Poor Nucleophiles Research Articles

ChemInform Abstract: Direct N‐Cyclopropylation of Secondary Acyclic Amides Promoted by Copper.

AbstractThe N‐cyclopropylation of aromatic and aliphatic secondary amines (I), known as poor nucleophiles, is accomplished using a simple and inexpensive copper system.

Reactivity in Nucleophilic Vinylic Substitution (SNV):SNVπ versus SNVσ Mechanistic Dichotomy

The intrinsic electronic factors that determine reactivity in prototypical identity nucleophilic vinylic substitution reactions, X(-) + ViX → XVi + X(-) (Vi = vinyl), have been studied by performing quantum chemical calculations (OPBE/6-311++G(d,p)). Of the two limiting reaction types envisaged--the S(N)Vπ and S(N)Vσ mechanisms--the former is preferred for most combinations of nucleophiles and substrates, except for the combination of unactivated substrates and poor nucleophiles, as seen for the much studied reactions Cl(-) + CH2CHCl and Br(-) + CH2CHBr. It was found that periodic trends for S(N)Vπ are essentially the same as those previously reported for nucleophilic aromatic substitution, S(N)Ar, while intrinsic S(N)Vσ nucleophilicity parallels aliphatic S(N)2. It is therefore concluded that S(N)V reactivity in general can be understood in terms of this mechanistic dichotomy. Furthermore, a few representative reactions were analyzed applying two complementary schemes for energy decomposition analysis.

Efficient 18 F Labeling of Cysteine-Containing Peptides and Proteins Using Tetrazine– Trans -Cyclooctene Ligation

18F positron emission tomography (PET) has a number of attributes that make it clinically attractive, including nearly 100% positron efficiency, very high specific radioactivity, and a short half-life of ≈ 110 minutes. However, the short half-life of 18F and the poor nucleophilicity of fluoride introduce challenges for the incorporation of 18F into complex molecules. Recently, the tetrazine-trans-cyclooctene ligation was introduced as a novel 18F labeling method that proceeds with fast reaction rates without catalysis. Herein we report an efficient method for 18F labeling of free cysteines of peptides and proteins based on sequential ligation with a bifunctional tetrazinyl-maleimide and an 18F-labeled trans-cyclooctene. The newly developed method was tested for site-specific labeling of both c(RGDyC) peptide and vascular endothelial growth factor (VEGF)-SH protein. Starting with 4 mCi of 18F-trans-cyclooctene and only 10 μg of tetrazine-RGD (80-100 μM) or 15 μg of tetrazine-VEGF (6.0 μM), 18F-labeled RGD peptide and VEGF protein could be obtained within 5 minutes in 95% yield and 75% yield, respectively. The obtained tracers were then evaluated in mice. In conclusion, a highly efficient method has been developed for site-specific 18F labeling of cysteine-containing peptides and proteins. The special characteristics of the tetrazine-trans-cyclooctene ligation provide unprecedented opportunities to synthesize 18F-labeled probes with high specific activity for PET applications.

ChemInform Abstract: Preparation of Substituted Benzimidazoles and Imidazopyridines Using 2,2,2‐Trichloroethyl Imidates.

The preparation of benzimidazoles and imidazopyridines has been achieved under mild conditions using 2,2,2-trichloroethyl imidates as the acylating agents. The reactions proceed smoothly in isopropyl alcohol at 70 °C. In cases where the acylation was rapid but the cyclization proceeded slowly, addition of sodium acetate proved to be beneficial. For substrates with poor nucleophilicity, modification of the solvent to the more inert tert-amyl alcohol, which can also achieve higher temperature, allowed for superior reactions.

Direct N-cyclopropylation of secondary acyclic amides promoted by copper

The N-cyclopropylation of aromatic and aliphatic secondary acyclic amides, known to be poor nucleophiles, has been accomplished using a simple and cheap copper system. The corresponding tertiary acyclic amides, which constitute a wide family of biologically active compounds, have been obtained in good to excellent yields.

Preparation of Substituted Benzimidazoles and Imidazopyridines Using 2,2,2-Trichloroethyl Imidates

The preparation of benzimidazoles and imidazopyridines has been achieved under mild conditions using 2,2,2-trichloroethyl imidates as the acylating agents. The reactions proceed smoothly in isopropyl alcohol at 70 °C. In cases where the acylation was rapid but the cyclization proceeded slowly, addition of sodium acetate proved to be beneficial. For substrates with poor nucleophilicity, modification of the solvent to the more inert <i>tert</i>-amyl alcohol, which can also achieve higher temperature, allowed for superior reactions.

Efficient N‐Terminal Labeling of Proteins by Use of Sortase

Efficient N‐Terminal Labeling of Proteins by Use of Sortase

Abstract 370: Tetrazine trans-cyclooctene ligation: An efficient 18F labeling method for cysteine containing peptides and proteins

Abstract 18F PET has a number of attributes that make it clinically attractive, including almost 100% positron efficiency, very high specific radioactivity, and short half-life of ∼110 min. However, the short half-life of 18F and the poor nucleophilicity of fluoride make it difficult to incorporate 18F in complex molecules. Recently, the tetrazine-trans-cyclooctene ligation has been introduced as a novel 18F labeling method that proceeds with fast reaction rates without any catalysis. To further explore the scope of this reaction, herein we reported an efficient method for 18F-lableing of free cysteine-containing bioligands based on the tetrazine-trans-cyclooctene ligation. The newly developed method was tested for site specific labeling of both c(RGDyC) and VEGF-SH protein. Starting with 4 mCi of 18F-trans-cyclooctene and only 10 μg of tetrazine-RGD (80-100 µM) or 15 μg of tetrazine-VEGF (6.0 µM), the 18F labeled RGD peptide or VEGF protein could be obtained in 95% yield and 75% yield within five minutes. The obtained tracers were then evaluated in small animals. In conclusion, a highly efficient method has been developed for site-specific 18F labeling of cysteine containing peptides and proteins. The special characteristics of the tetrazine-trans-cyclooctene ligation provide unprecedented opportunities to synthesize 18F-labeled probes with high specific activity for PET applications. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 370. doi:1538-7445.AM2012-370

Factors Favoring Efficient Bifunctional Catalysis. Study of a Ruthenium(II) Hydrogenation Catalyst Containing an N-Heterocyclic Carbene with a Primary Amine Donor

An alcohol-assisted outer-sphere bifunctional mechanism is proposed for the H2 hydrogenation of ketones catalyzed by the ruthenium(II) precatalyst [RuCp*(C–NH2)py]PF6 (2; Cp* = pentamethylcyclopentadienyl ligand, C–NH2 = N-heterocyclic carbene (NHC) with a tethered primary amine donor, py = pyridine) when activated by an alkoxide base. It has a high activity (turnover frequency (TOF) of up to 17 600 h–1) and selectivity for the H2 hydrogenation of ketones at 25 °C and 8 bar of H2 pressure in the presence of alcohols. Computational studies of a model neutral ruthenium(II) hydride amine complex, RuCp(C–NH2)H (Cp = cyclopentadienyl ligand), using density functional theory (DFT) methods reveal a low free energy barrier for the transfer of a proton/hydride couple to the ketone in the outer coordination sphere. In contrast, the related iridium(III) hydride amine complex [IrCp(C–NH2)H]+ is predicted to have a high barrier for hydride transfer to the ketone due to the poor nucleophilicity of this cationic hydride...

DNA-catalyzed reactivity of a phosphoramidate functional group and formation of an unusual pyrophosphoramidate linkage

During in vitro selection for DNA-catalyzed lysine reactivity, we identified a deoxyribozyme that instead catalyzes nucleophilic attack of a phosphoramidate functional group at a 5'-triphosphate-RNA, forming an unusual pyrophosphoramidate (N-P(V)-O-P(V)) linkage. This finding highlights the relatively poor nucleophilicity of nitrogen using nucleic acid catalysts, indicating a major challenge for future experimental investigation.

Simple palladium‐catalyzed C–N bond formation for poor nucleophilicity of aminonaphthalenes

Aromatic amines is not used commonly in allylic amination, presumably because of their less nucleophilic nature compared with the more extensively used benzylamine or relatively stable anionic nitrogen nucleophiles. An eco‐friendly method for C–O bond activation of allylic acetates using palladium associated with ligands in water leading to N‐allylation was described in this study. The palladium‐catalyzed allylic amination of allylic acetate with aminonaphthalenes gave 34–95% yields to the corresponding N‐allylic aminonaphthalenes. Copyright © 2011 John Wiley &amp; Sons, Ltd.

Organic chemistry: an acid-base approach

Organic chemistry: an acid-base approach

A Simple Copper-Catalyzed Synthesis of Tertiary Acyclic Amides

The N-arylation of aromatic and aliphatic secondary acyclic amides, known to be poor nucleophiles, has been accomplished using a simple and cheap copper catalytic system. The corresponding tertiary acyclic amides, which can be found in numerous biologically active compounds, have been obtained in good to excellent yields.

Enzymatic synthesis of activated esters and their subsequent use in enzyme-based peptide synthesis

Chemoenzymatic peptide synthesis is potentially the most cost-efficient technology for the synthesis of short and medium-sized peptides. However, there are still some limitations when challenging peptides, e.g. containing sterically demanding acyl donors, non-proteinogenic amino acids or proline residues, are to be synthesized. To remedy these limitations, special ester moieties have been used that are specifically recognized by the enzyme, e.g. guanidinophenyl, carboxamidomethyl (Cam) or trifluoroethyl (Tfe) esters, which, unfortunately, are notoriously difficult to synthesize chemically. Herein, we demonstrate that Cam and Tfe esters are very useful for Alcalase-CLEA mediated peptide synthesis using sterically demanding and non-proteinogenic acyl donors as well as poor nucleophiles, and combinations thereof. Furthermore, these esters can be efficiently synthesized by using the lipase Cal-B or Alcalase-CLEA. Finally, it is shown that the ester synthesis by Cal-B and subsequent peptide synthesis by Alcalase-CLEA can be performed simultaneously using a two-enzyme-one-pot approach with glycolamide or 2,2,2-trifluoroethanol as additive.

Total Synthesis of the Bacteroides fragilis Zwitterionic Polysaccharide A1 Repeating Unit

Nearly all bacteria capsular polysaccharides are T-cell-independent antigens that do not promote immunoglobulin class switching from IgM to IgG nor memory responses. In contrast, zwitterionic polysaccharides activate T-cell-dependent immune responses by major histocompatability complex class II presentation, a mechanism previously believed to be reserved for peptidic antigens. The best studied zwitterionic polysaccharide, polysaccharide A1 (PS A1) is found on the capsule of the commensal bacteria Bacteroides fragilis . Its potent immunomodulatory properties have been linked to postoperative intra-abdominal abscess formation. Here, we report the synthesis of the PS A1 tetrasaccharide repeating unit (2) as a tool to investigate the biological role of this polysaccharide. A modular synthetic strategy originating from the reducing end of the PS A1 repeating unit was unsuccessful and illustrated the limitations of glycosylation reactions between highly armed glycosylating agents and poor nucleophiles. Thus, a [3 + 1] glycosylation relying on trisaccharide 5 and pyruvalated galactose 6 was used to complete the first total synthesis of the PS A1 repeating unit (2).

Automation for Optimised Production of Fluorine-18-Labelled Radiopharmaceuticals

Most F-18 radiolabelling is currently done by nucleophilic substitution using no-carrier-added [F18]-fluoride. F-18 radionuclide produced in the cyclotron is a poor nucleophile that is unreactive in aqueous media and must undergo a number of processes to maximise reactivity. First it must be isolated from the target material (separation), then dried to remove traces of water (drying) and dissolved in an anhydrous solvent together with the precursor to initiate reaction (labelling). The intermediate labelled product then may need to be hydrolysed (de-protection) and finally, separated from the crude mixture (purification). An automated radiolabelling module is essential for the development and production of PET radiopharmaceuticals for performing basic functions such as transfer of fluids and heating and stirring. Sounds easy, but in reality the requirements of PET radiochemistry create unique challenges for the automated system. Such challenges are; radiation resistance and chemical compatibility of materials, reliability of control components, size constraints due to the need for shielding, product sterility and safety to the operator. Advances in computing hardware and software have had a major impact on automation of radiolabelling. Simplified program control and visualization of components and sensors has made the radiochemists work easier and safer. Modern synthesizer programs incorporate real-time displays of hardware status and trend graphs of various parameters (radioactivity, temperature, pressure) so that the synthesizer is no longer a “black box”. Finally, miniaturisation of components and more recently the design of “microfluidic reactors” have shown potential for further improving the radiolabelling process.

A Novel Family of Onium Salts Based Upon Isonitroso Meldrum's Acid Proves Useful as Peptide Coupling Reagents

AbstractA new family of uronium salts (HTMU, HMMU, and HDmPyMU) based on isonitroso Meldrum's acid (HONM) are reported as stand‐alone coupling reagents. Amide bond formation with the use of these reagents occurred more quickly than that with other uronium salts as a result of the presence of a neighboring group effect with a cyclic structure. Thus, these novel onium salts were often more effective in the acylation of poor nucleophiles and in the control of optical purity than related Oxyma‐ and benzotriazole‐based reagents. Among the HONM derivatives, HMMU showed the best performance in reducing racemization and assembling demanding sequences such as the Aib‐ACP decapeptide or analogues of Leu‐enkephalin pentapeptide. Furthermore, the scope and limitations of the use of HONM as an additive in combination with carbodiimides is discussed.

Control of Periplasmic Interdomain Thiol:Disulfide Exchange in the Transmembrane Oxidoreductase DsbD

The bacterial protein DsbD transfers reductant from the cytoplasm to the otherwise oxidizing environment of the periplasm. This reducing power is required for several essential pathways, including disulfide bond formation and cytochrome c maturation. DsbD includes a transmembrane domain (tmDsbD) flanked by two globular periplasmic domains (nDsbD/cDsbD); each contains a cysteine pair involved in electron transfer via a disulfide exchange cascade. The final step in the cascade involves reduction of the Cys103-Cys109 disulfide of nDsbD by Cys461 of cDsbD. Here we show that a complex between the globular periplasmic domains is trapped in vivo only when both are linked by tmDsbD. We have found previously (Mavridou, D. A., Stevens, J. M., Ferguson, S. J., & Redfield, C. (2007) J. Mol. Biol.370 ,643 -65817544440) that the attacking cysteine (Cys461) in isolated cDsbD has a high pKa value (10.5) that makes this thiol relatively unreactive toward the target disulfide in nDsbD. Here we show using NMR that active-site pKa values change significantly when cDsbD forms a complex with nDsbD. This modulation of pKa values is critical for the specificity and function of cDsbD. Uncomplexed cDsbD is a poor nucleophile, allowing it to avoid nonspecific reoxidation; however, in complex with nDsbD, the nucleophilicity of cDsbD increases permitting reductant transfer. The observation of significant changes in active-site pKa values upon complex formation has wider implications for understanding reactivity in thiol:disulfide oxidoreductases.

Enzyme action: lock up your waters?: Water and active sites

Water is thought of as the universal solvent for biological macromolecules, and its interaction with the different amino acid side chains of proteins determines their folding. Only a small proportion of the water associated with enzymes is tightly bound, but this can play crucial roles in determining the rates and specificities of reactions. Water itself is a relatively poor nucleophile, and enzymes can employ different strategies to facilitate hydrolytic reactions.

Using 3′-Bridging Phosphorothiolates To Isolate the Forward DNA Cleavage Reaction of Human Topoisomerase IIα

The ability to cleave DNA is critical to the cellular and pharmacological functions of human type II topoisomerases. However, the low level of cleavage at equilibrium and the tight coupling of the cleavage and ligation reactions make it difficult to characterize the mechanism by which these enzymes cut DNA. Therefore, to establish a system that isolates topoisomerase II-mediated DNA scission from ligation, oligonucleotide substrates were developed that contained a 3'-bridging phosphorothiolate at the scissile bond. Scission of these substrates generates a 3'-terminal -SH moiety that is a poor nucleophile relative to the normal 3'-terminal -OH group. Consequently, topoisomerase II cannot efficiently ligate phosphorothiolate substrates once they are cleaved. The characteristics of topoisomerase IIalpha-mediated cleavage of phosphorothiolate oligonucleotides were identical to those seen with wild-type substrates, except that no ligation was observed. This unidirectional accumulation of cleavage complexes provided critical information regarding coordination of the protomer subunits of topoisomerase IIalpha and the mechanism of action of topoisomerase II poisons. Results indicate that the two enzyme subunits are partially coordinated and that cleavage at one scissile bond increases the degree of cleavage at the other. Furthermore, anticancer drugs such as etoposide and amsacrine that strongly inhibit topoisomerase II-mediated DNA ligation have little effect on the forward scission reaction. In contrast, abasic sites that increase levels of cleavage complexes without affecting ligation stimulate the forward rate of scission. Phosphorothiolate substrates provide significant advantages over traditional "suicide substrates" and should be valuable for future studies on DNA scission and the topoisomerase II-DNA cleavage complex.