Diboronic Acid Anhydride-Catalyzed Direct Peptide Bond Formation Enabled by Hydroxy-Directed Dehydrative Condensation

Controlled synthesis of superhydrophilic flower-like hierarchical porous diboronate affinity materials for capturing biomarkers

BACKGROUND

Boronate affinity chromatography represents a powerful analytical technique for the selective separation and enrichment of biomolecules containing cis-diol moieties, including carbohydrates, glycoproteins, and other cis-dihydroxy compounds. While boronate affinity materials (BAMs) have shown promise in glycosylation-based separation and analysis, their practical application is hindered by non-biocompatible binding pH, low enrichment efficiency for low-abundance samples, non-specific adsorption, and limited loading capacity. To address these limitations, this work focuses on developing flower-like hierarchical porous diboronate affinity materials (FHP-DBAMs) with enhanced binding strength, selectivity, and capacity for cis-diol-containing biomolecules.

RESULTS

FHP-DBAM was synthesized via a facile sol-gel method, using tetrahydroxydiboron as a hydrophilic diboronic acid monomer. The electron-withdrawing nature and hydrophilicity of diboronate affinity mechanism enable FHP-DBAM to operate at lower pH values (pH ≥ 5), addressing the biocompatibility issue. DFT and experiment calculations confirm the enhanced cis-diol binding affinity of diboronate affinity mechanism compared with monoboronate affinity mechanism, resulting in a remarkably low dissociation constant (DFT Kd = 6.74 × 10-5 M, experiment Kd = 9.95 × 10-5 M) for FHP-DBAM. Furthermore, the unique flower-like hierarchical porous structure provides a high surface area and nanoconfinement effect, significantly boosting target molecule loading capacity and affinity reaction kinetics. Compared to traditional BAMs, FHP-DBAM exhibits over ten times higher loading capacity. As a proof-of-concept, FHP-DBAM successfully captures the biomarker GM1 in breast cancer cells MCF-7 with high efficiency.

SIGNIFICANCE AND NOVELTY

This work introduces diboronate affinity mechanism and flower-like hierarchical porous structure as new solution to overcome the limitations of conventional BAMs. FHP-DBAMs achieve lower binding pH, enhanced selectivity, and stronger binding stability through diboronate affinity mechanism. The unique flower-like porous structure maximizes surface area and active sites, addressing low enrichment efficiency and loading capacity. These advancements are critical for the efficient and biocompatible separation of cis-diol-containing biomolecules.

Gem-Diboronic Acids: A Motif for Anion Recognition in Competitive Media

Gem-diboronic acid derivatives have previously been demonstrated to facilitate substrate binding within a metal's secondary coordination sphere, but their use as an anion recognition motif has not been explored. Here, we introduce the gem-diboronic acid motif as a highly effective group for recognition of oxoanions in aqueous solution. Anion receptors based on this motif demonstrate higher binding affinities than other common neutral motifs such as amides and (thio)ureas, and display a unique selectivity profile. Studies with a receptor bearing two gem-diboronic acid groups, receptor 2, indicate that the interaction with anions is highly directional. Despite its simplicity, receptor 2 represents one of the most selective receptors for malonate reported to date.

Synthesis of N-methyl secondary amides via diboronic acid anhydride-catalyzed dehydrative condensation of carboxylic acids with aqueous methylamine

In this study, we present the first catalytic methodology for synthesizing N-methyl secondary amides via dehydrative condensation of hydroxycarboxylic acids with readily available and safe aqueous methylamine, employing diboronic acid anhydride (DBAA) as the catalyst. DBAA catalysis can also be applied to direct amidations using aqueous ethylamine or aqueous dimethylamine. Moreover, we demonstrate the applicability of this catalytic system for the concise synthesis of eight biologically active compounds containing β-amino alcohol motifs, including halostachine, synephrine, longimammine, phenylephrine, metanephrine, normacromerine, etilefrine, and macromerine.

An Electrochemical Design for a General Catalytic Carboxylic Acid Substitution Platform via Anhydrides at Room Temperature: Amidation, Esterification, and Thioesterification

An original concept for catalytic electrochemical dehydration has enabled a suite of acid substitutions, including amidation, esterification, and thioesterification, through a linchpin anhydride formed in situ. By avoiding stoichiometric dehydrating agents, this method addresses a leading challenge in organic synthesis and green chemistry. It also proceeds without acid additives at room temperature, accesses a diverse range of product structures, is easily scaled, and enabled the first example of catalytic peptide coupling at room temperature.

Improved Electrochemical Peptide Synthesis Enabled by Electron-Rich Triaryl Phosphines

While remarkable progress has been made in the development of peptide medicines, many problems related to peptide synthesis remain unresolved. Previously, we reported electrochemical peptide synthesis using a phosphine as a potentially recyclable coupling reagent. However, there was room for improvement from the point of view of reaction efficiency, especially in the carboxylic acid activation step and the peptide bond formation step. To overcome these challenges, we searched for the optimal phosphine. Among phosphines with various electronic properties, we found that electron-rich triaryl phosphines improved the reaction efficiency. Consequently, we successfully performed electrochemical peptide synthesis on sterically hindered and valuable amino acids. We also synthesized oligopeptides that were challenging with our previous method. Finally, we examined the effect of substituents on the phosphine cations, and gained some insights into reactivity, which will aid researchers designing reactions involving phosphine cations.

Organoboron catalysis for direct amide/peptide bond formation

Amides and peptides are ubiquitous functional groups found in several natural and artificial materials, and they are essential for the advancement of life and material sciences. In particular, their relevance in clinical medicine and drug discovery has increased in recent years. Dehydrative condensation of readily available carboxylic acids with amines is the most "direct" method for amide synthesis; however, this methodology generally requires a stoichiometric amount of condensation agent (coupling reagent). Catalytic direct dehydrative amidation has become an "ideal" methodology for synthesizing amides from the perspective of green chemistry, with water as the only byproduct in principle, high atom efficiency, environmentally friendly, energy saving, and safety. Conversely, organoboron compounds, such as boronic acids, which are widely used in various industries as coupling reagents for Suzuki-Miyaura cross-coupling reactions or pharmaceutical structures, are environmentally friendly molecules that have low toxicity and are easy to handle. Based on the chemical properties of organoboron compounds, they have potential Lewis acidity and the ability to form reversible covalent bonds with dehydration, making them attractive as catalysts. This review explores studies on the development of direct dehydrative amide/peptide bond formation reactions from carboxylic acids using organoboron catalysis, classifying them based on chemical bonding and catalysis over approximately 25 years, from the early developmental days to 2023.

Development of boronic acid catalysts for direct amidation of aromatic carboxylic acids using fluorescence-based screening

Direct amidation of carboxylic acids with amines holds significant importance; therefore, catalytic processes involving boronic acids have undergone extensive investigation. However, studies focused on the amidation of aromatic carboxylic acids remain limited. In this study, we introduce a fluorescence-based screening methodology employing an anthracene derivative probe, facilitating the rapid evaluation of various amidation catalysts. Using this approach, boronic acids were evaluated for their catalytic potential. Our findings reveal that 2-hydroxyphenylboronic acid (C7), previously deemed inefficient for aliphatic acids, effectively catalyzes the amidation of aromatic acids. The catalysts identified through this method consistently achieved high yields, reaching up to 98% across a broad spectrum of substrates.

Emergent Organoboron Acid Catalysts

Organoboron acids are stable, organic-soluble Lewis acids with potential application as catalysts for a wide variety of chemical reactions. In this review, we summarize the utility of boronic and borinic acids, as well as boric acid, as catalysts for organic transformations. Typically, the catalytic processes exploit the Lewis acidity of trivalent boron, enabling the reversible formation of a covalent bond with oxygen. Our focus is on recent developments in the catalysis of dehydration, carbonyl condensation, acylation, alkylation, and cycloaddition reactions. We conclude that organoboron acids have a highly favorable prospectus as the source of new catalysts.

Peptide coupling using recyclable bicyclic benziodazolone

We report a greener peptide coupling using bicyclic benziodazolone and triarylphosphine as coupling reagents. Bicyclic benziodazolone also works as a base and can be recovered as the corresponding iodine(I) compound after use, which can be converted to the original iodine(III) reagent by electrolytic oxidation.

Hydroxy-directed peptide bond formation from α-amino acid-derived inert esters enabled by boronic acid catalysis

A boronic acid-catalyzed peptide bond formation from α-amino acid methyl esters is described. The catalysis showed high chemoselectivity for β-hydroxy-α-amino esters, affording the peptides in high to excellent yields with high functional group tolerance. This hydroxy-directed peptide bond formation could be applicable to oligopeptide syntheses. This is the first successful example of organoboron-catalyzed peptide bond formation from α-amino acid-derived inert esters.

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.

Concise Synthesis of 2,5-Diketopiperazines via Catalytic Hydroxy-Directed Peptide Bond Formations

2,5-Diketopiperazines (DKPs) with hydroxymethyl functional groups are essential structures found in many bioactive molecules and functional materials. We have established a simple protocol for the concise synthesis of this type of DKPs through diboronic acid anhydride-catalyzed hydroxy-directed peptide bond formations. The sequential reactions in this report, which consist of three steps, an intermolecular catalytic condensation reaction in which water is the only byproduct, a simple deprotection of the nitrogen-protecting group, and an intramolecular cyclization, enabled the synthesis of functionalized DKPs in high to excellent yields without any intermediate purification. The utility of this protocol has been demonstrated by synthesizing natural products, phomamide and Cyclo(Deala-l-Leu).

Expeditious Access to the B3NO2 Heterocycle Enabling Modular Derivatization

DATB (1,3-dioxa-5-aza-2,4,6-triborinane) is a unique six-membered heterocycle exhibiting proficient catalytic activity in direct dehydrative amidation. Reported herein is an improved synthetic protocol for DATB derivatives featuring a concise two-step chromatography-free process. Suzuki-Miyaura coupling assembled 2,6-dibromoaniline derivatives and 1,2-phenylenediboronic acid to afford dimeric B-spiroborate salts. Acidic untying of the spiroborates gave rise to the DATB ring system with various substituents.

Heterocyclic Boron Acid Catalyzed Dehydrative Amidation of Aliphatic/Aromatic Carboxylic Acids with Amines

A commercially available and versatile dehydrative amidation catalyst, featuring a thianthrene boron acid structure, has been developed. The catalyst shows high catalytic activity to both aliphatic and less reactive aromatic carboxylic acid substrates, including several bioactive or clinical molecules with a carboxylic acid group.

Less Is More: N(BOH)2 Configuration Exhibits Higher Reactivity than the B3NO2 Heterocycle in Catalytic Dehydrative Amide Formation

Diboron substructures have emerged as a promising scaffold for the catalytic dehydrative amidation of carboxylic acids and amines. This Letter describes the design, synthesis, and evaluation of the first isolable N(BOH)₂ compound as an amidation catalyst. The new catalyst outperforms the previously reported B₃NO₂ heterocycle catalyst, with respect to turnover frequency, albeit the former gradually decomposes upon exposure to amines. This work opens up an avenue for designing a better catalyst for direct amidation.

Fusion of Aza- and Oxadiborepins with Furans in a Reversible Ring-Opening Process Furnishes Versatile Building Blocks for Extended π-Conjugated Materials

A modular synthesis of both difurooxa- and difuroazadiborepins from a common precursor is demonstrated. Starting from 2,2'-bifuran, after protection of the positions 5 and 5' with bulky silyl groups, formation of the novel polycycles proceeds through opening of the furan rings to a dialkyne and subsequent re-cyclization in the borylation step. The resulting bifuran-fused diborepins show pronounced stability, highly planar tricyclic structures, and intense blue light emission. Deprotection and transformation into dibrominated building blocks that can be incorporated into π-extended materials can be performed in one step. Detailed DFT calculations provide information about the aromaticity of the constituent rings of this polycycle.

Organocatalytic Activation of Inert Hydrosilane for Peptide Bond Formation

We describe the development of a reliable catalytic protocol for peptide bond formation that is generally applicable to natural and unnatural α-amino acids, β-amino acids, and peptides bearing various functional groups. A 10 mol % loading of HSi[OCH(CF₃)₂]₃ as a catalyst was sufficient to guarantee a consistently high yield of the resulting peptide. This method facilitates the sustainable utilization of natural resources by using a catalyst and an auxiliary based on earth-abundant silicon.

A diselenobis-functionalized magnetic catalyst based on iron oxide/silica nanoparticles suggested for amidation reactions

In this study, a new heterogeneous magnetic catalytic system based on selenium-functionalized iron oxide nanoparticles is presented and suggested for facilitating amide/peptide bonds formation. The prepared nanocatalyst, entitled as "Fe3O4/SiO2-DSBA" (DSBA stands for 2,2'-diselanediylbis benzamide), has been precisely characterized for identifying its physicochemical properties. As the most brilliant point, the catalytic performance of the designed system can be mentioned, where only a small amount of Fe3O4/SiO2-DSBA (0.25 mol%) has resulted in 89% reaction yield, under a mild condition. Also, given high importance of green chemistry, convenient catalyst particles separation from the reaction medium through its paramagnetic property (ca. 30 emu·g-1) should be noticed. This particular property provided a substantial opportunity to recover the catalyst particles and successfully reuse them for at least three successive times. Moreover, due to showing other excellences, such as economic benefits and nontoxicity, the presented catalytic system is recommended to be scaled up and exploited in the industrial applications.

Thionyl Fluoride-Mediated One-Pot Substitutions and Reductions of Carboxylic Acids

Thionyl fluoride (SOF₂) is an underutilized reagent that is yet to be extensively studied for its synthetic applications. We previously reported that it is a powerful reagent for both the rapid syntheses of acyl fluorides and for one-pot peptide couplings, but the full scope of these nucleophilic acyl substitutions had not been explored. Herein, we report one-pot thionyl fluoride-mediated syntheses of peptides and amides (35 examples, 45-99% yields) that were not explored in our previous study. The scope of thionyl fluoride-mediated nucleophilic acyl substitutions was also expanded to encompass esters (24 examples, 64-99% yields) and thioesters (11 examples, 24-96% yields). In addition, we demonstrate that the scope of thionyl fluoride-mediated one-pot reactions can be extended beyond nucleophilic acyl substitutions to mild reductions of carboxylic acids using NaBH₄ (13 examples, 33-80% yields).

On the Copper-Promoted Backbone Arylation of Histidine-Containing Peptides Using Triarylbismuthines

We report herein our detailed investigation on the histidine-directed backbone arylation of histidine-containing peptides using triarylbismuth reagents. The reaction proceeds on the backbone NH of the amino acid that precedes the histidine, the so-called n–1 position. The protocol is applicable to dipeptides where the histidine is located at the C-terminus and to tripeptides where the histidine occupies the central position. The transformation is promoted by copper(II) acetate in the presence of phenanthroline (Phen) and diisopropylethylamine in dichloromethane at 50 °C under oxygen. An excellent scope was observed for the triarylbismuthines. In all cases, the imidazole ring of the histidine is protected with a trityl group to prevent the arylation of the side chain. An ATCUN-like model is proposed to explain the observed results.

Methyltrimethoxysilane (MTM) as a Reagent for Direct Amidation of Carboxylic Acids

Methyltrimethoxysilane [MTM, CH₃Si(OMe)₃] has been demonstrated to be an effective, inexpensive, and safe reagent for the direct amidation of carboxylic acids with amines. Two simple workup procedures that provide the pure amide product without the need for further purification have been developed. The first employs an aqueous base-mediated annihilation of MTM. The second involves simple product crystallization from the reaction mixture providing a low process mass intensity direct amidation protocol.

Rapid and column-free syntheses of acyl fluorides and peptides using ex situ generated thionyl fluoride

Thionyl fluoride (SOF₂) was first isolated in 1896, but there have been less than 10 subsequent reports of its use as a reagent for organic synthesis. This is partly due to a lack of facile, lab-scale methods for its generation. Herein we report a novel protocol for the ex situ generation of SOF₂ and subsequent demonstration of its ability to access both aliphatic and aromatic acyl fluorides in 55-98% isolated yields under mild conditions and short reaction times. We further demonstrate its aptitude in amino acid couplings, with a one-pot, column-free strategy that affords the corresponding dipeptides in 65-97% isolated yields with minimal to no epimerization. The broad scope allows for a wide range of protecting groups and both natural and unnatural amino acids. Finally, we demonstrated that this new method can be used in sequential liquid phase peptide synthesis (LPPS) to afford tri-, tetra-, penta-, and decapeptides in 14-88% yields without the need for column chromatography. We also demonstrated that this new method is amenable to solid phase peptide synthesis (SPPS), affording di- and pentapeptides in 80-98% yields.

Heteroelement Analogues of Benzoxaborole and Related Ring Expanded Systems

The review covers the chemistry of organoboron heterocycles structurally related to benzoxaboroles where one of the carbon atoms in a boracycle or a fused benzene ring is replaced by a heteroelement such as boron, silicon, tin, nitrogen, phosphorus, or iodine. Related ring expanded systems including those based on naphthalene and biphenyl cores are also described. The information on synthetic methodology as well as the basic structural and physicochemical characteristics of these emerging heterocycles is complemented by a presentation of their potential applications in organic synthesis and medicinal chemistry, the latter aspect being mostly focused on the promising antimicrobial activity of selected compounds.

6-Halo-2-pyridone as an efficient organocatalyst for ester aminolysis

It was found that 6-halo-2-pyridones catalysed ester aminolysis in which not only reactive aryl esters but also relatively less reactive methyl and benzyl esters could be used as a substrate. The reaction could be performed without strictly dry and anaerobic conditions and the 6-chloro-2-pyridone catalyst could be recovered quantitatively after reaction. The method could be applied to dipeptide synthesis from methyl or benzyl esters of amino acids, where a high enantiomeric purity of the products was maintained. The mechanism involving dual activation of ester and amine substrates through hydrogen bonding between catalyst and substrates is proposed where 6-halo-2-pyridones act as a bifunctional Brønsted acid/base catalyst.

6-Halo-2-pyridones effectively catalyse ester aminolysis as bifunctional catalysts. This reaction did not require any special conditions and was operationally convenient.

Amide bond formation: beyond the dilemma between activation and racemisation

The development of methods for amide bond formation without recourse to typical condensation reagents has become an emerging research area and has been actively explored in the past quarter century. Inspired by the structure of vitamin B12, we have developed a metal-templated macrolactamisation that generates a new wave towards classical macrolactam synthesis. Further, distinct from the extensively used methods with condensation reagents or catalysts based on catalyst/reagent control our metal-catalysed methods based on substrate control can effectively address long-standing challenges such as racemisation in the field of peptide chemistry. In addition, the substrate-controlled strategy demonstrates the feasibility of "remote" peptide bond-forming reaction catalysed by a metal-ligand complex. Moreover, an originally designed hydrosilane/aminosilane system can avoid not only racemisation but also unnecessary waste production. This feature article documents our discovery and application of our original approaches in amide bond formation.

Dithiophene-Fused Oxadiborepins and Azadiborepins: A New Class of Highly Fluorescent Heteroaromatics

Access to dithiophene-fused oxadiborepins and the first azadiborepins attained via a modular synthesis route are presented. The new compounds emit intense blue light, some of which demonstrate fluorescence quantum yields close to unity. Cyclic voltammetry (CV) revealed electrochemically reversible one-electron reduction processes. The weak aromatic character of the novel 1,2,7-azadiborepin ring is demonstrated with in-depth theoretical investigations using nucleus-independent chemical shift (NICS) scans and anisotropy of the induced current density (ACID) calculations.