Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents

Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure-activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N-B bond is a new strategy for PBP1b inhibition.

Dynamic hydrazone crosslinked salecan/chondroitin sulfate hydrogel platform as a promising wound healing Strategy: A comparative study on antibiotic and probiotic delivery

Natural polysaccharide-based active-ingredient carriers have been a source of great concern for a long time. In order to explore potential antibiotics and probiotics carriers, a novel injectable chondroitin sulfate/salecan (CS) hydrogel was constructed by forming dynamic hydrazone bonds. Scanning electron microscope (SEM), proton nuclear magnetic resonance (1H NMR), Fourier transform infrared spectroscopy (FTIR), bacteriostatic test, and rheological experiments were used to investigate the chemical structure, inherent morphology, and enzymatic corruption of the hydrogel in vitro. The resulting hydrogels exhibited ideal probiotics loading capacity, drug release behavior, excellent antimicrobial activity and variable properties. Crucially, owing to its exceptional biocompatibility and reversible crosslinking network, this hydrogel can function as a three-dimensional extracellular matrix for cells, enabling cells to maintain high vitality and proliferation, and promote wound healing. The aforementioned findings indicated that this novel hydrogel can be a promising candidate as an active-ingredient carrier and scaffold material for tissue engineering.

A melanin-like polymer bearing phenylboronic units as a suitable bioplatform for living cell display technology

Surface display of functional groups with specific reactivity around living cells is an emerging, low cost and highly eco-compatible technology that serves multiple applications, ranging from basic biochemical studies to biomedicine, therapeutics and environmental sciences. Conversely to classical methods exploiting hazardous organic synthesis of precursors or monovalent functionalization via genetics, here we perform functional decoration of individual living microalgae using suitable biocoatings based on polydopamine, a melanin-like synthetic polymer. Here we demonstrate the one-pot synthesis of a functional polydopamine bearing phenylboronic units which can decorate the living cell surfaces via a direct ester formation between boronic units and surface glycoproteins. Furthermore, biosorption of fluorescent sugars on functionalized cell membranes is triggered, demonstrating that these organic coatings act as biocompatible soft shells, still functional and reactive after cell engineering.

In situ bioorthogonal-modulation of m6A RNA methylation in macrophages for efficient eradication of intracellular bacteria

N6-Methyladenosine (m6A) methylation plays a critical role in controlling the RNA fate. Emerging evidence has demonstrated that aberrant m6A methylation in immune cells such as macrophages could alter cell homeostasis and function, which can be a promising target for disease treatment. Despite tremendous progress in regulating the level of m6A methylation, the current methods suffer from the time-consuming operation and annoying off-target effect, which hampers the in situ manipulation of m6A methylation. Here, a bioorthogonal in situ modulation strategy of m6A methylation was proposed. Well-designed covalent organic framework (COF) dots (CIDM) could deprotect the agonist prodrug of m6A methyltransferase, resulting in a considerable hypermethylation of m6A modification. Simultaneously, the bioorthogonal catalyst CIDM showed oxidase (OXD)-mimic activity that further promoted the level of m6A methylation. Ultimately, the potential therapeutic effect of bioorthogonal controllable regulation of m6A methylation was demonstrated through intracellular bacteria eradication. The remarkable antimicrobial outcomes indicate that upregulating m6A methylation in macrophages could reprogram them into the M1 phenotype with high bactericidal activity. We believe that our bioorthogonal chemistry-controlled epigenetics regulatory strategy will provide a unique insight into the development of controllable m6A methylation.

Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously

Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.

Peptide Boronic Acids by Late-Stage Hydroboration on the Solid Phase

Organoboron compounds have a wide range of applications in numerous research fields, and methods to incorporate them in biomolecules are much sought after. Here, on-resin chemical syntheses of aliphatic and vinylogous peptide boronic acids are presented by transition metal-catalyzed late-stage hydroboration of alkene and alkyne groups in peptides and peptoids, for example on allyl- and propargylglycine residues, using readily available chemicals. These methods yield peptide boronic acids with much shorter linkers than previously reported on-resin methods. Furthermore, the methods are regio- and stereoselective, compatible with all canonical amino acid residues and can be applied to short, long, and in part even "difficult" peptide sequences. In a feasibility study, the protected peptide vinylboronic acids are further derivatized by the Petasis reaction using salicylaldehyde derivatives. The ability of the obtained peptide boronic acids to reversibly bind to carbohydrates is demonstrated in a catch-release model experiment using a fluorescently labeled peptide boronic acid on cross-linked dextran beads. In summary, this highlights the potential of the target compounds for drug discovery, glycan-specific target recognition, controlled release, and diagnostics.

Boron catalysis in a designer enzyme

Enzymes play an increasingly important role in improving the benignity and efficiency of chemical production, yet the diversity of their applications lags heavily behind chemical catalysts as a result of the relatively narrow range of reaction mechanisms of enzymes. The creation of enzymes containing non-biological functionalities facilitates reaction mechanisms outside nature's canon and paves the way towards fully programmable biocatalysis1-3. Here we present a completely genetically encoded boronic-acid-containing designer enzyme with organocatalytic reactivity not achievable with natural or engineered biocatalysts4,5. This boron enzyme catalyses the kinetic resolution of hydroxyketones by oxime formation, in which crucial interactions with the protein scaffold assist in the catalysis. A directed evolution campaign led to a variant with natural-enzyme-like enantioselectivities for several different substrates. The unique activation mode of the boron enzyme was confirmed using X-ray crystallography, high-resolution mass spectrometry (HRMS) and 11B NMR spectroscopy. Our study demonstrates that genetic-code expansion can be used to create evolvable enantioselective enzymes that rely on xenobiotic catalytic moieties such as boronic acids and access reaction mechanisms not reachable through catalytic promiscuity of natural or engineered enzymes.

Chemoselective umpolung of thiols to episulfoniums for cysteine bioconjugation

Cysteine conjugation is an important tool in protein research and relies on fast, mild and chemoselective reactions. Cysteinyl thiols can either be modified with prefunctionalized electrophiles, or converted into electrophiles themselves for functionalization with selected nucleophiles in an independent step. Here we report a bioconjugation strategy that uses a vinyl thianthrenium salt to transform cysteine into a highly reactive electrophilic episulfonium intermediate in situ, to enable conjugation with a diverse set of bioorthogonal nucleophiles in a single step. The reactivity profile can connect several nucleophiles to biomolecules through a short and stable ethylene linker, ideal for introduction of infrared labels, post-translational modifications or NMR probes. In the absence of reactive exogenous nucleophiles, nucleophilic amino acids can react with the episulfonium intermediate for native peptide stapling and protein-protein ligation. Ready synthetic access to isotopologues of vinyl thianthrenium salts enables applications in quantitative proteomics. Such diverse applications demonstrate the utility of vinyl-thianthrenium-based bioconjugation as a fast, selective and broadly applicable tool for chemical biology.

Structural and spectroscopic characterization of large boron heterocyclic radicals: Matrix infrared spectroscopy and quantum chemical calculations

Six boron heterocyclic radicals with different conformations or configurations were synthesized in solid neon and identified by matrix isolation infrared spectroscopy as well as quantum-chemical calculations. The ground-state boron atom selectively attacks the C = C bond of cycloheptene forming η2 (1,2)-BC7H12 complex (A), which contains a chair conformation and a boat conformation. Species A isomerizes to the 2,3,4,5,6,7-hexahydroborocine radical (B), which involves an eight-membered boron heterocyclic ring and also has two isomers observed. The 1-(prop-1-en-1-yl)-2,3,4-dihydro borole radical (C) with E-configuration and Z-configuration is generated as the final product under UV light irradiation through ring contraction reaction and the hydrogen atom transfer reaction. The observation of species A and further photo-isomerization to species C is consistent with theoretical predictions that these reactions are thermodynamically exothermic and kinetically facile. This work not only provides a possible route for future design and synthesis of corresponding borole derivatives, but also provides new insights into the structural and spectroscopic information of boron heterocyclic radicals with different conformations and configurations.

The linkage-type and the exchange molecule affect the protein-labeling efficiency of iminoboronate probes

Reversible bioorthogonal conjugation reactions have been exploited in the chemoproteomic field to prepare protein labeling reagents and to visualize labeled proteins. We recently demonstrated that reversible iminoboronates can be used to prepare probes from fragment libraries and that the linkage subsequently can be used to detect the labeled proteins. In this study, we determined the effect of the stability of the iminoboronate linkage on the efficiency of the labeling protocol. Our study reveals that the linkage should be stable enough to allow for efficient targeting, but should be labile enough to detect the labeled protein. Acyl hydrazides were identified as the most suitable handles for the probe synthesis step. Anthranilic hydrazides and N-hydroxy semicarbazides were found to be the most efficient read-out molecules. With these novel exchange molecules, native probe-labeled proteins could be visualized under physiological conditions.

Polyol recognition in catalysis: toward selective modification of glycosylated polypeptides with boronic acid-rhodium(II) catalysts

Proximity-induced methodologies for peptide and protein modification have been developed using recognition elements like inhibitors, antibodies, or affinity tags on amino acids. However, the recognition of saccharides for chemical modification remains widely unexplored. Studies exploring boronic acids and their derivatives have shown their alluring capabilities as selective molecular recognition elements for saccharides, and in this study we describe the application of these ideas to the discovery of a catalytic proximity-induced methodology for covalent modification of glycopeptides using boronic acids as a saccharide recognition element.

A Versatile Route to Acyl (MIDA)Boronates

A modular approach to highly functional acyl (MIDA)boronates is described. It involves the generation of the hitherto unknown radical derived from acetyl (MIDA)boronate and its capture by various alkenes, including electronically unbiased, unactivated alkenes. In contrast to the anion of acetyl (MIDA)boronate, which has not so far been employed in synthesis, the corresponding radical is well behaved and readily produced from the novel α-xanthyl acetyl (MIDA)boronate. This shelf-stable, easily prepared solid is a convenient acyl (MIDA)boronate transfer agent that provides a direct entry to numerous otherwise inaccessible structures, including latent 1,4-dicarbonyl derivatives that can be transformed into B(MIDA) substituted pyrroles and furans. A competition experiment indicated the acyl (MIDA)boronate substituted radical to be more stable than the all-carbon acetonyl radical but somewhat less reactive in additions to alkenes.

Desulfurative Borylation of Small Molecules, Peptides, and Proteins

We introduce a direct conversion of alkyl thiols into boronic acids, facilitated by a water-soluble phosphine, 1,3,5-triaza-7-phosphaadamantane (PTA), in conjunction with tetrahydroxydiboron (B2(OH)4), acting as both a radical initiator and a boron source. This desulfurative borylation reaction has been successfully applied to various substrates, including cysteine residues in oligopeptides and small proteins, primary alkyl thiols found in pharmaceutical compounds, disulfides, and selenocysteine. Optimization of reaction conditions was undertaken to reduce the formation of unwanted reactions, such as the reduction of alanyl or other primary radicals, and to prevent deleterious reactions between the phosphine and N-terminal amine that lead to methylene adducts by utilizing a buffer containing glycine-glycine (GG) dipeptide. The developed method is characterized by its operational simplicity and robustness. Moreover, its compatibility with various functional groups present in peptides and proteins makes it a promising tool for late-stage functionalization, extending its potential application across a broad spectrum of chemical and biological targets.

LiOtBu-Promoted trans-Stereoselective and β-Regioselective Hydroboration of Propargyl Alcohols

A convenient and efficient trans-stereoselective and β-regioselective hydroboration of propargyl alcohols was achieved simply with LiOtBu as the base and (Bpin)2 as the boron reagent in dimethyl sulfoxide at room temperature. Both terminal and internal propargyl alcohols with diverse structures and functional groups underwent the transformation smoothly to produce β-Bpin-substituted (E)-allylic alcohols, of which the synthetic potentials were demonstrated by the downstream conversions of boronate, alkenyl, and hydroxyl groups.

N-Terminal Cysteine Bioconjugation with (2-Cyanamidophenyl)boronic Acids Enables the Direct Formation of Benzodiazaborines on Peptides

Benzodiazaborines (BDABs) have emerged as a valuable tool to produce stable and functional bioconjugates via a click-type transformation. However, the current available methods to install them on peptides lack bioorthogonality, limiting their applications. Here, we report a strategy to install BDABs directly on peptide chains using (2-cyanamidophenyl)boronic acids (2CyPBAs). The resulting BDAB is stabilized through the formation of a key intramolecular B-N bond. This technology was applied in the selective modification of N-terminal cysteine-containing functional peptides.

Alkynone β-trifluoroborates: A new class of amine-specific biocompatible click reagents

Amine-targeting reactions that work under biocompatible conditions or in water are green processes that are extremely useful for the synthesis of functional materials and biotherapeutics. Unfortunately, despite the usefulness of this reaction, there are very few good amine-specific click methods reported thus far. Here, we report an amine-specific click reagent using alkynone β-trifluoroborates as the electrophiles. These boron-containing alkynyl reagents exhibit extremely high chemoselectivity toward amines even in the presence of thiols. The resulting oxaboracycle products are bench-stable, displaying the reactivities of both organoborates and enaminones. Intrinsic advantages of this methodology include benign reaction conditions, operational simplicity, remarkable product stability, and excellent chemoselectivity, which satisfy the criteria of click chemistry and demonstrate the high potential in bioconjugation. Hence, this water-based chemical approach is also applicable to the modification of native amino acids, peptides, and proteins. Ultimately, the essential role of water during the reaction was elucidated.

Empowering boronic acids as hydroxyl synthons for aryne induced three-component coupling reactions

Boronic acids have become one of the most prevalent classes of reagents in modern organic synthesis, displaying various reactivity profiles via C-B bond cleavage. Herein, we describe the utilization of a readily available boronic acid as an efficient surrogate of hydroxide upon activation via fluoride complexation. The hitherto unknown aryne induced ring-opening reaction of cyclic sulfides and three-component coupling of fluoro-azaarenes are developed to exemplify the application value. Different from metal hydroxides or water, this novel hydroxy source displays mild activation conditions, great functionality tolerance and structural tunability, which shall engender a new synthetic paradigm and in a broad context offer new blueprints for organoboron chemistry. Detailed computational studies also recognize the fluoride activation mode, provide in-depth insights into the unprecedented mechanistic pathway and elucidate the reactivity difference of ArB(OH) x F y complexes, which fully support the experimental data.

Analysis of tri-benzeneboronic esters of monosaccharides formed in aqueous solution by MALDI-TOF MS and DFT calculations

The affinity interactions between boronic acids and sugars have been successfully exploited in many fields, such as the sensing of saccharides, selective enrichment of glycoconjugates, and drug delivery. However, despite multiple techniques having been adopted to investigate the reaction of boronate affinity, the pathway of boronate esters formation under aqueous conditions remains controversial. We report a MALDI-MS approach to investigate the interactions between phenylboronic acid and monosaccharides in neutral aqueous solution by using polylevodopa as an innovative substrate instead of conventional matrix. A series of unusual tri-benzeneboronic esters were then revealed. The mass spectrometry data indicate that they bear a dibenzenepyroboronate cyclic ester moiety with seven-membered ring or eight-membered ring. With the aid of theoretical computations, their most likely geometrical structures are elucidated, and these tri-benzeneboronic esters are proposed to be formed via a boroxine binding monosaccharide pathway. This work provides more insight into the mechanism of boronate affinity interaction between boronic acid and sugars and proves the developed MALDI-MS approach is promising for studying interactions between small molecules.

Copper-Catalyzed Borylation of Styrenes by 1,8-Diaminonaphthalene-Protected Diboronic Acid

We report a concise synthesis of 1,8-diaminonaphthalene-protected diboronic acid (B₂(dan)₂), which is a promising borylating agent. B₂(dan)₂ is a bench-stable compound, and it could be utilized for Cu-catalyzed borylation of styrene derivatives. The reaction proceeded in a highly selective manner, and the products were isolated in up to 97% yields. Mechanistic studies revealed that a borate species would be a key intermediate for the borylation reaction.

Single-Molecule Interconversion between Chiral Configurations of Boronate Esters Observed in a Nanoreactor

Isomers of some chemical compounds may be dynamically interconvertible. Due to a lack of sensing methods with a sufficient resolution, however, direct monitoring of such processes can be difficult. Engineered Mycobacterium smegmatis porin A (MspA) nanopores can be applied as nanoreactors so that chemical reactions can be directly monitored. Here, an MspA modified with a phenylboronic acid (PBA) adapter was prepared and was used to observe dynamic interconversion between chiral configurations of boronate esters, which appears as telegraphic switching on top of nanopore events. The mechanism of this behavior was further confirmed by trials with different halogenated catechols, dopamine, adenosine, 1,2-propanediol, and (2R,3R)-2,3-butanediol, and its generality has been demonstrated. These results suggest that an engineered MspA possesses an exceptional resolution in its monitoring of chemical reaction processes and may inspire the future design of nanopore small-molecule sensors.

Dual-Boronic Acid Reagents That Combine Dynamic and Covalent Bioconjugation

Boronic acids and boronate esters find appreciable use in chemical biology. Molecules containing orthogonal boronic acid pairs can be utilized for sequential metal-catalyzed cross-couplings for facile preparation of complex bioconjugates including protein-protein conjugates. In this paper, we expand bis-boronic acid reagents for tandem covalent and dynamic bioconjugation. Sequential cross-coupling of 2-nitroarylboronic acid with cysteine residues and condensation of phenylboronic acid with salicylhydroxamic acids (SHA) readily afforded bioconjugates under physiological conditions with dual covalent and dynamic linkages. Both small molecule- and macromolecule-protein conjugates were amenable with this approach and reversible upon addition of excess unfunctionalized SHA or reactive oxygen species. These investigations provide new insights into the kinetic stability of SHA adducts.

Photocatalytic direct borylation of carboxylic acids

The preparation of high value-added boronic acids from cheap and plentiful carboxylic acids is desirable. To date, the decarboxylative borylation of carboxylic acids is generally realized through the extra step synthesized redox-active ester intermediate or in situ generated carboxylic acid covalent derivatives above 150 °C reaction temperature. Here, we report a direct decarboxylative borylation method of carboxylic acids enabled by visible-light catalysis and that does not require any extra stoichiometric additives or synthesis steps. This operationally simple process produces CO₂ and proceeds under mild reaction conditions, in terms of high step economy and good functional group compatibility. A guanidine-based biomimetic active decarboxylative mechanism is proposed and rationalized by mechanistic studies. The methodology reported herein should see broad application extending beyond borylation.

Allyl phenyl selenides as H2O2 acceptors to develop ROS-responsive theranostic prodrugs

Reactive oxygen species (ROS)-responsive prodrugs have received significant attention due to their capacity to target tumors to relieve the side effects caused by chemotherapy. Herein, a series of novel H₂O₂-activated theranostic prodrugs (CPTSe1-CPTSe7) were developed containing allyl phenyl selenide moieties as H₂O₂ acceptors. Compared with conventional boronate ester-based prodrug CPT-B, CPTSe1 was more stable in human plasma and showed a more complete release of camptothecin (CPT) in H₂O₂ inducing experiment. The selectively activated fluorescence signals of CPTSe1 in tumor cells make it useful for real-time monitoring of CPT release and H₂O₂ detection. Furthermore, excellent selectivity of CPTSe1 was achieved for tumor cells over normal cells. Our results provide a new platform for the development of H₂O₂-responsive theranostic prodrugs.

Boron-Assisted Selective Citrulline Modification under Mild Conditions

Protein citrullination is one type of protein post-translational modification. Previous methods entail the use of a strongly acidic condition (pH <1), which impedes its exploration under physiological and pathological conditions. Here, we developed a biocompatible method based on o-boron-assisted citrulline modification. We demonstrated that this method enables selective and mainly irreversible modification of citrulline residues under neutral conditions. We expect that it will provide a valuable tool for the study of protein citrullination.

Reversible and Highly Ordered Biointerfaces for Efficient Capture and Nondestructive Release of Circulating Tumor Cells

The engineering strategy of artificial biointerfaces is vital for governing their performances in bioanalysis and diagnosis. Highly ordered arrangement of affinity ligands on the interface surface facilitates efficient interaction with target molecules, whereas biointerfaces aimed at drug delivery or rare cell isolation require sophisticated stimuli-response mechanisms. However, it is still challenging to facilely fabricate biointerfaces possessing the two features. Herein, we endow a biointerface with both reversibility and capability to orderly assemble affinity ligands by introducing boronic acid moieties alone. By boronate conjugation via glycosylation sites, avidin was well arranged at the surface of boronic acid-decorated carbon nitride nanosheets for the assembly of biotinylated aptamers. The ordered orientation of aptamers largely relieved their inactivation caused by inter-strand entanglement, facilitating significant increase in cell affinity for the isolation of circulating tumor cells (CTCs). The reversible boronate conjugation also facilitated mild release of CTCs by acid fructose with high cell viability. This engineered interface was capable of isolating CTCs from the peripheral blood of tumor-bearing mice and cancer patients. The successful utilization of the isolated CTCs in the downstream drug susceptibility test and mutation analysis demonstrated the clinical potential of this biointerface for the early diagnosis of cancers and precision medicine.

Applications of the Reversible Boronic Acids/Boronate Switch to Nucleic Acids

Over the last decades, boron and nucleic acids chemistries have gained a lot of attention for biological, medicinal and analytical applications. Our laboratory has a long-standing interest in both chemistries and owing to the ability of boronic acids to react with cis-diol function in aqueous media we developed over the years a variety of applications ranging from molecular recognition and sensing to the development of reversible dynamic systems in which the natural phosphodiester linkage was replaced by a boronate. In this account, we summarize research results from our group from our preliminary studies on molecular recognition of ribonucleosides to the dynamic assembly of functional DNAzymes. In particular, the various parameters influencing the dynamic nature of these reversible covalent bonds able to respond to external stimuli are discussed. Finally, current challenges and opportunities for boron-based nucleic acids are also addressed.

Investigating a Boronate-Affinity-Guided Acylation Reaction for Labelling Native Antibodies

The excellent molecular recognition capabilities of monoclonal antibodies (mAbs) have opened up exciting opportunities for biotherapeutic discovery. Taking advantage of the full potential of this tool necessitates affinity ligands capable of conjugating directly with small molecules to a defined degree of biorthogonality, especially when modifying natural Abs. Herein, a bioorthogonal boronate-affinity-based Ab ligand featuring a 4-(dimethylamino)pyridine and an S-aryl thioester to label full-length Abs is reported. The photoactivatable linker in the acyl donor facilitated purification of azide-labelled Ab (N₃ -Ab) was quantitatively cleaved upon brief exposure to UV light while retaining the original Ab activity. Click reactions enabled the precise addition of biotin, a fluorophore, and a pharmacological agent to the purified N₃ -Abs. The resulting immunoconjugate showed selectivity against targeted cells. Bioorthogonal traceless design and reagentless purification allow this strategy to be a powerful tool to engineer native antibodies amenable to therapeutic intervention.

Diazaborines oxidize slowly with H2O2 but rapidly with peroxynitrite in aqueous buffer

Reactive oxygen species (ROS) such as hydrogen peroxide (H₂O₂) and peroxynitrite (ONOO^-) oxidize arylboronic acids to their corresponding phenols. When used in molecular imaging probes and in ROS-responsive molecules, however, simple arylboronic acids struggle to discriminate between H₂O₂ and ONOO^- because of their fast rate of reaction with both ROS. Here, we show that diazaborines (DABs) react slowly with H₂O₂ but rapidly with peroxynitrite in an aqueous buffer. In addition to their slow reaction with H₂O₂, the immediate product of DAB oxidation with H₂O₂ and ONOO^- can yield a kinetically trapped CN Z-isomer that slowly equilibrates with its E-isomer. Taken together, our work shows that diazaborines exhibit enhanced kinetic discrimination between H₂O₂ and ONOO^- compared to arylboronic acids, opening up new opportunities for diazaborine-based tools in chemical biology.

Synthesis, structure, properties and antimicrobial activity of para trifluoromethyl phenylboronic derivatives

The [2-formyl-4-(trifluoromethyl)phenyl]boronic acid as well as its benzoxaborole and bis(benzoxaborole) derivatives were obtained and their properties studied. The 2-formyl compound displays an unusual structure in the crystalline state, with a significant twist of the boronic group, whereas in DMSO solution it tautomerizes with formation of a cyclic isomer. All the studied compounds exhibit relatively high acidity as well as a reasonable antimicrobial activity. Docking studies showed interactions of all the investigated compounds with the binding pocket of Candida albicans LeuRS. High activity against Bacillus cereus was determined for the 2-formyl compound as well as for the novel bis(benzoxaborole), whereas the studied benzoxaborole shows high antifungal action with MIC values equal to 7.8and 3.9 μg/mL against C. albicans and A. niger respectively. None of the studied compounds exhibits reasonable activity against E. coli.

Dual Stimuli-Responsive Dynamic Covalent Peptide Tags: Toward Sequence-Controlled Release in Tumor-like Microenvironments

Dynamic covalent chemistry (DCvC) has emerged as a versatile synthetic tool for devising stable, stimuli-responsive linkers or conjugates. The interplay of binding affinity, association and dissociation constants exhibits a strong influence on the selectivity of the reaction, the conversion rate, as well as the stability in aqueous solutions. Nevertheless, dynamic covalent interactions often exhibit fast binding and fast dissociation events or vice versa, affecting their conversion rates or stabilities. To overcome the limitation in linker design, we reported herein dual responsive dynamic covalent peptide tags combining a pH responsive boronate ester with fast association and dissociation rates, and a redox-active disulfide with slow formation and dissociation rate. Precoordination by boronic acid-catechol interaction improves self-sorting and selectivity in disulfide formation into heterodimers. The resulting bis-peptide conjugate exhibited improved complex stability in aqueous solution and acidic tumor-like extracellular microenvironment. Furthermore, the conjugate responds to pH changes within the physiological range as well as to redox conditions found inside cancer cells. Such tags hold great promise, through cooperative effects, for controlling the stability of bioconjugates under dilution in aqueous media, as well as designing intelligent pharmaceutics that react to distinct biological stimuli in cells.

Chiral Benzothiazole Monofluoroborate Featuring Chiroptical and Oxygen-Sensitizing Properties: Synthesis and Photophysical Studies

Advances in personalized medicine are prompting the development of multimodal agents, that is, molecules that combine properties promoting various diagnostic and therapeutic applications. General approaches exploit chemical conjugation of therapeutic agents with contrast agents or the design of multimodal nanoplatforms. Herein, we report the design of a single molecule that exhibits potential for different diagnostic modes as well as the ability to sensitize oxygen, thus offering potential for photodynamic therapy. Exceptionally, this work involves the synthesis and chiral resolution of an enantiomeric pair of chiral monofluoroborates that contain a stereogenic boron atom. Combining experimental and theoretical chiroptical studies allowed the unambiguous determination of their absolute configuration. Photophysical investigations established the ability of this compound to sensitize oxygen even in the absence of heavy atoms within its structure. The synthesis of a chiral benzothiazole monofluoroborate paves a way to multimodal diagnostic tools (fluorescence and nuclear imaging) while also featuring potential therapeutic applications owing to its ability to activate oxygen to its singlet state for use in photodynamic therapy.

Boronic acid with high oxidative stability and utility in biological contexts

Despite their desirable attributes, boronic acids have had a minimal impact in biological contexts. A significant problem has been their oxidative instability. At physiological pH, phenylboronic acid and its boronate esters are oxidized by reactive oxygen species at rates comparable to those of thiols. After considering the mechanism and kinetics of the oxidation reaction, we reasoned that diminishing electron density on boron could enhance oxidative stability. We found that a boralactone, in which a carboxyl group serves as an intramolecular ligand for the boron, increases stability by 10⁴-fold. Computational analyses revealed that the resistance to oxidation arises from diminished stabilization of the p orbital of boron that develops in the rate-limiting transition state of the oxidation reaction. Like simple boronic acids and boronate esters, a boralactone binds covalently and reversibly to 1,2-diols such as those in saccharides. The kinetic stability of its complexes is, however, at least 20-fold greater. A boralactone also binds covalently to a serine side chain in a protein. These attributes confer unprecedented utility upon boralactones in the realms of chemical biology and medicinal chemistry.

Fluorescent-Oxaboroles: Synthesis and Optical Property by Sugar Recognition

The optical property of fluorescent unit-conjugated aliphatic oxaboroles has been investigated. The oxaboroles provide good fluorescence quantum yields and selective recognition toward D-ribose and D-ribose containing molecules. The molecular recognition induced significant fluorescence quenching. The property of the boroles showed the possibility of the boron-based nicotinamide adenine dinucleotide (NAD) sensor probe.

Slow-Onset, Potent Inhibition of Mandelate Racemase by 2-Formylphenylboronic Acid. An Unexpected Adduct Clasps the Catalytic Machinery

o-Carbonyl arylboronic acids such as 2-formylphenylboronic acid (2-FPBA) are employed in biocompatible conjugation reactions with the resulting iminoboronate adduct stabilized by an intramolecular N-B interaction. However, few studies have utilized these reagents as active site-directed enzyme inhibitors. We show that 2-FPBA is a potent reversible, slow-onset inhibitor of mandelate racemase (MR), an enzyme that has served as a valuable paradigm for understanding enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. Kinetic analysis of the progress curves for the slow onset of inhibition of wild-type MR using a two-step kinetic mechanism gave Ki and Ki* values of 5.1 ± 1.8 and 0.26 ± 0.08 μM, respectively. Hence, wild-type MR binds 2-FPBA with an affinity that exceeds that for the substrate by ∼3000-fold. K164R MR was inhibited by 2-FPBA, while K166R MR was not inhibited, indicating that Lys 166 was essential for inhibition. Unexpectedly, mass spectrometric analysis of the NaCNBH3-treated enzyme-inhibitor complex did not yield evidence of an iminoboronate adduct. 11B nuclear magnetic resonance spectroscopy of the MR·2-FPBA complex indicated that the boron atom was sp3-hybridized (δ 6.0), consistent with dative bond formation. Surprisingly, X-ray crystallography revealed the formation of an Nζ-B dative bond between Lys 166 and 2-FPBA with intramolecular cyclization to form a benzoxaborole, rather than the expected iminoboronate. Thus, when o-carbonyl arylboronic acid reagents are employed to modify proteins, the structure of the resulting product depends on the protein architecture at the site of modification.

Boronic Acid Pairs for Sequential Bioconjugation

Boronic acids can play diverse roles when applied in biological environments, and employing boronic acid structures in tandem could provide new tools for multifunctional probes. This Letter describes a pair of boronic acid functional groups, 2-nitro-arylboronic acid (NAB) and (E)-alkenylboronic acid (EAB), that enable sequential cross-coupling through stepwise nickel- and copper-catalyzed processes. The selective coupling of NAB groups enables the preparation of stapled peptides, protein-protein conjugates, and other bioconjugates.

Recent Developments and Strategies for Mutually Orthogonal Bioorthogonal Reactions

Over the past decade, several different metal-free bioorthogonal reactions have been developed to enable simultaneous double-click labeling with minimal-to-no competing cross-reactivities; such transformations are termed 'mutually orthogonal'. More recently, several examples of successful triple ligation strategies have also been described. In this minireview, we discuss selected aspects of the development of orthogonal bioorthogonal reactions over the past decade, including general strategies to drive future innovations to achieve simultaneous, mutually orthogonal click reactions in one pot.

Boronic acid complexes with amino phenolic N,O-ligands and their use for non-covalent protein fluorescence labeling

Phenylboronic acid (PBA) forms neutral tetrahedral N,O-coordinated 6-membered cyclic complexes with stability constants reaching the values as large as 1.3 × 10⁴ M^-1 at pH 7.4 in water with amino phenolic compounds including 2-(2'-hydroxyphenyl)-1H-benzimidazole (HPBI) often used for protein probing and labeling. The crystal structures of isolated complexes demonstrate unusually high for boronate adducts degree of the tetrahedral character of the boron atom with short B-N bonds in agreement with their high solution stability. The complexation of PBA with HPBI, causes a strong enhancement of the fluorescence of the "enol" form of the ligand, increases the affinity of the dye to a protein (bovine serum albumin) and makes more pronounced the shift in emission maximum induced by the protein binding. Similar, but larger effects are observed with an amino HPBI derivative and with a stronger boronic acid benzoxaborole. Thus, the binding constant to the protein about 2 × 10⁴ M^-1 for free HPBI increases to 1.2 × 10⁶ M^-1 for the complex of 5-amino-HPBI with benzoxaborole making it suitable for an efficient non-covalent protein labeling or bioconjugation.

Modular Approaches to Synthesize Activity- and Affinity-Based Chemical Probes

Combinatorial and modular methods to synthesize small molecule modulators of protein activity have proven to be powerful tools in the development of new drug-like molecules. Over the past decade, these methodologies have been adapted toward utilization in the development of activity- and affinity-based chemical probes, as well as in chemoproteomic profiling. In this review, we will discuss how methods like multicomponent reactions, DNA-encoded libraries, phage displays, and others provide new ways to rapidly screen novel chemical probes against proteins of interest.

Rapid and Selective Chemical Editing of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) via CuII -Catalyzed β-Borylation of Dehydroamino Acids

We report the fast and selective chemical editing of ribosomally synthesized and post-translationally modified peptides (RiPPs) by β-borylation of dehydroalanine (Dha) residues. The thiopeptide thiostrepton was modified efficiently using CuII -catalysis under mild conditions and 1D/2D NMR of the purified product showed site-selective borylation of the terminal Dha residues. Using similar conditions, the thiopeptide nosiheptide, lanthipeptide nisin Z, and protein SUMO_G98Dha were also modified efficiently. Borylated thiostrepton showed an up to 84-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity was maintained in thiostrepton and nosiheptide. The introduced boronic-acid functionalities were shown to be valuable handles for chemical mutagenesis and in a reversible click reaction with triols for the pH-controlled labeling of RiPPs.

Synthesis of functionalized copillar[4+1]arenes and rotaxane as heteromultivalent scaffolds

In this study, novel copillar[4+1]arenes were used as central heteromultivalent scaffolds via orthogonal couplings with a series of biologically relevant molecules such as carbohydrates, α-amino acids, biotin and phenylboronic acid. Further modifications by introducing maleimides or cyclooctyne groups provided molecular probes adapted to copper-free click chemistry. An octa-azidated fluorescent rotaxane bearing two distinct ligands was also generated in a fully controlled manner.

Boronic Acid-Mediated Activity Control of Split 10-23 DNAzymes

The 10-23 DNAzyme is an artificially developed Mg2+ -dependent catalytic oligonucleotide that can cleave an RNA substrate in a sequence-specific fashion. In this study, new split 10-23 DNAzymes made of two nonfunctional fragments, one of which carries a boronic acid group at its 5' end, while the other has a ribonucleotide at its 3' end, were designed. Herein it is demonstrated that the addition of Mg2+ ions leads to assembly of the fragments, which in turn induces the formation of a new boronate internucleoside linkage that restores the DNAzyme activity. A systematic evaluation identified the best-performing system. The results highlight key features for efficient control of DNAzyme activity through the formation of boronate linkages.