Solid-phase synthesis of dysidiolide-derived protein phosphatase inhibitors

Biologically active natural products can be regarded as evolutionary selected and biologically validated starting points in structural space for the development of compound libraries. For libraries designed and synthesized around a given natural product, a higher hit rate and the identification of biologically relevant hits can be expected, justifying a probably higher investment in the development of the corresponding syntheses. This approach requires the development of complex multistep reaction sequences on the solid phase. Employing the protein phosphatase Cdc25 inhibitor dysidiolide as an example, we demonstrate that this goal can be achieved successfully. The reaction sequences developed led to dysidiolide analogues in overall 8-12 linear steps with the longest sequence on the solid support amounting to up to 11 sequential transformations. The desired products were obtained in overall yields ranging from 6% to 27% and in multimilligram amounts starting from 100 mg of resin. The transformations applied include a variety of very different reaction types widely used in organic synthesis (i.e., an asymmetric cycloaddition employing a removable chiral auxiliary, different organometallic transformations, olefination reactions, different oxidation reactions, acidic hydrolyses, and a nucleophilic substitution). Biological investigation of the eight dysidiolide analogues synthesized showed that they inhibit Cdc25C in the low micromolar range with the IC(50) value varying by a factor of 20 and that they display considerable and differing biological activities in cytotoxicity assays employing different cancer cell lines.     

Biology‐Oriented Combined Solid‐ and Solution‐Phase Synthesis of a Macroline‐Like Compound Collection

Macrolines constitute a class of natural products that has more than 100 members and displays diverse biological activities. These compounds feature a cycloocta[b]indole scaffold that represents an interesting target structure for biology‐oriented synthesis (BIOS). We have presented a solid‐phase synthesis of isomerically pure cycloocta[b]indoles by employing the Pictet–Spengler reaction and the Dieckmann cyclization as key steps. The scope of this reaction sequence was investigated in more detail by using various additional diversification procedures, such as Pd‐catalyzed Sonogashira or Suzuki couplings on a solid phase, thus allowing, for example, the generation of 10‐substituted cycloocta[b]indole derivatives. Finally, solution‐phase decoration of the cycloocta[b]indole skeleton by reduction and saponification was evaluated, thereby further extending the scope of the solid‐phase synthesis.     

In‐Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors

A one bead–one compound screening format is presented. Following solid‐phase synthesis on a photolabile linker, library compounds were readily released and screened inside polymer beads. The release of screening compounds was readily controlled by varying photolysis time and light intensity. Dose‐response experiments were carried out to effectively distinguish high‐ and low‐affinity ligands. A library containing 55 800 compounds was synthesized and screened in a fluorometric assay, thereby identifying potent HDAC inhibitors with IC₅₀ values in the nanomolar range.     

On‐Bead Screens Sample Narrower Affinity Ranges of Protein–Ligand Interactions Compared to Equivalent Solution Assays

Conceptually, on‐bead screening is one of the most efficient high‐throughput screening (HTS) methods. One of its inherent advantages is that the solid support has a dual function: it serves as a synthesis platform and as a screening compartment. Compound purification, cleavage and storage and extensive liquid handling are not necessary in bead‐based HTS. Since the establishment of one‐bead one‐compound library synthesis, the properties of polymer beads in chemical reactions have been thoroughly investigated. However, the characterization of the kinetics and thermodynamics of protein–ligand interactions on the beads used for screening has received much less attention. Consequently, the majority of reported on‐bead screens are based on empirically derived procedures, independent of measured equilibrium constants and rate constants of protein binding to ligands on beads. More often than not, on‐bead screens reveal apparent high affinity binders through strong protein complexation on the matrix of the solid support. After decoding, resynthesis, and solution testing the primary hits turn out to be unexpectedly weak binders, or may even fall out of the detection limit of the solution assay. Only a quantitative comparison of on‐bead binding and solution binding events will allow systematically investigating affinity differences as function of protein and small molecule properties. This will open up routes for optimized bead materials, blocking conditions and other improved assay procedures. By making use of the unique features of our previously introduced confocal nanoscanning (CONA) method, we investigated the kinetic and thermodynamic properties of protein–ligand interactions on TentaGel beads, a popular solid support for on‐bead screening. The data obtained from these experiments allowed us to determine dissociation constants for the interaction of bead‐immobilized ligands with soluble proteins. Our results therefore provide, for the first time, a comparison of on‐bead versus solution binding thermodynamics. Our data indicate that affinity ranges found in on‐bead screening are indeed narrower compared to equivalent interactions in homogeneous solution. A thorough physico‐chemical understanding of the molecular recognition between proteins and surface bound ligands will further strengthen the role of on‐bead screening as an ultimately cost‐effective method in hit and lead finding.     

Solid‐Phase Synthesis of Polyamine Spider Toxins and Correlation with the Natural Products by HPLC‐MS/MS

A recently developed new and divergent approach for the solid‐phase synthesis of polyamines and polyamine derivatives was extended to the preparation of linear pentamines, and it was applied to the synthesis of three quartets of isomeric polyamine spider toxins. The twelve synthetic acylpolyamines were investigated by HPLC‐UV(DAD)‐MS and HPLC‐UV(DAD)‐MS/MS and compared with the natural products in the complex mixture of the venom of Agelenopsis aperta. The comparative investigation supported the structures and assignments of seven previously found toxins and allowed the identification of an additional five polyamine derivatives in the natural sample. The MS/MS study of the isomerically pure polyamine derivatives revealed furthermore a characteristic pattern for the fragmentation of these compounds, which can possibly be used as evidence in the trace analysis of other polyamine derivatives.     

Highly Efficient Synthesis and Assay of Protein‐Imprinted Nanogels by Using Magnetic Templates

We report an approach integrating the synthesis of protein‐imprinted nanogels (“plastic antibodies”) with a highly sensitive assay employing templates attached to magnetic carriers. The enzymes trypsin and pepsin were immobilized on amino‐functionalized solgel‐coated magnetic nanoparticles (magNPs). Lightly crosslinked fluorescently doped polyacrylamide nanogels were subsequently produced by high‐dilution polymerization of monomers in the presence of the magNPs. The nanogels were characterised by a novel competitive fluorescence assay employing identical protein‐conjugated nanoparticles as ligands to reversibly immobilize the corresponding nanogels. Both nanogels exhibited K_d<10 pM for their respective target protein and low cross‐reactivity with five reference proteins. This agrees with affinities reported for solid‐phase‐synthesized nanogels prepared using low‐surface‐area glass‐bead supports. This approach simplifies the development and production of plastic antibodies and offers direct access to a practical bioassay.     

Spatially Resolved Derivatization of Solid‐Phase‐Synthesis Beads with Fluorescent Dendrimers: Creation of Localized Microdomains

Second and third generation Newkome‐type trifurcated dendrimers, containing either a coumarin or dansyl fluorescent probe at the dendrimer core, have been synthesized and attached to ArgoGel ^® solid‐phase‐synthesis beads. Subsequent reaction with rhodamine dye shows that the dye can penetrate throughout the beads to acylate the remaining sites. Thus, it is possible to achieve a spatially resolved microdomain for library formation at the core of the dendrimer, primarily on the bead's periphery, and a second microdomain suitable for derivatization by other reagents such as encoding tags and fluorescent sensors.     

Toward the Total Synthesis of Onchidin,a Cytotoxic Cyclic Depsipeptide from a Mollusc

The total synthesis of onchidin ( 1 ), a cytotoxic, C₂‐symmetric cyclic decadepsipeptide from a marine mollusc, according to the published structure, is described. A novel β‐amino acid, (2S,3S)‐3‐amino‐2‐methyl‐7‐octynoic acid (AMO), was efficiently prepared in high yield with high diastereo‐ and enantioselectivity based on a catalytic asymmetric three‐component Mannich‐type reaction with a chiral zirconium catalyst. The formation of sterically unfavorable N‐methyl amide and hindered ester bonds were successfully demonstrated, and final macrocyclization was achieved at a secondary‐amide site. Completion of the synthesis of 1 suggested that a revision of the structure of the natural product is required. Two diastereomers were also synthesized as candidates for the actual structure of onchidin. Furthermore, efficient solid‐phase methods were employed for the combinatorial synthesis of other derivatives to clarify the real structure of onchidin. The solid‐phase assembly of a pentadepsipeptide containing all the building blocks was established followed by dimeric cyclization in solution.     

Preparation and characterization of crosslinked poly(N,N‐diethylacrylamide‐co‐2‐hydroxyethyl methacrylate) resins and their application as support in solid‐phase peptide synthesis

Novel hydrophilic and thermosensitive poly(N,N‐diethylacrylamide‐co‐2‐hydroxyethyl methacrylate) resins were prepared by inverse suspension polymerization with N,N′‐methylenebis(acrylamide) as a crosslinker. The effects of chemical composition and degree of crosslinking on the polymerization were investigated. The polymer resins were characterized by elemental analysis, infrared spectroscopy, differential scanning calorimetry, and scanning electron microscopy. The thermosensitivity of the crosslinked resins was demonstrated by their lower critical swelling temperatures. The swelling and deswelling volume of the beads in water varied depending on the molar fraction of the N,N‐diethylacrylamide. These beads swelled extensively in a variety of common solvents. They had high loadings of functional hydroxyl groups and were used as supports in the solid‐phase synthesis of an oligopeptide. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1681–1690, 2003     

Total synthesis of natural dysidiolide

Dysidiolide (1), a novel sesterterpenoid previously isolated from the Caribbean sponge Dysidea etheria de Laubenfels, inhibits the action of the protein phosphatase, cdc25A. The authors establish a novel total synthesis of natural dysidiolide (1) using intramolecular Diels-Alder reaction as the key step from optically active cyclohexenone 3. Decalin, the core structure of 1, was constructed by intramolecular Diels-Alder reaction of the diene ester generated by elimination of the phenyl sulfoxide group from sulfoxide ester 6 prepared from cyclohexenone 3. Diastereoselective methylation at C-7, alkylation at C-6, and deoxygenation of C-12 and C-24 positions gave the fully substituted bicyclic core of 1. The two side chains of the bicyclic core were further extended so as to afford natural dysidiolide (1). The total yield of this synthesis exceeds that of previous syntheses of 1.     

Anti‐inflammatory bioactive equivalence of combinatorial components β‐carboline alkaloids identified in Arenaria kansuensis by two‐dimensional chromatography and solid‐phase extraction coupled with liquid–liquid extraction enrichment technology

Bioactive equivalent combinatorial components play a critical role in herbal medicines. However, how to discover and enrich them efficiently is a question for herbal pharmaceuticals researchers. In our work, a novel two‐dimensional reversed‐phase/hydrophilic interaction high‐performance liquid chromatography method was established to perform real‐time components trapping and combining for preparation and isolation of coeluting components. Arenaria kansuensis was taken as an example, and solid‐phase extraction coupled with liquid–liquid extraction as a simple and efficient method for enriching trace components, reversed phase column coupled with hydrophilic interaction liquid chromatography XAmide column as two‐dimensional chromatography technology for isolation and preparation of coeluting constituents, enzyme‐linked immune‐sorbent assay as bio‐guided assay, and anti‐inflammatory bioactivity evaluation for bioactive constituents. A combination of 12 β‐carboline alkaloids was identified as anti‐inflammatory bioactive equivalent combinatorial components from A. kansuensis , which accounts for 1.9% w/w of original A. kansuensis . This work answers the key question of which are real anti‐inflammatory components from A. kansuensis and provides a fast and efficient approach for discovering and enriching trace β‐carboline alkaloids from herbal medicines for the first time. More importantly, the discovery of bioactive equivalent combinatorial components could improve the quality control of herbal products and inspire a herbal medicine based on combinatorial therapeutics.     

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.     

A miniaturized arrayed assay format for detecting small molecule-protein interactions in cells

Background: Two complementary approaches to studying the cellular function of proteins involve alteration of function either by mutating protein-encoding genes or by binding a small molecule to the protein. A mutagen can generate millions of genetic mutations; correspondingly, split-pool synthesis can generate millions of unique ligands attached to individual beads. Genetic screening of mutations is relatively straightforward but, in contrast, split-pool synthesis presents a challenge to current methods of screening for compounds that alter protein function. The methods used to screen natural products are not feasible for large libraries composed of covalently immobilized compounds on synthesis beads. The sheer number of compounds synthesized by split-pool synthesis, and the small quantity of individual compound attached to each bead require assay miniaturization for efficient screening.Results: We present a miniaturized cell-based technique for the screening of ligands prepared by split-pool synthesis. Spatially defined droplets with uniform volumes of approximately 50–150 nanoliters (depending on well dimensions) are arrayed on plastic devices prepared using a combination of photolithography and polymer molding. Using this microtechnology, approximately 6,500 assays using either yeast cells or mammalian tissue culture can be performed within the dimensions of a standard 10 cm petri dish. We demonstrate that the biological effect of a small molecule prepared by split-pool synthesis can be detected in this format following its photorelease from a bead.Conclusions: The miniaturized format described here allows uniformly sized nanodroplets to be arrayed on plastic devices. The design is amenable to a large number of biological assays and the spatially arrayed format ensures uniform and controlled ligand concentrations and should facilitate automation of assays. The screening method presented here provides an efficient means of rapidly screening large numbers of ligands made by split-pool synthesis in both yeast and mammalian cells.     

Direct from solid natural products to pure compounds in a single step: Coupling online extraction with high‐speed counter‐current chromatography

Extraction is the most important step in the purification of bioactive compounds from natural products. This study introduces a simple online extraction strategy coupled with high‐speed counter‐current chromatography for efficient extraction and purification of bioactive components from solid natural products. For online extraction strategy, 1.0 g of ground Mangnolia officinalis or Piper nigrum was loaded into a guard column, which was then positioned on the manual injection valve instead of the sample loop. Bioactive components were directly extracted by the mobile phase of high‐speed counter‐current chromatography, and then transferred into high‐speed counter‐current chromatography for purification. In addition, the compatibility of the developed methodology for direct purification of bioactive components from fresh M. officinalis was successfully demonstrated. Obviously, in comparison with traditional offline heat‐reflux extraction, online extraction avoided the instrument, time, solvent, and energy consumption, and purified two phenolic compounds (honokiol and magnolol) from M. officinalis and three alkaloids (piperyline, piperine, and piperanine) from P. nigrum with high extraction efficiency. The superiority of the developed methodology is to establish an easy, rapid, and efficient technique for the purification of a wide variety of bioactive components from solid natural products.     

Advances in the development of molecularly imprinted polymers for the separation and analysis of proteins with liquid chromatography

This review documents recent advances in the design, synthesis, characterization, and application of molecularly imprinted polymers in the form of monoliths and particles/beads for the use in the separation and analysis of proteins with solid‐phase extraction or liquid chromatography. The merits of three‐dimensional molecular imprinting, whereby the molecular template is randomly embedded in the polymer, and two‐dimensional imprinting, in which the template is confined to the surface, are described. Target protein binding can be achieved by either using the entire protein as a template or by using a protein substructure as template, that is, a peptide, as in the "epitope" approach. The intended approach and strategy then determine the choice of polymerization method. A synopsis has been provided on methods used for the physical, chemical, and functional characterizations and associated performance evaluations of molecularly imprinted and nonimprinted control polymers, involving a diverse range of analytical techniques commonly used for low and high molecular mass analytes. Examples of recent applications demonstrate that, due to the versatility of imprinting methods, molecularly imprinted monoliths or particles/beads can be adapted to protein extraction/depletion and separation procedures relevant to, for example, protein biomarker detection and quantification in biomedical diagnostics and targeted proteomics.     

Oxyfold: A Simple and Efficient Solid‐Supported Reagent for Disulfide Bond Formation

The synthesis and use of novel polymer‐supported reagents for disulfide bond formation is described. This family of supported reagents consists of a series of oxidized methionines grafted onto a solid support. Their cost and the simplicity of their preparation through N‐carboxyanhydride polymerization on beads make them reactants of choice for the formation of disulfide bridges in peptides.     

Metal Oxide Assisted Preparation of Core–Shell Beads with Dense Metal–Organic Framework Coatings for the Enhanced Extraction of Organic Pollutants

Dense and homogeneous metal–organic framework (MOF) coatings on functional bead surfaces are easily prepared by using intermediate sacrificial metal oxide coatings containing the metal precursor of the MOF. Polystyrene (PS) beads are coated with a ZnO layer to give ZnO@PS core–shell beads. The ZnO@PS beads are reactive in the presence of 2‐methylimidazole to transform part of the ZnO coating into a porous zeolitic imidazolate framework‐8 (ZIF‐8) external shell positioned above the internal ZnO precursor shell. The obtained ZIF‐8@ZnO@PS beads can be easily packed in column format for flow‐through applications, such as the solid‐phase extraction of trace priority‐listed environmental pollutants. The prepared material shows an excellent permeance to flow when packed as a column to give high enrichment factors, facile regeneration, and excellent reusability for the extraction of the pollutant bisphenol A. It also shows an outstanding performance for the simultaneous enrichment of mixtures of endocrine disrupting chemicals (bisphenol A, 4‐tert‐octylphenol and 4‐n‐nonylphenol), facilitating their analysis when present at very low levels (<1 μg L^?1) in drinking waters. For the extraction of the pollutant bisphenol A, the prepared ZIF‐8@ZnO@PS beads also show a superior extraction and preconcentration capacity to that of the PS beads used as precursors and the composite materials obtained by the direct growth of ZIF‐8 on the surface of the PS beads in the absence of metal oxide intermediate coatings.     

Solid‐Phase Combinatorial Synthesis and Biological Evaluation of Destruxin E Analogues

The solid‐phase combinatorial synthesis of cyclodepsipeptide destruxin E has been demonstrated. The combinatorial synthesis of cyclization precursors 8 was achieved by using a split and pool method on SynPhase Lanterns. The products were successfully macrolactonized in parallel in the solution phase by using 2‐methyl‐6‐nitrobenzoic anhydride and 4‐(dimethylamino)pyridine N‐oxide to afford macrolactones 9 , and the subsequent formation of an epoxide in the side chain gave 18 member destruxin E analogues 6 . Biological evaluation of analogues 6 indicated that the N‐MeAla residue was crucial to the induction of morphological changes in osteoclast‐like multinuclear cells (OCLs). Based on structure–activity relationships, azido‐containing analogues 15 were then designed for use as a molecular probe. The synthesis and biological evaluation of analogues 15 revealed that 15 b , in which the Ile residue was replaced with a Lys(N₃) residue, induced morphological changes in OCLs at a sufficient concentration, and modification around the Ile residue would be tolerated for attachment of a chemical tag toward the target identification of destruxin E ( 1 ).     

Development of an Electrochemical Immunoassay Based on the Use of an Eight‐Electrodes Screen‐Printed Array Coupled with Magnetic Beads for the Detection of Antimicrobial Sulfonamides in Honey

In this work an electrochemical immunoassay, based on a direct competitive assay, was developed using magnetic beads as solid phase and carbon screen‐printed arrays as transducers for the detection of sulfonamides in food matrices such as honey. Magnetic beads coated with protein A were modified by immobilisation of specific antibodies and then the competition between the target analyte and the corresponding analyte‐labelled with an enzyme was carried out; after the immunosensing step, beads were captured by a magnet onto the working surfaces of a screen‐printed eight‐electrodes array for a multiple electrochemical detection. Screen‐printed eight‐electrodes arrays were chosen as transducers due to the possibility to repeat multiple analysis and to test different samples simultaneously. Alkaline Phosphatase (AP) was used as enzyme label and Differential Pulse Voltammetry (DPV) as fast electrochemical technique. Calibration curves demonstrate that the developed electrochemical immunoassay was able to detect this class of drugs in standard solutions at low concentrations (ng/mL levels). The short incubation times (25 min) and the fast electrochemical measurement (10 sec) make of these systems a possible alternative to classic ELISA tests.