Construction and application of a novel library: Fourier transform infrared wavelet coefficients library

This article aims at designing a wavelet alternative to Fourier transform infrared spectra (FTIR). In order to select the most suitable wavelet parameters to perform, several decomposition levels and 53 wavelets were tested by trial and error approach, respectively. The result indicated that discrete meyer wavelet (dmey) associated with its third decomposition level was very efficient for this purpose. On the base of it, a novel library named as Fourier transform infrared wavelet coefficients library (FTIR-WC) has been constructed. Finally, two tools such as library search and structure elucidation were developed to evaluate the capability of the new library system. The results obtained were also compared with those from FTIR library by a variety of indices. The results suggested that the new library performed better but with less volume. This work is expected to propose a novel and practical strategy in infrared spectroscopic analysis.     

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)).     

Rational principles of compound selection for combinatorial library design

It is practically impossible in a short period of time to synthesize and test all compounds in any large exhaustive chemical library. We discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for both targeted and diverse library design. For targeted library design, we consider principles based on the similarity to lead molecules. In the case of diverse library design, we discuss algorithms aimed at the selection of both diverse and representative subsets of the entire chemical library space. We illustrate methodologies with several practical examples.     

Efficient resolution of racemic 1,1'-bi-2-naphthol with chiral selectors identified from a small library

Efficient resolution of racemic 1,1'-bi-2-naphthol, a well-studied analyte in chiral separation, was achieved using selectors developed from a small library. Separation factors (up to 7.2) obtained are significantly higher than the ones reported previously for this analyte. The library consists of 121 members and it does not contain the pi deficient 3,5-dinitrobenzoyl (Dnb) group. These highly efficient stationary phases may lead to the practical large-scale chromatographic resolution of enantiomers of 1,1'-bi-2-naphthol, which are widely used as chiral auxiliaries and ligands in asymmetric synthesis.     

Solution-phase parallel synthesis of a 1,2,7-trialkyl-1H-imidazo[4,5-g]quinoxalin-6-ol library scaffold

This paper describes solution-phase parallel synthesis of a library with a novel 1,2,7-trialky-1H-imidazo[4,5-g]quinoxalin-6-ol scaffold and three points of diversity. The library is prepared using 1,5-difluoro-2,4-dinitrobenzene as the starting material and commercially available chemicals as the building blocks. A new, inexpensive, and practical apparatus for parallel filtration is also described.     

A statistical-based approach to assessing the fidelity of combinatorial libraries encoded with electrophoric molecular tags. Development and application of tag decode-assisted single bead LC/MS analysis

A statistical sampling protocol is described to assess the fidelity of libraries encoded with molecular tags. The methodology, termed library QA, is based on the combined application of tag decode analysis and single bead LC/MS. The physical existence of library compounds eluted from beads is established by comparing the molecular weight predicted by tag decode with empirical measurement. The goal of sampling is to provide information on overall library fidelity and an indication of the performance of individual library synthons. The minimal sampling size n for library QA is l0 x the largest synthon set. Data are reported as proportion (p) +/- lower and upper boundary (lb-ub) computed at the 95% confidence level (alpha = 0.05). As a practical demonstration, library QA was performed on a 25,200-member library of statine amides (size = 40 x 63 x 10). Sampling was conducted three times at n approximately 630 beads per run for a total of 1902 beads. The overall proportions found for the three runs were consistent with one another: p = 84.4%, lb-ub = 81.5-87.2%; p = 83.1%, lb-ub = 80.2-85.95; and p = 84.5%, lb-ub = 81.8-87.3%, suggesting the true value of p is close to 84% compound confirmation. The performance pi of individual synthons was also computed. Corroboration of QA data with biological screening results obtained from assaying the library against cathepsin D and plasmepsin II is discussed.     

组合化学法在筛选真空紫外荧光材料中的应用

综述了近年来组合化学法在筛选新型真空紫外荧光材料研究方面取得的进展, 包括组合材料库的并行合成和高通量表征技术, 并重点介绍了组合材料库的设计艺术, 最后列举了组合化学法筛选真空紫外荧光材料体系研究的实例及结果.     

Practical solid-phase parallel synthesis of Delta(5)-2-oxopiperazines via N-acyliminium ion cyclization

A practical solid-phase strategy for the synthesis of Delta(5)-2-oxopiperazines via N-acyliminium ion cyclization has been developed. A key step in the library synthesis is tandem acidolytic cleavage with subsequent in situ iminium formation, followed by stable enamide transformation. This approach is exemplified by the preparation of a 192-member pilot library using bromoacetal resins without further purification.     

Library design practices for success in lead generation with small molecule libraries

The generation of novel structures amenable to rapid and efficient lead optimization comprises an emerging strategy for success in modern drug discovery. Small molecule libraries of sufficient size and diversity to increase the chances of discovery of novel structures make the high throughput synthesis approach the method of choice for lead generation. Despite an industry trend for smaller, more focused libraries, the need to generate novel lead structures makes larger libraries a necessary strategy. For libraries of a several thousand or more members, solid phase synthesis approaches are the most suitable. While the technology and chemistry necessary for small molecule library synthesis continue to advance, success in lead generation requires rigorous consideration in the library design process to ensure the synthesis of molecules possessing the proper characteristics for subsequent lead optimization. Without proper selection of library templates and building blocks, solid phase synthesis methods often generate molecules which are too heavy, too lipophilic and too complex to be useful for lead optimization. The appropriate filtering of virtual library designs with multiple computational tools allows the generation of information-rich libraries within a drug-like molecular property space. An understanding of the hit-to-lead process provides a practical guide to molecular design characteristics. Examples of leads generated from library approaches also provide a benchmarking of successes as well as aspects for continued development of library design practices.     

Decoding a PNA encoded peptide library by PCR: the discovery of new cell surface receptor ligands

The ability to screen and identify new ligands for cell surface receptors has been a long-standing goal as it might allow targeting of pharmaceutically relevant receptors, such as integrins or G protein coupled receptors. Here, we present a method to amplify hits from a library of PNA-tagged peptides. To this end, human cells, overexpressing either integrins or the CCR6 receptor, were treated with a 10,000 member PNA-encoded peptide library. Extraction of the PNA tags from the surface of the cells was followed by a PNA-tag to DNA translation and amplification enabling decoding of the tags via microarray hybridization. This approach to ligand discovery facilitates screening for differences in surface-receptor ligands and/or receptor expression between different cell types, and opens up a practical approach to PNA-tag amplification.     

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.     

Exploratory Study on the RNA‐Binding Structural Motifs by Library Screening Targeting pre‐miRNA‐29 a

The metabolic stream of microRNA (miRNA) production, the so‐called maturation process of miRNAs, became one of important metabolic paths for drug‐targeting to modulate the expression of genes related to a number of diseases. We carried out discovery studies on small molecules binding to the precursor of miR‐29a (pre‐miR‐29a) from a chemical library containing 41 119 compounds (AQ library) by the fluorescent indicator displacement (FID) assay using the xanthone derivative X2SdiMe as a fluorescent indicator. The FID assay provided 1075 compounds, which showed an increase of fluorescence. These compounds were subsequently submitted to a binding analysis in a surface plasmon resonance (SPR) assay on a pre‐miR‐29a immobilized surface. 21 hit compounds were identified with a good reproducibility in the binding. These compounds have not been reported to bind to RNA until now and can be classified into two groups on the basis of the kinetics in the binding. To gain more information on the motif structures that could be necessary for the binding to pre‐miR‐29a, 19 substructures were selected from the hit compounds. The substructure library (SS library) which consisted of 362 compounds was prepared from the AQ library. An SPR assay of the SS library on pre‐miR‐29a‐immobilized surface suggested that five substructures could potentially be important structural motifs to bind to pre‐miR‐29a. These studies demonstrate that the combination of FID‐based screening of chemical library and subsequent SPR assay would be one way for obtaining practical solutions for the discovery of molecules which bind to the target pre‐miRNAs.     

A novel frequency distribution selection method for efficient plate layout of a diverse combinatorial library.

A deterministic method (frequency distribution method) for selecting compounds from a partitioned virtual combinatorial library for efficient synthesis is presented here. The method is based on reagent frequency analysis and can be applied to any library of molecules distributed in any given partitioned chemical space (cluster, cell-based, etc.). Compound selection by reagent frequency distribution can produce a unique, diverse set of molecules that adequately represents the library while requiring the least amount of compounds to be synthesized and minimizing the number of different reagents that must be used. This method also provides a practical solution to the configuration of plate layout. Because the method essentially identifies "expensive" regions in the chemical space to synthesize for a desired diversity or similarity coverage, decisions concerning the necessity to synthesize these compounds can be addressed. Minimum compound generation and efficient plate layout results in savings both in time of synthesis and cost of materials. This method always results in a discrete solution, which can be used for any given library size as well as any combination of reagents and is also readily adaptable to robotic automation.     

Dynamic combinatorial chemistry

Dynamic combinatorial chemistry is based on the reversible combination of initial building blocks to form dynamic combinatorial libraries. It has recently emerged as an efficient strategy to detect and to evaluate affinity between the library products and a target molecule. In this review, examples from various fields of chemistry and biochemistry are presented and extensively discussed. The last section deals with the practical aspects for implementing this approach.     

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.     

Near-infrared libraries in the pharmaceutical industry: a solution for identity confirmation

The construction of near-infrared spectral libraries as an alternative to qualitative analysis methods for identifying pharmaceutical raw materials is proposed. Various conceptual and practical aspects of library construction are assessed and discussed. The procedure is demonstrated by constructing a library including NIR spectra for 125 different raw materials using the correlation coefficient as the discriminating criterion. Compounds with very similar spectra can be identified by constructing sub-cascading libraries branching off the main one that are developed by using chemometric procedures with higher discriminating ability. The construction of sub-libraries and their performance and discriminating power in three different situations are illustrated. The proposed methodology affords the expeditious unequivocal identification of all the compounds included in a library.     

A solution- and solid-phase approach to tetrahydroquinoline-derived polycyclics having a 10-membered ring

With the goal of library generation using a polycyclic derivative 5 having an enamide functional group, a simple and practical, enantioselective synthesis of tetrahydroquinoline derivative 2 was achieved. The phenolic hydroxyl group in compound 2 was utilized as an anchoring site for solid-phase synthesis. The ring closing metathesis approach yielded the desired polycyclic product 5 on solid phase in five steps (overall 40% yield). Compound 5 is a novel scaffold for the library generation of natural product-like polycyclics having a functionalized medium ring for obtaining a new class of small molecules to be utilized as chemical probes.     

Focused combinatorial library design based on structural diversity, druglikeness and binding affinity score

The advent of focused library and virtual screening has reduced the disadvantage of combinatorial chemistry and changed it to a realizable and cost-effective tool in drug discovery. Usually, genetic algorithms (GAs) are used to quickly finding high-scoring molecules by sampling a small subset of the total combinatorial space. Therefore, scoring functions play essential roles in focused library design. Reported here is our initial attempt to establish a new approach for generating a target-focused library using the combination of the scores of structural diversity and binding affinity with our newly improved drug-likeness scoring functions. Meanwhile, a software package, named LD1.0, was developed on the basis of the new approach. One test on a cyclooxygenase (COX)2-focused library successfully reproduced the structures that have been experimentally studied as COX2-selective inhibitors. Another test is on a peroxisome proliferator-activated receptors gamma-focused library design, which not only reproduces the key fragments in the approved (thiazolidinedione) TZD drugs, but also generates some new structures that are more active than the approved drugs or published ligands. Both of the two tests took approximately 15% of the running time of the ordinary molecular docking method. Thus, our new approach is an effective, reliable, and practical way for building up a properly sized focused library with a high hit rate, novel structure, and good ADME/T profile.     

Rapid analysis of flavonoids based on spectral library development in positive ionization mode using LC-HR-ESI-MS/MS

Natural product screening in plants has always been a difficult task due to the complex nature of the plant material and diverse structures of the compounds present in them. Flavonoids are important and diverse class of plant secondary metabolites with numerous medicinal activities. The present study focuses on the development of a high-resolution tandem mass spectral library for the rapid and authentic identification of common flavonoids. A total of forty flavonoid standards belong to class flavones, isoflavones, flavanones, flavanols and anthocyanins were pooled into two solutions applying logP-based strategy. The flavonoids were analyzed using LC-QTOF-MS high-resolution mass spectrometer with optimization of different instrumental parameters to achieve good sensitivity. The library was built by incorporating names, molecular formulae, exact masses, and MS, and MS/MS spectra of analyzed flavonoids using Bruker Library Editor tool. The fragmentation pattern observed for the standard compounds were compared to the fragments reported in the literature. To assess the practical implications, an extract of tea sample was analyzed and screened using the developed library, which resulted in the identification of three common flavonoids based on their HR-ESI-MS/MS spectral features. The established LC-HR-MS/MS method can be used for the targeted identification of flavonoids in complex samples like food material from different botanical families.