Ynamides as Racemization-Free Coupling Reagents for Amide and Peptide Synthesis

Optimization of peptide synthesis time and sustainability using novel eco-friendly binary solvent systems with induction heating on an automated peptide synthesizer

On December 12th, 2023, the European Commission took regulatory action to amend Annex XVII of REACH, imposing restrictions on the use of N,N-dimethylformamide (DMF) within the EU market owing to its high toxicity. Historically, DMF has been widely considered the gold standard for solid-phase peptide synthesis (SPPS). Being urgent to propose alternative solvents, we tested the suitability of non-hazardous neat and mixed solvents. Notably, binary solvent mixtures containing dimethyl sulfoxide as one of the solvent partners demonstrated high efficacy in solubilizing reagents while maintaining the desired swelling characteristics of common resins. A series of binary solvent mixtures were tested in automated SPPS, both at room temperature and high temperature, employing the PurePep® Chorus synthesizer, which enabled controlled induction heating between 25 and 90°C with oscillation mixing. The performances were assessed in challenging peptide sequences, i.e., ACP (65-74), and in longer and aggregating sequences like SARS-CoV-2 RBM (436-507) and β-amyloid (1-42). Furthermore, as part of the proposed sustainable approach to minimize the utilization of hazardous solvents, we coupled the novel PurePep EasyClean catch-and-release purification technology. This work, addressing regulatory compliance, emphasizes the crucial role of green chemistry in advancing safer and more environmentally friendly practices in SPPS.

A Type of Stable Amides Behaves as Acyl Transfer Reagents upon Visible-Light Irradiation through Self-Aromatization

Organic molecules with light-modifiable reactivity are important in many fields because they can serve as the "switch" for light to trigger chemical processes. Herein, we disclose a new type of stable non-twisted amides, the reactivity of which can be turned on by light as acyl transfer reagents. Upon photo-activation, these amides react with various nucleophiles including amines, phenols, hydroxide, thiols, boronic acids, and alkynes either under metal-free or metal-catalysis conditions. This reactivity hinges on the design and synthesis of a photo-activatable reagent (7-nitro-5,6-dihydrophenanthridine), which undergoes self-aromatization enabled by an internal oxidant under light. This masked acyl donor group is anticipated to be useful in scenarios where light is preferred to trigger a chemical process.

A General and Highly Versatile Heterogeneous Pd-Catalyzed Oxidative Aminocarbonylation of Alkynes with Aromatic and Aliphatic Amines

An efficient heterogeneous catalytic system for the oxidative aminocarbonylation of alkynes and amines in the presence of CO/O2 to afford substituted propiolamides has been developed. The active nanocatalyst, [Pd/Mg3Al-LDH]-300(D), is composed by Pd nanoaggregates (2-3 nm average particle size) stabilized over a partially dehydrated [Mg3Al-LDH] matrix. The methodology has resulted widely applicable, being the first catalytic system, either homogeneous or heterogeneous, able to activate not only aliphatic amines but also poorly-nucleophilic aromatic amines. In fact, >60 substituted propiolamides have been synthesized in good to excellent isolated yields through this methodology, being 27 novel compounds. An important characterization effort (XRD, 27Al MAS NMR, TGA, TPD-CO2, BET area, XPS, HAADF-HRSTEM and HRTEM) and optimization of the synthesis conditions of the optimal catalyst has been performed. This study, together with a series of kinetic and mechanistic essays, indicates that the optimal catalyst is composed by Pd(0) species stabilized in a partially dehydrated/dehydroxylated LDH material with a Mg/Al molar ratio of 3 and a small crystallite size. All the experimental data indicates that the in situ formation of [PdI2] active species in the material surface together with the presence of a matrix with the optimal acid/base properties are key aspects of this process.

Kinase Inhibition via Small Molecule-Induced Intramolecular Protein Cross-Linking

Remarkable progress has been made in the development of cysteine-targeted covalent inhibitors. In kinase drug discovery, covalent inhibitors capable of targeting other nucleophilic residues (i.e. lysine, or K) have emerged in recent years. Besides a highly conserved catalytic lysine, almost all human protein kinases possess an equally conserved glutamate/aspartate (e.g. E/D) that forms a K-E/D salt bridge within the enzyme's active site. Electrophilic ynamides were previously used as effective peptide coupling reagents and to develop E/D-targeting covalent protein inhibitors/probes. In the present study, we report the first ynamide-based small-molecule inhibitors capable of inducing intramolecular cross-linking of various protein kinases, leading to subsequent irreversible inhibition of kinase activity. Our strategy took advantage of the close distance between the highly conserved catalytic K and E/D residues in a targeted kinase, thus providing a conceptually general approach to achieve irreversible kinase inhibition with high specificity and desirable cellular potency. Finally, this ynamide-facilitated, ligand-induced mechanism leading to intramolecular kinase cross-linking and inhibition was unequivocally established by using recombinant ABL kinase as a representative.

Recent advances in asymmetric synthesis of chiral amides and peptides: racemization-free coupling reagents

Over past decades, chiral amides and peptides have emerged as powerful and versatile compounds due to their various biological activities and interesting molecular architectures. Although some chiral condensation reagents have been applied successfully for their synthesis, the introduction of racemization-free methods of amino acid activation have shown lots of advantages in terms of their low cost and low toxicity. In this review, advancements in amide and peptide synthesis using racemization-free coupling reagents over the last 10 years are summarized. Various racemization-free coupling reagents have been applied in the synthesis of enantioselective amides and peptides, including ynamides, allenones, HSi[OCH(CF3)2]3, Ta(OMe)5, Nb(OEt)5, Ta(OEt)5, TCFH-NMI, water-removable ynamides, DBAA, DATB, o-NosylOXY, TCBOXY, Boc-Oxyma, NDTP, 9-silafluorenyl dichlorides, the Mukaiyama reagent, EDC and T3P. The racemization-free reagents described in this review provide an alternative greener option for the asymmetric synthesis of chiral amides and peptides. We hope that this review will inspire further studies and developments in this field.

Liquid Chromatographic Enantioseparation of Newly Synthesized Fluorinated Tryptophan Analogs Applying Macrocyclic Glycopeptides-Based Chiral Stationary Phases Utilizing Core-Shell Particles

Due to the favorable features obtained through the incorporation of fluorine atom(s), fluorinated drugs are a group with emerging pharmaceutical importance. As their commercial availability is still very limited, to expand the range of possible candidates, new fluorinated tryptophan analogs were synthesized. Control of enantiopurity during the synthesis procedure requires that highly efficient enantioseparation methods be available. In this work, the enantioseparation of seven fluorinated tryptophans and tryptophan was studied and compared systematically to (i) develop analytical methods for enantioselective separations and (ii) explore the chromatographic features of the fluorotrytophans. For enantioresolution, macrocyclic glycopeptide-based selectors linked to core-shell particles were utilized, applying liquid chromatography-based methods. Application of the polar-ionic mode resulted in asymmetric and broadened peaks, while reversed-phase conditions, together with mobile-phase additives, resulted in baseline separation for all studied fluorinated tryptophans. The marked differences observed between the methanol and acetonitrile-containing eluent systems can be explained by the different solvation abilities of the bulk solvents of the applied mobile phases. Among the studied chiral selectors, teicoplanin and teicoplanin aglycone were found to work effectively. Under optimized conditions, baseline separations were achieved within 6 min. Ionic interactions were semi-quantitatively characterized and found to not influence enantiorecognition. Interestingly, fluorination of the analytes does not lead to marked changes in the chromatographic characteristics of the methanol-containing eluents, while larger differences were noticed when the polar but aprotic acetonitrile was applied. Experiments conducted on the influence of the separation temperature indicated that the separations are enthalpically driven, with only one exception. Enantiomeric elution order was found to be constant on both teicoplanin and teicoplanin aglycone-based chiral stationary phases (L < D) under all applied chromatographic conditions.

Ynamide Coupling Reagents: Origin and Advances

Since the pioneering work of Curtius and Fischer, chemical peptide synthesis has witnessed a century's development and evolved into a routine technology. However, it is far from perfect. In particular, it is challenged by sustainable development because the state-of-the-art of peptide synthesis heavily relies on legacy reagents and technologies developed before the establishment of green chemistry. Over the past three decades, a broad range of efforts have been made for greening peptide synthesis, among which peptide synthesis using unprotected amino acid represents an ideal and promising strategy because it does not require protection and deprotection steps. Unfortunately, C → N peptide synthesis employing unprotected amino acids has been plagued by undesired polymerization, while N → C inverse peptide synthesis with unprotected amino acids is retarded by severe racemization/epimerization owing to the iterative activation and aminolysis of high racemization/epimerization susceptible peptidyl acids. Consequently, there is an urgent need to develop innovative coupling reagents and strategies with novel mechanisms that can address the long-standing notorious racemization/epimerization issue of peptide synthesis.This Account will describe our efforts in discovery of ynamide coupling reagents and their application in greening peptide synthesis. Over an eight-year journey, ynamide coupling reagents have evolved into a class of general coupling reagents for both amide and ester bond formation. In particular, the superiority of ynamide coupling reagents in suppressing racemization/epimerization enabled them to be effective for peptide fragment condensation, and head-to-tail cyclization, as well as precise incorporation of thioamide substitutions into peptide backbones. The first practical inverse peptide synthesis using unprotected amino acids was successfully accomplished by harnessing such features and taking advantage of a transient protection strategy. Ynamide coupling reagent-mediated ester bond formation enabled efficient intermolecular esterification and macrolactonization with preservation of α-chirality and the configuration of the conjugated α,β-C-C double bond. To make ynamide coupling reagents readily available with reasonable cost and convenience, we have developed a scalable one-step synthetic method from cheap starting materials. Furthermore, a water-removable ynamide coupling reagent was developed, offering a column-free purification of the target coupling product. In addition, the recycle of ynamide coupling reagent was accomplished, thereby paving the way for their sustainable industrial application.As such, this Account presents the whole story of the origin, mechanistic insights, preparation, synthetic applications, and recycle of ynamide coupling reagents with a perspective that highlights their future impact on peptide synthesis.

Acid-Catalyzed Highly Enantioselective Synthesis of α-Amino Acid Derivatives from Sulfinamides and Alkynes

An enantioselective difunctionalization of activated alkynes using chiral sulfinamide reagents is developed. It is an atom and chirality transfer process that allows for the modular synthesis of optically active α-amino acid derivatives under mild conditions. The reaction proceeds through an acid-catalyzed [2,3]-sigmatropic rearrangement mechanism with predictable stereochemistry and a broad scope.

Pinpointing Acidic Residues in Proteins

It is of great importance to pinpoint specific residues or sites of a protein in biological contexts to enable desired mechanism of action for small molecules or to precisely control protein function. In this regard, acidic residues including aspartic acid (Asp) and glutamic acid (Glu) hold great potential due to their great prevalence and unique function. To unlock the largely untapped potential, great efforts have been made recently by synthetic chemists, chemical biologists and pharmacologists. Herein, we would like to highlight the remarkable progress and particularly introduce the electrophiles that exhibit reactivity to carboxylic acids, the light-induced reactivities to carboxylic acids and the genetically encoded noncanonical amino acids that allow protein manipulations at acidic residues. We also comment on certain unresolved challenges, hoping to draw more attention to this rapidly developing area.

The dipicolylamino group as an efficient leaving group for amide bond formation via hexafluoroisopropyl ester

Peptide dipicolylamide was prepared by the solid-phase method. The amide was activated by Cu(II) ions in hexafluoroisopropanol and converted to the corresponding active ester. It was condensed with the C-terminal segment to realize segment coupling. The method was successfully applied to the synthesis of an atrial natriuretic peptide and RNase T1.

Catalyst-free late-stage functionalization to assemble α-acyloxyenamide electrophiles for selectively profiling conserved lysine residues

Covalent probes coupled with chemical proteomics represent a powerful method for investigating small molecule and protein interactions. However, the creation of a reactive warhead within various ligands to form covalent probes has been a major obstacle. Herein, we report a convenient and robust process to assemble a unique electrophile, an α-acyloxyenamide, through a one-step late-stage coupling reaction. This procedure demonstrates remarkable tolerance towards other functional groups and facilitates ligand-directed labeling in proteins of interest. The reactive group has been successfully incorporated into a clinical drug targeting the EGFR L858R mutant, erlotinib, and a pan-kinase inhibitor. The resulting probes have been shown to be able to covalently engage a lysine residue proximal to the ATP-binding pocket of the EGFR L858R mutant. A series of active sites, and Mg2+, ATP-binding sites of kinases, such as K33 of CDK1, CDK2, CDK5 were detected. This is the first report of engaging these conserved catalytic lysine residues in kinases with covalent inhibition. Further application of this methodology to natural products has demonstrated its success in profiling ligandable conserved lysine residues in whole proteome. These findings offer insights for the development of new targeted covalent inhibitors (TCIs).

Inverse Peptide Synthesis Using Transient Protected Amino Acids

Peptide therapeutics have experienced a rapid resurgence over the past three decades. While a few peptide drugs are biologically produced, most are manufactured via chemical synthesis. The cycle of prior protection of the amino group of an α-amino acid, activation of its carboxyl group, aminolysis with the free amino group of a growing peptide chain, and deprotection of the N-terminus constitutes the principle of conventional C → N peptide chemical synthesis. The mandatory use of the Nα-protecting group invokes two additional operations for incorporating each amino acid, resulting in poor step- and atom-economy. The burgeoning demand in the peptide therapeutic market necessitates cost-effective and environmentally friendly peptide manufacturing strategies. Inverse peptide chemical synthesis using unprotected amino acids has been proposed as an ideal and appealing strategy. However, it has remained unsuccessful for over 60 years due to severe racemization/epimerization during N → C peptide chain elongation. Herein, this challenge has been successfully addressed by ynamide coupling reagent employing a transient protection strategy. The activation, transient protection, aminolysis, and in situ deprotection were performed in one pot, thus offering a practical peptide chemical synthesis strategy formally using unprotected amino acids as the starting material. Its robustness was exemplified by syntheses of peptide active pharmaceutical ingredients. It is also amenable to fragment condensation and inverse solid-phase peptide synthesis. The compatibility to green solvents further enhances its application potential in large-scale peptide production. This study offered a cost-effective, operational convenient, and environmentally benign approach to peptides.

Copper-catalyzed room-temperature cross-dehydrogenative coupling of secondary amides with terminal alkynes: a chemoselective synthesis of ynamides

A copper-catalyzed aerobic oxidative cross-dehydrogenative coupling reaction between secondary amides and terminal alkynes has been developed. With the aid of ligands and 3 Å molecular sieves, ynamides can be efficiently synthesized at room temperature and conveniently scaled up. A legitimate mechanism involving nitrogen-centred radicals and copper trivalent intermediates has been proposed.

Regio- and Stereocontrolled Hydrohalogenation of Ynamides with N-Halosuccinimides (NXS) as the Halogen Source: Synthesis of (E)-α-Haloenamides

Presented herein is a facile stereoselective construction of synthetically versatile chiral and achiral (E)-α-haloenamides under mild conditions utilizing N-halosuccinimides and diphenylphosphine oxide. This reaction is metal-free, mild, efficient, very rapid, and practical and highlights the synthetic versatility of ynamides. The reaction has a broad substrate scope; both chiral and achiral ynamides have been transformed into the corresponding (E)-α-haloenamides within a very short period of time without compromising selectivity or complexity.

Synthesis of Chiral Diarylmethylamides via Catalytic Asymmetric Aza-Michael Addition of Amides to ortho-Quinomethanes

Chiral diarylmethylamides are a privileged skeleton in many bioactive molecules. However, the enantioselective synthesis of such molecules remains a long-standing challenge in organic synthesis. Herein, we report a chiral bifunctional squaramide catalyzed asymmetric aza-Michael addition of amides to in situ generated ortho-quinomethanes, affording enantioenriched diarylmethylamides in good yields with excellent enantioselectivities. This work not only provides a new strategy for the construction of the diarylmethylamides but also represents the practicability of amides as nitrogen-nucleophiles in asymmetric organocatalysis.

Copper-Catalyzed Regio- and Stereoselective Hydroarylation of Ynamide

Presented herein is a copper-catalyzed trans-hydroarylation of ynamides. The reaction showcases the assembly of boronic acids across the carbon-carbon triple bond of ynamides. The reaction proceeds under mild conditions offering a complementary approach for the versatile synthesis of multifunctional (E)-α,β-disubstituted enamides. Moreover, the hydroarylation process is highly regio- and stereoselective. The transformation shows a broad scope (30 examples) and tolerates a wide range of labile functional groups. Control experiments provide substantive evidence supporting the mechanistic cycle and the observed selectivity.

Expedient and divergent synthesis of unnatural peptides through cobalt-catalyzed diastereoselective umpolung hydrogenation

The development of a reliable method for asymmetric synthesis of unnatural peptides is highly desirable and particularly challenging. In this study, we present a versatile and efficient approach that uses cobalt-catalyzed diastereoselective umpolung hydrogenation to access noncanonical aryl alanine peptides. This protocol demonstrates good tolerance toward various functional groups, amino acid sequences, and peptide lengths. Moreover, the versatility of this reaction is illustrated by its successful application in the late-stage functionalization and formal synthesis of various representative chiral natural products and pharmaceutical scaffolds. This strategy eliminates the need for synthesizing chiral noncanonical aryl alanines before peptide formation, and the hydrogenation reaction does not result in racemization or epimerization. The underlying mechanism was extensively explored through deuterium labeling, control experiments, HRMS identification, and UV-Vis spectroscopy, which supported a reasonable CoI/CoIII catalytic cycle. Notably, acetic acid and methanol serve as safe and cost-effective hydrogen sources, while indium powder acts as the terminal electron source.

4-Iodine N-Methylpyridinium-Mediated Peptide Synthesis

Through systematic optimization of halopyridinium compounds, we established a peptide coupling protocol utilizing 4-iodine N-methylpyridinium (4IMP) for solid-phase peptide synthesis (SPPS). The 4IMP coupling reagent is easily prepared, bench stable, and cost-effective. Employing 4IMP in the SPPS process has showcased remarkable chemoselectivity and efficiency, effectively eliminating racemization and epimerization. This achievement has been substantiated through the successful synthesis of a range of peptides via the direct utilization of commercially available amino acid substrates for SPPS.

Epimerisation in Peptide Synthesis

Epimerisation is basically a chemical conversion that includes the transformation of an epimer into another epimer or its chiral partner. Epimerisation of amino acid is a side reaction that sometimes happens during peptide synthesis. It became the most avoided reaction because the process affects the overall conformation of the molecule, eventually even altering the bioactivity of the peptide. Epimerised products have a high similarity of physical characteristics, thus making it difficult for them to be purified. In regards to amino acids, epimerisation is very important in keeping the chirality of the assembled amino acids unchanged during the peptide synthesis and obtaining the desirable product without any problematic purification. In this review, we report several factors that induce epimerisation during peptide synthesis, including how to characterise and affect the bioactivities. To avoid undesirable epimerisation, we also describe several methods of suppressing the process.

AITF (4-acetamidophenyl triflimide) mediated synthesis of amides, peptides and esters

A simple, broadly applicable protocol for amidation and esterification reactions is described. Thereby, 4-acetamidophenyl triflimide (AITF), a crystalline stable reagent, is employed for the activation of carboxylic acids. The use of AITF as a coupling agent is demonstrated in the synthesis of peptides, amides and esters under mild conditions in good to excellent yields. Notably, peptide segment condensations were also accomplished. A diverse array of synthetic protocols showcasing a broad substrate scope and good functional group compatibility were accomplished. Herein, we systematically summarized the use of AITF in peptide synthesis strategies.

Recyclable gold(I)-catalyzed heterocyclization of ynamides with benzyl or indolyl azides towards 2-aminoindoles or 3-amino-β-carbolines

A highly efficient heterogeneous gold(I)-catalyzed heterocyclization of ynamides with benzyl or indolyl azides has been achieved in 1,2-dichloroethane under mild conditions via a heterogenized α-imino gold carbene intermediate using 5 mol% of SBA-15-anchored strongly hindered NHC-gold(I) complex [IPr-SBA-15-AuNTf2] as the catalyst, delivering a wide range of valuable 2-aminoindoles or 3-amino-β-carbolines in mostly good to excellent yields with high regioselectivity. Furthermore, the new heterogenized NHC-gold(I) complex displays the same catalytic activity as IPrAuNTf2 and is facile to recover by centrifugation of the reaction mixture and can be reused at least seven times without any appreciable drop in its catalytic activity.

Practical N-to-C peptide synthesis with minimal protecting groups

Accessible drug modalities have continued to increase in number in recent years. Peptides play a central role as pharmaceuticals and biomaterials in these new drug modalities. Although traditional peptide synthesis using chain-elongation from C- to N-terminus is reliable, it produces large quantities of chemical waste derived from protecting groups and condensation reagents, which place a heavy burden on the environment. Here we report an alternative N-to-C elongation strategy utilizing catalytic peptide thioacid formation and oxidative peptide bond formation with main chain-unprotected amino acids under aerobic conditions. This method is applicable to both iterative peptide couplings and convergent fragment couplings without requiring elaborate condensation reagents and protecting group manipulations. A recyclable N-hydroxy pyridone additive effectively suppresses epimerization at the elongating chain. We demonstrate the practicality of this method by showcasing a straightforward synthesis of the nonapeptide DSIP. This method further opens the door to clean and atom-efficient peptide synthesis.

Synthesis and evaluation of alkoxy-substituted enamides against influenza A virus in vitro and in vivo

Alkoxy-substituted enamides are often used as synthetic intermediates due to their special reactivity. To the best our knowledge, the biological activity of alkoxy-substituted amines has never been reported so far. We have synthesized a series of alkoxy-substituted enamides to study their anti-influenza A virus activity in vitro and in vivo. Among these compounds, compound E-2o had the best antiviral activity (EC50 = 2.76 ± 0.67 μM) and low cytotoxicity (CC50 = 662.87 ± 24.85 μM). The mechanism of action of this compound was preliminarily explored by us. It alleviated the cytopathic effects and cell death caused by different subtypes of influenza A virus. Different drug delivery methods and timed dosing experiments had shown that E-2o had the best therapeutic effect and mainly played a role in the early stages of virus replication. The expansion of influenza viruses in cells was inhibited by reducing ROS accumulation, cell apoptosis, and autophagy. Alkoxy-substituted enamide E-2o reduced the production of interferon and other pro-inflammatory factors in the RIG-Ⅰ pathway and its downstream NF-κB was induced by influenza A virus in vitro and in vivo. It avoided damage in the mice which was caused by excessive inflammatory factors. In addition, the weight loss and lung lesion damage in mice caused by influenza virus were improved by compound E-2o. Therefore, Alkoxy-substituted enamide E-2o could inhibit the replication of influenza viruses in vivo and in vitro, and has the potential to be developed into a drug for treating influenza.

Multicomponent Reactions for Expeditious Construction of β-Indole Carboxamide Amino Amides

A multicomponent reaction of N-indole carboxylic acids, aldehydes, amines, and C2 building blocks can be transformed to structurally diverse β-indole carboxamide amino amides. In this multicomponent reaction, the ynamides and triazenyl alkynes act as the C2 building block, and this protocol features readily available starting materials, high atom economy, and mild reaction conditions. Besides, the acyl triazene group in the product can be easily transformed to differential groups to expand the structural diversity.

Concise total synthesis and structure revision of metacridamides A and B

Concise total synthesis of metacridamides A and B was accomplished through repetitive vinylogous Mukaiyama aldol reactions and ynamide-mediated macrolactonization. Spectral data of both synthetic products were identical to those of the natural products, resulting in the revision of the absolute configuration of the C-9 position to be S.

Development of a nitrogen-bound hydrophobic auxiliary: application to solid/hydrophobic-tag relay synthesis of calpinactam

In the last couple of decades, technologies and strategies for peptide synthesis have advanced rapidly. Although solid-phase peptide synthesis (SPPS) and liquid-phase peptide synthesis (LPPS) have contributed significantly to the development of the field, there have been remaining challenges for C-terminal modifications of peptide compounds in SPPS and LPPS. Orthogonal to the current standard approach that relies on installation of a carrier molecule at the C-terminus of amino acids, we developed a new hydrophobic-tag carbonate reagent which facilitated robust preparation of nitrogen-tag-supported peptide compounds. This auxiliary was easily installed on a variety of amino acids including oligopeptides that have a broad range of noncanonical residues, allowing simple purification of the products by crystallization and filtration. We demonstrated a de novo solid/hydrophobic-tag relay synthesis (STRS) strategy using the nitrogen-bound auxiliary for total synthesis of calpinactam.

Ynamide Coupling Reagent for the Chemical Cross-Linking of Proteins in Live Cells

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is a powerful method for the study of protein structure and protein-protein interactions (PPIs). However, the chemical probes used in the CXMS are limited to bidentate reactive warheads, and the available zero-length cross-linkers are restricted to 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM). To alleviate this issue, an efficient coupling reagent, sulfonyl ynamide, was developed as a new zero-length cross-linker that can connect high-abundance carboxyl residues (D/E) with lysine (K) to form amide bonds in the absence of any catalyst. Significant improvement in the cross-linking efficiency and specificity in comparison with traditional EDC/NHS was achieved with model proteins, which includes inter- and intramolecular conjugations. The cross-linked structures were validated by X-ray crystallography. Importantly, this coupling reagent can be successfully used to capture interacting proteins in the whole proteome and can be a useful reagent for probing potential protein-protein interactions in situ.

Triflylpyridinium as Coupling Reagent for Rapid Amide and Ester Synthesis

An effective method has been developed to facilitate the synthesis of amides and esters at ambient temperature within 5 min, in which a stable and easily accessible triflylpyridinium reagent is used. Remarkably, this method not only has a wide range of substrate compatibility but also could realize the scalable synthesis of peptide and ester via a continuous flow process. Moreover, excellent chirality retentions are presented during activation of carboxylic acid.

A one-step base-free synthesis of N-arylamides via modified pivaloyl mixed anhydride mediated amide coupling

Pivalic anhydride is shown to be an effective reagent for direct amidation of carboxylic acids with N-alkyl anilines. The only by-product of this reaction is nontoxic pivalic acid, which can be easily removed by aqueous workup. The reactions are conducted under mild conditions and found to be compatible with a range of carboxylic acids, including aromatic, heterocyclic, acrylic, and aliphatic carboxylic acids and amino acids generating the desired amides in short reaction times.

Modular enantioselective access to β-amino amides by Brønsted acid-catalysed multicomponent reactions

β-Amino acids are structural motifs widely found in therapeutic natural products, novel biomimetic polymers and peptidomimetics. As a convergent method, the synthesis of stereoenriched β-amino amides through the asymmetric Mannich reaction requires specialized amide substrates or a metal catalyst for enolate formation. By a redesign of the Ugi reaction, a conceptually different solution to prepare chiral β-amino amides was established using ambiphilic ynamides as two-carbon synthons. The modulation of ynamides or oxygen nucleophiles concisely furnished three classes of β-amino amides with generally good efficiency as well as excellent chemo- and stereo-control. The utility is verified in the preparation of over 100 desired products that bear one or two contiguous carbon stereocentres, including those that directly incorporate drug molecules. This advance also provides a synthetic shortcut to other valuable structures. The amino amides could be elaborated into β-amino acids, anti-vicinal diamines, γ-amino alcohols and β-lactams or undergo transamidation with amino acids and amine-containing pharmaceuticals.

Cyclotrimetaphosphate-assisted ruthenium catalyst for the hydration of nitriles and oxidation of primary amines to amides under aerobic conditions in water

Amide bonds are ubiquitous and regarded as an essential constituent of many biologically active drug molecules and fine chemicals. We report a practical and operationally simple ruthenium-based catalytic system for the hydration of nitriles and aerobic oxidation of primary amines to the corresponding amides. Both reactions proceed without any external oxidant in water under aerobic conditions and exhibit a broad substrate scope. The mechanistic investigation was executed with the aid of control experiments and kinetic and spectroscopic studies of the reaction mixture.

Gold-Catalyzed Regio- and Stereoselective α-Acyloxy-β-Alkynylation of Ynol Ethers

Enol esters and conjugated enynes are valuable structural motifs for synthetic chemistry and material sciences. Herein, the synthesis of tetra-substituted enol ester 2-iodobenzoate derivatives was achieved in good yields at room temperature through a gold-catalyzed acyloxyalkynylation of sensitive ynol ethers with ethynylbenziodoxolones (EBXs), the latter acting as bifunctional reactants. The conversion is highly regioselective with a broad substrate scope. Mechanistically, an Au(III) species is the key intermediate of an Au(I)/Au(III) redox cycle. The reaction is synthetically useful and can easily be scaled up to gram scale.

Ynamides in Radical Reactions: A Route to Original Persubstituted 2-Aminofurans

Mn(OAc)₃/Cu(OAc)₂-mediated reaction between ynamides, derived from oxazolidone or 3-methylindole carboxylate, and cyclic α-dicarbonyl radicals led to the one-pot synthesis of 2-aminofurans. The transformation involves addition of the α-dicarbonyl radical to ynamide, oxidation to ketene-iminium, and polar cyclization steps to provide original persubstituted 2-aminofurans in good to excellent yields. This work represents the first radical route for the synthesis of furans from ynamides.

Regio- and stereospecific cis-hydrophenoxylation of ynamides with acidic phenols

Herein we describe a self-acid-enabled chemo-, regio-, and stereospecific cis-hydrophenoxylation of ynamides under reagent-free conditions. The presence of a non-polar solvent such as toluene was found to be beneficial to facilitate the rate-limiting proton transfer between phenols and ynamides to form an intimate ion pair, which is followed by a swift nucleophilic attack of the phenolate oxygen on keteniminium, fulfilling the overall hydrofunctionalization event. This protocol is operationally simple and easily scalable, tolerates a wide variety of functional groups, and shows good compatibility with the requirements of modern green chemistry.

Peptide-based drug discovery: Current status and recent advances

The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.

High-valent Cu(III)-CF3 compound-mediated esterification reaction

Cu(III)-CF₃ compounds are reported herein as novel coupling reagents to mediate ester synthesis from carboxyl acids and alcohols/phenols. Carboxylic acids are transformed to trifluoromethyl ester and acyl fluoride activated species that interact with each other. The broad substrate scope and late-stage application of this method are demonstrated. This study opens up new opportunities to develop interesting reactions using Cu(III)-CF₃ compounds without transferring a CF₃ group to the products.

N-Acetyl-l-phenylalanine Racemization during TBTU Amidation: An In-Depth Study for the Synthesis of Anti-Inflammatory 2-(N-Acetyl)-l-phenylalanylamido-2-deoxy-d-glucose (NAPA)

A thorough study on the amidation conditions of N-acetyl-l-phenylalanine using TBTU and various bases is reported for the synthesis of 2-(N-acetyl)-l-phenylalanylamido-2-deoxy-d-glucose (NAPA), a promising drug for the treatment of joints diseases. TBTU-mediated diastereoselective amidation reaction with 1,3,4,6-tetra-O-acetyl-β-d-glucosamine always gave racemization of N-acetyl-l-phenylalanine. The stereochemical retention under amidation conditions was studied in detail in the presence of difference bases and via other control experiments, evidencing the possibility to reduce racemization using pyridine as base.

Organo-cyanamides: convenient reagents for catalytic amidation of carboxylic acids

An unprecedented DMAP-catalysed amidation of aryl and alkyl carboxylic acids with organo-cyanamides has been developed. Unlike the use of N-cyano-N-phenyl-p-methylbenzenesulfonamide (NCTS) as an electrophilic cyanating reagent, an unusual desulfonylation/decyanation reaction model has been disclosed for the first time. Remarkable features of this reaction include readily available substrates, simple operation and broad scope, enabling the efficient synthesis of structurally diverse amides. The synthetic utility of this protocol was demonstrated by the late-stage amidation of bioactive carboxylic acids and a scale-up reaction.

A Facile Synthesis of 2-Oxazolines via Dehydrative Cyclization Promoted by Triflic Acid

2-oxazolines are common moieties in numerous natural products, pharmaceuticals, and functional copolymers. Current methods for synthesizing 2-oxazolines mainly rely on stoichiometric dehydration agents or catalytic dehydration promoted by specific catalysts. These conditions either generate stoichiometric amounts of waste or require forcing azeotropic reflux conditions. As such, a practical and robust method that promotes dehydrative cyclization while generating no byproducts would be attractive to oxazoline production. Herein, we report a triflic acid (TfOH)-promoted dehydrative cyclization of N-(2-hydroxyethyl)amides for synthesizing 2-oxazolines. This reaction tolerates various functional groups and generates water as the only byproduct. This method affords oxazoline with inversion of α-hydroxyl stereochemistry, suggesting that alcohol is activated as a leaving group under these conditions. Furthermore, the one-pot synthesis protocol of 2-oxazolines directly from carboxylic acids and amino alcohols is also provided.

Transamidation of aromatic amines with formamides using cyclic dihydrogen tetrametaphosphate

Amide fragments are found to be one of the key constituents in a wide range of natural products and pharmacologically active compounds. Herein, we report a simple and efficient procedure for transamidation with a cyclic dihydrogen tetrametaphosphate. The protocol is simple, does not require any additives, and encompasses a broad substrate scope. To comprehend the mechanism of the present methodology, detailed spectroscopic and kinetic studies were undertaken.

Synthesis of Amide Enol 2-Iodobenzoates by the Regio- and Stereoselective Gold-Catalyzed Acyloxyalkynylation of Ynamides with Hypervalent Iodine Reagents

Multisubstituted alkenes are accessible by a gold-catalyzed acyloxyalkynylation of ynamides with ethynylbenziodoxolones (EBXs) with perfect atom-economy. The EBX reagents transfer both the carboxylate as well as the alkynyl entity. Overall, this cascade comprises the in situ generation of an alkynyl gold(III) species, a stereoselective C(sp)-C(sp²) bond formation, and a C-O coupling at the alkynyl position of the ynamides. This reaction proceeds under mild conditions and accepts a wide range of substrates. A number of tetrasubstituted amide enol 2-iodobenzoates bearing different functional groups were obtained in good to excellent yields. DFT calculations explain the observed regioselectivity. The synthetic potential of the reaction was further demonstrated by a number of selected follow-up transformations.

Amine Activation: "Inverse" Dipeptide Synthesis and Amide Function Formation through Activated Amino Compounds

A copper(II)/HOBt-catalyzed procedure for the synthesis of dipeptides and "general" amides has been developed using microwave irradiation to considerably hasten the reaction. As an alternative to using traditional carboxylic acid activation, the method relies on the use of N-acyl imidazoles as activated amino partners. By doing so, a nonconventional way to reach dipeptides and amides has been proposed through the challenging and less studied N → C direction synthesis. A series of dipeptides and "general" amides have been successfully synthesized, and the applicability of the method has been illustrated in gram-scale syntheses. The mild reaction conditions proposed are completely adequate for couplings in the presence of sensitive amino acids, affording the products without detectable racemization. Furthermore, experimental observations prompted us to propose a plausible reaction pathway for the couplings.

Ynamide Electrophile for the Profiling of Ligandable Carboxyl Residues in Live Cells and the Development of New Covalent Inhibitors

Covalent inhibitors with an electrophilic warhead have received considerable attention due to their remarkable pharmacological properties. However, the electrophilic warhead in covalent drugs is often an α, β-unsaturated amide, and the targets are mainly cysteine or lysine residues. Thus, the development of novel electrophiles that can target other amino acids is highly desirable. Ynamide, a useful and versatile building block, is commonly employed in the construction of various compounds in organic synthesis. The performance of this functional group in a proteome-wide environment has been studied here for the first time, and it has been shown that it can efficiently modify carboxyl residues in situ and in vitro. Upon incorporation of this ynamide warhead into the pharmacophores of kinase inhibitors, the resulting compound showed moderate inhibition against the EGFR L858R mutant but not against EGFR WT. This novel electrophilic group can be used in the development of new types of covalent inhibitors.

Co-Crystal Structure-Guided Optimization of Dual-Functional Small Molecules for Improving the Peroxygenase Activity of Cytochrome P450BM3

We recently developed an artificial P450–H₂O₂ system assisted by dual-functional small molecules (DFSMs) to modify the P450BM3 monooxygenase into its peroxygenase mode, which could be widely used for the oxidation of non-native substrates. Aiming to further improve the DFSM-facilitated P450–H₂O₂ system, a series of novel DFSMs having various unnatural amino acid groups was designed and synthesized, based on the co-crystal structure of P450BM3 and a typical DFSM, N-(ω-imidazolyl)-hexanoyl-L-phenylalanine, in this study. The size and hydrophobicity of the amino acid residue in the DFSM drastically affected the catalytic activity (up to 5-fold), stereoselectivity, and regioselectivity of the epoxidation and hydroxylation reactions. Docking simulations illustrated that the differential catalytic ability among the DFSMs is closely related to the binding affinity and the distance between the catalytic group and heme iron. This study not only enriches the DFSM toolbox to provide more options for utilizing the peroxide-shunt pathway of cytochrome P450BM3, but also sheds light on the great potential of the DFSM-driven P450 peroxygenase system in catalytic applications based on DFSM tunability.

Regio- and Stereoselective Addition to gem-Difluorinated Ene-Ynamides: Access to Stereodefined Fluorinated Dienes

The first synthesis of gem-difluorinated ene-ynamides is presented via deprotonation of trifluoromethylated N-allenamides and δ extrusion of fluorine. These highly reactive building blocks, owing to their dual functional groups, offer a unique entry to difluorinated dienes and to stereodefined, monofluoro-substituted dienes. Stereoselective addition to the ynamide moiety led to difluorinated dienes. A stereocontrolled domino δ elimination reaction followed by an addition/elimination sequence from trifluoromethylated N-allenamides provided exclusively stereodefined monofluorinated ene-ynamides.

Metal-free hydroalkoxylation of ynesulfonamides with alcohols

Efforts for developing a convenient and expeditious method for synthesizing alkoxy-substituted enamides via nucleophilic addition of alcohols to ynesulfonamides are described. This sequence is completely regioselective and highly stereoselective, and leads to the hydroalkoxylation products in high yields under mild reaction conditions.

Ynamide-Mediated Thioamide and Primary Thioamide Syntheses

Environmentally friendly ynamide-mediated thioamidation of monothiocarboxylic acids with amines or ammonium hydroxide for the syntheses of thioamides and primary thioamides is described. Simple and mild reaction conditions enable the reaction to tolerate a wide variety of functional groups such as hydroxyl group, ester, tertiary amine, ketone, and amide moieties. Readily available NaSH served as the sulfur source, avoiding the use of toxic, expensive, and malodorous organic sulfur reagents and making this strategy environmentally friendly and practical. Importantly, the stereochemical integrity of α-chiral monothiocarboxylic acids was maintained during the activation step and subsequent aminolysis process, thus offering a racemization-free strategy for peptide C-terminal modification. Furthermore, a number of thioamide-modified drugs were prepared in good yields by using this protocol and the synthesized primary thioamides were transformed into backbone thiazolyl modified peptides.