Combinatorial Biomimetic Chemistry: Parallel Synthesis of a Small Library of β‐Hairpin Mimetics Based on Loop III from Human Platelet‐Derived Growth Factor B

Combinatorial diversity in hypervariable β‐hairpin loops is exploited by the immune system to select binding sites on antibodies for a wide variety of different protein antigens. In a first step towards mimicking this strategy in vitro, for the selection of novel protein ligands, an approach is described here for the parallel synthesis of small libraries of conformationally defined β‐hairpin protein epitope mimetics. Starting from a protruding hairpin loop in platelet‐derived growth factor B (PDGF‐B), 8 and 12 residues were first transplanted from the protein to a D ‐Pro‐L ‐Pro template, to afford the cyclic peptide‐loop mimetics 1 and 2 , respectively. NMR and MD studies in aqueous solution show that both mimetics populate conformations which closely mimic the β‐hairpin in the crystal structure of the native protein (Fig. 5). Based on 1 as a scaffold, a library of 24 mimetics was synthesized in which the four residues at the tip of the loop (VRKK) were held constant, and flanking residues at positions 1, 2, 7, and 8 in the hairpin were varied (Fig. 7). The library was prepared by parallel synthesis in a two‐stage solid‐phase assembly/solution‐phase cyclization process. The products were analyzed by MS, NMR, and CD. 2D‐NOESY revealed for most library members characteristic long‐range NOEs that show that the hairpin conformation is stably maintained. The results suggest that this approach may be useful for the synthesis of much larger libraries of peptide and protein mimetics based on a β‐hairpin scaffold.     

Screening of Three Transition Metal‐Mediated Reactions Compatible with DNA‐Encoded Chemical Libraries

The construction of DNA‐encoded chemical libraries (DECLs) crucially relies on the availability of chemical reactions, which are DNA‐compatible and which exhibit high conversion rates for a large number of diverse substrates. In this work, we present our optimization and validation procedures for three copper and palladium‐catalyzed reactions (Suzuki cross‐coupling, Sonogashira cross‐coupling, and copper(I)‐catalyzed alkyne‐azide cycloaddition (CuAAC)), which have been successfully used by our group for the construction of large encoded libraries.     

LC‐MS analysis for the components captured by ECV304 cell from extract of Aconitum szechenyianum Gay.

A novel method of cell affinity screening (CAS), cell affinity capture coupled with LC‐MS analysis, was developed for screening the bioactive compounds related to cardiovascular diseases from the natural product libraries. One of the major characteristics lies in its function in affinity‐capturing and separating the bioactive components from the natural product libraries in vitro. Another characteristic is its use in analyzing and identifying the target compounds, by employing high‐performance liquid chromatography and mass spectrometry. CAS was used for screening the bioactive components from the alkaloid extract derived from Aconitum szechenyianum Gay. Of the five components found to be bound to the oxidative‐damaged endothelial cells, the two compounds identified, mesaconitine and aconitine, were recognized in the literature as being related to cardiovascular diseases. Copyright © 2008 John Wiley & Sons, Ltd.     

A Genetically Encoded,Phage‐Displayed Cyclic‐Peptide Library

Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic‐peptide ligands for therapeutic targets, phage‐displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage‐display technique in which its displayed peptides are cyclized through a proximity‐driven Michael addition reaction between a cysteine and an amber‐codon‐encoded N^?‐acryloyl‐lysine (AcrK). Using a randomized 6‐mer library in which peptides were cyclized at two ends through a cysteine–AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4‐ to 6‐fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.     

A Genetically Encoded,Phage‐Displayed Cyclic‐Peptide Library

Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic‐peptide ligands for therapeutic targets, phage‐displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage‐display technique in which its displayed peptides are cyclized through a proximity‐driven Michael addition reaction between a cysteine and an amber‐codon‐encoded N^?‐acryloyl‐lysine (AcrK). Using a randomized 6‐mer library in which peptides were cyclized at two ends through a cysteine–AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4‐ to 6‐fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.     

Liquid‐phase synthesis of mixture‐based bicyclic β‐lactam libraries

Five sets of 27‐membered combinatorial libraries of alicyclic β‐lactams were prepared via liquid‐phase Ugi 4‐center 3‐component reactions (U‐4C‐3CR) utilizing 3 different cis β‐amino acids, 3 different isonitriles and 5×3 sets of aldehydes. Through combinations of the building blocks of one of these libraries, all of the possible sublibraries were also generated. A few azetidinone derivatives were synthesized individually by parallel synthesis.     

A Gold‐Catalyzed Domino Cyclization Enabling Rapid Construction of Diverse Polyheterocyclic Frameworks

We report herein an efficient gold(I)‐catalyzed post‐Ugi domino dearomatization/ipso‐cyclization/Michael sequence that enables access to libraries of diverse (hetero)arene‐annulated tricyclic heterocycles. This process affords novel complex polycyclic scaffolds in moderate to good yields from readily available acyclic precursors with excellent chemo‐, regio‐, and diastereoselectivity. The power of this strategy has been demonstrated by the rapid synthesis of 40 highly functionalized polyheterocycles bearing indole, pyrrole, (benzo)furan, (benzo)thiophene, pyrazole, and electron‐rich arene groups in two operational steps.     

Formation of 1,3‐Thiazol‐5(4H)‐imines and 1,3‐Oxazol‐5(4H)‐imines in Aib‐Containing Thiopeptides

When tripeptides of type Axx^t‐Aib‐Axx‐OH were coupled with amino acid methyl esters by means of commonly used coupling reagents, the formation of 1,3‐thiazol‐5(4H)‐imines and 1,3‐oxazol‐5(4H)‐imines was observed. With the aim of understanding which structure elements are required for this reaction, several model peptides have been prepared according to our recently described methodology, a modification of the ‘azirine/oxazolone method', followed by selective isomerization of the peptide thioamides. In addition, attempts to prepare peptides that contain more than one C=S group by the same methodology also led to the formation of 1,3‐thiazol‐5(4H)‐imine‐containing derivatives. An additional C=S group can be introduced into the peptide, when the 1,3‐thiazol‐5(4H)‐imines were treated with H₂S, although mixtures of epimers were obtained. The structures of an endothiohexapeptide, two 1,3‐thiazol‐5(4H)‐ones, and two peptides containing a 1,3‐thiazol‐5(4H)‐imine moiety have been established by X‐ray crystal‐structure analysis.     

Identification of avocado (Persea americana) pulp proteins by nano‐LC‐MS/MS via combinatorial peptide ligand libraries

Avocado (Persea americana) proteins have been scarcely studied despite their importance, especially in food related allergies. The proteome of avocado pulp was explored in depth by extracting proteins with capture by combinatorial peptide ligand libraries at pH 7.4 and under conditions mimicking reverse‐phase capture at pH 2.2. The total number of unique gene products identified amounts to 1012 proteins, of which 174 are in common with the control, untreated sample, 190 are present only in the control and 648 represent the new species detected via combinatorial peptide ligand libraries of all combined eluates and likely represent low‐abundance proteins. Among the 1012 proteins, it was possible to identify the already known avocado allergen Pers a 1 and different proteins susceptible to be allergens such as a profilin, a polygalacturonase, a thaumatin‐like protein, a glucanase, and an isoflavone reductase like protein.     

Expressed Sequence Tag Analysis of the Dinoflagellate Lingulodinium polyedrum During Dark Phase¶

To collect information on gene expression during the dark period in the luminous dinoflagellate Lingulodinium polyedrum, normalized complementary DNA (cDNA) libraries were constructed from cells collected during the first hour of night phase in a 12:12 h light‐dark cycle. A total of 4324 5′‐end sequence tags were isolated. The sequences were grouped into 2111 independent expressed sequence tags (EST) from which 433 groups were established by similarity searches of the public nonredundant protein database. Homology analysis of the total sequences indicated that the luminous dinoflagellate is more similar to land plants and animals (vertebrates and invertebrates) than to prokaryotes or algae. We also isolated three bioluminescence‐related (luciferase and two luciferinbinding proteins [LBP]) and 37 photosynthesis‐related genes. Interestingly, two kinds of LBP genes occur in multiple copies in the genome, in contrast to the single luciferase gene. These cDNA clones and EST sequence data should provide a powerful resource for future genome‐wide functional analyses for uncharacterized genes.     

A Practical,Water‐Soluble,Ionic Scavenger for the Solution‐Phase Syntheses of Amides

A new ionic, water‐soluble scavenger for acyl chlorides, 1‐(2‐aminoethyl)pyridinium bromide ( 1 ), has been investigated. Compound 1 was used for the rapid and simple purification of a series of benzamides and sulfonamides (Table) obtained by solution‐phase synthesis from the corresponding amines (Scheme). The inexpensive scavenger, which can be prepared on large scale, was shown to readily ‘eliminate’ excess acyl chlorides (reagent) by simple aqueous extraction. The amides purified in this way were obtained in excellent yields and purities (Table), which makes 1 a versatile new reagent, especially for the combinatorial solution‐phase synthesis of amide libraries.     

Leader Peptide‐Free In Vitro Reconstitution of Microviridin Biosynthesis Enables Design of Synthetic Protease‐Targeted Libraries

Microviridins are a family of ribosomally synthesized and post‐translationally modified peptides with a highly unusual architecture featuring non‐canonical lactone as well as lactam rings. Individual variants specifically inhibit different types of serine proteases. Here we have established an efficient in vitro reconstitution approach based on two ATP‐grasp ligases that were constitutively activated using covalently attached leader peptides and a GNAT‐type N‐acetyltransferase. The method facilitates the efficient in vitro one‐pot transformation of microviridin core peptides to mature microviridins. The engineering potential of the chemo‐enzymatic technology was demonstrated for two synthetic peptide libraries that were used to screen and optimize microviridin variants targeting the serine proteases trypsin and subtilisin. Successive analysis of intermediates revealed distinct structure–activity relationships for respective target proteases.     

Towards a full reference library of MSn spectra. II: A perspective from the library of pesticide spectra extracted from the literature/Internet

To gain perspective on building full transferable libraries of MSⁿ spectra from their diverse/numerous collections, a new library was built from 1723 MS^>1 spectra (mainly MS² spectra) of 490 pesticides and related compounds. Spectra acquired on different types of tandem instruments in various experimental conditions were extracted from 168 literature articles and Internet sites. Testing of the library was based on searches where 'unknown' and reference spectra originated from different sources (mainly from different laboratories) were cross‐compared. The NIST 05 MS² library was added to the reference spectra. The library searches were performed with all the test spectra or were divided into different subsamples containing (a) various numbers of replicate spectra of test compounds or (b) spectra acquired from different instrument types. Thus, the dependence of true/false search (identification) result rates on different factors was explored. The percentage of 1^st rank correct identifications (true positives) for the only 'unknown' mass spectrum and two and more reference spectra and matching precursor ion m/z values was 89%. For qualified matches, above the cut‐off match factor, that rate decreased to 80%. The corresponding rates based on the best match for two and more 'unknown' and reference spectral replicates were 89–94%. For quadrupole instruments, the rates were even higher: 91–95% (one 'unknown' spectrum) and 90–100% (two and more such spectra). This study shows that MS² spectral libraries generated from the numerous literature/Internet sources are not less efficient for the goal of identification of unknown compounds including pesticides than very common EI‐MS¹ libraries and are almost as efficient as the most productive from current MS² spectral databases. Such libraries may be used as individual reference databases or supplements to large experimental spectral collections covering many groups of abundant compounds and different types of tandem mass spectrometers. Copyright © 2011 John Wiley & Sons, Ltd.     

Nanomolar Inhibitors for Two Distinct Biological Target Families from a Single Synthetic Sequence: A Next Step in Combinatorial Library Design?

One common synthetic route creates small-molecule libraries directed toward two functionally distinct target families. The novel structural template 1 can independently display the necessary pharmacophore patterns for inhibition of members of two different biomolecular target families, the matrix metalloproteinases (MMPs) or the phosphodiesterases (PDEs). The incorporation of multiple target family directed design elements into combinatorial library design could help expedite the pharmaceutical lead discovery process. Z=OR′ (PDE4), H (MMPs).     

Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N‐formyl‐L‐valinamide and N‐formyl‐L‐phenylalaninamide

Employing introductory (3‐21G RHF) and medium‐size (6‐311++G** B3LYP) ab initio calculations, complete conformational libraries, containing as many as 27 conformers, have been determined for diamide model systems incorporating the amino acids valine (Val) and phenylalanine (Phe). Conformational and energetic properties of these libraries were analyzed. For example, significant correlation was found between relative energies from 6‐311++G** B3LYP and single‐point B3LYP/6‐311++G**//RHF/3‐21G calculations. Comparison of populations of molecular conformations of hydrophobic aromatic and nonaromatic residues, based on their ab initiorelative energies, with their natural abundance indicates that, at least for the hydrophobic core of proteins, the conformations of Val (Ile, Leu) and Phe (Tyr, Trp) are controlled by the local energetic preferences of the respective amino acids. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 732–751, 2001     

Electric‐Field Triggered Controlled Release of Bioactive Volatiles from Imine‐Based Liquid Crystalline Phases

Application of an electric field to liquid crystalline film forming imines with negative dielectric anisotropy, such as N‐(4‐methoxybenzylidene)‐4‐butylaniline (MBBA, 1 ), results in the expulsion of compounds that do not participate in the formation of the liquid crystalline phase. Furthermore, amines and aromatic aldehydes undergo component exchange with the imine by generating constitutional dynamic libraries. The strength of the electric field and the duration of its application to the liquid crystalline film influence the release rate of the expelled compounds and, at the same time, modulate the equilibration of the dynamic libraries. The controlled release of volatile organic molecules with different chemical functionalities from the film was quantified by dynamic headspace analysis. In all cases, higher headspace concentrations were detected in the presence of an electric field. These results point to the possibility of using imine‐based liquid crystalline films to build devices for the controlled release of a broad variety of bioactive volatiles as a direct response to an external electric signal.     

Synthesis of 7,8‐Dihydrothieno[3′,2′:4,5]pyrrolo[1,2‐a]pyrazin‐5(6H)‐ones Using a Modification of Four‐Component Ugi Reaction

We describe an efficient synthesis of novel 7,8‐dihydrothieno [3′,2′:4,5]pyrrolo[1,2‐a]pyrazin‐5(6H)‐one heterocyclic structures. The target compounds were prepared by a novel modification of four‐component Ugi reaction of heterocyclic bifunctional keto acids, isonitriles, and amines. We demonstrate the usefulness and versatility of the developed approach, which is amenable to production of combinatorial libraries.     

Solid‐Phase Synthesis of a 1‐Thio‐β‐d‐GlcNAc Carbohydrate Mimetic Library

The solid phase synthesis of N‐acetyl‐2‐deoxy‐1‐thio‐β‐d‐glucopyranoside derivatives by reacting an immobilized sugar thiol with Michael acceptors and α‐chloroketones, followed by ketone reductions, reductive aminations, acylations and alkylations was developed to yield a library of 1088 compounds. Such carbohydrate mimetic libraries are synthesized efficiently on the solid phase without the need for protection of the sugar hydroxyl groups. The library was designed for the identification of potential inhibitors of β‐d‐GlcNAc binding proteins.