Amide Coupling Reagent Research Articles

Porphyrin-Modified Beads for Use as Compensation Controls in Flow Cytometry

Flow cytometry can rapidly characterize and quantify diverse cell populations based on fluorescence measurements. The cells are first stained with one or more fluorescent reagents, each functionalized with a different fluorescent molecule (fluorophore) that binds to cells selectively based on their phenotypic characteristics, such as cell surface antigen expression. The intensity of fluorescence from each reagent bound to cells can be measured on the flow cytometer using channels that detect a specified range of wavelengths. When multiple fluorophores are used, the light from individual fluorophores often spills over into undesired detection channels, which requires a correction to the fluorescence intensity data in a process called compensation. Compensation control particles, typically polymer beads bound to a single fluorophore, are needed for each fluorophore used in a cell labeling experiment. Data from compensation particles from the flow cytometer are used to apply a correction to the fluorescence intensity measurements. This protocol describes the preparation and purification of polystyrene compensation beads covalently functionalized with the fluorescent reagent meso-tetra(4-carboxyphenyl) porphine (TCPP) and their application in flow cytometry compensation. In this work, amine-functionalized polystyrene beads were treated with TCPP and the amide coupling reagent EDC (N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride) at pH 6 and at room temperature for 16 h with agitation. The TCPP beads were isolated by centrifugation and resuspended in a pH 7 buffer for storage. TCPP-related particulates were observed as a byproduct. The number of these particulates could be reduced using an optional filtration protocol. The resultant TCPP beads were successfully used on a flow cytometer for compensation in experiments with human sputum cells labeled with multiple fluorophores. The TCPP beads proved stable following storage in a refrigerator for 300 days.

A sustainable, efficient, and potentially cost-effective approach to the antimalarial drug candidate MMV688533.

A 6-step synthesis of the antimalarial drug candidate MMV688533 is reported. Key transformations carried out under aqueous micellar conditions include two Sonogashira couplings and amide bond formation. Compared with the first-generation manufacturing process reported by Sanofi, the current route featuresppm levels of palladium loading, less material input, less organic solvent, and no traditional amide coupling reagents. The overall yield is improved ten-fold, from 6.4% to 67%.

Novel N-(4-thiocyanatophenyl)-1H-1,2,3-triazole-4-carboxamides exhibit selective cytotoxic activity at nanomolar doses towards human leukemic T-cells

The N-(4-thiocyanatophenyl)-1H-1,2,3-triazole-4-carboxamides were synthesized via the condensation of variety of 1H-1,2,3-triazole-4-carboxylic acids and 4-thiocyanatoaniline using CDI as amide coupling reagents. According to computer-aided calculations, all synthesized compounds are expected to have acceptable ADME profile for drug design. The antiproliferative potency of derivatives was evaluated towards different cell lines. The specific activity of four N-(4-thiocyanatophenyl)-1H-1,2,3-triazole-4-carboxamides (4a, 4b, 4c, 4f) was comparable to doxorubicin (GI50 = 0.65 μM) at nanomolar level against Jurkat cells in the range of GI50 0.63–0.69 μM. According to the results of toxicity studies of the compounds for HEK293, HaCaT, Balb/c 3T3 cells, compound 4a was selected for further studies as a biocompatible agent with promising anticancer activity in the NCI60 cell lines. A remarkable antiproliferative activity of compound 4a towards leukemia cell lines (SR, MOLT-4; CCRF-CEM; HL-60(TB); K-562; RPMI-8226) was observed and high cytotoxicity towards the CAKI-1 (kidney cancer), LOX IMVI (melanoma) and UO-31 (renal cancer) cells lines was detected. Compound 4a inhibits LOX IMVI cells growth at a GI50 value of 0.15 μM. COMPARE analysis to indicate potential mechanisms of action of novel compound, as well as in silico SwissTargetPrediction and SwissSimilarity were performed. Compound 4a induced morphological changes (apoptotic bodies, membrane blebbing, chromatin condensation), and DNA fragmentation in Jurkat T-cells. It reduced mitochondrial membrane potential and induced DNA damage in Jurkat cells without binding and/or intercalation to DNA molecule.

One-step synthesis of picolinohydrazides from fusaric acid: DFT, structural characterization and molecular inhibitory studies on metastatic tumor-derived exosomal and non-exosomal proteins

A new class of picolinohydrazide analogs (5–7) was synthesized via the one-pot reaction between fusaric acid (1) and aryl hydrazines (2–4) using amide coupling reagents. The synthesized compounds (5–7) were characterized using density-functional theory (DFT) computational spectroscopy, and instrumental methods. Global and local reactivity descriptors of these compounds were calculated at the B3LYP/6–311++g(d) level of theory to predict the reactivity and the reactive sites. The evaluated electronic properties (HOMO and LUMO) gave an insight into the molecular properties of the molecule. The charge distribution and molecular electrostatic potential facilitated the prediction of either the electrophilic or nucleophilic reactivity of these compounds. Extracellular heat shock protein-90 (HSP90) plays an essential role in tumor invasion while epidermal growth factor receptor (EGFR) is found at high levels on the surface of metastatic tumors. Blocking EGFR and HSP90 may predict metastatic spread. Molecular docking and molecular dynamics showed that picolinohydrazide analogs (5–7) act as inhibitors to the active-site cavity of the target proteins, i.e., EGFR and HSP90. The fluorine scaffold (6) has a potential binding free energy of -31.01 kcal mol−1 and -30.54 kcal mol−1 for EGFR and HSP90, respectively. The binding complex of fluorine scaffold (6) with EGFR and HSP90, respectively has also shown substantial stability in the post-dynamics analysis. Our results implicate the potential efficacy of novel adjunct therapeutic insights in treating advanced cancer.

Racemization-free synthesis of N\u03b1-2-thiophenoyl-phenylalanine-2-morpholinoanilide enantiomers and their antimycobacterial activity

Nα-2-thiophenoyl-d-phenylalanine-2-morpholinoanilide (MMV688845, IUPAC: N-(1-((2-morpholinophenyl)amino)-1-oxo-3-phenylpropan-2-yl)thiophene-2-carboxamide) from the Pathogen Box® library (Medicines for Malaria Ventures, MMV) is a promising lead compound for antimycobacterial drug development. Two straightforward synthetic routes to the title compound starting from phenylalanine or its Boc-protected derivative are reported. Employing Boc-phenylalanine as starting material and the T3P® and PyBOP® amide coupling reagents enables racemization-free synthesis, avoiding the need for subsequent separation of the enantiomers. The crystal structure of the racemic counterpart gives insight into the molecular structure and hydrogen bonding interactions in the solid state. The R-enantiomer of the title compound (derived from d-phenylalanine) exhibits activity against non-pathogenic and pathogenic mycobacterial strains, whereas the S-enantiomer is inactive. Neither of the enantiomers and the racemate of the title compound shows cytotoxicity against various mammalian cells.

Exploring Cyclic Sulfamidate Building Blocks for the Synthesis of Sequence-Defined Macromolecules.

The preparation of sequence-defined macromolecules using cyclic sulfamidates on solid-phase is outlined. The challenges surrounding an AB+CD approach are described with focus on understanding the formation of ring-opened side products when using amide coupling reagents. To avoid undesired side product formation, a strategy of iterative ring-openings of cyclic sulfamidates on solid-phase is explored. Ring-opening on primary and secondary amines is successfully reported, generating both linear and branched chain growth. However, attempts to selectively cleave N-sulfate bearing sp3 -hybridized groups cannot be demonstrated, limiting the overall building block scope for this methodology. Consequently, the active ring-opening of cyclic sulfamidates on amine-functionalized oligo(amidoamine) backbones is successfully applied to produce sequence-defined, N-sulfated macromolecules.

The design of novel 4,6-dimethoxyindole based hydrazide-hydrazones: Molecular modeling, synthesis and anticholinesterase activity

Biologically important hydrazide-hydrazone (–(C=O)NHN=CH) functionality was located at two different positions on 4,6-dimethoxyindole moiety and novel compounds 11a-c and 12a-c were generated by the condensation reactions of indole hydrazones 7 and 8, derived from the corresponding indole carbaldehydes 4 and 6, and carboxylic acids 9a-c in the presence of amide coupling reagent (EDC). The anticholinesterase potency was investigated towards the acetyl- and butrylcholinesterase enzymes (AChE and BChE) and complementary determination of biological potency was obtained by the evaluation of binding scores. The compound 11b resulted the best binding behaviors due to the hydrophobic interactions with the responsible amino acids on the different active sites of enzymes pocket. The structural analysis revealed that the most favorable binding pose was mainly dependent on the presence of aromatic moiety administered by the benzoic acid as well as the hydrazide-hydrazone linker but not related with the location on indole ring. Most importantly, the biological study was found to be compatible with the molecular modeling study and the highest inhibition was determined in the presence of compound 11b with the values of 83.31 and 73.55 for AChE and BChE, respectively.

Further applications of classical amide coupling reagents: Microwave-assisted esterification on solid phase.

Ester linkage (s) is a key chemical connector in organic chemistry, including natural products, peptides, and synthetic polymers. We herein describe a straightforward method for the efficient formation of ester linkage (s) on solid-phase. This method simply involves the use of amide coupling reagents under microwave irradiation. The robustness of this method relies on the use of classical solid-phase coupling reagents, heating by microwave irradiation, and a short time period, which results in high yields and the minimization of racemization.

Synthesis of Dicarba-closo-dodecaborane-1-carboxamides.

Amide bond formation is one of the most important chemical reactions. In peptide and organic chemistry, the application of amide coupling reagents is a routine strategy, but surprisingly not in carborane chemistry. Thus, we now report a fast, safe, and robust protocol to couple amines to m- and p-dicarba-closo-dodecaborane-1-carboxylic acids. The procedure comprises the activation of carboxylic acid with the coupling reagent (1-cyano-2-ethoxy-2-oxoethylidenaminooxy)(dimethylamino)morpholinocarbenium hexafluorophosphate, extraction of the product using the hydrophobic nature of the cluster, and a straightforward chromatographic purification. The protocol allows access to a variety of carborane-organic hybrid molecules suitable for application in multiple areas.

Unique physicochemical and catalytic properties dictated by the B3NO2 ring system.

The expansion of molecular diversity beyond what nature can produce is a fundamental objective in chemical sciences. Despite the rich chemistry of boron-containing heterocycles, the 1,3-dioxa-5-aza-2,4,6-triborinane (DATB) ring system, which is characterized by a six-membered B3NO2 core, remains elusive. Here, we report the synthesis of m-terphenyl-templated DATB derivatives, displaying high stability and peculiar Lewis acidity arising from the three suitably arranged boron atoms. We identify a particular utility for DATB in the dehydrative amidation of carboxylic acids and amines, a reaction of high academic and industrial importance. The three boron sites are proposed to engage in substrate assembly, lowering the entropic cost of the transition state, in contrast with the operative mechanism of previously reported catalysts and amide coupling reagents. The distinct mechanistic pathway dictated by the DATB core will advance not only such amidations, but also other reactions driven by multisite activation.

Two different behaviors in 4-ABT and 4,4′-DMAB surface enhanced Raman spectroscopy

In surface enhanced Raman scattering (SERS) community, the origin of b2-type bands of 4-aminobenenethiol (4-ABT) has been controversial until now, and the debate has positively contributed deeper understanding of SERS enhancement mechanism. Here, I report two experimental results to support chemical enhancement mechanism regarding origin of b2-type bands in 4-ABT SERS. At first, I compared the peak growth phenomena between 4-ABT and 4,4-dimercaptoazobenzene (4,4′-DMAB) SERS. After making that no b2-type bands were exhibited in SERS spectra both at 4-ABT and 4,4′-DMAB sides by treating strong reductant reagent like borohydride or applying strong negative electrochemical potential, 4-ABT side shows clear b2-type peak growth with laser irradiation, while 4,4′-DMAB side does not show any peak growth even with weak laser power, rather just shows abrupt peak appearance regardless of laser power. Secondly, amide coupling reagent was used to discriminate the property between 4-ABT and 4,4′-DMAB. When the reagent was flowed over 4-ABT and 4,4′-DMAB, of which their SERS fingerprints seem totally same because of laser irradiation, only the spectrum of 4-ABT changes after the treatment. The results verify that the amine group in 4-ABT still exists (not transformed to azo-compound), while strong b2-type bands were exhibited, which supports that b2-type bands in 4-ABT have no relationship with azo-compound (4,4′-DMAB). Copyright © 2016 John Wiley & Sons, Ltd.

ChemInform Abstract: Large‐Scale Applications of Amide Coupling Reagents for the Synthesis of Pharmaceuticals

AbstractReview: [116 refs.

Synthesis and preliminary evaluation of 5,7-dimethyl-2-aryl-3H-pyrrolizin-3-ones as angiogenesis inhibitors

Sunitinib (Sutent®) is a receptor tyrosine kinase (RTK) and angiogenesis inhibitor approved for the treatment of renal cell carcinomas, gastrointestinal stromal tumours and pancreatic neuroendocrine tumours. A key structural motif retained throughout medicinal chemistry efforts during sunitinib’s development was the indoline-2-one group. In the search for new anti-angiogenic scaffolds, we previously reported that non-indoline-2-one-based derivatives of semaxanib (SU5416, a structurally simpler sunitinib predecessor that underwent Phase III trials) are active as angiogenesis inhibitors, indicating that the group is not essential for activity. This Letter describes the synthesis and structure–activity relationships of another class of non-indoline-2-one angiogenesis inhibitors related to sunitinib/semaxanib; the 5,7-dimethyl-2-aryl-3H-pyrrolizin-3-ones. A focussed library of 19 analogues was prepared using a simple novel process, wherein commercially available substituted arylacetic acids activated with an amide coupling reagent (HBTU) were reacted with the potassium salt of 3,5-dimethyl-1H-pyrrole-2-carbaldehyde in one-pot. Screening of the library using a cell-based endothelial tube formation assay identified 6 compounds with anti-angiogenesis activity. Two of the compounds were advanced to the more physiologically relevant rat aortic ring assay, where they showed similar inhibitory effects to semaxanib at 10μg/mL, confirming that 5,7-dimethyl-2-aryl-3H-pyrrolizin-3-ones represent a new class of angiogenesis inhibitors.

Large-Scale Applications of Amide Coupling Reagents for the Synthesis of Pharmaceuticals

This review showcases various coupling reagents which have been implemented specifically for large-scale amide synthesis via the condensation of an acid and amine, while highlighting the benefits and drawbacks of each reagent on an industrial scale.

Enhanced electrocatalytic activity of oxygen reduction by cobalt-porphyrin functionalized with graphene oxide in an alkaline solution

Cobalt[5,15-(p-aminophenyl)-10,20-(pentafluorophenyl)porphyrin] (CoAPFP) functionalized with graphene oxide (GO) by N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (EDC hydrochloride) was used as an amide-coupling reagent (GO-CoAPFP). Electrochemical investigation revealed that ERGO-CoAPFP exhibited much better catalysis and better-improved oxygen reduction reaction (ORR) than GO-CoAPFP. ERGO-CoAPFP is a simple and facile method of improving electrocatalytic activity. The ERGO-CoAPFP catalysts were tested in ORR using electrochemical techniques such as cyclic voltammetry (CV) and rotating-ring-disk-electrode (RRDE) hydrodynamic voltammetry to quantitatively obtain the ORR kinetic constants and the reaction mechanisms on a glassy carbon electrode (GCE) in a 0.1 M KOH solution. The electrocatalytic oxygen reduction reaction of RRDE modified with ERGO-CoAPFP established a pathway of four-electron transfer reactions.

N,N′-Carbonyldiimidazole-Mediated Amide Coupling: Significant Rate Enhancement Achieved by Acid Catalysis with Imidazole·HCl

Over a series of 10 aromatic amines we show the rate of CDI mediated amidation to be significantly enhanced upon introduction of imidazole·HCl as a proton source for acid catalysis. Our work supports and provides an application for previous investigations into the imidazolium effect, thus increasing the scope of CDI as an amide-coupling reagent with aromatic amines. The influence of the relative pKa of the amines studied on the rate of reaction was also investigated.

Study of the Racemization Observed in the Amide Bond Forming Reaction on Silica Gel

Racemization resulting from the coupling of N-(3,5-dinitrobenzoyl)-L-leucine and 3-aminopropyl silica gel with several amide-coupling reagents is further investigated in order to explain the much higher degree of racemization on silica gel, as compared with the similar reaction in solution. Based on experiments using different types of solid supports, limited pore access and surface microchemical environment are ruled out as the possible reason for the higher degree of racemization that occurred on silica gel. Steric hindrance of the solid support is thought to have caused the amino group to be more basic relative to its nucleophilicity, leading to a higher degree of racemization.

Preparation of Dendrimer SAM on Au Substrate and Adsorption/Desorption of Poly-<I>L</I>-glutamate on the SAM

A self-assembled monolayer (SAM) of a dendrimer has been fabricated by covalent bonding of amine-terminated dendrimers to 3-mercaptopropionic acid SAM on an Au substrate, where an amide bond was formed between the amine and the carboxylic acid using amide-coupling reagents. Each reaction step was inspected by transmission surface-enhanced infrared absorption spectroscopy. Reaction was affected by solvents of the coupling reagents and concentrations of the coupling reagents and dendrimers. The pH-dependent adsorption/desorption behavior of sodium poly-L-glutamate (PGA) has been examined on the dendrimer SAM prepared. The adsorbed amount was abundant at acid pH below the pK(a) of carboxylate, while desorption from PGA-adsorbed dendrimer SAM prepared at acid pH proceeded as the pH was raised. The reaction was reversible and reproducible within 30 min under controlled pH, although the carboxylic acid species adsorbed at pH 4.2 was deprotonated to a carboxylate species after more than 30 min of desorption at pH 9.4.

Advances in the Applications of Polymer‐Supported Reagents for Organic Synthesis

AbstractFor Abstract see ChemInform Abstract in Full Text.

Advances in the Applications of Polymer-Supported Reagents for Organic Synthesis

This chapter discusses the new developments in polymer-supported reagents, with reagents grouped by different classes of chemical transformations. Polymer-supported acids and bases have been used extensively as ion-exchange resins for purifications and reagents for synthetic transformations. Their handling properties guarantee easy manipulations allowing rapid reaction optimization and parallel synthesis development. Using acids and bases, several reactions have been carried out. Some of these include the synthesis of dihydropyrimidones, oxidations and reductions, synthesis of carboxylic acids, and hydrogenation of alkenes. The Anelli oxidation of alcohols to aldehydes and ketones has been accomplished using polymer-supported nitroxyl radical catalysts. Various polymer-supported hydrides have been applied successfully to the reductions of both carbonyl and olefin groups. The sulfur and phosphorous transfer reagents are discussed. New polymer-supported reagents for sulfide transfer have been developed to avoid exposure to malodorous and toxic sulfur reagents. The chapter also reviews various esterification and amide-coupling reagents.