Ring Structure and Aromatic Substituent Effects on the pK a of the Benzoxaborole Pharmacophore

Applications of chromatographic methods in metabolomics: A review

Chromatography is a robust and reliable separation method that can use various stationary phases to separate complex mixtures commonly seen in metabolomics. This review examines the types of chromatography and stationary phases that have been used in targeted or untargeted metabolomics with methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. General considerations for sample pretreatment and separations in metabolomics are considered, along with the various supports and separation formats for chromatography that have been used in such work. The types of liquid chromatography (LC) that have been most extensively used in metabolomics will be examined, such as reversed-phase liquid chromatography and hydrophilic liquid interaction chromatography. In addition, other forms of LC that have been used in more limited applications for metabolomics (e.g., ion-exchange, size-exclusion, and affinity methods) will be discussed to illustrate how these techniques may be utilized for new and future research in this field. Multidimensional LC methods are also discussed, as well as the use of gas chromatography and supercritical fluid chromatography in metabolomics. In addition, the roles of chromatography in NMR- vs. MS-based metabolomics are considered. Applications are given within the field of metabolomics for each type of chromatography, along with potential advantages or limitations of these separation methods.

The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology

Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.

Modular Synthesis of Complex Benzoxaboraheterocycles through Chelation-Assisted Rh-Catalyzed [2 + 2 + 2] Cycloaddition

Benzoxaboraheterocycles (BOBs) are moieties of increasing interest in the pharmaceutical industry; however, the synthesis of these compounds is often difficult or impractical due to the sensitivity of the boron moiety, the requirement for metalation-borylation protocols, and lengthy syntheses. We report a straightforward, modular approach that enables access to complex examples of the BOB framework through a Rh-catalyzed [2 + 2 + 2] cycloaddition using MIDA-protected alkyne boronic acids. The key to the development of this methodology was overcoming the steric barrier to catalysis by leveraging chelation assistance. We show the utility of the method through synthesis of a broad range of BOB scaffolds, mechanistic information on the chelation effect, intramolecular alcohol-assisted BMIDA hydrolysis, and linear/cyclic BOB limits as well as comparative binding affinities of the product BOB frameworks for ribose-derived biomolecules.

Multifaceted personality and roles of heme enzymes in industrial biotechnology

Heme enzymes are the most prominent category of iron-containing metalloenzymes with the capability of catalyzing an astonishingly wide range of reactions like epoxidation, hydroxylation, demethylation, desaturation, reduction, sulfoxidation, and decarboxylation. Various enzymes in this category are P450s, heme peroxidases, catalases, myoglobin, cytochrome C, and others. Besides this, the natural promiscuity and amenability of these enzymes to protein engineering and evolution have also added several non-native reactions such as C-H, N-H, S-H insertions, cyclopropanation, and other industrially important reactions to their capabilities. Surprisingly, all of these reactions and their wide substrate scopes are attributed to changes in the active site scaffold of different heme enzymes as the center of all enzymes is constituted by a porphyrin ring containing iron. Multiple prominent research groups across the world, including 2018, Nobel Laureate Frances Arnold's group, have shown keen interest in engineering and evolving these enzymes for utilizing their industrial potential. Besides engineering the active site, researchers have also explored the possibility of these enzymes catalyzing non-native reactions by replacing the center porphyrin ring with other cofactors or by changing the iron in the porphyrin ring with other metal ions along with engineering the active site and thereby creating novel artificial metalloenzymes. Thus, in this mini-review from our group, for the first time, we are trying to catalog various activities catalyzed by heme enzymes and their engineered variants and their active usage in various industries along with shedding light on their potential for use in various applications in the future.

Elemental exchange: Bioisosteric replacement of phosphorus by boron in drug design

Continuous efforts are being directed toward the employment of boron in drug design due to its advantages and unique characteristics including a plethora of target engagement modes, lower metabolism, and synthetic accessibility, among others. Phosphates are components of multiple drug molecules as well as clinical candidates, since they play a vital role in various biochemical functions, being components of nucleotides, energy currency- ATP as well as several enzyme cofactors. This review discusses the unique chemistry of boron functionalities as phosphate bioisosteres - "the boron-phosphorus elemental exchange strategy" as well as the superiority of boron groups over other commonly employed phosphate bioisosteres. Boron phosphate-mimetics have been utilized for the development of enzyme inhibitors as well as novel borononucleotides. Both the boron functionalities described in this review-boronic acids and benzoxaboroles-contain a boron connected to two oxygens and one carbon atom. The boron atom of these functional groups coordinates with a water molecule in the enzyme site forming a tetrahedral molecule which mimics the phosphate structure. Although boron phosphate-mimetic molecules - FDA-approved Crisaborole and phase II/III clinical candidate Acoziborole are products of the boron-phosphorus bioisosteric elemental exchange strategy, this technique is still in its infancy. The review aims to promote the use of this strategy in future medicinal chemistry projects.

Correlations between the Electronic Structure and Energetics of the Catalytic Steps in Homogeneous Water Oxidation Catalysis

The development of an efficient electrocatalyst for the water oxidation reaction is limited by unfavorable scaling relations between catalytic intermediates, resulting in an overpotential. In contrast to heterogeneous catalysts, the electronic structure of homogeneous catalysts can be modified to a great extent due to a tailored ligand design. However, studies utilizing the tunability of organic ligands have rarely been conducted in a systematic manner and, as of yet, have not produced catalytic paths that avoid the aforementioned unfavorable scaling relations. To investigate the influence of electron-donating groups (EDGs) or electron-withdrawing groups (EWGs) on elementary steps in electrochemical water oxidation catalysis, cis-[Ru(bpy)2(H2O)]2+ (bpy = 2,2'-bipyridine) was selected as the scaffold that was modified with methyl, methoxy, chloro, and trifluoromethyl groups. This catalyst can undergo several electron transfer (ET), proton transfer (PT), and proton-coupled electron transfer (PCET) steps that were all probed experimentally. In this systematic study, it was found that PCET steps are relatively insensitive with respect to the presence of EDGs or EWGs, while the decoupled ET and PT steps are more heavily affected. However, the influence of the substituents decreases with an increasing oxidation state of Ru due to a lack of d-electrons available at the Ru center for π-backbonding to the bipyridine ligand. Therefore, the RuV/VI redox couple appears to be relatively unaffected by the substituent. Nevertheless, the implementation of EWGs can shift all oxidation events to a very narrow potential window. Not only do our findings illustrate how electronic substituents affect the entire potential energy landscape of the catalytic water oxidation reaction, but they also show that the cis-[Ru(bpy)2(H2O)]2+ compounds follow different design rules and scaling relations, as has been reported for every other oxygen evolution catalyst thus far.

Synthesis and Biophysical and Biological Studies of N-Phenylbenzamide Derivatives Targeting Kinetoplastid Parasites

The AT-rich mitochondrial DNA (kDNA) of trypanosomatid parasites is a target of DNA minor groove binders. We report the synthesis, antiprotozoal screening, and SAR studies of three series of analogues of the known antiprotozoal kDNA binder 2-((4-(4-((4,5-dihydro-1H-imidazol-3-ium-2-yl)amino)benzamido)phenyl)amino)-4,5-dihydro-1H-imidazol-3-ium (1a). Bis(2-aminoimidazolines) (1) and bis(2-aminobenzimidazoles) (2) showed micromolar range activity against Trypanosoma brucei, whereas bisarylimidamides (3) were submicromolar inhibitors of T. brucei, Trypanosoma cruzi, and Leishmania donovani. None of the compounds showed relevant activity against the urogenital, nonkinetoplastid parasite Trichomonas vaginalis. We show that series 1 and 3 bind strongly and selectively to the minor groove of AT DNA, whereas series 2 also binds by intercalation. The measured pKa indicated different ionization states at pH 7.4, which correlated with the DNA binding affinities (ΔTm) for series 2 and 3. Compound 3a, which was active and selective against the three parasites and displayed adequate metabolic stability, is a fine candidate for in vivo studies.

Expanding the Role of Boron in New Drug Chemotypes: Properties, Chemistry, Pharmaceutical Potential of Hemiboronic Naphthoids

New chemotypes and bioisosteres can open a new chemical space in drug discovery and help meet an urgent demand for novel agents to fight infections and other diseases. With the aim of identifying new boron-containing drug chemotypes, this article details a comprehensive evaluation of the pseudoaromatic hemiboronic naphthoids, benzoxaza- and benzodiazaborines. Relevant physical properties in aqueous media (acidity, solubility, log P, and stability) of prototypic members of four subclasses were determined. Both scaffolds are amenable to common reactions used in drug discovery, such as chemoselective Suzuki-Miyaura, Chan-Lam, and amidation reactions. Small model libraries were prepared to assess the scope of these transformations, and the entire collection was screened for antifungal (Candida albicans) and antibacterial activity (MRSA, Escherichia coli), unveiling promising benzoxazaborines with low micromolar minimum inhibitory concentration values. Select DMPK assays of representative compounds suggest promising drug-like behavior for all four subclasses. Moreover, several drug isosteres were evaluated for anti-inflammatory and anticancer activity as appropriate.

Recent research of BTK inhibitors: Methods of structural design, pharmacological activities, manmade derivatives and structure-activity relationship

Protein kinases constitute the largest group within the kinase family, and mutations and translocations of protein kinases due to genetic alterations are intimately linked to the pathogenesis of numerous diseases. Bruton's tyrosine kinase (BTK) is a member of the protein kinases and plays a pivotal role in the development and function of B cells. BTK belongs to the tyrosine TEC family. The aberrant activation of BTK is closely associated with the pathogenesis of B-cell lymphoma. Consequently, BTK has always been a critical target for treating hematological malignancies. To date, two generations of small-molecule covalent irreversible BTK inhibitors have been employed to treat malignant B-cell tumors, and have exhibited clinical efficacy in hitherto refractory diseases. However, these drugs are covalent BTK inhibitors, which inevitably lead to drug resistance after prolonged use, resulting in poor tolerance in patients. The third-generation non-covalent BTK inhibitor Pirtobrutinib has obtained approval for marketing in the United States, thereby circumventing drug resistance caused by C481 mutation. Currently, enhancing safety and tolerance constitutes the primary issue in developing novel BTK inhibitors. This article systematically summarizes recently discovered covalent and non-covalent BTK inhibitors and classifies them according to their structures. This article also provides a detailed discussion of binding modes, structural features, pharmacological activities, advantages and limitations of typical compounds within each structure type, providing valuable references and insights for developing safer, more effective and more targeted BTK inhibitors in future studies.

An endoscopically compatible fast-gelation powder forms Janus-adhesive hydrogel barrier to prevent postoperative adhesions

Postoperative adhesions occur widely in various tissues, bringing the risk of secondary surgery and increased medical burden. Hydrogel barriers with Janus-adhesive ability can achieve physical isolation of adjacent tissues and are therefore considered an ideal solution. However, integrating endoscopic delivery convenience and viscoelastic Janus hydrogel formation remains a great challenge. Here, we present a report of the in situ formation of Janus-adhesive hydrogel barrier using a sprayable fast-Janus-gelation (FJG) powder. We first methacrylate the polysaccharide macromolecules to break the intermolecular hydrogen bonds and impart the ability of rapid hydration. FJG powder can rapidly absorb interfacial water and crosslink through borate ester bonds, forming a toughly adhesive viscoelastic hydrogel. The Janus barrier can be simply formed by further hydrating the upper powder with cationic solution. We construct rat models to demonstrate the antiadhesions efficiency of viscoelastic FJG hydrogels in organs with different motion modalities (e.g., intestine, heart, liver). We also developed a low-cost delivery device with a standardized surgical procedure and further validated the feasibility and effectiveness of FJG powder in minimally invasive surgery using a preclinical translational porcine model. Considering the advantages in terms of therapeutic efficacy, clinical convenience, and commercialization, our results reveal the great potential of Janus-gelation powder materials as a next-generation antiadhesions barrier.

11B NMR Spectroscopy: Structural Analysis of the Acidity and Reactivity of Phenyl Boronic Acid-Diol Condensations

Phenyl boronic acids are valuable for medical diagnostics and biochemistry studies due to their ability to readily bind with carbohydrates in water. Incorporated in carbohydrates are 1,2-diols, which react with boronic acids through a reversible covalent condensation pathway. A wide variety of boronic acids have been employed for diol binding with differing substitution of the phenyl ring, with the goals of simplifying their synthesis and altering their thermodynamics of complexation. One method for monitoring their pK_a's and binding is ¹¹B NMR spectroscopy. Herein, we report a comprehensive study employing ¹¹B NMR spectroscopy to determine the pK_a of the most commonly used phenyl boronic acids and their binding with catechol or d,l-hydrobenzoin as prototypical diols. The chemical shift of the boronic acid transforming into the boronate ester was monitored at pHs ranging from 2 to 10. With each boronic acid, the results confirm (1) the necessity to use pHs above their pK_a's to induce complexation, (2) that the pK_a's change in the presence of diols, and (3) that ¹¹B NMR spectroscopy is a particularly convenient tool for monitoring these interconnected acidity and binding phenomena.

Unraveling the Silent Hydrolysis of Cyclic B-X/C═C Isosteres: The Striking Impact of a Single Heteroatom on the Aromatic, Acidic, and Dynamic Properties of Hemiboronic Phenanthroids

Although heterocyclic hemiboronic acids are represented in several recently approved drugs, many questions remain unanswered regarding the physical properties and reactivity of these boranol (BOH)-containing compounds in aqueous media. Over the past 60 years, studies on the acidic and aromatic character of 10-hydroxy-10,9-boroxarophenanthrene and its boraza analog have been conflicting. In contradiction with the Lewis acidic behavior of arylboronic acids in aqueous conditions, it has been proposed that the central boroheterocyclic ring of these borophenanthroids confers sufficient aromatic character to compel the boranol unit to behave as a Brønsted acid and favor the boron oxy conjugate base, thereby avoiding the disruption of cyclic resonance that would otherwise occur with a tetravalent boronate anion. These questions are addressed with a combination of physical and spectroscopic characterizations, X-ray crystallographic analysis, and computational studies. Although both oxa and aza derivatives are conclusively shown to behave as Lewis acids in aqueous solutions, according to pK_a measurements and MO and NICS calculations, only the boraza derivatives possess an appreciable aromatic character within the boroheterocyclic ring. For the first time, the possibility of dynamic chemical exchange via a reversible hydrolysis of the endocyclic B-heteroatom bond was examined using VT and EXSY NMR with suitable probe compounds. Whereas the boraza analog is static at neutral pH, its oxa analog undergoes a rapid hydrolytic ring opening-closing equilibrium with the transient boronic acid. Altogether, this study will guide the methodical application of these heterocycles as reaction catalysts, in bioconjugation, and as new-drug chemotypes and bioisosteres of pharmaceutically important classes of heterocycles.

Merging Electron Deficient Boronic Centers with Electron-Withdrawing Fluorine Substituents Results in Unique Properties of Fluorinated Phenylboronic Compounds

Fluorinated boron species are a very important group of organoboron compounds used first of all as receptors of important bioanalytes, as well as biologically active substances, including Tavaborole as an antifungal drug. The presence of substituents containing fluorine atoms increases the acidity of boronic compounds, which is crucial from the point of view of their interactions with analytes or certain pathogen's enzymes. The review discusses the electron acceptor properties of fluorinated boronic species using both the acidity constant (pK_a) and acceptor number (AN) in connection with their structural parameters. The NMR spectroscopic data are also presented, with particular emphasis on ¹⁹F resonance due to the wide range of information that can be obtained from this technique. Equilibria in solutions, such as the dehydration of boronic acid to form boroxines and their esterification or cyclization with the formation of 3-hydroxyl benzoxaboroles, are discussed. The results of the latest research on the biological activity of boronic compounds by experimental in vitro methods and theoretical calculations using docking studies are also discussed.

Reactive chemistry for covalent probe and therapeutic development

Bioactive small molecules that form covalent bonds with a target protein are important tools for basic research and can be highly effective drugs. This review highlights reactive groups found in a collection of thiophilic and oxophilic drugs that mediate pharmacological activity through a covalent mechanism of action (MOA). We describe the application of advanced proteomic and bioanalytical methodologies for assessing selectivity of these covalent agents to guide and inspire the search for additional electrophiles suitable for covalent probe and therapeutic development. While the emphasis is on chemistry for modifying catalytic serine, threonine or cysteine residues, we devote a substantial fraction of the review to a collection of exploratory reactive groups of understudied residues on proteins.

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.

How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features-Multifactor Studies

Substitution is well-known to modulate the physico-chemical properties of molecules. In this study, a combined, multifactor approach was employed to determine a plethora of substitution patterns using –Br and –O-H in 1,4-naphthoquinone and its derivatives. On the basis of classical Density Functional Theory (DFT), 25 models divided into three groups were developed. The first group contains 1,4-naphthoquinone and its derivatives substituted only by –Br. The second group consists of compounds substituted by –Br and one –O-H group. As a result of the substitution, an intramolecular hydrogen bond was formed. The third group also contains –Br as a substituent, but two –O-H groups were introduced and two intramolecular hydrogen bonds were established. The simulations were performed at the ωB97XD/6-311++G(2d,2p) level of theory. The presence of substituents influenced the electronic structure of the parent compound and its derivatives by inductive effects, but it also affected the geometry of the 2 and 3 groups, due to the intramolecular hydrogen bonding and the formation of a quasi-ring/rings. The static DFT models were applied to investigate the aromaticity changes in the fused rings based on the Harmonic Oscillator Model of Aromaticity (HOMA). The OH stretching was detected for the compounds from groups 2 and 3 and further used to find correlations with energetic parameters. The evolution of the electronic structure was analyzed using Hirshfeld atomic charges and the Substituent Active Region (cSAR) parameter. The proton reaction path was investigated to provide information on the modulation of hydrogen bridge properties by diverse substitution positions on the donor and acceptor sides. Subsequently, Car–Parrinello Molecular Dynamics (CPMD) was carried out in the double-bridged systems (group 3) to assess the cooperative effects in double –O-H-substituted systems. It was determined that the –O-H influence on the core of the molecule is more significant than that of –Br, but the latter has a major impact on the bridge dynamics. The competitive or synergic effect of two –Br substituents was found to depend on the coupling between the intramolecular hydrogen bridges. Thus, the novel mechanism of a secondary (cooperative) substituent effect was established in the double-bridged systems via DFT and CPMD results comparison, consisting of a mediation of the bromine substitutions’ influence by the cooperative proton transfer events in the hydrogen bridges.

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.

L-DOPA Dioxygenase Activity on 6-Substituted Dopamine Analogues

Dioxygenase enzymes are essential protein catalysts for the breakdown of catecholic rings, structural components of plant woody tissue. This powerful chemistry is used in nature to make antibiotics and other bioactive materials or degrade plant material, but we have a limited understanding of the breadth and depth of substrate space for these potent catalysts. Here we report steady-state and pre-steady-state kinetic analysis of dopamine derivatives substituted at the 6-position as substrates of L-DOPA dioxygenase, and an analysis of that activity as a function of the electron-withdrawing nature of the substituent. Steady-state and pre-steady-state kinetic data demonstrate the dopamines are impaired in binding and catalysis with respect to the cosubstrate molecular oxygen, which likely afforded spectroscopic observation of an early reaction intermediate, the semiquinone of dopamine. The reaction pathway of dopamine in the pre-steady state is consistent with a nonproductive mode of binding of oxygen at the active site. Despite these limitations, L-DOPA dioxygenase is capable of binding all of the dopamine derivatives and catalyzing multiple turnovers of ring cleavage for dopamine, 6-bromodopamine, 6-carboxydopamine, and 6-cyanodopamine. 6-Nitrodopamine was a single-turnover substrate. The variety of substrates accepted by the enzyme is consistent with an interplay of factors, including the capacity of the active site to bind large, negatively charged groups at the 6-position and the overall oxidizability of each catecholamine, and is indicative of the utility of extradiol cleavage in semisynthetic and bioremediation applications.

Development of structurally extended benzosiloxaboroles - synthesis and in vitro biological evaluation

The synthesis of potassium 6-hydroxy-7-chloro-1,1-dimethyl-3,3-difluorobenzo-1,2,3-siloxaborolate 5b from readily available 4-bromo-2-chlorophenol was developed. This compound proved useful in various derivatizations resulting in a wide range of O-functionalized benzosiloxaboroles. Reactions of 5b with selected substituted benzoyl chlorides gave rise to a series of respective derivatives with 6-benzoate side groups attached to the benzosiloxaborole core. Furthermore, treatment of 5b with substituted benzenesufonyl chlorides afforded several benzosiloxaboroles bearing functionalized benzenesulfonate moieties at the 6 position. The synthesis of related chloropyridine-2-yloxy substituted benzosiloxaboroles was accomplished by a standard approach involving silylation/boronation of appropriate heterodiaryl ethers. Investigation of biological activity of obtained compounds revealed that some benzoate and most benzenesulfonate derivatives exhibit high activity against Gram-positive cocci such as methicillin-sensitive Staphylococcus aureus ATCC 6538P as well as methicillin-resistant S. aureus ATCC 43300 with the MIC values in the range of 0.39–3.12 mg L⁻¹. Some benzenesulfonate derivatives showed also potent activity against Enterococcus faecalis ATCC 29212 and E. faecium ATCC 6057 with MIC = 6.25 mg L⁻¹. Importantly, for the most promising cocci-active benzenesulfonate derivatives the obtained MIC values were far below the cytotoxicity limit determined with respect to human normal lung fibroblasts (MRC-5). For those derivatives, the obtained IC₅₀ values were higher than 12.3 mg L⁻¹. The results of antimicrobial activity and cytotoxicity indicate that the tested compounds can be considered as potential antibacterial agents.

The synthesis of potassium 6-hydroxy-7-chloro-1,1-dimethyl-3,3-difluorobenzo-1,2,3-siloxaborolate 5b from readily available 4-bromo-2-chlorophenol was developed.

Synthesis of Fluorinated Aminoalkylboronic Acids from Amphoteric α-Boryl Aldehydes

Our ongoing search for underdeveloped functional group combinations has brought to light α-fluorinated aminoalkylboronic acids, a new class of molecules featuring the B-CF linkage. These compounds can now be generated from secondary amines and α-boryl aldehydes through electrophilic fluorination of boryl enamines or enamides. Fluorinated β-aminoalkylboronic acids show no signs of degradation under ambient conditions. We present evidence for the involvement of chair-like motifs, favored over the acyclic forms by up to 1.7±0.1 kcal mol^-1 in water and held together by an amine-boronate hydrogen bond. Fluorinated β-aminoalkylboronic acids are stable over a wide pH range and are characterized by a pK_a of 3.4, which is the lowest of any alkylboronic acid.

Lewis or Brønsted? A Rectification of the Acidic and Aromatic Nature of Boranol-Containing Naphthoid Heterocycles

Boron-containing heterocycles are important in a variety of applications from drug discovery to materials science; therefore a clear understanding of their structure and reactivity is desirable to optimize these functions. Although the boranol (B-OH) unit of boronic acids behaves as a Lewis acid to form a tetravalent trihydroxyborate conjugate base, it has been proposed that pseudoaromatic hemiboronic acids may possess sufficient aromatic character to act as Brønsted acids and form a boron oxy conjugate base, thereby avoiding the disruption of ring aromaticity that would occur with a tetravalent boronate anion. Until now no firm evidence existed to ascertain the structure of the conjugate base and the aromatic character of the boron-containing ring of hemiboronic "naphthoid" isosteres. Here, these questions are addressed with a combination of experimental, spectroscopic, X-ray crystallographic, and computational studies of a series of model benzoxazaborine and benzodiazaborine naphthoids. Although these hemiboronic heterocycles are unambiguously shown to behave as Lewis acids in aqueous solutions, boraza derivatives possess partial aromaticity provided their nitrogen lone electron pair is sufficiently available to participate in extended delocalization. As demonstrated by dynamic exchange and crossover experiments, these heterocycles are stable in neutral aqueous medium, and their measured pK_a values are consistent with the ability of the endocyclic heteroatom substituent to stabilize a partial negative charge in the conjugate base. Altogether, this study corrects previous inaccuracies and provides conclusions regarding the properties of these compounds that are important toward the methodical application of hemiboronic and other boron heterocycles in catalysis, bioconjugation, and medicinal chemistry.

Progress in the medicinal chemistry of organoboron compounds

The review aims to draw attention to the latest advances in the organoboron chemistry and therapeutic use of organoboron compounds. The synthetic strategies towards boron-containing compounds with proven in vitro and/or in vivo biological activities, including derivatives of boronic acids, benzoxaboroles, benzoxaborines and benzodiazaborines, are summarized. Approaches to the synthesis of hybrid structures containing an organoboron moiety as one of the pharmacophores are considered, and the effect of this modification on the pharmacological activity of the initial molecules is analyzed. On the basis of analysis of the published data, the most promising areas of research in the field of organoboron compounds are identified, including the latest methods of synthesis, modification and design of effective therapeutic agents.

The bibliography includes 246 references.

Potential of Biocatalysis in Pharmaceuticals

Biocatalysis has been continuously evolving as an essential tool which is playing a significant role in the industrial synthesis of chemicals, active pharmaceuticals, pharmaceutical intermediates, etc. where the high-yielding chemo-, regio-, and enantioselective reactions are needed. Despite its vital importance, industrial biocatalysis is facing certain limitations such as operational stability, economic viability, efficient recovery, and reusability. The limitations mentioned can be overcome by the isolation of specific enzyme producers from extreme environment by protein engineering, bioinformatics, and recombinant DNA technologies. Recently, chemoenzymatic pathway and biological cascade reactions have also been developed and designed to perform the synthesis of pharmaceuticals. In this chapter, we compile the broad applications of biocatalysts in the synthesis of pharmaceuticals.

Chemoresponsive polymer systems for selective molecular recognition of organic molecules in biological systems

Smart polymer materials that respond to a chemical stimulus are applied for the construction of biomedical devices and purification/separation systems. Small organic molecules are a particular type of stimulus. Their abnormal concentration indisputably indicates certain diseases. They are also hazardous environment contaminants. Polymer materials, which structure is selectively changed in the presence of a defined organic compound are promising in view of regulation of certain biomedical functions, as well as in view of chemical detectors construction. This review summarizes the state of the art in the self-assemblies of amphiphilic copolymers and polymer networks sensitive toward organic species, with an emphasis on the reports from the last decade. We focus on the relationship between the selectivity of introduced receptor moieties responsible for the change of material structure, the overall structure of material and its functionality.

NMR quantification of H-bond donating ability for bioactive functional groups and isosteres

The H-bond donating ability for 127 compounds including drug fragments and isosteres have been quantified using a simple and rapid method with ³¹P NMR spectroscopy. Functional groups important to medicinal chemistry were evaluated including carboxylic acids, alcohols, phenols, thioic acids and nitrogen group H-bond donors. ³¹P NMR shifts for binding to a phosphine oxide probe have a higher correlation with equilibrium constants for H-bonding (log K^H_A) than acidity (pK_a), indicating that these binding experiments are representative of H-bonding ability and not proton transfer. Additionally, ³¹P NMR binding data for carboxylic acid isosteres correlates with physicochemical properties such as lipophilicity, membrane permeability and plasma protein binding. This method has been used to evaluate the H-bond donating ability of small molecule drug compounds such as NSAIDs and antimicrobials.

Differential Sensing of Saccharides Based on an Array of Fluorinated Benzosiloxaborole Receptors

Fluorinated benzosiloxaboroles–silicon congeners of benzoxaboroles, were synthesized and tested as molecular receptors for mono- and disaccharides. The receptors differed in the Lewis acidity of the boron center as well as in the number of potential binding sites. The calculated stability constants indicated different binding affinity of benzosiloxaborole derivatives towards selected saccharides, enabling their classification using a receptor array-based sensing. Unique fluorescence fingerprints were created on the basis of competitive interactions of the studied receptors with both Alizarin Red S (ARS) and tested saccharide molecules. Detailed chemometric analysis of the obtained fluorescence data (based on partial least squares-discriminant analysis and hierarchical clustering analysis) provided the differential sensing of common saccharides, in particular the differentiation between glucose and fructose. In addition, DFT calculations were carried out to shed light on the binding mechanism under different pH conditions.

Boronic acid and diol-containing polymers: how to choose the correct couple to form "strong" hydrogels at physiological pH

Dynamic covalent hydrogels crosslinked by boronate ester bonds are promising materials for biomedical applications. However, little is known about the impact of the crosslink structure on the mechanical behaviour of the resulting network. Herein, we provide a mechanistic study on boronate ester crosslinking upon mixing hyaluronic acid (HA) backbones modified, on the one hand, with two different arylboronic acids, and on the other hand, with three different saccharide units. Combining rheology, NMR and computational analysis, we demonstrate that carefully selecting the arylboronic-polyol couple allows for tuning the thermodynamics and molecular exchange kinetics of the boronate ester bond, thereby controlling the rheological properties of the gel. In particular, we report the formation of "strong" gels (i.e. featuring slow relaxation dynamics) through the formation of original complex structures (tridentate or bidentate complexes). These findings offer new prospects for the rational design of hydrogel scaffolds with tailored mechanical response.

5-Trifluoromethyl-2-formylphenylboronic Acid

2-Formylphenylboronic acids display many interesting features, not only from synthetic but also from an application as well as structural points of view. 5-Trifluoromethyl-2-formyl phenylboronic acid has been synthesized and characterized in terms of its structure and properties. The presence of an electron-withdrawing substituent results in a considerable rise in the acidity in comparison with its analogues. In some solutions, the title compound isomerizes with formation of the corresponding 3-hydroxybenzoxaborole. Taking into account the probable mechanism of antifungal action of benzoxaboroles, which blocks the cytoplasmic leucyl-tRNA synthetase (LeuRS) of the microorganism, docking studies with the active site of the enzymes have been carried out. It showed possible binding of the cyclic isomer into the binding pocket of Candida albicans LeuRS, similar to that of the recently approved benzoxaborole antifungal drug (AN2690, Tavaborole, Kerydin). In case of Escherichia coli LeuRS, the opened isomer displays a much higher inhibition constant in comparison with the cyclic one. The antimicrobial activity of the title compound was also investigated in vitro, showing moderate action against Candida albicans. The compound reveals higher activity against Aspergillus niger as well as bacteria such as Escherichia coli and Bacillus cereus. In case of Bacillus cereus, the determined Minimum Inhibitory Concentration (MIC) value is lower than that of AN2690 (Tavaborole). The results confirm potential of 2-formylphenylboronic acids as antibacterial agents and give a hint of their possible mechanism of action.

Self-crosslinking smart hydrogels through direct complexation between benzoxaborole derivatives and diols from hyaluronic acid

By tailoring the structure of benzoxaborole (BOR), self-crosslinking hydrogels based on hyaluronic acid (HA) modified with BOR derivatives are obtained for the first time through the direct BOR-HA diol complexation at physiological pH.

Efficient Heterogeneous Palladium-Catalyzed Oxidative Cascade Reactions of Enallenols to Furan and Oxaborole Derivatives

A heterogeneous palladium-catalyzed oxidative cyclization of enallenols has been developed for the construction of highly substituted furan and oxaborole derivatives. The heterogeneous catalyst (Pd-AmP-MCF) exhibits high activity, high site- and stereoselectivity, and efficient palladium recyclability in the transformations.

Benzoxaboroles-Novel Autotaxin Inhibitors

Autotaxin (ATX) is an extracellular enzyme that hydrolyses lysophosphatidylcholine (LPC) to lysophosphatidic acid (LPA), which has a role in the mediation of inflammation, fibrosis and cancer. ATX is a drug target that has been the focus of many research groups during the last ten years. To date, only one molecule, Ziritaxestat (GLPG1690) has entered the clinic; it is currently in Phase 3 clinical trials for idiopathic pulmonary fibrosis. Other small molecules, with different binding modes, have been investigated as ATX inhibitors for cancer including compounds possessing a boronic acid motif such as HA155. In this work, we targeted new, improved inhibitors of ATX that mimic the important interactions of boronic acid using a benzoxaborole motif as the acidic warhead. Furthermore, we aimed to improve the plasma stability of the new compounds by using a more stable core spacer than that embedded in HA155. Compounds were synthesized, evaluated for their ATX inhibitory activity and ADME properties in vitro, culminating in a new benzoxaborole compound, 37, which retains the ATX inhibition activity of HA155 but has improved ADME properties (plasma protein binding, good kinetic solubility and rat/human plasma stability).

Bis-benzoxaboroles: Design, Synthesis, and Biological Evaluation as Carbonic Anhydrase Inhibitors

The synthesis, characterization, and biological evaluation of a series of compounds incorporating two or three benzoxaborole moieties is reported. Three different synthetic strategies were used to explore within this series as much chemical space as possible, all starting from the 6-aminobenzoxaborole reagent: amide coupling, imine bond formation, and squarate coupling. Eleven new compounds were isolated in pure form, and single crystals were obtained for two of them. These compounds were then evaluated as carbonic anhydrase inhibitors against the cytosolic hCA I and II and the transmembrane hCA IV, IX, and XII isoforms. While the benzoxaborole scaffold has been recently introduced as a new chemotype for carbonic anhydrase inhibition, these new multivalent derivatives exhibited superior inhibitory activity against the tumor-associated isoform hCA IX. In particular, compared to monovalent 6-aminobenzoxaborole (K _I = 813 nM) and 6-carboxybenzoxaborole (K _I = 400 nM), derivative 2h characterized by a glutamic acid structural core and two benzoxaborole moieties was found to be more potent (K _I = 64 nM) and more selective over human hCA II.

Spectrophotometric determination of α-hydroxytropolone pK a values: A structure-acidity relationship study

α-Hydroxytropolones (αHTs) have a wealth of biological activity owing to their ability to serve as metalbinding fragments for many therapeutically valuable dinuclear metalloenzymes. They also have the potential to exist in as many as 4 protonation states under aqueous acidic or basic conditions. The following details how UV absorption can be used to generate pK a values on a series of αHTs. The studies also provide some knowledge into how the acidity and basicity change with some different functional groups. These studies thus provide new strategies and knowledge that could be valuable in leveraging αHTs as metal-binding fragments in drug-development pursuits.

Design of N-Benzoxaborole Benzofuran GSK8175-Optimization of Human Pharmacokinetics Inspired by Metabolites of a Failed Clinical HCV Inhibitor

We previously described the discovery of GSK5852 (1), a non-nucleoside polymerase (NS5B) inhibitor of hepatitis C virus (HCV), in which an N-benzyl boronic acid was essential for potent antiviral activity. Unfortunately, facile benzylic oxidation resulted in a short plasma half-life (5 h) in human volunteers, and a backup program was initiated to remove metabolic liabilities associated with 1. Herein, we describe second-generation NS5B inhibitors including GSK8175 (49), a sulfonamide-N-benzoxaborole analog with low in vivo clearance across preclinical species and broad-spectrum activity against HCV replicons. An X-ray structure of NS5B protein cocrystallized with 49 revealed unique protein-inhibitor interactions mediated by an extensive network of ordered water molecules and the first evidence of boronate complex formation within the binding pocket. In clinical studies, 49 displayed a 60–63 h half-life and a robust decrease in viral RNA levels in HCV-infected patients, thereby validating our hypothesis that reducing benzylic oxidation would improve human pharmacokinetics and lower efficacious doses relative to 1.

Dopamine/2-Phenylethylamine Sensitivity of Ion-Selective Electrodes Based on Bifunctional-Symmetrical Boron Receptors

Piperazine-based compounds bearing two phenylboronic acid or two benzoxaborole groups (PBPA and PBBB) were applied as dopamine receptors in polymeric membranes (PVC/DOS) of ion-selective electrodes. The potentiometric sensitivity and selectivity of the sensors towards dopamine were evaluated and compared with the results obtained for 2-phenylethylamine. Since the developed electrodes displayed strong interference from 2-phenylethylamine, single-molecule geometry optimizations were performed using the density functional theory (DFT) method in order to investigate the origin of dopamine/2-phenylethylamine selectivity. The results indicated that phenylboronic acid and benzoxaborole receptors bind dopamine mainly through the dative B⁻N bond (like 2-phenylethylamine) and the potentiometric selectivity is mainly governed by the higher lipophilicity of 2-phenylethylamine.

Structure-Reactivity Relationships in Boronic Acid-Diol Complexation

Boronic acids have found widespread use in the field of biomaterials, primarily through their ability to bind with biologically relevant 1,2- and 1,3-diols, including saccharides and peptidoglycans, or with polyols to prepare hydrogels with dynamic covalent or responsive behavior. Despite a wide range of boronic acid architectures that have been previously considered, there is a need for greater understanding of the structure-reactivity relationships that govern binding affinity to diols. In this study, various boronic acids and other organoboron compounds were investigated to determine their pK a and their binding constants with the biologically relevant diols including sorbitol, fructose, and glucose. Boronic acid pK a values were determined through spectroscopic titration, whereas binding constants were determined by fluorescence spectroscopy during competitive binding studies. Key structure-reactivity relationships clearly indicated that both boronic acid structure and solution pH must be carefully considered. By considering a variety of boronic acids with systematically varied electronics and sterics, these results provide guidance during selection of organoboron compounds in sensing, delivery, and materials chemistry.

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

Kinetoplastid parasites-trypanosomes and leishmanias-infect millions of humans and cause economically devastating diseases of livestock, and the few existing drugs have serious deficiencies. Benzoxaborole-based compounds are very promising potential novel anti-trypanosomal therapies, with candidates already in human and animal clinical trials. We investigated the mechanism of action of several benzoxaboroles, including AN7973, an early candidate for veterinary trypanosomosis. In all kinetoplastids, transcription is polycistronic. Individual mRNA 5'-ends are created by trans splicing of a short leader sequence, with coupled polyadenylation of the preceding mRNA. Treatment of Trypanosoma brucei with AN7973 inhibited trans splicing within 1h, as judged by loss of the Y-structure splicing intermediate, reduced levels of mRNA, and accumulation of peri-nuclear granules. Methylation of the spliced leader precursor RNA was not affected, but more prolonged AN7973 treatment caused an increase in S-adenosyl methionine and methylated lysine. Together, the results indicate that mRNA processing is a primary target of AN7973. Polyadenylation is required for kinetoplastid trans splicing, and the EC50 for AN7973 in T. brucei was increased three-fold by over-expression of the T. brucei cleavage and polyadenylation factor CPSF3, identifying CPSF3 as a potential molecular target. Molecular modeling results suggested that inhibition of CPSF3 by AN7973 is feasible. Our results thus chemically validate mRNA processing as a viable drug target in trypanosomes. Several other benzoxaboroles showed metabolomic and splicing effects that were similar to those of AN7973, identifying splicing inhibition as a common mode of action and suggesting that it might be linked to subsequent changes in methylated metabolites. Granule formation, splicing inhibition and resistance after CPSF3 expression did not, however, always correlate and prolonged selection of trypanosomes in AN7973 resulted in only 1.5-fold resistance. It is therefore possible that the modes of action of oxaboroles that target trypanosome mRNA processing might extend beyond CPSF3 inhibition.