Synthesis Of Combinatorial Libraries Research Articles

Novel aqueous one-pot RAFT process for the rapid and combinatorial synthesis of complex star polymer biomaterial libraries

Novel aqueous one-pot RAFT process for the rapid and combinatorial synthesis of complex star polymer biomaterial libraries

Price-Focused Analysis of Commercially Available Building Blocks for Combinatorial Library Synthesis.

Combinatorial libraries are synthesized by combining smaller reagents (building blocks), the price of which is an important component of the total costs associated with the synthetic exercise. A significant portion of commercially available reagents are too expensive for large scale work. In this study, 13 commonly used reagent classes in combinatorial library synthesis (primary and secondary amines, carboxylic acids, alcohols, ketones, aldehydes, boronic acids, acyl halides, sulfonyl chlorides, isocyanates, isothiocyanates, azides and chloroformates) were analyzed with respect to the cost, physicochemical properties (molecular weight and calculated logP), chemical diversity, and 3D-likeness using a large data set. The results define the chemical space accessible under a constraint of limited financial resources.

A Robust and Versatile Method of Combinatorial Chemical Synthesis of Gene Libraries via Hierarchical Assembly of Partially Randomized Modules.

A major challenge in gene library generation is to guarantee a large functional size and diversity that significantly increases the chances of selecting different functional protein variants. The use of trinucleotides mixtures for controlled randomization results in superior library diversity and offers the ability to specify the type and distribution of the amino acids at each position. Here we describe the generation of a high diversity gene library using tHisF of the hyperthermophile Thermotoga maritima as a scaffold. Combining various rational criteria with contingency, we targeted 26 selected codons of the thisF gene sequence for randomization at a controlled level. We have developed a novel method of creating full-length gene libraries by combinatorial assembly of smaller sub-libraries. Full-length libraries of high diversity can easily be assembled on demand from smaller and much less diverse sub-libraries, which circumvent the notoriously troublesome long-term archivation and repeated proliferation of high diversity ensembles of phages or plasmids. We developed a generally applicable software tool for sequence analysis of mutated gene sequences that provides efficient assistance for analysis of library diversity. Finally, practical utility of the library was demonstrated in principle by assessment of the conformational stability of library members and isolating protein variants with HisF activity from it. Our approach integrates a number of features of nucleic acids synthetic chemistry, biochemistry and molecular genetics to a coherent, flexible and robust method of combinatorial gene synthesis.

ChemInform Abstract: Total Synthesis of (+)‐Antimycin A3b on Solid Supports.

A straightforward and convergent total synthesis of (+)-antimycin A3b is reported. Four fragments were assembled on a solid support and the fully functionalized seco acid was cyclized in the solution phase. This synthetic route minimized the number of manipulations in the solution phase and is useful for a combinatorial library synthesis.

Zinc Chloride Catalyzed Regioselective Nitration of Aromatic Hydrocarbons Using Tetrachlorosilane-Sodium Nitrate Homogeneous System

The development of a new silane reagent derived from tetrachlorosilane (TCS) was applied in the present work. TCS-sodium nitrate (NaNO3) binary reagent and zinc chloride (ZnCl2) were reported here as a homogeneous nitrating system. The later was used for the efficient mono nitration, in most cases, with high para-regioselectivity. The nitration proceeded smoothly under mild condition, fairly clean and in good yields. This readily available and inexpensive system is superior to other methods by avoidance of the use of corrosive nitrating reagents and therefore considered to be convenient in terms of risk reduction, economic advantages and environment protection. The present protocol was convenient and applicable to a variety of aromatic hydrocarbons and could be amenable to high throughput synthesis of combinatorial libraries for potential drug development, which needs to be studied as part of future investigations.

Pseudo-five-component domino strategy for the combinatorial library synthesis of [1,6] naphthyridines-an on-water approach.

This work features the base-promoted on-water synthesis of [1,6]-naphthyridines from methyl ketones, malononitrile and phenols or thiols. The reaction conditions were carefully tuned to drive the product selectivity from 3H-pyrroles to [1,6]-naphthyridines. The advantages of this method lie in its simplicity, cost effectiveness, and environmental friendliness, representing a new effort toward the on-water synthesis of [1,6]-naphthyridines without starting from a nitrogen-containing heterocycle and highlighting the versatility of the nitrile functional group.

Assessing the combinatorial potential of the RiPP cyanobactin tru pathway.

Ribosomally produced natural products, the RiPPs, exhibit features that are potentially useful in the creation of large chemical libraries using simple mutagenesis. RiPPs are encoded on ribosomal precursor peptides, but they are extensively posttranslationally modified, endowing them with properties that are useful in drug discovery and biotechnology. In order to determine which mutations are acceptable, strategies are required to determine sequence selectivity independently of the context of flanking amino acids. Here, we examined the absolute sequence selectivity of the trunkamide cyanobactin pathway, tru. A series of random double and quadruple simultaneous mutants were synthesized and produced in Escherichia coli. Out of a total of 763 mutated amino acids examined in 325 unique sequences, 323 amino acids were successfully incorporated in 159 sequences, leading to >300 new compounds. Rules for tru sequence selectivity were determined, which will be useful for the design and synthesis of combinatorial biosynthetic libraries. The results are also interpreted in comparison to the known natural products of tru and pat cyanobactin pathways.

Total Synthesis of (+)‐Antimycin A3b on Solid Supports

A straightforward and convergent total synthesis of (+)-antimycin A3b is reported. Four fragments were assembled on a solid support and the fully functionalized seco acid was cyclized in the solution phase. This synthetic route minimized the number of manipulations in the solution phase and is useful for a combinatorial library synthesis.

Current perspectives on applications of shikimic and aminoshikimic acids in pharmaceutical chemistry

Current perspectives on applications of shikimic and aminoshikimic acids in pharmaceutical chemistry Dulce Catalina Díaz Quiroz, Susy Beatriz Carmona, Francisco Bolívar, Adelfo Escalante Department of Cellular Engineering and Biocatalysis, Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México Abstract: Aromatic metabolism comprises the shikimic acid (SA) and the aminoshikimic acid (ASA) pathways. The SA pathway is the common route for the biosynthesis of aromatic amino acids and other metabolites in bacteria, higher plants, fungi, and Apicomplexa parasites, but this pathway is absent in mammals. A variant of the SA pathway known as the ASA pathway branches off from the normal pathway in some bacteria, and its final product, 3-amino-5-hydroxybenzoic acid, is the precursor for many aminoglycoside antibiotics such as kanamycin, neomycin, butirosin, and spectinomycin. The SA pathway includes the key intermediate SA, which is the precursor for the chemical synthesis of the drug oseltamivir phosphate, known commercially as Tamiflu®, an efficient inhibitor of the neuraminidase enzyme of the seasonal influenza viruses types A and B, avian influenza virus H5N1, and human influenza virus H1N1. Meanwhile, the intermediate of the ASA pathway, ASA, is an attractive candidate for use as the core scaffold for the synthesis of combinatorial libraries and is a potential alternative to SA as a precursor for oseltamivir phosphate synthesis. In this review, we discuss the relevance of the key intermediates SA and ASA as scaffold molecules for the synthesis of diverse chemicals. We highlight the current and potential pharmaceutical applications of these molecules and discuss the main strategies for the production of these aromatic compounds from natural sources and the application of metabolic engineering strategies in diverse bacterial strains for production through biotechnological processes. Keywords: aromatic metabolism, shikimic acid, aminoshikimic acid, oseltamivir phosphate, medical applications, metabolic engineering

Three-Component Synthesis of 4-Aroyl-2(1),4,5,7-Tetrahydropyrazolo[3,4-b]Pyridin-6-Ones and Their Properties

Inspired by the concept of multicomponent reactions, a novel one-pot synthesis involving arylglyoxals, 5-aminopyrazoles, and Meldrum's acid has been developed and employed for the creation of a small library of 4-aroyl-2(1),4,5,7-tetrahydropyrazolo- (3,4-b)pyridin-6-ones. The alkylation, acylation, reduction, and oxidation reactions of 4-aroyl-3-methyl-2,4,5,7-tetrahydropyrazolo(3,4-b)pyridin-6-ones have been studied. In last two decades the multicomponent reactions (MCRs) have been recognized as a highly powerful synthetic strategy for the combinatorial synthesis of compound libraries and have received significant attention (1-6). A central issue in MCRs research is the synthesis of nitrogen heterocycles, since this group of organic compounds holds a special place among pharmaceutically and agro- chemically important natural and synthetic products. Pyrazolopyridines among different azoloazines have received more attention as one of the "privileged medicinal scaffolds" which are used for the development of new drug candidates of various applications. Numerous methods for the synthesis of systems incorporating a pyrazolopyridine moiety have been reported with respect to their different structures (7-17). In the past several years, we and others have developed various MCRs based on interaction Meldrum's acid or its derivatives with carbonyl compounds and different nitrogen-containing 1,3-binucleophiles that can provide facile route to partially hydrogenated fused heterocyclic systems for chemical and biomedical purposes, some natural alkaloids and their analogs (4-6, 17, 18). For example, three-component reactions of 5-aminopyrazoles with aromatic, heterocyclic, or some aliphatic aldehydes and Meldrum's acid were shown to provide facile access to 4-aryl-4,5,6,7-tetrahydropyrazolo(3,4-b)pyridin-6-ones (17, 19-22). Unfortu- nately, there are only two reaction centers suitable for further chemical modification in their structure (21). For this reason, the introduction of a new chemically active group, such as carbonyl moiety, in tetrahydropyrazolo(3,4-b)- pyridin-6-one scaffold is a prioritary synthetic task for us. We have selected arylglyoxals as possible building blocks to be used in MCR with 5-aminopyrazoles and Meldrum's acid. They would be able to provide an additional carbonyl group in target heterocycles. These 1,2-dicarbonyl compounds are widely used in the design of different heterocycles (23). Nevertheless, in scientific literature there are no publications concerning one-pot synthesis of tetrahydropyrazolo(3,4-b)pyridin- 6-one derivatives on the base of glyoxals, 5-aminopyrazoles, and Meldrum's acid.

Total Synthesis of (+)‐Antimycin A3b on Solid Supports

AbstractA straightforward and convergent total synthesis of (+)‐antimycin A3b is reported. Four fragments were assembled on a solid support and the fully functionalized seco acid was cyclized in the solution phase. This synthetic route minimized the number of manipulations in the solution phase and is useful for a combinatorial library synthesis.

Liquid-Phase Combinatorial Library Synthesis: Recent Advances and Future Perspectives

Liquid-phase combinatorial library synthesis is commonly developed into the viable alternatives or adjunct across the broad spectrum of polymer-supported organic chemistry. It includes the use of soluble polymer supports in the combinatorial synthesis of peptides and small-molecular library compounds which act as catalyst and reagent supports. It also includes high throughput biological screening with generation and evaluation of chemical leads for drug discovery development. In this review, liquid-phase combinatorial library synthesis is shown as the most efficient method of choice for the synthesis of most of the combinatorial library compounds with specific approaches from different groups that state potentials of solution-phase combinatorial synthesis.

Ligand engineering using yeast surface display.

The genotype-phenotype linkage provided by display technologies enables efficient synthesis, analysis, and selection of combinatorial protein libraries. This approach tremendously expands the protein sequence space that can be efficiently evaluated for a selectable function. It thereby provides a key element in identification and directed evolution of novel or improved protein function. Here, yeast surface display is described in the context of selection for binding function. Yeast culture and multiple approaches to magnetic- and fluorescence-based protein selection are presented in detail.

Reversible Cyclic Peptide Libraries for the Discovery of Affinity Ligands

A novel strategy is presented for the identification of cyclic peptide ligands from combinatorial libraries of reversible cyclic depsipeptides. A method for the solid-phase synthesis of individual cyclic depsipeptides and combinatorial libraries of these compounds is proposed, which employs lactic acid (Lact) and the dipeptide ester (Nα-Ac)-Ser(Ala)- as linkers for dilactonization. Upon alkaline treatment of the beads selected by screening a model library, the cyclic depsipeptides are linearized and released from the solid support to the liquid phase, to be sequenced via single-step tandem mass spectrometry (MS/MS). The protocol presented for library synthesis provides for wide structural diversity. Two model sequences, VVWVVK and AAWAAR, were chosen to present different structural examples for depsipeptide libraries and demonstrate the process of sequence determination by mass spectrometry. Further, a case study using the IgG binding cyclic depsipeptide cyclo[(Nα-Ac)-S(A)-RWHYFK-Lact-E] is presented to demonstrate the process of library screening and sequence determination on the selected beads. Finally, a method is shown for synthesis of the irreversible cyclic peptide corresponding to the proposed depsipeptide structure, to make the ligand stable to the aqueous acid and alkaline conditions encountered in affinity chromatographic applications. The cyclic peptide ligand was synthesized on a poly(methacrylate) resin and used for chromatographic binding of the target IgG.

ChemInform Abstract: Nitrogen‐Containing Privileged Structures and Their Solid‐Phase Combinatorial Synthesis

AbstractReview: 240 refs.

Synthesis of Small Combinatorial Libraries of Natural Products: Identification and Quantification of New Long‐chain 3‐Methyl‐2‐alkanones from the Root Essential Oil of Inula helenium L. (Asteraceae)

Recently, a potent anti-staphylococcal activity of Inula helenium L. (Asteraceae) root essential oil was reported. Also, bioassay guided fractionation of the oil pointed to eudesmane sesquiterpene lactones and a series of unidentified constituents as the main carriers of the observed activity. To identify nine new constituents (long-chain 3-methyl-2-alkanones) from a fraction of this root essential oil with a low minimum inhibitory concentration value (0.8 µg/mL) by employing a synthetic methodology that leads to the formation of a small combinatorial library of these compounds. The identity of these constituents was inferred from mass spectral fragmentation patterns and GC retention data. A library of 3-methyl-2-alkanones (C11 -C19 homologous series) was synthesised in three steps starting from methyl acetoacetate and the corresponding alkyl halides. The synthetic library was also screened for in vitro anti-microbial activity. Gas chromatographic analyses of I. helenium essential oil samples with spiked compounds from the synthesised library corroborated the tentative identifications of the long-chain 3-methyl-2-alkanones. The availability of these anti-microbial compounds from this library made it possible to construct GC/FID calibration curves and determine their content in the plant material: 0.08 - 24.2 mg/100 g of dry roots. The small combinatorial library approach enabled the first unequivocal identification of long-chain 3-methyl-2-alkanones as plant secondary metabolites, and, also, allowed determination of not only a single compound and biological properties, but those of a group of structurally related compounds.

Screening bicyclic peptide libraries for protein-protein interaction inhibitors: discovery of a tumor necrosis factor-α antagonist.

Protein-protein interactions represent a new class of exciting but challenging drug targets, because their large, flat binding sites lack well-defined pockets for small molecules to bind. We report here a methodology for chemical synthesis and screening of large combinatorial libraries of bicyclic peptides displayed on rigid small-molecule scaffolds. With planar trimesic acid as the scaffold, the resulting bicyclic peptides are effective for binding to protein surfaces such as the interfaces of protein-protein interactions. Screening of a bicyclic peptide library against tumor necrosis factor-α (TNFα) identified a potent antagonist that inhibits the TNFα-TNFα receptor interaction and protects cells from TNFα-induced cell death. Bicyclic peptides of this type may provide a general solution for inhibition of protein-protein interactions.

Combinatorial synthesis of alloy libraries with a progressive composition gradient using laser engineered net shaping (LENS): Hydrogen storage alloys

The laser engineered net shaping technique was applied as a fast synthesis method for preparing libraries of binary and ternary alloys. Compositional gradient libraries of Fe–Ti alloys and four different FeTiNi samples were fabricated from elemental powders. A continuous gradient sample and discrete gradient samples (25 and 188 samples) were deposited. Ternary alloys were prepared from pre-blended powder mixtures. Chemical composition measurements showed that samples of different compositions can be synthesized. XRD phase analysis indicated that structures close to equilibrium or occasionally quenched are obtained after the process. The microstructure of the prepared samples was analyzed. The hydrogen storage properties of the selected samples were investigated. After laser deposition, the samples were found to absorb significant quantities of hydrogen with just a simple activation. The method was determined to be very useful for discovering new ternary and multicomponent alloys for hydrogen storage.

Nitrogen Containing Privileged Structures and their Solid Phase Combinatorial Synthesis

The existence of preferred molecular scaffolds that possess inherent biological activity, called privileged structures, is now well recognized. Such privileged structures not only provide enhanced drug-like properties but also give new hits for developing leads. The synthesis of combinatorial libraries, especially with the insertion of privileged substructures into heterocyclic moieties containing nitrogen, provides for a greater probability of the discovery of novel lead compounds using chemical transformation. The review focuses on the progress in the solid-phase synthetic strategies of nitrogen containing privileged structures over the years.

Discovery of 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides as potent agonists of TGR5 via sequential combinatorial libraries

Optimization of a high-throughput screening hit led to the discovery of a new series of 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides as highly potent agonists of TGR5. This novel chemotype was rapidly developed through iterative combinatorial library synthesis. It was determined that in vitro agonist potency correlated with functional activity data from human peripheral blood monocytes.