Kinetic and in silico structural characterization of norbelladine O-methyltransferase of Amaryllidaceae alkaloids biosynthesis.

Amaryllidaceae alkaloids are a diverse group of alkaloids exclusively reported from the Amaryllidaceae plant family. In planta, their biosynthesis is still not fully characterized; however, a labeling study established 4'-O-methylnorbelladine as the key intermediate compound of the pathway. Previous reports have characterized O-methyltransferases from several Amaryllidaceae species. Nevertheless, the formation of the different O-methylnorbelladine derivatives (3'-O-methylnorbelladine, 4'-O-methylnorbelladine, and 3'4'-O-dimethylnorbelladine), the role, and the preferred substrates of O-methyltransferases are not clearly understood. In this study, we performed the biochemical characterization of an O-methyltransferase candidate from Narcissus papyraceus (NpOMT) in vitro and in vivo, following biotransformation of norbelladine in Nicotiana benthamiana having transient expression of NpOMT. Docking analysis was further used to investigate substrate preferences, as well as key interacting residues of NpOMT. Our study shows that NpOMT methylates norbelladine preferentially at the 4'-OH position in vitro and in planta. Interestingly, NpOMT also catalyzed the synthesis of 3',4'-O-dimethylnorbelladine from norbelladine and 4'-O-methylnorbelladine during in vitro enzymatic assay. Furthermore, we show that NpOMT methylates 3,4-dihydroxybenzylaldehyde and caffeic acid in a nonregiospecific manner to produce meta/para monomethylated products. This study reveals a novel catalytic potential of an Amaryllidaceae O-methyltransferase and its ability to regioselectively methylate norbelladine in the heterologous host N. benthamiana.

Structure of epoxide hydrolase 2 from Mangifera indica throws light on the substrate specificity determinants of plant epoxide hydrolases.

Epoxide hydrolases (EHs) are a group of ubiquitous enzymes that catalyze hydrolysis of chemically reactive epoxides to yield corresponding dihydrodiols. Despite extensive studies on EHs from different clades, generic rules governing their substrate specificity determinants have remained elusive. Here, we present structural, biochemical and molecular dynamics simulation studies on MiEH2, a plant epoxide hydrolase from Mangifera indica. Comparative structure-function analysis of nine homologs of MiEH2, which include a few AlphaFold structural models, show that the two conserved tyrosines (MiEH2Y152 and MiEH2Y232) from the lid domain dissect substrate binding tunnel into two halves, forming substrate-binding-pocket one (BP1) and two (BP2). This compartmentalization offers diverse binding modes to their substrates, as exemplified by the binding of smaller aromatic substrates, such as styrene oxide (SO). Docking and molecular dynamics simulations reveal that the linear epoxy fatty acid substrates predominantly occupy BP1, while the aromatic substrates can bind to either BP1 or BP2. Furthermore, SO preferentially binds to BP2, by stacking against catalytically important histidine (MiEH2H297) with the conserved lid tyrosines engaging its epoxide oxygen. Residue (MiEH2L263) next to the catalytic aspartate (MiEH2D262) modulates substrate binding modes. Thus, the divergent binding modes correlate with the differential affinities of the EHs for their substrates. Furthermore, long-range dynamical coupling between the lid and core domains critically influences substrate enantioselectivity in plant EHs.

Mechanistic study of the Ni-catalyzed hydroalkylation of 1,3-dienes: The origins of regio- and enantioselectivities and a further rational design.

The development of the catalytic regio- and enantioselective hydrofunctionalization of 1,3-dienes remains a challenge and requires deep insight into the reaction mechanisms. We herein thoroughly studied the reaction mechanism of the Ni-catalyzed hydroalkylation of 1,3-dienes with ketones by density functional theory (DFT) calculations. It reveals that the reaction is initiated by stepwise oxidative addition of EtO-H followed by 1,3-diene migratory insertion to generate the alkylnickel(II) intermediate, rather than the experimentally proposed ligand-to-ligand hydrogen transfer (LLHT) mechanism. In addition, we rationalized the role of t BuOK in the subsequent addition of enolate of ketone and transmetalation process. Based on the whole catalysis, the CC reductive elimination step, turns out to be the rate- and enantioselectivity-determining step. Furthermore, we disclosed the origins of the regio- and enantioselectivity of the product, and found that the 1,2-selectivity lies in the combination effects of the ligand-substrate electrostatic interactions, orbital interactions and Pauli repulsions, while the enantioselectivity mainly arises from substrate-ligand steric repulsions. Based on mechanistic study, new biaryl bisphosphine ligands affording higher enantioselectivity were designed, which will help to improve current catalytic systems and develop new transition-metal-catalyzed hydroalkylations.

Regioselective Deacetylation in Nucleosides and Derivatives.

Nucleoside analogues are a promising class of natural compounds in the pharmaceutical industry, and many antiviral, antibacterial and anticancer drugs have been created through structural modification of nucleosides scaffold. Acyl protecting groups, especially the acetyl group, play an important role in the protection of hydroxy groups in nucleoside synthesis and modification; consequently, numerous methodologies have been put forth for the acetylation of free nucleosides. However, for nucleosides that contain different O- and N-based functionalities, selective deprotection of the acetyl group(s) in nucleosides has been studied little, despite its practical significance in simplifying the preparation of partially or differentially substituted nucleoside intermediates. In this mini-review, recent approaches for regioselective deacetylation in acetylated nucleosides and their analogues are summarized and evaluated. Different regioselectivities (primary ester, secondary ester, full de-O-acetylation, and de-N-acetylation) are summarized and discussed in each section.

Engineering of a Baeyer-Villiger monooxygenase to Improve Substrate Scope, Stereoselectivity and Regioselectivity.

Baeyer-Villiger monooxygenases belong to a family of flavin-binding proteins that catalyze the Baeyer-Villiger (BV) oxidation of ketones to produce lactones or esters, which are important intermediates in pharmaceuticals or sustainable materials. Phenylacetone monooxygenase (PAMO) from Thermobifida fusca with moderate thermostability catalyzes the oxidation of aryl ketone substrates, but is limited by high specificity and narrow substrate scope. In the present study, we applied loop optimization by loop swapping followed by focused saturation mutagenesis in order to evolve PAMO mutants capable of catalyzing the regioselective BV oxidation of cyclohexanone and cyclobutanone derivatives with formation of either normal or abnormal esters or lactones. We further modulated PAMO to increase enantioselectivity. Crystal structure studies indicate that rotation occurs in the NADP-binding domain and that the high B-factor region is predominantly distributed in the catalytic pocket residues. Computational analyses further revealed dynamic character in the catalytic pocket and reshaped hydrogen bond interaction networks, which is more favorable for substrate binding. Our study provides useful insights for studying enzyme-substrate adaptations.

Biological Evaluation of Isosteric Applicability of 1,3-Substituted Cuneanes as m-Substituted Benzenes Enabled by Selective Isomerization of 1,4-Substituted Cubanes.

We herein evaluate a biological applicability of 1,3-substituted cuneanes as an isostere of m-substituted benzenes based on its structural similarity. An investigation of a method to obtain 1,3-substituted cuneanes by selective isomerization of 1,4-substituted cubanes enables this attempt by giving a key synthetic step to obtain a cuneane analogs of pharmaceuticals having m-substituted benzene moiety. Biological evaluation of the synthesized analogs and in silico study of the obtained result revealed a potential usage of cuneane skeleton in medicinal chemistry.

Chemo-Enzymatic Synthesis of Isomeric I-branched Polylactosamines Using Traceless Blocking Groups.

Poly-N-acetyl lactosamines (polyLacNAc) are common structural motifs of N- and O-linked glycan, glycosphingolipids and human milk oligosaccharides. They can be branched by the addition of ß1,6-linked N-acetyl-glucosamine (GlcNAc) moieties to internal galactoside (Gal) residues by the I-branching enzyme beta-1,6-N-acetylglucosaminyltransferase 2 (GCNT2). I-branching has been implicated in many biological processes and is also associated with various diseases such as cancer progression. Currently, there is a lack of methods that can install, in a regioselective manner, I-branches and allows the preparation of isomeric poly-LacNAc derivatives. Here, we described a chemo-enzymatic strategy that addresses this deficiency and is based on the enzymatic assembly of an oligo-LacNAc chain that at specific positions is modified by a GlcNTFA moiety. Replacement of the trifluoroacetyl (TFA) moiety by tert-butyloxycarbonyl (Boc) gives compounds in which the galactoside at the proximal site is blocked from modification by GCNT2. After elaboration of the antennae, the Boc group can be removed, and the resulting amine acetylated to give natural I-branched structures. It is also shown that fucosides can function as a traceless blocking group that can provide complementary I-branched structures from a single precursor. The methodology made it possible to synthesize a library of polyLacNAc chains having various topologies.

The Effect of Conformational Freedom vs Restriction on the Rate in Asymmetric Hydrogenation: Iridium-Catalyzed Regio- and Enantioselective Monohydrogenation of Dienones.

Transition metal-catalyzed asymmetric hydrogenation constitutes an efficient strategy for the preparation of chiral molecules. When dienes are subjected to hydrogenation, control over regioselectivity still presents a large challenge and the fully saturated alkane is often yielded. A few successful monohydrogenations of dienes have been reported, but hitherto these are only efficient for dienes comprised of two distinctly different olefins. Herein, the reactivity of a conjugated carbonyl compound as a function of their conformational freedom is studied, based on a combined experimental and theoretical approach. It was found that alkenes in the (s)-cis conformation experience a large rate acceleration while (s)-trans restrained alkenes undergo hydrogenation slowly. Ultimately, this reactivity aspect was exploited in a novel method for the monohydrogenation of dienes based on conformational restriction ((s)-cis vs (s)-trans). This mode of discrimination conceptually differs from existing monohydrogenations and dienones constructed of two olefins similar in nature could efficiently be hydrogenated to the chiral alkene (up to 99 % ee). The extent of regioselection is even powerful enough to overcome the conventional reactivity order of substituted olefins (di>tri>tetra). This high yielding and atom-economical protocol provides an interesting opportunity to instal a stereogenic center on a carbocycle, while leaving a synthetically useful alkene untouched.

Gold Trifluoromethyl Complexes as Efficient Regioselective Catalysts in Alkyne Hydration.

Gold(III) complexes containing trifluoromethyl ligands are efficient catalysts in the hydration of alkynes, operating at low catalyst loadings, without additives, using environmentally friendly solvents and at mild conditions (60 °C). Hydration of terminal and internal alkynes provides the corresponding ketones in quantitative yields without special precautions as dry solvents or inert atmospheres. Remarkably, hydration of asymmetric internal alkynes proceeds with moderate to notable regioselectivities, providing mixtures of the two possible isomers with ratios up to 90 : 10.

Elucidating Mechanism and Selectivity in Pyridine Functionalization Through Silylium Catalysis.

The functionalization of aromatic N-heterocycles through silylium activation demonstrates exceptional selectivity and efficiency. Density functional theory (DFT) calculations unveil the detailed silylium catalysis mechanism and elucidate the origins of selectivity in this reaction. The phosphoramidimidate sulfonamide (PADI) precatalyst orchestrates of the catalytic cycle via three elementary steps. The Brønsted acidity of precatalyst significantly influences both the formation of silylium-based Lewis acid active species and the silylium activation of pyridine. Unlike disulfonimide (DSI)-type precatalysts, both Tf2NH and PADI precatalysts with strong acidities can easily promote the generation of activated silylium pyridine species. A semi-enclosed 'rigid' electronegative cavity in PADI-type anions constructs a well-defined recognition site, facilitating engagement with the positively charged silylium pyridine species. Due to the high electrophilicity and less steric demand at the C4-position of the pyridine substrate, the product with C4-regioselectivity was predominantly generated.

Unexpectedly Regioselective Diels-Alder Reactions of New Unsymmetrical Benzoquinones: A Convenient Synthetic Entry to Uniquely Substituted Decalins.

We report flexible synthesis of new unsymmetrically 2,6-disubstituted benzoquinones (33 examples) and a systematic study of their reactivity in the Diels-Alder reaction. The Diels-Alder reactions of selected unsymmetrical benzoquinones with seemingly similar substituents were found to proceed with high regioselectivity and the formation of selected experimentally observed main products was rationalized by theoretical (DFT) calculations. The findings can be exploited in the convenient preparation of densely substituted and stereochemically defined decalins with unique angular substituents at ring fusion. We also demonstrate the usefulness of this methodology in complex molecule synthesis through the total synthesis of a novel forskolin analog possessing an ethyl group at the fusion of the rings B and C.

Interrogating Explicit Solvent Effects on the Mechanism and Site-Selectivity of Aryl Halide Oxidative Addition to L2Pd(0).

We report a study of solvent effects on the rate, selectivity, and mechanism of (hetero)aryl (pseudo)halide oxidative addition to Pd(PCy3)2 as an exemplar of L2Pd(0) species. First, 2-chloro-3-aminopyridine is observed to undergo faster oxidative addition in toluene compared to more polar solvents, which is not consistent with the trend we observe with many other 2-halopyridines. We attribute this to solvent basicity hydrogen-bonding (pKHB) between solvent and substrate. Greater hydrogen-bond donation from the substrate leads to a more electron-rich aromatic system, and therefore slower oxidative addition. We demonstrate how this affects rate and site-selectivity for hydrogen-bond donating substrates. Second, electron-deficient multihalogenated pyridines exhibit improved site-selectivity in polar solvents, which we attribute to different C-X sites undergoing oxidative addition by two different mechanisms. The C-X site that favours the more polar nucleophilic displacement transition state is preferred over the site that favours a less-polar 3-centered transition state. Finally, (hetero)aryl triflates consistently undergo faster oxidative addition in more polar solvents, which we attribute to highly polar nucleophilic displacement transition states. This leads to improved site-selectivity for C-OTf oxidative addition, even in the presence of highly reactive 2-pyridylhalides.

Regioselective Synthesis of Hamilton-Receptor-Fullerene Oligo-Adducts for the Supramolecular Binding of Cyanuric Derivatives.

A new concept for the regioselective synthesis of Hamilton-receptor and cyanurate-functionalized oligo adducts of the fullerene C60 was developed. Based on an in-situ deprotection and click-post-functionalization approach with novel azido precursors, the corresponding fullerene hexakis-adducts with octahedral addition patterns and up to twelve Hamilton-receptor/cyanurate moieties surrounding the fullerene sphere were synthesized. The versatility of this approach was further demonstrated by the synthesis of Hamilton-receptor/cyanurate functionalized fullerene mono-adducts, which are not accessible by direct cyclopropanation. Several fullerene target compounds were purified by simple washing procedures of the solid crude reaction mixture without the need for chromatography. The resulting fullerene mono- and hexakis-adducts were fully characterized and their supramolecular properties were investigated by NMR-spectroscopy and isothermal titration calorimetry (ITC).

Remote Fluorination of α,ß-Unsaturated Carbonyls via Silyl Dienol Ethers.

We report a general, regioselective, and metal free γ-fluorination of α,ß-unsaturated carbonyls via silyl dienol ethers that are readily prepared from simple ketones and aldehydes. The transformation displays broad scope including 27 cyclic and acyclic siloxydienes providing γ-fluoro compounds in 28-91 % yield. Notably, the reported conditions are also suitable for the synthesis of challenging tertiary fluorides. The regioselectivity of the reaction was studied on a series of acyclic siloxydienes and was observed to be sensitive to the conformational flexibility of the substrate. Diversification of the γ-fluorocarbonyls demonstrates the promise of fluorine as a stereocontrol element.

The Effect of Basic Ligands and Alkenes on the Regioselectivity of C-H Additions of Tertiary Amines to Alkenes.

Highly regioselective C-H alkylation reactions of tertiary anilines and tertiary alkyl amines with simple alkenes have been achieved by the use of imidazolin-2-iminato scandium alkyl complexes. This protocol provided an efficient and atom-economical route to structurally diverse tertiary amine derivatives. The basic ligand, a coordinating THF in the catalyst and the substitution of alkene substrates were found to switch the regioselectivity of the C-H alkylation reactions of tertiary anilines presumably due to the generation of different types of catalytically active species or the formation of relatively stable intermediates. On the basis of the deuterium labeling experiments and KIE experiments, possible catalytical cycles were provided to understand the reaction mechanism as well as the regioselectivity.

Achieving Regioselectivity for Remote C-H Activation by Substructure Conformations: an Approach of Paralogous Cytochrome P450 Enzymes.

For advanced synthetic intermediates or natural products with multiple unactivated and energetically similar C(sp3)-H bonds, controlling regioselectivity for the C-H activation is particularly challenging. The use of cytochrome P450 enzymes (CYPs) is a promising solution to the 'regioelectivity' challenge in remote C-H activation. Notably, CYPs and organic catalysts share a fundamental principle: they strive to control the distance and geometry between the metal reaction center and the target C-H site. Most structural analyses of the regioselectivity of CYPs are limited to the active pocket, particularly when explaining why regioselectivity could be altered by enzyme engineering through mutagenesis. However, the substructures responsible for forming the active pocket in CYPs are well known to display complex dynamic changes and substrate-induced plasticity. In this context, we highlight a comparative study of the recently reported paralogous CYPs, IkaD and CftA, which achieve different regioselectivity towards the same substrate ikarugamycin by distinct substructure conformations. We propose that substructural conformation-controlled regioselectivity might also be present in CYPs of other natural product biosynthesis pathways, which should be considered when engineering CYPs for regioselective modifications.

Divergent Synthesis of Pyrazoles via Manganese Pincer Complex Catalyzed Acceptorless Dehydrogenative Coupling Reactions.

This report detailed the synthesis of multi-substituted pyrazoles through the acceptorless dehydrogenative coupling (ADC) reaction catalyzed by a well-defined manganese(I)-pincer complex. Symmetrically substituted pyrazoles were synthesized by reacting 1,3-diols with hydrazines. Unsymmetrically substituted pyrazoles were selectively made via the ADC of primary alcohols with methyl hydrazones. Water and hydrogen are liberated as the green byproducts. The endurance of these methodologies has been presented by producing 30 substrates with varied functionalities. Model reactions were scaled up to demonstrate practicability. The reaction rate and order were measured to transparent the involvement of the reagents during catalysis. Control experiments elucidated the plausible reaction mechanisms.

Regioselective Electrochemical Construction of Csp2-Csp2 Linkage at C5-C5' Position of 2-Oxindoles via an Intermolecular Anodic Dehydrogenative Coupling.

Applying electricity as a reagent in synthetic organic chemistry has attracted particular attention from synthetic chemists worldwide as an environmentally benign and cost-effective technique. Herein, we report the construction of the Csp2-Csp2 linkage at the C5-C5' position of 2-oxindole utilizing electricity as the traceless oxidant in an anodic dehydrogenative homo-coupling process. A variety of 3,3-disubstituted-2-oxindoles were subjected to dimerization, achieving yields of up to 70% through controlled potential electrolysis at an applied potential of 1.5 V versus Ag/Ag+ nonaqueous reference electrode. This electro-synthetic approach facilitates the specific assembly of C5-C5' (para-para coupled) dimer of 3,3-disubstituted-2-oxindole without the necessity of any external oxidants or additives and DFT (Density Functional Theory) calculations provided confirmation of this pronounced regioselectivity. Furthermore, validation through control experiments and voltammetric analyses substantiated the manifestation of radical-radical coupling (or biradical pathway) for the dimerization process.

REACTION KINETICS OF THE BENZYLATION OF ADENINE IN DMSO: REGIO-SELECTIVITY GUIDED BY ENTROPY.

The factors governing the regio-selectivity of the alkylation of adenine have been of interest for many years due to the biological importance of adenine derivatives, however, no reaction kinetic studies have been conducted. Herein, we report the rate constants and activation parameters of the benzylation of adenine under basic conditions in DMSO in the absence and presence of 15-crown-5 ether using real-time 1H NMR spectroscopy. The reaction is second-order for the formation of the N9- and N3-benzyladenine products, with a regio-selectivity factor 2.3 in favour of the N9-adduct. The Gibbs free energy of activation amounts to 87±2 kJ mol-1 for both reactions. The formation of the N9-adduct is more activated by 7 kJ mol-1, but its effect is offset by a less negative activation entropy, demonstrating that the long-contested reason for the regioselectivity in the benzylation of adenine is dominated by compensation of entropy and enthalpy in the transition state. The kinetic parameters obtained in the presence of the 15-crown-5 ether indicate that the crown ether forms a complex with an adenine-sodium ion-pair, increasing the activation barrier. However, the Gibbs free energy in the absence and presence of the crown ether remains constant.

Br-to-Cl Transformation Guided the Formation of Polyhalogenated Dibenzo-p-dioxins/Dibenzofurans.

Polyhalogenated dibenzo-p-dioxins/dibenzofurans (PXDD/Fs) are commonly released into the environment as byproducts of combustion processes, accompanied by flue gases. Chlorinated (Cl) and brominated (Br) precursors play crucial roles in forming PXDD/Fs. However, the specific contributions of Cl-precursors and Br-precursors to PXDD/Fs formation have not been fully elucidated. Herein, we demonstrate that the formation of Br-precursors can increase the fraction of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) congeners substituted at specific positions, such as 1,2,3,4,6,7,8-HpCDD, OCDD, 2,3,4,7,8-PeCDF, and 2,3,4,6,7,8-HxCDF. This is attributed to the electrophilic chlorination reaction of the Br-precursors, which includes the Br-to-Cl transformation pathway, following the principle of regioselectivity. The observed formation of polybrominated/chlorinated dibenzo-p-dioxins/benzofurans (PBCDD/Fs) from 1,2-dibromobenzene (1,2-DiBBz) as a Br precursor provides direct evidence supporting the proposed Br-to-Cl transformation. Quantum chemical calculations are employed to discuss the principle of regioselectivity in the Br-to-Cl transformation, clarifying the priority of the position for electrophilic chlorination. Additionally, the concentration of PCDD/Fs formed from 1,2-DiBBz is 1.6 µg/kg, comparable to that of polybrominated dibenzo-p-dioxins/dibenzofurans (PBDD/Fs) (2.4 µg/kg), highlighting the potential of brominated organic pollutants as precursors for PCDD/Fs formation. This study provides three potential pathways for PCDD/Fs formation from Br-precursors, establishing a theoretical foundation for elucidating the formation mechanism of PXDD/Fs in the coexistence of Cl and Br.