Nucleophilic Substrates Research Articles

Synthesis of N-heterocyclic compounds using N,N-dimethylacetamides as an electrophilic carbon source.

In this study, N-heterocyclic compounds were synthesized using nitrogen-containing nucleophilic substrates and electrophilic carbon sources derived from N,N-dimethylacetamide (DMAc). Depending on the nucleophilic groups, N-heterocyclic compounds such as 4-quinazolinones, pyrrole-quinoxalines, and dihydro-benzothiadiazine dioxides were produced. Carbon, adjacent to the nitrogen in DMAc, was activated in the presence of FeCl3·6H2O and di-t-butyl peroxide (DTBP). This procedure was considered an economical synthetic method because it utilized iron catalysts and DMAc as an electrophilic carbon source and a solvent.

Synthetic Amine Linkers for Efficient Sortagging.

Enzymatic site-specific bioconjugation techniques, in particular sortase-mediated ligation, are increasingly used to generate conjugated proteins for a wide array of applications. Extension of the utility and practicality of sortagging for diverse purposes is critically dependent on further improvement of the efficiency of sortagging reactions with a wider structural variety of substrates. We present a comprehensive comparative mass spectrometry screening study of synthetic nonpeptidic incoming amine nucleophile substrates of Staphylococcus aureus Sortase A enzyme. We have identified the optimal structural motifs among the chemically diverse set of 452 model primary and secondary amine-containing sortagging substrates, and we demonstrate the utility of representative amine linkers for efficient C-terminal biotinylation of nanobodies.

Friedel Crafts Reactions Revisited: Some Applications in Heterogeneous Catalysis#

Abstract: Important organic reactions require the use of catalysts. The Friedel-Crafts reactions were discovered by Charles Friedel and James Mason Crafts in 1887. They are an essential catalytic process since they are widely applied in different areas such as fuels, cleaning, and pharmacological products. The reaction is usually carried out in the presence of Lewis acids or Brønsted acids in a homogeneous medium, with the nucleophilic aromatic substrate in excess. Although there is still work in the literature on the Friedel- Crafts reaction in a homogeneous medium using metal halides, the tendency is to replace these catalysts, which generate effluents that are harmful to the environment. Heterogeneous catalysts using solid acids show advantages over homogeneous catalysts, especially concerning separating products from the reaction medium, recycling, and reusing. This paper presents a mini-review focusing on the use of solid acids in Friedel-Crafts reactions.

Substrate Trapping in Polyketide Synthase Thioesterase Domains: Structural Basis for Macrolactone Formation.

Emerging antibiotic resistance requires continual improvement in the arsenal of antimicrobial drugs, especially the critical macrolide antibiotics. Formation of the macrolactone scaffold of these polyketide natural products is catalyzed by a modular polyketide synthase (PKS) thioesterase (TE). The TE accepts a linear polyketide substrate from the termina PKS acyl carrier protein to generate an acyl-enzyme adduct that is resolved by attack of a substrate hydroxyl group to form the macrolactone. Our limited mechanistic understanding of TE selectivity for a substrate nucleophile and/or water has hampered development of TEs as biocatalysts that accommodate a variety of natural and non-natural substrates. To understand how TEs direct the substrate nucleophile for macrolactone formation, acyl-enzyme intermediates were trapped as stable amides by substituting the natural serine OH with an amino group. Incorporation of the unnatural amino acid, 1,3-diaminopropionic acid (DAP), was tested with five PKS TEs. DAP-modified TEs (TE DAP ) from the pikromycin and erythromycin pathways were purified and tested with six full-length polyketide intermediates from three pathways. The erythromycin TE had permissive substrate selectivity, whereas the pikromycin TE was selective for its native hexaketide and heptaketide substrates. In a crystal structure of a native substrate trapped in pikromycin TE DAP , the linear heptaketide was curled in the active site with the nucleophilic hydroxyl group positioned 4 Å from the amide-enzyme linkage. The curled heptaketide displayed remarkable shape complementarity with the TE acyl cavity. The strikingly different shapes of acyl cavities in TEs of known structure, including those reported here for juvenimicin, tylosin and fluvirucin biosynthesis, provide new insights to facilitate TE engineering and optimization.

Carbene-Catalyzed Enantioselective Addition of Sulfinate to Ketones.

A carbene-catalyzed enantioselective addition of sulfinate to ketones between 2-benzoylbenzaldehyde and sulfonyl chloride is disclosed. Up to now, the carbon and heteroatom nucleophiles have effectively undergone catalytic enantioselective addition to carbonyl molecules to introduce functionalities and chirality. Sulfone, as an important class of sulfur-containing functional groups, represents highly valuable motifs in medicines and natural products. It remains undeveloped for the catalytic asymmetric addition of sulfinate to carbonyls. Herein we disclosed the first catalytic enantioselective addition of sulfinate to ketones for the synthesis of sulfones via N-heterocyclic carbene (NHC) catalysis. The sulfonyl chloride behaves both as an oxidant and as a nucleophilic substrate in this carbene-catalyzed process. Experimental studies suggested that the Breslow intermediate can be SET oxidized by sulfonyl chloride to generate the sulfonyl radical. This novel synthetic approach for the asymmetric addition of sulfinate to carbonyls can also be used to modify the commercially available functional molecules.

Molecular and Structural Basis for Cγ-C Bond Formation by PLP-Dependent Enzyme Fub7.

Pyridoxal 5'-phosphate (PLP)-dependent enzymes that catalyze γ-replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP-dependent enzymes, CndF and Fub7, has unveiled unique C-C bond forming capabilities, enabling the biocatalytic synthesis of alkyl- substituted pipecolic acids from O-acetyl-L-homoserine and β-keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone-derived enolates as carbon nucleophiles, revealing Fub7's capacity for substrate-dependent regioselective α-alkylation of unsymmetrical ketones. Through an integrated approach combining X-ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.

Molecular and Structural Basis for Cγ−C Bond Formation by PLP‐Dependent Enzyme Fub7

AbstractPyridoxal 5’‐phosphate (PLP)‐dependent enzymes that catalyze γ‐replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP‐dependent enzymes, CndF and Fub7, has unveiled unique C−C bond forming capabilities, enabling the biocatalytic synthesis of alkyl‐ substituted pipecolic acids from O‐acetyl‐L‐homoserine and β‐keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone‐derived enolates as carbon nucleophiles, revealing Fub7’s capacity for substrate‐dependent regioselective α‐alkylation of unsymmetrical ketones. Through an integrated approach combining X‐ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.

A Ruthenophosphanorcaradiene as a Synthon for an Ambiphilic Metallophosphinidene.

Reaction of the ruthenium carbene complex Cp*(IPr)RuCl (1) (IPr = 1,3-bis(Dipp)imidazol-2-ylidene; Dipp = 2,6-diisopropylphenyl) with sodium phosphaethynolate (NaOCP) led to intramolecular dearomatization of one of the Dipp substituents on the Ru-bound carbene to afford a Ru-bound phosphanorcaradiene, 2. Computations by DFT reveal a transition state characterized by a concerted process whereby CO migrates to the Ru center as the P atom adds to the π system of the aryl group. The phosphanorcaradiene possesses ambiphilic properties and reacts with both nucleophilic and electrophilic substrates, resulting in rearomatization of the ligand aryl group with net P atom transfer to give several unusual metal-bound, P-containing main-group moieties. These new complexes include a metallo-1-phospha-3-azaallene (Ru─P═C═NR), a metalloiminophosphanide (Ru─P═N─R), and a metallophosphaformazan (Ru─P(═N─N═CPh2)2). Reaction of 2 with the carbene 2,3,4,5-tetramethylimidazol-2-ylidene (IMe4) produced the corresponding phosphaalkene DippP═IMe4.

Using BpyAla to generate copper artificial metalloenzymes: a catalytic and structural study.

Artificial metalloenzymes (ArMs) have emerged as a promising avenue in the field of biocatalysis, offering new reactivity. However, their design remains challenging due to the limited understanding of their protein dynamics and how the introduced cofactors alter the protein scaffold structure. Here we present the structures and catalytic activity of novel copper ArMs capable of (R)- or (S)-stereoselective control, utilizing a steroid carrier protein (SCP) scaffold. To incorporate 2,2'-bipyridine (Bpy) into SCP, two distinct strategies were employed: either Bpy was introduced as an unnatural amino acid (2,2'-bipyridin-5-yl)alanine (BpyAla) using amber stop codon expression or via bioconjugation of bromomethyl-Bpy to cysteine residues. The resulting ArMs proved to be effective at catalysing an enantioselective Friedel-Crafts reaction with SCP_Q111BpyAla achieving the best selectivity with an enantioselectivity of 72% ee (S). Interestingly, despite using the same protein scaffold, different attachment strategies for Bpy at the same residue (Q111) led to a switch in the enantiopreference of the ArM. X-ray crystal structures of SCP_Q111CBpy and SCP_Q111BpyAla ArMs with bound Cu(ii) ions unveiled crucial differences in the orientation of the catalytic centre. Combining structural information, alanine scanning studies, and computational analysis shed light on the distinct active sites of the ArMs, clarifying that these active sites stabilise the nucleophilic substrate on different sides of the electrophile leading to the observed switch in enantioselectivity. This work underscores the importance of integrating structural studies with catalytic screening to unravel the intricacies of ArM behaviour and facilitate their development for targeted applications in biocatalysis.

Release of Redox Additives Via Megasonic Energy for High Selectivity/Low-Stress STI CMP

The advancements in a wide array of semiconductor manufacturing processing have been pivotal for the extension of Moore’s law the Chemical Mechanical Planarization (CMP) process has become an area of focus due to the stringent surface topography requirements. CMP utilizes complex slurry formulations containing abrasive nanoparticles and additives to reduce substrate defectivity and achieve angstrom-level uniformity. One area that has gained significant attention is Shallow Trench Isolation (STI), where the modulation and control of the surface oxidation state of the ceria, specifically the Ce3+ state, is critical to TEOS removal. In the Ce3+ state, defect states (i.e., oxygen vacancies (Ovacs)) on the surface are highly electron deficient (i.e., electrophilic) and allow the nucleophilic substrate to complex. By modulating the electrophilic properties of the particle, the kinetics of surface complexations required for effective TEOS removal can be controlled. This work focuses on developing stimuli-responsive capsules that can be added to STI slurry formulations to promote the controlled release of redox-active additives that can be used to drive the oxidation state of the CeO2 nanoparticle (Ce3+/Ce4+). By encapsulating the additive in a polymeric system, the reactive properties of the slurry are limited until the additive is released. In this work, megasonic action was employed to disrupt the capsules releasing the additives on demand to facilitate the modulation of the CeO2 surface redox states. Results have shown that the addition of a controlled-release capsule with an additive resulted in the increase of Ovacs at the CeO2 surface. This led to an increase from 1800 Å/min to 3450 Å/min using a constant 2.0 W/cm2 continuous flow megasonic flux. Furthermore, the overall defectivity decreased significantly with respect to both particle contamination and surface scratching. Lastly, the nature of the polymeric capsule has been shown to enhance selectivity between TEOS and silicon nitride and preliminarily appears to be megasonic flux dependent.

Control of Substrate Conformation by Hydrogen Bonding in a Retaining β-Endoglycosidase.

Bacterial β-glycosidases are hydrolytic enzymes that depolymerize polysaccharides such as β-cellulose, β-glucans and β-xylans from different sources, offering diverse biomedical and industrial uses. It has been shown that a conformational change of the substrate, from a relaxed 4 C1 conformation to a distorted 1 S3 /1,4 B conformation of the reactive sugar, is necessary for catalysis. However, the molecular determinants that stabilize the substrate's distortion are poorly understood. Here we use quantum mechanics/molecular mechanics (QM/MM)-based molecular dynamics methods to assess the impact of the interaction between the reactive sugar, i. e. the one at subsite -1, and the catalytic nucleophile (a glutamate) on substrate conformation. We show that the hydrogen bond involving the C2 exocyclic group and the nucleophile controls substrate conformation: its presence preserves sugar distortion, whereas its absence (e.g. in an enzyme mutant) knocks it out. We also show that 2-deoxy-2-fluoro derivatives, widely used to trap the reaction intermediates by X-ray crystallography, reproduce the conformation of the hydrolysable substrate at the experimental conditions. These results highlight the importance of the 2-OH⋅⋅⋅nucleophile interaction in substrate recognition and catalysis in endo-glycosidases and can inform mutational campaigns aimed to search for more efficient enzymes.

Systematic study of nucleophile additions to 1-bromo-4-(trifluorovinyloxy)benzene: A versatile intermediate toward fluorinated ethers of synthetic interest

The nature of the structural configuration of fluorinated ethers has been widespread as a crucial component for improving high performance polymers, industrial agrochemicals, and targets for important pharmaceutical drugs. This is a result of countless advances in organo-fluorine methodologies with this unique substructure in order to overcome many traditional synthetic challenges. In this work, we expand on the preparation of fluorinated ethers by introducing hetero-nucleophiles to a highly electrophilic aryl trifluorovinyl ether affording a new class of difunctional aryl/alkyl fluorinated ethers that would serve as useful intermediates. The facile reaction chemistry of various nucleophile substrates, effect of base concerning regio-selectivity, and structural elucidation trends of the synthesized aryl/alkyl fluoroethers will be discussed.

Expanding the β-substitution reactions of serine synthase through mutagenesis of aromatic active site residues

The Gram-negative bacterium, Fusobacterium nucleatum, possesses a fold II type pyridoxal 5′-phosphate-dependent enzyme that catalyzes the reversible β-replacement of l-cysteine and l-serine, generating H2S and H2O, respectively. This enzyme, termed serine synthase (FN1055), contains an active site Asp232 that serves as a general base in the activation of a water molecule for nucleophilic attack of the ⍺-aminoacrylate intermediate. A network of hydrophobic residues surrounding Asp232 are key to catalysis as they increase the basicity of the side chain. However, these residues severely restrict the range of nucleophilic substrates that can react with the ⍺-aminoacrylate, making the enzyme an ineffective biocatalyst for noncanonical amino acid biosynthesis. Herein, we systematically substituted four aromatic active residues (Trp99, Phe125, Phe148 and Phe234) to an alanine to determine their catalytic importance in serine/cysteine synthase reactions and if their substitution could broaden the scope of nucleophiles that could react with the ⍺-aminoacrylate intermediate. All four single site mutants W99A, F125A, F148A, and F234A could form the ⍺-aminoacrylate intermediate upon reaction with either l-cysteine or l-serine; however, the rate constant associated with the elimination of the β-hydroxyl group from l-serine was 150 to 200-fold lower in the F125A and F148A variants. Substitution of Phe125 and Phe148, situated ∼3–4 Å from the general base, also abolished the serine synthase reaction due to their inability to activate a water molecule for nucleophilic attack of the ⍺-aminoacrylate. Overall, the mutational studies indicate that the clustering of aromatic residues disproportionately benefits the serine synthase reaction as they increase the binding affinity for l-cysteine, decrease the binding of the product, l-serine, and promote the activation of a water molecule. Notably, the aminoacrylate species present in F125A and F148A was able to react with thiophenol, signifying that serine synthase has biocatalytic potential in the synthesis of noncanonical amino acids.

Enzymatic Synthesis of l-Methionine Analogues and Application in a Methyltransferase Catalysed Alkylation Cascade.

Chemical modification of small molecules is a key step for the development of pharmaceuticals. S-adenosyl-l-methionine (SAM) analogues are used by methyltransferases (MTs) to transfer alkyl, allyl and benzyl moieties chemo-, stereo- and regioselectively onto nucleophilic substrates, enabling an enzymatic way for specific derivatisation of a wide range of molecules. l-Methionine analogues are required for the synthesis of SAM analogues. Most of these are not commercially available. In nature, O-acetyl-l-homoserine sulfhydrolases (OAHS) catalyse the synthesis of l-methionine from O-acetyl-l-homoserine or l-homocysteine, and methyl mercaptan. Here, we investigated the substrate scope of ScOAHS from Saccharomyces cerevisiae for the production of l-methionine analogues from l-homocysteine and organic thiols. The promiscuous enzyme was used to synthesise nine different l-methionine analogues with modifications on the thioether residue up to a conversion of 75 %. ScOAHS was combined with an established MT dependent three-enzyme alkylation cascade, allowing transfer of in total seven moieties onto two MT substrates. For ethylation, conversion was nearly doubled with the new four-enzyme cascade, indicating a beneficial effect of the in situ production of l-methionine analogues with ScOAHS.

Comparing Condensed and Hydrolysable Tannins for Mechanical Foaming of Furanic Foams: Synthesis and Characterization

This study examined the potential of hydrolysable tannin in comparison to condensed tannins for the production of furanic foams. The results indicate that chestnut tannin presents lower reactivity and requires a stronger acid for the polymerization. Additionally, foamability and density were found to be dependent on both surfactant concentration and tannin type, allowing lower densities for mimosa tannin and lower thermal conductivities for chestnut-based foams. Mimosa tannin was found to have the highest compression strength, followed by quebracho and chestnut, promising thermal conductivity of around 50 mW/m·K for 300 kg/m3 foams, which suggests that chestnut foams have the potential to performing highly when the density is reduced. Chemical analysis revealed that the methylene moieties of the furanics are non-specific and produces new covalent bonds with nucleophilic substrates: -OH groups and free-positions in the flavonoids. Overall, this study opens new perspectives for the application of hydrolysable tannins in polymer and material science.

Unconventional Transformations of Difluorocarbene with Amines and Ethers.

ConspectusFluorine-containing compounds are extensively involved in various fields originating from intriguing and unique characteristics of fluorine atom; notably, in pharmaceuticals, the involvement of a fluorine atom or a fluorine-containing group is a chief technique for improving the pesticide effect and developing new drugs. Difluorocarbene, one of the most important and powerful fluorine-containing reagents, is widely employed and studied in many areas mainly to assemble gem-difluoromethyl molecules, including but not limited to the abundant reactions between difluorocarbene with nucleophilic substrates, Wittig reaction with ketones or aldehydes, cascade reaction with both a nucleophile and an electrophile, or [2+1] cycloaddition with alkenes or alkynes. However, its unconventional and intriguing protocols beyond as a difluoromethyl synthon have rarely been studied, and thus, it is highly desired given its abundance, inexpensiveness and peculiar properties. In this Account, we mainly discuss our discovery with unconventional transformations of difluorocarbene, instead of as a sole difluoromethyl source (different from other dihalocarbene), actually can serve as an electron acceptor to activate C-X bonds (X = N and O) and thus promote a myriad of fascinating transformations for the assembly of versatile valuable products with various aza-compounds (primary/secondary/tertiary amines as well as NH3 and NaNH2 and so on) and aliphatic ethers in the absence of transition metals and expensive ligands. Inspired by the electron-deficient characteristics of difluorocarbene, we first found that the isocyanides could be readily formed in situ when the unoccupied orbital of difluorocarbene meets the lone-pair of primary amines; in basic condition, a cascade defluorination and cyclizations could afford plethora of valuable N-containing heterocycles. Meanwhile, we disclosed that cyano anion could be accessible in situ as well when difluorocarbene and NaNH2 or NH3 were mixed up in suitable basic conditions, and thus a series of aryl nitrile compounds were obtained in the presence of Pd catalysis and ArI. Interestingly, when difluorocarbene encountered secondary amines, formamides were rendered under mild reactions. Of note, concomitant functionalizations of C and N moieties via cleavage of the unstrained C(sp3)-N bond in the absence of metal and oxidant are sparce, which indeed significantly add versatility and diversity to products. Gratifyingly, by uitilizing difluorocarbene and cyclic tertiary amines, we achieved difluorocarbene-mediated deconstructive functionalizations for the first time, showing successive C(sp3)-N bond scission of amines and simultaneous functionalization of C and N atoms which would be introduced into the products in the absence of transition metals and oxidants. This method provides a brand-new while very universal synthetic pathway to selectively cleave inert unactivated Csp3-N bonds, in which halodifluoromethyl reagents act as both C1 synthon and halo (Cl, Br, I) sources. Fascinatingly, nitrogen ylides are generated in situ from difluorocarbene and tertiary amines, and an intriguing and universal approach for deaminative arylation or alkenylation of tertiary amines was disclosed for the first time in appropriate basic conditions, which represents an intriguing reaction mode to lead to a formal transition-metal free Suzuki cross coupling. Besides, we also disclosed that difluorocarbene could proceed novel atom recombination to render meaningful 2-fluoroindoles or 3-(2,2-difluoroethyl)-2-fluoroindoles from ortho-vinylanilines, 3-fluorined oxindoles from 2-aminoarylketones, in which difluorocarbene acts as a C1 synthon and F1 source simultaneously. Last but not the least, we recently found that the lone-pair-electron of oxygen could trap difluorocarbene as well to form oxonium ylide, which eventually leads to C-O bond cleavage with the formation of difluoromethyl ethers.

Paracatalytic induction: Subverting specificity in hedgehog protein autoprocessing with small molecules.

Paracatalytic inducers are antagonists that shift the specificity of biological catalysts, resulting in non-native transformations. In this Chapter we describe methods to discover paracatalytic inducers of Hedgehog (Hh) protein autoprocessing. Native autoprocessing uses cholesterol as a substrate nucleophile to assist in cleaving an internal peptide bond within a precursor form of Hh. This unusual reaction is brought about by HhC, an enzymatic domain that resides within the C-terminal region of Hh precursor proteins. Recently, we reported paracatalytic inducers as a novel class of Hh autoprocessing antagonists. These small molecules bind HhC and tilt the substrate specificity away from cholesterol in favor of solvent water. The resulting cholesterol-independent autoproteolysis of the Hh precursor generates a non-native Hh side product with substantially reduced biological signaling activity. Protocols are provided for in vitro FRET-based and in-cell bioluminescence assays to discover and characterize paracatalytic inducers of Drosophila and human hedgehog protein autoprocessing, respectively.

Unusual catalytic hydrogenation caused by photoinduced solid frustrated Lewis pairs

Most homogeneously FLP-catalyzed hydrogenation reactions that follow cleavage of H2 occur via protonation of substrates followed by hydride transfer. This order of activated H-transfer unavoidably limits the application scope of currently FLP-catalyzed hydrogenation to nucleophilic substrates. Herein, we report an unusual inverse H-transfer order in which photoinduced solid In2O3-FLPs catalyze the hydrogenated dehalogenation of aryl halides with H2. After the generation of active FLPs of In-OH+ and In-[Ov]H- via H2 splitting on In2O3 surface upon irradiation, a series of aryl halides were readily activated and initiated at the In-[Ov]H- sites and then dehalogenated with high yields. By combining this work with detailed studies on H/D kinetic isotope effects and activation energies of hydrogenated dehalogenation, we demonstrate that initial hydride transfer mediated by photoinduced solid FLPs is more effective than common proton transfer to initiate hydrogenation of these substrates.

Structure and Catalytic Mechanism of Radical SAM Methylases.

Methyl transfer is essential in myriad biological pathways found across all domains of life. Unlike conventional methyltransferases that catalyze this reaction through nucleophilic substitution, many members of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily use radical-based chemistry to methylate unreactive carbon centers. These radical SAM methylases reductively cleave SAM to generate a highly reactive 5'-deoxyadenosyl radical, which initiates a broad range of transformations. Recently, crystal structures of several radical SAM methylases have been determined, shedding light on the unprecedented catalytic mechanisms used by these enzymes to overcome the substantial activation energy barrier of weakly nucleophilic substrates. Here, we review some of the discoveries on this topic over the last decade, focusing on enzymes for which three-dimensional structures are available to identify the key players in the mechanisms, highlighting the dual function of SAM as a methyl donor and a 5'-deoxyadenosyl radical or deprotonating base source. We also describe the role of the protein matrix in orchestrating the reaction through different strategies to catalyze such challenging methylations.

Polyphenols from Thinned Young Apples: HPLC-HRMS Profile and Evaluation of Their Anti-Oxidant and Anti-Inflammatory Activities by Proteomic Studies.

The qualitative profile of thinned apple polyphenols (TAP) fraction (≈24% of polyphenols) obtained by purification through absorbent resin was fully investigated by LC-HRMS in positive and negative ion mode and using ESI source. A total of 68 polyphenols were identified belonging to six different classes: flavanols, flavonols, dihydrochalchones, flavanones, flavones and organic and phenolic acids. The antioxidant and anti-inflammatory activities were then investigated in cell models with gene reporter for NRF2 and NF-κB and by quantitative proteomic (label-free and SILAC) approaches. TAP dose-dependently activated NRF2 and in the same concentration range (10–250 µg/mL) inhibited NF-κB nuclear translocation induced by TNF-α and IL-1α as pro-inflammatory promoters. Proteomic studies elucidated the molecular pathways evoked by TAP treatment: activation of the NRF2 signaling pathway, which in turn up-regulates protective oxidoreductases and their nucleophilic substrates such as GSH and NADPH, the latter resulting from the up-regulation of the pentose phosphate pathway. The increase in the enzymatic antioxidant cellular activity together with the up-regulation of the heme-oxygenase would explain the anti-inflammatory effect of TAP. The results suggest that thinned apples can be considered as a valuable source of apple polyphenols to be used in health care products to prevent/treat oxidative and inflammatory chronic conditions.