Electrophilic Functional Groups Research Articles

Nucleophiles promotes the decomposition of electrophilic functional groups of tetracycline in ZVI/H2O2 system: Efficiency and mechanism

Nucleophiles promotes the decomposition of electrophilic functional groups of tetracycline in ZVI/H2O2 system: Efficiency and mechanism

Postpolymerization Modification by Nucleophilic Addition to Styrenic Carbodiimides.

Carbodiimides are electrophilic functional groups that react with select nucleophiles under mild conditions. However, their potential as platforms for postpolymerization modification has been relatively underexplored. We describe the synthesis and radical polymerization of a styrenic carbodiimide which undergoes rapid nucleophilic addition with primary and secondary alkyl amines under ambient conditions, even in the presence of other protic nucleophiles. The monomer is amenable to both free and controlled radical (co)polymerization, and we further demonstrate the utility of this approach by preparing covalent adaptable networks through guanylation of the styrenic carbodiimide with difunctional amines. These materials exhibit a variation in relaxation times according to both the guanidine structure and concentration, providing a facile means for tuning dynamic behavior.

Chemoproteomic Profiling Reveals that Anticancer Natural Product Dankastatin B Covalently Targets Mitochondrial VDAC3.

Chlorinated gymnastatin and dankastatin alkaloids derived from the fungal strain Gymnascella dankaliensis have been reported to possess significant anticancer activity but their mode of action is unknown. These members possess electrophilic functional groups that can might undergo covalent bond formation with specific proteins to exert their biological activity. To better understand the mechanism of action of this class of natural products, we mapped the proteome-wide cysteine reactivity of the most potent of these alkaloids, dankastatin B, by using activity-based protein profiling chemoproteomic approaches. We identified a primary target of dankastatin B in breast cancer cells as cysteine C65 of the voltage-dependent anion-selective channel on the outer mitochondrial membrane VDAC3. We demonstrated direct and covalent interaction of dankastatin B with VDAC3. VDAC3 knockdown conferred hypersensitivity to dankastatin B-mediated antiproliferative effects in breast cancer cells, thus indicating that VDAC3 was at least partially involved in the anticancer effects of this natural product. Our study reveals a potential mode of action of dankastatin B through covalent targeting of VDAC3 and highlights the utility of chemoproteomic approaches in gaining mechanistic understanding of electrophilic natural products.

Acyl Azolium-Photoredox-Enabled Synthesis of β-Keto Sulfides.

α-Heteroatom functionalization is a key strategy for C-C bond formation in organic synthesis, as exemplified by the addition of a nucleophile to electrophilic functional groups, such as iminium ions; oxocarbenium ions; and their sulfur analogues, sulfenium ions. We envisioned a photoredox-enabled radical Pummerer-type reaction realized through the single-electron oxidation of a sulfide. Following this oxidative event, α-deprotonation would afford α-thio radicals that participate in radical-radical coupling reactions with azolium-bound ketyl radicals, thereby accessing a commonly proposed mechanistic intermediate of the radical-radical coupling en route to functionalized additive Pummerer products. This system provides a complementary synthetic approach to highly functionalized sulfurous products, including modification of methionine residues in peptides, and beckons further exploration in C-C bond formations previously limited in the standard two-electron process.

Enantioselective Catalysis by the Umpolung of Conjugate Acceptors Involving N-Heterocyclic Carbene or Organophosphine 1,4-Addition

ConspectusConjugate acceptors are one of the most common electrophilic functional groups in organic synthesis. While useful in a diverse range of transformations, their applications are largely dominated by the reactions from which their name is derived (i.e., as an acceptor of nucleophiles in the conjugate position). In 2014, we commenced studies focused on their ability to undergo polarity inversion through the conjugate addition of Lewis base catalysts. The first step in this process provides an enolate, from which the well-developed Rauhut-Currier (RC) and Morita-Baylis-Hillman (MBH) reactions can occur; however, tautomerization to provide a species in which the β-carbon of the conjugate acceptor can now act as a donor is also possible. When we commenced studies on this topic, reaction designs with this type of species, particularly when accessed using N-heterocyclic carbenes (NHCs), had been reported on only a handful of occasions. Despite a lack of development, conceptually it was felt that reactions taking advantage of polarity switching by Lewis base conjugate addition have a number of desirable features. Perhaps the most significant is the potential to reimagine a ubiquitous functional group as an entirely new synthon, namely, a donor to electrophiles from the conjugate position.Our work has focused on catalysis with both simple conjugate acceptors and also those embedded within more complicated substrates; the latter has allowed a series of cycloisomerizations and annulation reactions to be achieved. In most cases, the reactions have been possible using enantioenriched chiral NHCs or organophosphines as the Lewis base catalysts thereby delivering enantioselective approaches to novel cyclic molecules. While related chemistry can be accessed with either family of catalyst, in all cases reactions have been designed to take advantage of one or the other. In addition, a fine balance exists between reactions that exploit the initially formed enolate and those that involve the polarity-inverted β-anion. In our studies, this balance is addressed through substrate design, although catalyst control may also be possible. We consider the chemistry discussed in this Account to be in its infancy. Significant challenges remain to be addressed before our broad aim of discovering a universal approach to the polarity inversion of all conjugate acceptors can be achieved. These challenges broadly relate to chemoselectivity with substrates bearing multiple electrophilic functionalities, reliance upon the use of conjugate acceptors, and catalyst efficiency. To address these challenges, advances in catalyst design and catalyst cooperativity are likely required.

Covalent Modifier Discovery Using Hydrogen/Deuterium Exchange-Mass Spectrometry.

Covalent ligands are generally filtered out of chemical libraries used for high-throughput screening, because electrophilic functional groups are considered to be pan-assay interference compounds (PAINS). Therefore, screening strategies that can distinguish true covalent ligands from PAINS are required. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for evaluating protein stability. Here, we report a covalent modifier screening approach using HDX-MS. In this study, HDX-MS was used to classify peroxisome proliferator-activated receptor γ (PPARγ) and vitamin D receptor ligands. HDX-MS could discriminate the strength of ligand-protein interactions. Our HDX-MS screening method identified LT175 and nTZDpa, which can bind concurrently to the PPARγ ligand-binding domain (PPARγ-LBD) with synergistic activation. Furthermore, iodoacetic acid was identified as a novel covalent modifier that stabilizes the PPARγ-LBD.

Covalent chemical probes for protein kinases

Small-molecule chemical probes are crucial tools to study the function of unexplored proteins in biological systems, thereby directly impacting preclinical target validation. Being one of the largest protein families in humans, protein kinases are currently among the most important and fruitful molecular targets in drug discovery. However, a significant fraction of the human “kinome” is still understudied and growing efforts in the scientific community aim at the development of specific chemical tool compounds for such “dark” kinases. Covalent targeting has proven to be a valid and rational strategy towards high-quality chemical probes enabling superior potencies, high selectivities and sustained target engagement. In the kinase field, the targeting of non-catalytic cysteine residues has been particularly fruitful and there is an increasing interest in addressing other residues, such as lysine or tyrosine. Herein, we discuss the properties and generation of covalent kinase inhibitors, with a special emphasis on electrophilic functional groups that can be used as “warheads”. Moreover, we highlight studies showcasing the development of covalent chemical probes targeting cysteine and lysine residues in an irreversible or reversible-covalent manner.

A Nucleophilic Chemical Probe Targeting Electrophilic Functional Groups in an Untargeted Way to Explore Cysteine Modulators in Natural Products.

The vital roles of biologically relevant cysteines have been discovered from proteins that are promising targets for new drugs or chemical tools. Therefore, new electrophilic small molecules that can covalently modulate these cysteines have attracted immense interest. Because of their extremely wide chemical diversity, electrophilic natural products (NPs) have been studied as promising sources of cysteine modulators. Previous studies have developed chemical probes to facilitate the detection and isolation of electrophilic NPs. To address the problems with the current methods, including their low sensitivity, high false-positive rate, and dependence on performing manual processing with a plethora of spectra, we report a chemical probe that can first covalently capture electrophilic NPs from natural resources and then produce sensitive reporter ion signals that are specific for the detected NPs. We applied this untargeted method to explore electrophilic NPs from natural resources and found that the complexity of electrophilic NPs was beyond our expectations. We used this chemical probe to identify a new electrophilic furanosesterterpene (BG-1) from an extract of Ginkgo biloba that targets the Cys207 of acyl-CoA thioesterase 7 (ACOT7).

Anodic corrosion of heteroatom doped graphene oxide supports and its influence on the electrocatalytic oxygen evolution reaction

Transition metal-based electrocatalysts supported on carbon substrates face the challenges of anodic corrosion of carbon during oxygen evolution reaction at high oxidation potential. The role of electrophilic functional groups (carbonyl, pyridinic, thiol, etc.) incorporated in graphene oxide has been studied towards the anodic corrosion resistance. Heteroatom functionalized carbon supports possess modified electronic properties, surface oxygen content, and hydrophilicity, which are crucial in governing electrochemical corrosion in the alkaline oxidative environment. Evidently, electron-withdrawing groups in NGO support (pyridinic, cyano, nitro, etc) and its lower oxygen content impart maximum corrosion resistance and anodic stability in comparison to the other sulfur-doped and co-doped graphene oxide support. In this report, we establish the baseline evaluation of carbon-supported OER electrocatalysts by a systematic analysis of activity and substrate corrosion resistance. The result of this study establishes the role of surface composition of the doped supports while for designing a stable, corrosion-resistant OER electrocatalyst.

HPLC-MS Analysis of Four Potential Genotoxic Impurities in Alogliptin Pharmaceutical Materials.

Pyridine, 3-aminopyridine, 4-dimethylaminopyridine, and N, N-dimethylamine are reactive bases that may be used in the preparation of the pharmaceutical ingredient alogliptin (ALO). They are considered as potentially genotoxic impurities (PGIs) since they contain electrophilic functional groups. Therefore, they should be monitored at the allowed limits in ALO. The aim of this study was to develop a novel liquid chromatography-mass spectrometry (LC-MS) method to estimate quantities of pyridine, 3-aminopyridine, 4-dimethylaminopyridine, and N, N-dimethylaniline impurities in ALO drug material. The separation was performed on Kromasil CN (250 mm × 3.9 mm, 3.5 µm) column in reversed phase mode. The mobile phase was a mixture of water-methanol (55:45, v/v) containing 2.5 mM ammonium acetate and 0.1% formic acid. Impurities were detected by MS in selected ion monitoring mode at m/z = 80, 95, 122, and 123 for pyridine, 3-aminopyridine, N, N-dimethylaniline, and 4-dimethylaminopyridine, respectively. The flow rate of the method was 0.5 mL/min. The sensitivity of the method was excellent at levels much less than the allowed limits. The method had excellent linearity in the concentration ranges of Quantitation Limit (QL)-150% of allowed limits and coefficients of determination were above 0.9990. The recovery ratios were in the range of 93.56-110.28%. Results showed good linearity, precision, accuracy, sensitivity, selectivity, robustness, and solution stability. The studied method was applied to test two samples of raw materials and one sample of tablets. The method discussed here could be very useful for controlling potentially genotoxic impurities (PGIs) levels in ALO during its synthesis, and for QC testing of ALO raw materials before using them in the preparation of pharmaceutical products.

Eletrophilic Chemistry of Tranilast Is Involved in Its Anti-Colitic Activity via Nrf2-HO-1 Pathway Activation.

Tranilast (TRL), a synthetic derivative of a tryptophan metabolite, is an anti-allergic drug used to treat bronchial asthma. We investigated how TRL activated the nuclear factor-erythroid 2 p45-related factor 2 (Nrf2)-hemeoxygenase-1 (HO-1) pathway based on the electrophilic chemistry of the drug and whether TRL activity contributed to the treatment of rat colitis. In human colon carcinoma cells, TRL activated Nrf2, as represented by an increase in nuclear Nrf2 and induction of Nrf2-dependent luciferase and, subsequently, HO-1, a target gene product of Nrf2. TRL activation of Nrf2 and induction of HO-1 were completely prevented by chemical reduction of the electrophilic functional group (α, β-unsaturated carbonyl group) in the drug. In parallel, TRL was reactive with the nucleophilic thiol group in N-acetylcysteine, forming a covalent adduct. Moreover, TRL, but not reduced TRL, binds to Kelch-like ECH-associated protein 1 (KEAP1), releasing Nrf2. TRL administration ameliorated colonic damage and inflammation in rats with dinitrobenzene sulfonic acid-induced colitis, which was partly compromised by the chemical reduction of TRL or co-treatment with an HO-1 inhibitor. Our results suggest that TRL activated the Nrf2-HO-1 pathway via covalent binding to KEAP1, partly contributing to TRL amelioration in rat colitis.

Modeling the Binding and Conformational Energetics of a Targeted Covalent Inhibitor to Bruton's Tyrosine Kinase.

Targeted covalent inhibitors (TCIs) bind to their targets in both covalent and noncovalent modes, providing exceptionally high affinity and selectivity. These inhibitors have been effectively employed as inhibitors of protein kinases, with Taunton and coworkers (Nat. Chem. Biol. 2015, 11, 525-531) reporting a notable example of a TCI with a cyanoacrylamide warhead that forms a covalent thioether linkage to an active-site cysteine (Cys481) of Bruton's tyrosine kinase (BTK). The specific mechanism of the binding and the relative importance of the covalent and noncovalent interactions is difficult to determine experimentally, and established simulation methods for calculating the absolute binding affinity of an inhibitor cannot describe the covalent bond-forming steps. Here, an integrated approach using alchemical free-energy perturbation and QM/MM molecular dynamics methods was employed to model the complete Gibbs energy profile for the covalent inhibition of BTK by a cyanoacrylamide TCI. These calculations provide a rigorous and complete absolute Gibbs energy profile of the covalent modification binding process. Following a classic thiol-Michael addition mechanism, the target cysteine is deprotonated to form a nucleophilic thiolate, which then undergoes a facile conjugate addition to the electrophilic functional group to form a bond with the noncovalently bound ligand. This model predicts that the formation of the covalent linkage is highly exergonic relative to the noncovalent binding alone. Nevertheless, noncovalent interactions between the ligand and individual amino acid residues in the binding pocket of the enzyme are also essential for ligand binding, particularly van der Waals dispersion forces, which have a larger contribution to the binding energy than the covalent component in absolute terms. This model also shows that the mechanism of covalent modification of a protein occurs through a complex series of steps and that entropy, conformational flexibility, noncovalent interactions, and the formation of covalent linkage are all significant factors in the ultimate binding affinity of a covalent drug to its target.

Accessing aliphatic alcohols for metallaphotoredox catalyzed C(sp3)-arylation

Common cross-coupling reactions to obtain C(sp²)–C(sp³)-bonds are hampered by the abundance of nucleophilic and electrophilic functional groups. Recently in <i>Nature</i>, Dong and MacMillan developed a mild activation of a diverse range of alcohols with an <i>N</i>-heterocyclic carbene (NHC) salt and merged it with nickel photoredox dual catalytic arylation.

The spectrum between substrates and inhibitors: Pinpointing the binding mode of dengue protease ligands with modulated basicity and hydrophobicity

Peptides can be inhibitors and substrates of proteases. The present study describes the inhibitor- vs. substrate-like properties of peptidic ligands of dengue protease which were designed to provide insight into their binding modes. Of particular interest was the localization of the cleavable peptide bond and the placement of hydrophobic elements in the binding site. The findings provide clues for the design of covalent inhibitors in which electrophilic functional groups bind to the catalytic serine, and in addition for the development of inhibitors that are less basic than the natural substrate and therefore have an improved pharmacokinetic profile. We observed a tendency of basic elements to favor a substrate-like binding mode, whereas hydrophobic elements decrease or eliminate enzymatic cleavage. This indicates a necessity to include basic elements which closely mimic the natural substrates into covalent inhibitors, posing a challenge from the chemical and pharmacokinetic perspective. However, hydrophobic elements may offer opportunities to develop non-covalent inhibitors with a favorable ADME profile and potentially improved target-binding kinetics.

Copper-Catalyzed Highly Enantioselective 1,4-Protoboration of Terminal 1,3-Dienes

Copper-Catalyzed Highly Enantioselective 1,4-Protoboration of Terminal 1,3-Dienes

One-Pot Synthetic Approaches for the Construction of Isochroman-4-ones and Benzoxazin-3-ones Using O,P-Acetals

AbstractA method for synthesizing six-membered heterocyclic compounds was developed based on the features of O,P-acetals. Sequential reactions of intramolecular cyclization between the methylene carbon atom of O,P-acetal and its electrophilic functional group (ester or protected carbamate) was followed by Horner–Wadsworth–Emmons (HWE) olefination with various aldehydes. The developed one-pot method yielded isochroman-4-one and benzoxazin-3-one derivatives with an alkylidene moiety.

A versatile living polymerization method for aromatic amides.

Polycondensation polymers typically follow step-growth kinetics assuming all functional groups are equally likely to react with one another. If the reaction rates with the chain end can be selectively accelerated, living polymers can be obtained. Here we report on two chlorophosphonium iodide reagents that have been synthesized from triphenylphosphine and tri(o-methoxyphenyl)phosphine. The former activates aromatic carboxylic acids as acid chlorides in the presence of secondary aromatic amines and the latter even in the presence of primary aromatic amines. These reagents allow p-aminobenzoic acid derivatives to form solution-stable activated monomers that polymerize in a living fashion in the presence of amine initiators. Other aryl amino acids and even dimers of aryl amino acids can be polymerized in a living fashion when slowly added to the phosphonium salt in the presence of an amine initiator. Diblock copolymers and triblock terpolymers of aryl amino acids can be prepared even in the presence of electrophilic functional groups.

Development and validation of an analytical method for quantitative determination of three potentially genotoxic impurities in vildagliptin drug material using HPLC-MS.

A novel high-performance liquid chromatography-mass spectrometry method was developed to determine the quantities of pyridine, 4-dimethylaminopyridine, and N, N-dimethylaniline impurities in vildagliptin drug material. These impurities are reactive bases that may be used in synthesis of vildagliptin pharmaceutical ingredients. They are considered as potentially genotoxic impurities since they contain electrophilic functional groups. Therefore, these impurities should be monitored at the allowed limits in vildagliptin. Hence a high-performance liquid chromatography-mass spectrometry method was developed to quantify the amounts of these impurities in vildagliptin. The column was KROMASIL CN (250mm × 3.9mm, 3.5μm) in reversed-phase mode. The mobile phase was a mixture of water-methanol (55:45) containing 2.5mM ammonium acetate and 0.1% formic acid. The mass spectrometer was used to detect the amounts of impurities using selected ionization monitoring mode at m/z=80, 122, and 123 for pyridine, N, N-dimethylaniline, and 4-dimethylaminopyridine, respectively. The flow rate was 0.5mL/min. The sensitivity of the method was excellent at levels very less than the allowed limits. The method had excellent linearity in the concentration ranges of limit of quantification-150% of the permitted level with coefficients of determination above 0.9990. The recovery ratios were in the range of 93.70-108.63%. Results showed good linearity, precision, accuracy, sensitivity, selectivity, robustness, and solution stability.

Docking-based virtual screening studies aiming at the covalent inhibition of SARS-CoV-2 MPro by targeting the cysteine 145

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 which has infected millions of people worldwide. The main protease of SARS-CoV-2 (MPro) has been recognized as a key target for the development of antiviral compounds. Taking advantage of the X-ray crystal complex with reversible covalent inhibitors interacting with the catalytic cysteine 145 (Cys145), we explored flexible docking studies to select alternative compounds able to target this residue as covalent inhibitors. First, docking studies of three known electrophilic compounds led to results consistent with co-crystallized data validating the method for SARS-CoV-2 MPro covalent inhibition. Then, libraries of soft electrophiles (overall 41 757 compounds) were submitted to docking-based virtual screening resulting in the identification of 17 molecules having their electrophilic group close to the Cys145 residue. We also investigated flexible docking studies of a focused approved covalent drugs library including 32 compounds with various electrophilic functional groups. Among them, the calculations resulted in the identification of four compounds, namely dimethylfumarate, fosfomycin, ibrutinib and saxagliptin, able first, to bind to the active site of the protein and second, to form a covalent bond with the catalytic cysteine.

Recent Advances in the Synthesis of Sulfonylureas

AbstractSulfonylureas are employed in a variety of applications including use as drugs to treat type II diabetes and as plant growth regulators or herbicides. Traditionally, the synthesis of sulfonylureas has been accomplished either by the treatment of sulfamides with isocyanates in the presence of a base or through sulfonamides conversion into N‐sulfonyl isocyanates or N‐sulfonyl carbamate derivatives which provide the corresponding sulfonylureas upon treatment with amines. Both approaches are severely limited by the weak nucleophilicity of sulfamides and by the difficulty in synthesizing and handling isocyanate species. Such a drawback could be mitigated by the emergence of protocols establishing the labile electrophilic functional groups in situ so that their coupling with nucleophilic partners takes place in one‐pot. Recently, the development of environmentally friendly methods to prepare sulfonylurea containing compounds without using harmful reagents has attracted considerable attention. The aim of the minireview is to explore the different protocols emerged in the literature to generate sulfonylureas giving importance to the reaction mechanisms of crucial synthetic steps.