Part 3. a novel stereocontrolled, in situ, solution- and solid-phase, Aza Michael approach for high-throughput generation of tetrahydroaminoquinoline-derived natural-product-like architectures

With the goal of rapidly accessing tetrahydroquinoline-based natural-product-like polycyclic architectures, herein, we report an unprecedented, in situ, stereocontrolled Aza Michael approach in solution and on the solid phase. The mild reaction conditions required to reach the desired target are highly attractive for the use of this method in library generation. To our knowledge, this approach has not been used before, and it opens a novel route leading to a wide variety of tetrahydroquinoline-derived bridged tricyclic derivatives.     

Part 1. modular approach to obtaining diverse tetrahydroquinoline-derived polycyclic skeletons for use in high-throughput generation of natural-product-like chemical probes

A practical synthesis of a tetrahydroaminoquinoline scaffold (12) was developed that used a stereocontrolled aza Michael as the key reaction. Three tetrahydroquinoline alkaloid-like, tricyclic derivatives 16, 18, and 19 with different medium to macrocyclic ring skeletons were obtained, using this scaffold as the starting material, in a modular manner. The macrocyclic compounds with an isolated olefin and an electron-deficient olefin were obtained by ring-closing metathesis approaches. Compounds 16 and 18 are unique and contain bridged 10- and 12-membered functionalized rings. The NMR studies of these compounds revealed interesting information on the conformation of the bicyclic scaffolds that was dependent on the nature and the size of the macrocyclic rings. Finally, this modular methodology, using compound 21 anchored onto the solid support, successfully led to the generation of different macrocyclic derivatives, 23, 25, and 27 in solid-phase synthesis. The solid-phase synthesis approach outlined in this article has the potential to generate tetrahydroquinoline-based tricyclic compounds containing different medium to macrocyclic architectures.     

Solution- and solid-phase, modular approaches for obtaining different natural product-like polycyclic architectures from an aminoindoline scaffold for combinatorial chemistry

With the goal of developing a modular approach leading to different indoline alkaloid natural-product-like tricyclic derivatives having an unsaturated lactam (see compounds 13, 14, and 16), an aminoindoline-based bicyclic scaffold 10 was obtained from 9. The selective deprotection of the indoline NTeoc or benzylic NHAlloc in compound 10, followed by N-acryloylation and then subjection to a ring-closing metathesis reaction, successfully led to obtaining two different architectures (13/14 and 16) having an unsaturated lactam functionality. This modular solution-phase methodology was then developed on solid phase. To achieve this objective, the aminoindoline bicyclic scaffold having an additional hydroxyl group could be immobilized onto the solid support using alkylsilyl linker-based polystyrene macrobeads, giving 18. By applying a ring-closing metathesis approach, 20 (tricyclic derivative with seven-membered-ring unsaturated lactam) and 23 (tricyclic derivative with eight-membered-ring unsaturated lactam) were then obtained from 18 in a number of steps.     

Benzofuran-derived cyclic beta-amino acid scaffold for building a diverse set of flavonoid-like probes and the discovery of a cell motility inhibitor

We report here a practical, enantioselective synthesis of benzofuran-derived, cyclic trans-beta-amino acid scaffold. In two cases, tricyclic derivatives having six- and eight-membered unsaturated lactams were obtained from this versatile scaffold. To explore the biological applications, these compounds were subjected to cell-based assays, using NIH3T3 mouse cells to examine their potency as cell motility inhibitors and identified 18 as a potent cell motility inhibitor (IC50 approximately 40 microM in chamber cell migration assay).     

Search for improved host architectures: application of de novo structure-based design and high-throughput screening methods to identify optimal building blocks for multidentate ethers

This paper presents a computational approach to the deliberate design of improved host architectures. The approach, which involves the use of computer-aided design software, is illustrated by application to cation hosts containing multiple aliphatic ether oxygen binding sites. De novo molecule building software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for generating and screening millions of potential bidentate building block structures. Enhanced cation binding affinity can be achieved when highly organized building blocks are used to construct macrocyclic hosts.     

S1P1-selective in vivo-active agonists from high-throughput screening: off-the-shelf chemical probes of receptor interactions, signaling, and fate

The essential role of the sphingosine 1-phosphate (S1P) receptor S1P(1) in regulating lymphocyte trafficking was demonstrated with the S1P(1)-selective nanomolar agonist, SEW2871. Despite its lack of charged headgroup, the tetraaromatic compound SEW2871 binds and activates S1P(1) through a combination of hydrophobic and ion-dipole interactions. Both S1P and SEW2871 activated ERK, Akt, and Rac signaling pathways and induced S1P(1) internalization and recycling, unlike FTY720-phosphate, which induces receptor degradation. Agonism with receptor recycling is sufficient for alteration of lymphocyte trafficking by S1P and SEW2871. S1P(1) modeling and mutagenesis studies revealed that residues binding the S1P headgroup are required for kinase activation by both S1P and SEW2871. Therefore, SEW2871 recapitulates the action of S1P in all the signaling pathways examined and overlaps in interactions with key headgroup binding receptor residues, presumably replacing salt-bridge interactions with ion-dipole interactions.     

Tentoxin as a scaffold for drug discovery. Total solid-phase synthesis of tentoxin and a library of analogues

[reaction: see text] A solid-phase method for the synthesis of tentoxin has been developed. Two key steps-dehydration and N-alkylation-are carried out while the peptide is anchored to the resin. The method, which has been validated by the preparation of a library of tentoxin analogues, should be applicable to the generation of further libraries that have the tentoxin scaffold structure, as well as other structures containing N-alkylated didehydroamino acids.     

Nucleotides. Part LV. Synthesis and application of a novel linker for solid-phase synthesis of modified oligonucleotides

Various bifunctional amino-protecting groups such as the phthaloyl, succinyl, and glutaryl group were investigated as potential linker molecules for attachment to solid-support materials. Pentane-1,3,5-tricarboxylic acid 1,3-anhydride ( 16 ) offered the best properties and reacted with the amino groups of differently sugar-protected adenosine (see 20 and 22 ), cytidine (see 29 ), and guanosine derivatives (see 32 ) to the corresponding 2-(2-carboxyethyl)glutaryl derivatives 23 , 24 , 30 , and 33 . The usefulness of the new linker-type molecules was demonstrated by the solid-support synthesis of the potentially antivirally active 3′-deoxyadenylyl-(2′–5′)-2′-adenylic acid 2′-{2-[(adenin-9-yl)methoxy]ethyl} ester ( 38 ) starting from the 2′-end with N⁶,N⁶-[2-(2-carboxyethyl)glutaryl]-9-{{2-[(4,4′-dimethoxytrityl)ethoxy]methyl}adenine ( 12 ).     

Towards new camptothecins. Part 2: Synthesis of the ABCD ring scaffold substituted by a carboxyl group in the 5-position

In the context of formation of camptothecins substituted by a carbonyl function on position 5 of cycle C, synthesis of a new keto tetrahydroindolizine was realized. This compound was obtained from the reaction of Bredereck's reagent with an indolizine derived from pyroglutamic acid. That yielded a dimethylaminovinyl group whose NaIO₄ oxidation gave a ketone. The indolizinone obtained was reacted in Friedlander condition to give the ABCD ring scaffold of camptothecins substituted by a methoxycarbonyl group on the 5-position. It was also shown that, if it is desired, a 5-carboxamide group does not need to be introduced at the beginning of the synthesis sequence.     

Synthesis of HyBeacons and dual-labelled probes containing 2'-fluorescent groups for use in genetic analysis

An FMOC-protected 2'-hydroxyethyl uridine phosphoramidite has been used to synthesise fluorescein-labelled HyBeacon probes and "FAM-ROX" dual-labelled fluorogenic oligonucleotides.     

Free radical reactions for heterocycle synthesis. Part 7: 2-Bromobenzoic acids as building blocks in the construction of spirobenzolactones and spirobenzolactams

A straightforward 2-step parallel synthesis for structurally diversified spiro compounds is developed. 2-Bromobenzoic acids are used as common building blocks to couple with a series of conjugated enoles or enamines. Sequential intramolecular free radical Michael additions lead to formation of spirobenzolactones, spirobenzolactams, spirobenzolactone-lactams, spiorbenzolactone-thiolactones, spiordilactones, and bridged-spirolactones.     

Photochemical fishing approaches for identifying target proteins and elucidating the structure of a ligand-binding region using carbene-generating photoreactive probes.

Photoaffinity labeling enables the direct probing of a target protein through a covalent bond between a ligand and its binding protein, and even a complex formed by weak interactions can be isolated by the method. The photochemical fishing approach accelerates the throughput, isolating crosslinked complexes and analyzing the structure of the ligand binding site within the protein. We used carbene-generating phenyldiazirine for this approach because practical examinations had shown that the phenyldiazirine functioned as the powerful barb on the hook. Improving the synthetic pathways of the photoprobes and using chemoselective-integrated photoreactive units makes possible the easy and rapid preparation of carbene-generating photoreactive probes including the derivatives in peptides, proteins, DNAs, and carbohydrates. This review also shows several recent impacts of photoaffinity labeling, including the in vivo preparation of photoreactive proteins in living cells.     

The development of room temperature phosphorescence into a new technique for chemical determinations: Part 2. Analytical considerations of room temperature phosphorimetry

The rapidly developing technique of room temperature phosphorimetry is discussed from a practical analytical standpoint in this second part of the review. Basic factors concerning the technique such as methods of sample preparation, special instrumentation employed, and quantitative capability are presented, together with a listing of the variety of organic compounds reported to display room temperature phosphorescence. Potential applications of room temperature phosphorimetry and the advantages of sensitivity and selectivity afforded by this technique are discussed.     

Free radical reactions for heterocycle synthesis. Part 6: 2-Bromobenzoic acids as building blocks in the construction of nitrogen heterocycles

A general method to construct a variety of nitrogen heterocycles is introduced. 2-Bromobenzoic acids or acid chlorides are used as the common building blocks to couple with appropriate nitrogen-containing compounds. Sequential aryl radical cyclizations including conjugate additions, spirocyclizations, homolytic and ipso aromatic substitutions, and 1,5-hydrogen atom transfers are employed to prepare tri- and tetracyclic isoindolinones, benzolactams, isoquinolinones, azabenzoisocoumarins, and bridged-azabicyclic compounds.     

The learning machine in quantitative chemical analysis: Part 2. Potentiometric titrations of mixtures of three bases

Computer-calculated curves for the titration of mixtures of one strong base and two weak bases are used in the training and testing of a linear learning machine. The results indicate that multicategory classifiers can be calculated from a computer-generated training set of titration curves in which a random error of ±0.01 unit in the pH values is introduced. The relative error in the predictions for concentrations of bases not included in the training set was of the orderof ± 1% for concentration ratios up to 10:1 when δpK_b for the weak bases exceeded 1 pK unit and for K_b1 ? 5 × 10^-4 and K_b2 ? 10^-9. Calculation of the first derivative of the volume of titrant versus pH curves as a preprocessing step was necessary to obtain this accuracy for the weak bases, whereas the volume of titrant versus pH curves had to be used directly in the determination of the strong base. Predictions of concentrations of actual samples were in agreement with the computer-calculated results.     

Achieving traceable chemical measurements: inter-laboratory evaluation of a simplified technique for isotope dilution mass spectrometry. Part 2. Methodology for high accuracy analysis of organic analytes

A high accuracy measurement procedure developed and validated at LGC has been transferred to a number of expert UK laboratories, and their experience in applying the technique has been evaluated by inter-laboratory comparisons. It is an “exact matching” calibration procedure for analysis of organic analytes using isotope dilution mass spectrometry (IDMS). This calibration procedure uses a calibration blend and a sample blend with closely matched isotope amount ratios, and is an iterative process, culminating in the calibration blend and sample blend having identical isotope amount ratios. It is capable of high accuracy, since systematic errors in the determination of the isotope amount ratios are cancelled out. A series of four inter-laboratory comparisons of increasing difficulty were carried out involving a number of expert laboratories. The first three comparisons used gas chromatography mass spectrometry (GC–MS) analysis of the pesticide metabolite (pp′-dichlorodiphenyl) dichloroethylene (pp′-DDE), involving both conventional calibration and IDMS exact matching procedures for pp′-DDE in a solvent and a complex liquid matrix (corn oil). The fourth comparisons utilised liquid chromatography mass spectrometry (LC–MS) and involved the analysis of sulphamethazine (4-amino-N-(4,6 dimethyl-2 pyrimidinyl) benzenesulphonamide) in solvent using IDMS and conventional calibration techniques. Following the first trial, a workshop for participants was held on the use of the exact matching procedure together with a short course on uncertainty estimation. The results of the comparisons clearly showed the superior accuracy of using IDMS with the exact matching procedure for both GC–MS and LC–MS applications. These comparisons and the workshop have enabled the methodology to be transferred to UK industry, helping to improve UK measurement capability.

     

Achieving traceable chemical measurements: inter-laboratory evaluation of a simplified technique for isotope dilution mass spectrometry. Part 2. Methodology for high accuracy analysis of organic analytes

A high accuracy measurement procedure developed and validated at LGC has been transferred to a number of expert UK laboratories, and their experience in applying the technique has been evaluated by inter-laboratory comparisons. It is an “exact matching” calibration procedure for analysis of organic analytes using isotope dilution mass spectrometry (IDMS). This calibration procedure uses a calibration blend and a sample blend with closely matched isotope amount ratios, and is an iterative process, culminating in the calibration blend and sample blend having identical isotope amount ratios. It is capable of high accuracy, since systematic errors in the determination of the isotope amount ratios are cancelled out. A series of four inter-laboratory comparisons of increasing difficulty were carried out involving a number of expert laboratories. The first three comparisons used gas chromatography mass spectrometry (GC–MS) analysis of the pesticide metabolite (pp′-dichlorodiphenyl) dichloroethylene (pp′-DDE), involving both conventional calibration and IDMS exact matching procedures for pp′-DDE in a solvent and a complex liquid matrix (corn oil). The fourth comparisons utilised liquid chromatography mass spectrometry (LC–MS) and involved the analysis of sulphamethazine (4-amino-N-(4,6 dimethyl-2 pyrimidinyl) benzenesulphonamide) in solvent using IDMS and conventional calibration techniques. Following the first trial, a workshop for participants was held on the use of the exact matching procedure together with a short course on uncertainty estimation. The results of the comparisons clearly showed the superior accuracy of using IDMS with the exact matching procedure for both GC–MS and LC–MS applications. These comparisons and the workshop have enabled the methodology to be transferred to UK industry, helping to improve UK measurement capability.     

Preparation of N-Fmoc-Protected β2- and β3-Amino Acids and their use as building blocks for the solid-phase synthesis of β-peptides

N-Fmoc-Protected (Fmoc = (9H-fluoren-9-ylmethoxy)carbonyl) β-amino acids are required for an efficient synthesis of β-oligopeptides on solid support. Enantiomerically pure Fmoc-β³-amino acids β³: side chain and NH₂ at C(3)(= C(β)) were prepared from Fmoc-protected (S)- and (R)-α-amino acids with aliphatic, aromatic, and functionalized side chains, using the standard or an optimized Arndt-Eistert reaction sequence. Fmoc-β²- Amino acids (β² side chain at C(2), NH₂ at C(3)(= C(β))) configuration bearing the side chain of Ala, Val, Leu, and Phe were synthesized via the Evans' chiral auxiliary methodology. The target β³-heptapeptides 5–8 , a β³- pentadecapeptide 9 and a β²-heptapeptide 10 were synthesized on a manual solid-phase synthesis apparatus using conventional solid-phase peptide synthesis procedures (Scheme 3). In the case of β³-peptides, two methods were used to anchor the first β-amino acid: esterification of the ortho-chlorotrityl chloride resin with the first Fmoc-β-amino acid 2 (Method I, Scheme 2) or acylation of the 4-(benzyloxy)benzyl alcohol resin (Wang resin) with the ketene intermediates from the Wolff rearrangement of amino-acid-derived diazo ketone 1 (Method II, Scheme 2). The former technique provided better results, as exemplified by the synthesis of the heptapeptides 5 and 6 (Table 2). The intermediate from the Wolff rearrangement of diazo ketones 1 was also used for sequential peptide-bond formation on solid support (synthesis of the tetrapeptides 11 and 12 ). The CD spectra of the β²- and β³-peptides 5 , 9 , and 10 show the typical pattern previously assigned to an (M) 3₁ helical secondary structure (Fig.). The most intense CD absorption was observed with the pentadecapeptide 9 (strong broad negative Cotton effect at ca. 213 nm); compared to the analogous heptapeptide 5 , this corresponds to a 2.5 fold increase in the molar ellipticity per residue!     

Utility of 4,6-dichloro-2-(methylthio)-5-nitropyrimidine. Part 3: Regioselective solid-phase synthesis of a 2,6,8,9-tetrasubstituted purine library

The first regiocontrolled solid-phase synthesis of a 2,6,8,9-tetrasubstituted purine library was performed through on-resin elaboration of 4,6-dichloro-2-(methylthio)-5-nitropyrimidine. A series of primary amines were loaded on ArgoGel-MB-CHO resin via reductive amination to yield secondary amines. Subsequent attachment of the starting pyrimidine core unit and C6-chloride substitution by primary amines yielded the resin-bound 4,6-disubstituted-2-methylthio-5-nitropyrimidines. Oxone^® mediated oxidation of the 2-methylthio moiety to the corresponding sulfone allowed facile substitution at the 2-position. CrCl₂ assisted reduction of the nitro group, followed by acid catalyzed orthoester cyclization and finally TFA mediated cleavage provided the tetrasubstituted purine final products. Most of the final purines were cleaved in good to excellent yield and purity, however, it was found that bulky groups at N9 hindered cyclization in C8-substituted derivatives. For these systems, LC purification of the crude cleavage products provided the target purines in high purity.