Homology Modeling and Molecular Docking Studies of (S)‐Scoulerine 9‐O‐Methyltransferase from Coptis chinensis

(S)‐Scoulerine 9‐O‐methyltransferase (SMT), belonging to the S‐adenosyl‐L‐methionine (SAM)‐dependent O‐methyltransferase family, is an essential enzyme in the berberine biosynthetic pathways. In order to study the interactions of SMT with its substrate and further to understand the catalytic mechanism and substrate specificity, a three dimensional model of SMT from Coptis chinensis was constructed by homology modeling using the crystal structure of caffeic acid/5‐hydroxyferulic acid 3/5‐O‐methyltransferase (COMT) as a template. The three dimensional structure of SMT, which was mainly composed of α‐helices and some β‐sheets, was similar to that of COMT. In contrast with COMT, the non‐conserved residues in the substrate binding pocket of SMT might be responsible for their differences in the substrate specificity. Val119 and Asp254 in SMT were the key residues for orienting substrate for methylation as both residues had H‐bonds with (S)‐scoulerine. The methylation of (S)‐scoulerine involved deprotonation of the 9‐hydroxyl group by His253 and Asp254 in SMT followed by a nucleophilic attack on the SAM‐methyl resulting in the product, (S)‐tetrahydrocolumbamine.     

Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane‐1,2‐dione Hydrolase: From CC Bond Cleavage to CC Bond Ligation

ThDP‐dependent cyclohexane‐1,2‐dione hydrolase (CDH) catalyzes the C? C bond cleavage of cyclohexane‐1,2‐dione to 6‐oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH‐H28A is much less able to catalyze the C? C bond formation, while the ability for C? C bond cleavage is still intact. The double variant CDH‐H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane‐1,2‐dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54–94 % enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane‐2,3‐dione are alternative donor substrates for C? C bond formation. Thus, the very rare aldehyde–ketone cross‐benzoin reaction has been solved by design of an enzyme variant.     

Semiempirical simulation of a theta‐class glutathione S‐transferase‐catalyzed glutathione attack to the allelochemical DIMBOA

We evaluated by the semiempirical method PM3 possible mechanisms of a putative interaction between a cereal allelochemical, the cyclic hydroxamic acid 2,4‐dihydroxy‐7‐metoxy‐2H‐1,4‐benzoxazin‐3(4H)‐one (DIMBOA), and the tripeptide glutathione (GSH) inside the active site of a theta‐class glutathione S‐transferase. Based on a preliminary study of transition states from DIMBOA reactions with methanethiolate as a simple model of GSH, we investigated the roles of catalytic residues of the enzyme during nucleophilic additions of GSH to the carbonyl groups of DIMBOA and of its phenol/aldehyde isomer inside the active site model. Our results suggest that a tyrosine residue, Tyr113, makes the most important contributions for the catalytic mechanism. In the modeled reaction steps, Tyr113 behaves as a double hydrogen bond donor catalyst for nucleophilic additions of GSH to substrates: It initially helps stabilize the strongly nucleophilic reduced GSH with a hydrogen bond intermediated by a water molecule; during substrate approach, small conformational changes enable the residue to make a direct hydrogen bond to the substrate group that develop negative charge after addition of reduced GSH. © 2002 Wiley Periodicals, Inc.; Int J Quantum Chem, 2002     

Nucleophile Promiscuity of Engineered Class II Pyruvate Aldolase YfaU from E. Coli

Pyruvate‐dependent aldolases exhibit a stringent selectivity for pyruvate, limiting application of their synthetic potential, which is a drawback shared with other existing aldolases. Structure‐guided rational protein engineering rendered a 2‐keto‐3‐deoxy‐l ‐rhamnonate aldolase variant, fused with a maltose‐binding protein (MBP‐YfaU W23V/L216A), capable of efficiently converting larger pyruvate analogues, for example, those with linear and branched aliphatic chains, in aldol addition reactions. Combination of these nucleophiles with N‐Cbz‐alaninal (Cbz=benzyloxycarbonyl) and N‐Cbz‐prolinal electrophiles gave access to chiral building blocks, for example, derivatives of (2S,3S,4R)‐4‐amino‐3‐hydroxy‐2‐methylpentanoic acid (68 %, d.r. 90:10) and the enantiomer of dolaproine (33 %, d.r. 94:6) as well as a collection of unprecedented α‐amino acid derivatives of the proline and pyrrolizidine type. Conversions varied between 6–93 % and diastereomeric ratios from 50:50 to 95:5 depending on the nucleophilic and electrophilic components.     

Two‐step synthesis of new 1,2,4,5‐tetrahydrospiro‐[3H‐2‐benzazepine‐3,4′‐piperidines] from 4‐iminopiperidines

New spiro[3H‐2‐benzazepine‐3,4′‐piperidines] and their precursors, N‐substituted 4‐allyl‐4‐N‐benzyl‐aminopiperidines, have been prepared as potential psychotic agents from readily available 4‐iminopiperidines, by a sequence of reactions that included nucleophilic addition of Grignard reagents and Bronsted acid‐mediated intramolecular cyclisation. Some of the compounds prepared have been tested in albine mice for spontaneous motor activity. All compounds prepared were characterized by ir and ¹H nmr spectroscopies and cg‐ms spectrometry.     

A kinetic study of the high temperature rearrangement of 4‐ethyl‐3,5‐diphenyl‐4H‐1,2,4‐triazole

The kinetics of the thermal rearrangement 4‐ethyl‐3,5‐diphenyl‐4H‐1,2,4‐triazoles, 1 , to the corresponding 1‐ethyl‐3,5‐diphenyl‐1‐alkyl‐1H‐1,2,4‐triazoles, 2 , was studied in 15‐Crown‐5 and octadecane at 330 °C. The reaction was very slow in octadecane but proceed well in 15‐Crown‐5. The reaction order for the reaction was not constant but changed from an initial second order rate law towards a first order rate law as the reaction progressed. This was confirmed by the concentration dependent reaction order, n_c, which was larger than the time dependent rate law, n_t. The rationale for the observation was, that at high substrate concentrations the reaction order was second order while at lower concentrations a competing solvent assisted reaction plays an increasing important role. The data were in agreement with a mechanism in which the neutral 4‐alkyl‐triazoles in an intermolecular nucleophilic displacement reaction form a triazolium triazolate, which in a subsequent nucleophilic reaction gives the observed product.     

Gold‐catalyzed Reactions of 3‐Alkynyloxireno[2, 3‐b]chromenones to Form 3(2H)‐Furanones via a Domino Pathway

3(2H)‐Furanones are efficiently generated from 3‐alkynyl oxireno[2,3‐b]chromenones by an Au/DDQ‐catalyzed domino reaction through a pathway composed of cyclization, C? C cleavage, nucleophilic addition, oxidation, and nucleophilic addition. It was found that stoichiometric AuCl₃ or catalytic Au with stoichiometric DDQ can oxidize the benzylic sp³ C? H bond to facilitate nucleophilic addition.     

Regioselective Insertion of o‐Carborynes into the α‐CH Bond of Tertiary Amines: Synthesis of α‐Carboranylated Amines

o‐Carboryne can undergo α‐C? H bond insertion with tertiary amines, thus affording α‐carboranylated amines in very good regioselectivity and isolated yields. In this process, the nucleophilic addition of tertiary amines to the multiple bond of o‐carboryne generates a zwitterionic intermediate. An intramolecular proton transfer, followed by a nucleophilic attack leads to the formation of the final product. Thus, regioselectivity is highly dependent upon the acidity of α‐C? H proton of tertiary amines. This approach serves as an efficient methodology for the preparation of a series of 1‐aminoalkyl‐o‐carboranes.     

4,5‐Bis(furoylsulfanyl)‐1,3‐dithiole‐2‐thione

The title compound, C₁₃H₆O₄S₅, possesses crystallographically imposed mirror symmetry, with the atoms of the C=S group lying on the mirror plane. It is an example of the general formula [RCO]₂(dmit), where R is a furan ring and dmit is 2‐thioxo‐1,3‐dithiole‐4,5‐dithiol­ate. The components exhibit some polarization of their mol­ecular–electronic structure. The dmit and furan moieties exhibit a high degree of conjugation, as the introduction of C=O connecting the conjugated furan (donor) and dmit (acceptor) rings forms a good conjugated system with high delocalization. A polar three‐dimensional framework is built from a combination of inter­molecular contacts, namely S⋯S inter­actions and C—H⋯O hydrogen bonding. The structural characteristics lead to good second‐order non‐linear optical properties.     

Structural Snapshots of α‐1,3‐Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases

Glycosyltransferases (GTs) are a key family of enzymes that catalyze the synthesis of glycosidic bonds in all living organisms. The reaction involves the transfer of a glycosyl moiety and can proceed with retention or inversion of the anomeric configuration. To date, the catalytic mechanism of retaining GTs is a topic of great controversy, particularly for those enzymes containing a putative nucleophilic residue in the active site, for which the occurrence of a double‐displacement mechanism has been suggested. We report native ternary complexes of the retaining glycosyltransferase α‐1,3‐galactosyltransferase (α3GalT) from Bos taurus , which contains such a nucleophile in the active site, in a productive mode for catalysis in the presence of its sugar donor UDP‐Gal, the acceptor substrate lactose, and the divalent cation cofactor. This new experimental evidence supports the occurrence of a front‐side substrate‐assisted S_Ni‐type reaction for α3GalT, and suggests a conserved common catalytic mechanism among retaining GTs.     

Mechanistic insight on (E)‐methyl 3‐(2‐aminophenyl)acrylate cyclization reaction by multicatalysis of solvent and substrate

The reaction mechanism of (E)‐methyl 3‐(2‐aminophenyl)acrylate ( A ) with phenylisothiocyanate ( B ) as well as the vital roles of substrate A and solvent water were investigated under unassisted, water‐assisted, substrate A ‐assisted, and water‐ A ‐assisted conditions. The reaction proceeds with four processes via nucleophilic addition, deprotonation and protonation, intramolecular cyclization with hydrogen transfer, and keto–enol tautomerization. According to the different H‐shift mode, two possible types of H‐shift P1 and P2 are carefully investigated to identify the most preferred pathway, differing in the ? NH₂ group deprotonation and ? CH group of A protonation processes. It is found that substrate A and water not only act as reactant and solvent, but also as catalyst, proton shuttle, and stabilizer in effectively lowering the energy barrier. Therefore, the results demonstrate that the strong donating and accepting ability of ? NH₂ group on A and the presence of bulk water are the keys to the title reaction proceed. © 2016 Wiley Periodicals, Inc.     

Regioselective Insertion of o‐Carborynes into the α‐C?H Bond of Tertiary Amines: Synthesis of α‐Carboranylated Amines

o‐Carboryne can undergo α‐C H bond insertion with tertiary amines, thus affording α‐carboranylated amines in very good regioselectivity and isolated yields. In this process, the nucleophilic addition of tertiary amines to the multiple bond of o‐carboryne generates a zwitterionic intermediate. An intramolecular proton transfer, followed by a nucleophilic attack leads to the formation of the final product. Thus, regioselectivity is highly dependent upon the acidity of α‐C H proton of tertiary amines. This approach serves as an efficient methodology for the preparation of a series of 1‐aminoalkyl‐o‐carboranes.     

Improvement of a Stereoselective Biocatalytic Synthesis by Substrate and Enzyme Engineering: 2‐Hydroxy‐(4′‐oxocyclohexyl)acetonitrile as the Model

Even if biocatalysis is finding increasing application, it still has to gain widespread use in synthetic chemistry. Reasons for this are limitations that enzymes have with regard to substrate range, reaction scope, and insufficient selectivity with unnatural compounds. These shortcomings can be challenged by enzyme and/or substrate engineering, which are employed to alter substrate specificity and enhance the enzyme selectivity toward unnatural substrates. Herein, these two approaches are coupled to improve the hydroxynitrile lyase catalyzed synthesis of 2‐hydroxy‐(4′‐oxocyclohexyl)acetonitrile ( 4 ). The ketone functionality is masked as an enol ether, and the oxynitrilase of Hevea brasiliensis is engineered towards this masked substrate to give the product with a high optical purity and to drastically lower the amount of enzyme needed.     

1,1′‐Dimethoxy‐3,3′‐dimethyl‐3,3′‐(hexane‐1,6‐diyl)bis(triazen‐2‐ium‐2‐olate): a nitric oxide donor

The title compound, C₁₀H₂₄N₆O₄, is the most stable type of nitric oxide (NO) donor among the broad category of discrete N‐diazeniumdiolates (NO adducts of nucleophilic small molecule amines). Sitting astride a crystallographic inversion center, the molecule contains a symmetric dimethylhexane‐1,6‐diamine structure bearing two planar O²‐methylated N‐diazeniumdiolate functional groups [N(O)=NOMe]. These two groups are parallel to each other and have the potential to release four molecules of NO. The methylated diazeniumdiolate substituent removes the negative charge from the typical N(O)=NO⁻ group, thereby increasing the stability of the diazeniumdiolate structure. The crystal was nonmerohedrally twinned by a 180° rotation about the real [101] axis. This is the first N‐based bis‐diazeniumdiolate compound with a flexible aliphatic main unit to have its structure analyzed and this work demonstrates the utility of stabilizing the N‐diazeniumdiolate functional group by methylation.     

Synthesis of Pyrano[3,2‐c]quinoline‐3‐carboxaldehyde and 3‐(Ethoxymethylene)‐pyrano[3,2‐c]quinolinone and Their Chemical Behavior toward Some Nitrogen and Carbon Nucleophiles

Synthesis of novel 3‐(ethoxymethylene)‐pyrano[3,2‐c]quinolinone and pyrano[3,2‐c]quinoline‐3‐carboxaldehyde was accomplished efficiently via a simple method. These two scaffolds were used as precursors to afford new biologically interesting products in good yield and short reaction times. The chemical reactivity of ethoxy methylene 2 and carboxaldehyde 3 toward different nucleophilic reagents was studied. Structures of the new synthesized compounds were elucidated by their analytical and spectral data.     

The Substrate Specificity of β, β‐Carotene 15,15′‐Monooxygenase

The synthesis of several substrate analogues of the enzyme β,β‐carotene 15,15′‐monooxygenase is reported. The substrate specificity of enriched enzyme fractions isolated from chicken intestinal mucosa was investigated. Regarding substrate binding/cleavage, these experiments demonstrate that i) any deviation from the `rod‐like' β,β‐carotene structure is not tolerated, ii) one `natural', unsubstituted β‐ionone ring is required, iii) the position and presence of the Me groups attached to the polyene chain is significant. These results suggest a hydrophobic barrel‐like substrate binding site in which the protein's amino acid residues through interaction with the Me groups, direct the central C=C bond in binding distance to the active site's metal‐oxo center, supporting the unique regiospecificity of cleavage to retinal (provitamin A).     

Reaction‐path calculations and crystal structures of 1,1′‐(ethylene‐1,2‐diyl)dipyridinium dichloride dihydrate and 1,1′‐(ethylene‐1,2‐diyl)dipyridinium dibromide

The design of new organic–inorganic hybrid ionic materials is of interest for various applications, particularly in the areas of crystal engineering, supramolecular chemistry and materials science. The monohalogenated intermediates 1‐(2‐chloroethyl)pyridinium chloride, C₅H₅NCH₂CH₂Cl⁺·Cl⁻, (I′), and 1‐(2‐bromoethyl)pyridinium bromide, C₅H₅NCH₂CH₂Br⁺·Br⁻, (II′), and the ionic disubstituted products 1,1′‐(ethylene‐1,2‐diyl)dipyridinium dichloride dihydrate, C₁₂H₁₄N₂²⁺·2Cl⁻·2H₂O, (I), and 1,1′‐(ethylene‐1,2‐diyl)dipyridinium dibromide, C₁₂H₁₄N₂²⁺·2Br⁻, (II), have been isolated as powders from the reactions of pyridine with the appropriate 1,2‐dihaloethanes. The monohalogenated intermediates (I′) and (II′) were characterized by multinuclear NMR spectroscopy, while (I) and (II) were structurally characterized using powder X‐ray diffraction. Both (I) and (II) crystallize with half the empirical formula in the asymmetric unit in the triclinic space group P. The organic 1,1′‐(ethylene‐1,2‐diyl)dipyridinium dications, which display approximate C2h symmetry in both structures, are situated on inversion centres. The components in (I) are linked via intermolecular O—H…Cl, C—H…Cl and C—H…O hydrogen bonds into a three‐dimensional framework, while for (II), they are connected via weak intermolecular C—H…Br hydrogen bonds into one‐dimensional chains in the [110] direction. The nucleophilic substitution reactions of 1,2‐dichloroethane and 1,2‐dibromoethane with pyridine have been investigated by ab initio quantum chemical calculations using the 6–31G** basis. In both cases, the reactions occur in two exothermic stages involving consecutive S_N2 nucleophilic substitutions. The isolation of the monosubstituted intermediate in each case is strong evidence that the second step is not fast relative to the first.     

A QM/MM Investigation of the Catalytic Mechanism of Metal‐Ion‐Independent Core 2 β1,6‐N‐Acetylglucosaminyltransferase

β1,6‐GlcNAc‐transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, and lung cancer cells, in leukemia cells, in the lymhomonocytes of multiple sclerosis patients, leukocytes from diabetes patients, and in conditions causing an immune deficiency. The result of the action of C2GnT is the core 2 structure that is essential for the further elongation of the carbohydrate chains of O‐glycans. The catalytic mechanism of this metal‐ion‐independent glycosyltransferase is of paramount importance and is investigated here by using quantum mechanical (QM) (density functional theory (DFT))/molecular modeling (MM) methods with different levels of theory. The structural model of the reaction site used in this report is based on the crystal structures of C2GnT. The entire enzyme–substrate system was subdivided into two different subsystems: the QM subsystem containing 206 atoms and the MM region containing 5914 atoms. Three predefined reaction coordinates were employed to investigate the catalytic mechanism. The calculated potential energy surfaces discovered the existence of a concerted S_N2‐like mechanism. In this mechanism, a nucleophilic attack by O6 facilitated by proton transfer to the catalytic base and the separation of the leaving group all occur almost simultaneously. The transition state for the proposed reaction mechanism at the M06‐2X/6‐31G** (with diffuse functions on the O1′, O5′, O_Glu, and O6 atoms) level was located at C1? O6=1.74 Å and C1? O1=2.86 Å. The activation energy for this mechanism was estimated to be between 20 and 29 kcal mol^?1, depending on the method used. These calculations also identified a low‐barrier hydrogen bond between the nucleophile O6H and the catalytic base Glu320, and a hydrogen bond between the N‐acetamino group and the glycosidic oxygen of the donor in the TS. It is proposed that these interactions contribute to a stabilization of TS and participate in the catalytic mechanism.     

Process Development through Solvent Engineering in the Biocatalytic Synthesis of the Heterocyclic Bulk Chemical ε‐Caprolactone

For an alternative synthetic approach toward the heterocyclic industrial chemical ε‐caprolactone, which is based on a biocatalytic oxidation of readily available cyclohexanol with air in aqueous media (using an alcohol dehydrogenase and a Baeyer–Villiger monooxygenase as enzyme components), a solvent engineering has been carried out identifying isooctane as a suitable co‐solvent. Biotransformations in an aqueous‐isooctane biphasic solvent system were found to proceed faster at both investigated substrate concentrations of 40 and 80 mm , respectively, compared with the analogous enzymatic reactions in pure aqueous medium. In addition, in all cases quantitative conversions were observed after a reaction time of 23 h when using isolated enzymes. The achievements indicate a high compatibility of isooctane [10%(v/v)] with the enzymes as well as the potential for an in situ removal of the organic reaction components, thus decreasing inhibition and/or destabilization effects of these organic components on the enzymes used. In contrast, so far, the use of recombinant whole‐cells gave less satisfactory results, which might be due to limitations of the permeation of, for example, the substrate through the cell membrane.     

Microwave‐assisted nucleophilic cleavage of 5,7‐dimethyl‐2‐phenyl‐1‐oxo‐lH‐pyrazolo[ 1,2‐a]pyrazol‐4‐ylium‐3‐olate to α‐phenylmalonamides

Three α‐phenylmalonamides have been prepared by the selective nucleophilic cleavage of 5,7‐dimethyl‐2‐phenyl‐1‐oxo‐1H‐pyrazolo[1,2‐a]pyrazol‐4‐ylium‐3‐olate in solventless microwave syntheses. The three weak nucleophiles employed were aniline, p‐chloroaniline and m‐toluidine. The α‐phenylmalonamides of these three aniline derivatives could not be prepared using the previously reported solvent syntheses via 3‐oxopyrazolo[1,2‐a]pyrazol‐8‐ylium‐1‐olates. All products were characterised using, infrared spectroscopy, ¹H nmr and electrospray mass spectrometry. The single crystal X‐ray structures of the starting pyrazolo‐[1,2‐a]pyrazole and α‐phenylmalon‐m‐toluidide are also reported.