening among synthesized compounds led to a series of new effective inhibitors of caspase-3, the most active of which possess effective inhibiting concentrations in the range of IC50 = 4–30 nM. The nonpeptide nature of the new chemotype offers potentially favorable pharmacokinetic parameters, while its belonging to large libraries (obtained by means of parallel combinatorial synthesis in solution) facilitates the subsequent optimization of active compounds.

A multidimensional overpressured layer chromatographic method for the characterization of tetrazine libraries

The recent combinatorial approach in synthetic organic chemistry started a new age in drug discovery. The generation of compound libraries in combination with high-throughput screening has become the method of choice for the production of new pharmacological leads for chemical optimization. Characterization and separation of such pool of compounds have been lagging behind the synthetic and screening methodologies. Overpressured layer chromatography (OPLC) is an instrumentalized planar liquid chromatographic technique associated with the use of optimized layers prepared from particles of narrow particle size distribution and small diameter. On one hand, uni-directional OPLC allows the simultaneous separation of large number of samples in minutes. On the other hand, two-dimensional OPLC offers multidimensional separation on a single layer. This paper shows the complete multidimensional separation of a tetrazine library prepared by parallel combinatorial synthesis. In general, this approach may become the method of choice for the characterization of compound libraries.

Combinatorial Parallel Synthesis of Biologically Active Libraries on Soluble Polymer Supports

AbstractFor Abstract see ChemInform Abstract in Full Text.

Solid‐Supported Reagents and Catalysts for the Preparation of Large Ring Compounds

AbstractFor Abstract see ChemInform Abstract in Full Text.

Solid-supported reagents and catalysts for the preparation of large ring compounds

Parallel combinatorial synthesis in solution using immobilized reagents, catalysts, and scavengers has emerged as a powerful technique for the preparation of diverse libraries of compounds. This technique has only recently been applied to the synthesis of large-ring compounds. In this comprehensive review several strategies are presented and discussed, including Pd-catalyzed allylic alkylation, Stille-coupling, macrolactonization and macrolactamization using solid supported reagents and catalysts. In several cases site isolation has allowed operation, of these macrocyclization reactions in concentrated solution (pseudo-dilution effect).

Parallel Combinatorial Synthesis of Azo Dyes

Parallel Combinatorial Synthesis of Azo Dyes

Parallel Combinatorial Synthesis of Azo Dyes: A Combinatorial Experiment Suitable for Undergraduate Laboratories

A parallel combinatorial synthesis of azo dyes experiment was developed that uses distinct colors to illustrate the concept of diversity and structure–function relationships. This experiment is suitable for undergraduate laboratories and has been used by both chemistry majors and nonmajors undergraduates in Miami University. Azo dyes can be prepared easily in one laboratory period and were chosen to illustrate the concept of diversity oriented synthesis. In the experiment, the positions of the laboratory are divided into a grid. Each student produces a unique azo dye, whose structure is coded according to his or her lab bench position. At the end of the experiment, a multifiber strip is dyed using the student's own synthetic dye. A colorful spectrum of azo dyes are produced collectively by the class.

Synthesis by microwave irradiation of a substituted benzoxazine parallel library with preferential relaxant activity for guinea pig trachealis

An efficient, facile, and practical parallel combinatorial synthesis of substituted-benzoxazines under microwave irradiation was described. The procedure involved the use of a microwave oven especially designed for organic synthesis suitable for parallel synthesis of solution libraries. A demonstration 19-membered library of substituted N,N-dimethyl- and N-methyl-benzoxazine amide derivatives, structurally related to the potassium channel opener cromakalim, was generated by both conventional and microwave procedures, achieving a reduction from 7 h to 30–36 min in library generation time for the microwave approach. All the synthesized compounds were tested using the in vitro models of rat aorta and guinea pig trachea rings pre-contracted with phenylephrine and carbachol, respectively. All N,N-dimethyl amide derivatives showed a relaxant activity higher on guinea pig trachea rings than on rat aorta rings.

Solid-Phase Combinatorial Synthesis of Peptide−Biphenyl Hybrids as Calpain Inhibitors,

[structure: see text] The combinatorial parallel synthesis of peptide-biphenyl hybrids on solid support using state of the art of peptide synthesis is reported. Key steps were the N to C addition of an amino moiety, hydrolysis of the methyl ester, and the absence of cross-linked compounds when the 2,2'-diamino-1,1'-biphenyl was incorporated. When tested for activity as calpain inhibitors, some of the compounds exhibited IC(50) values in the nanomolar range.

Synthesis of Chemiluminescent Esters: A Combinatorial Synthesis Experiment for Organic Chemistry Students

In this laboratory exercise, a peroxyoxalate chemiluminescence experiment has been integrated with a combinatorial synthesis experiment. Students prepare a number of esters, in reactions between acyl chlorides and phenols, and test the compounds for chemiluminescence. If the experiment is parallel combinatorial synthesis, each student prepares one to two esters; if the experiment is mix-and-split combinatorial synthesis, each student prepares two mixtures of esters. Results from the entire class are combined, and based on the results, the students identify general structural features of an active (chemiluminescent) ester. In addition to rubrene, which emits the most intense light, a number of inexpensive fluorophores are suitable for this experiment including chlorophyll and anthracene. The laboratory exercise is suitable for introductory organic chemistry students and can be modified for more advanced students.

Potential protease inhibitors based on a functionalized cyclic sulfamide scaffold.

Exploratory studies related to the design and synthesis of functionalized cyclic sulfamides (I) as potential inhibitors of proteolytic enzymes were carried out. The structural motif and three diversity sites embodied in the scaffold render it amenable to combinatorial parallel synthesis and the facile generation of lead discovery prospecting libraries. The scaffold was readily assembled starting with (DL) serine methyl ester, and a series of compounds was generated and screened against human leukocyte elastase. Modification of the P(1) recognition element, believed to be accommodated at the primary specificity site (S(1) subsite) of the enzyme, yielded compounds that inhibited the enzyme by an apparent hyperbolic partial mixed-type inhibition.

Focused Microwave-Assisted Parallel Synthesis of bis-Benzimidazoles

Combinatorial parallel synthesis of bis-benzimidazoles by focused (mono-modal) microwave irradiation is described. Polymer immobilized o-phenylenediamines as a versatile template was synthesized under microwave irradiation. The resulting PEG bound diamines was N-acylated with 4-fluoro-3-nitrobenzoic acid selectively in primary aromatic amino moiety. Nucleophilic aromatic substitution of the amide obtained was performer with different amines then cyclized to benzimidazole in acidic condition. Successive reduction, cyclization with various aldehydes yielded 5-(benzimidazol-2-yl)benzimidazoles. The desired products were released from the polymer support to afford the tri-substituted bis-benzimidazoles in good yields and purity.

Basic Concepts of “Cation Pool” and “Cation Flow” Methods and Their Applications in Conventional and Combinatorial Organic Synthesis.

AbstractFor Abstract see ChemInform Abstract in Full Text.