Catalytic Base Research Articles

Structural and functional analysis of SAM-dependent N-methyltransferases involved in ovoselenol and ovothiol biosynthesis.

Thio/selenoimidazole Nπ-methyltransferases are an emerging family of enzymes catalyzing the final step in the production of the S/Se-containing histidine-derived antioxidants ovothiol and ovoselenol. These enzymes, prevalent in prokaryotes, show minimal sequence similarity to other methyltransferases, and the structural determinants of their reactivities remain poorly understood. Herein, we report ligand-bound crystal structures of OvsM from the ovoselenol pathway as well as a member of a previously unknown clade of standalone ovothiol-biosynthetic Nπ-methyltransferases, which we have designated OvoM. Unlike previously reported ovothiol methyltransferases, which are fused as a C-terminal domain to the sulfoxide synthase OvoA, OvoMs function independently. Comparative structural analyses reveal conserved, ligand-induced conformational changes, suggesting similar behavior in dual-domain OvoA enzymes. Mutagenesis supports a model where OvoA domain rearrangement facilitates substrate recognition via a critical Tyr residue in the domain linker. Biochemical studies identify an essential active-site Asp, likely serving as a catalytic base in the SN2-like nucleophilic substitution reaction.

Alkyl bistriflimidate-mediated electrochemical deaminative functionalization.

An efficient electrochemical strategy for the deaminative functionalization of alkyl amines has been described. The alkyl bistriflimidates were readily accessed by the treatment of alkyl amines with trifluoromethanesulfonic anhydride and unprecedentedly employed for C-N bond activation. They can be applied to a range of transformations, including borylation, sulfuration, selenation, sulfonation, Additionally, deaminative esterification and amidation can be performed under catalytic base conditions. The protocol features an undivided cell without the use of transition metal- or photo-catalysts and exhibits high conversion and stability in flow reactors.

Between scents and sterols: Cyclization of labdane-related diterpenes as model systems for enzymatic control of carbocation cascades.

The citrus scent arises from the volatile monoterpene limonene, whose cyclic nature can be viewed as a miniaturized form of the poly-cyclic sterol triterpenoids. In particular, as these rings are all formed from poly-isoprenyl precursors via carbocation cascades. However, the relevant reactions are initiated by distinct mechanisms, either lysis/ionization of an allylic diphosphate ester bond, as in limonene synthases, or protonation of a terminal olefin or epoxide, as in lanosterol synthases. Labdane-related diterpenoids are unique in their utilization of both types of reactions. With over 7,000 such natural products known, this pair of reactions clearly generates privileged scaffolds, hydrocarbon backbones from which biological activity is readily derived. Moreover, the relevant enzymes serve as model systems for terpene cyclization more generally. Indeed, investigation of their enzymatic structure-function relationships has highlighted the importance of catalytic base positioning within the active site cavity in specifying product outcome. Conversely, comparison to the cyclases for other types of terpenoid natural products suggests new directions for discovery and/or engineering of the catalytic activity of those from labdane-related diterpenoid biosynthesis.

Unveiling the GT114 family: Structural characterization of A075L, a glycosyltransferase from Paramecium bursaria chlorella virus-1 (PBCV-1).

Protein A075L is a β-xylosyltransferase that participates in producing the core of the N-glycans found in VP54, the major viral capsid protein of Paramecium bursaria chlorella virus-1 (PBCV-1). In this study, we present an X-ray crystallographic analysis of the apo form of A075L, along with its complexes with the sugar donor and with a trisaccharide acceptor. The protein structure shows a typical GT-B folding, with two Rossmann-like fold domains, in which the acceptor substrate binds to the N-terminal region, and the nucleotide-sugar donor binds to the C-terminal region. We propose that the catalytic mechanism follows a direct displacement SN2-like reaction, where Asp73 serves as a catalytic base that deprotonates the incoming nucleophile of the acceptor, facilitating direct displacement of the UDP with the inversion of the anomeric configuration of the acceptor without metal ion dependence, while the interactions with side chains of Arg158 and Arg208 stabilize the developing negative charge. Using isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, high-performance liquid chromatography, and molecular dynamics simulations, the catalytic activity and specificity of this enzyme have been unraveled.

NHC‐Catalyzed, Microwave‐Assisted and Base‐Dependent Reactions of Substituted Cinnamaldehydes Towards γ‐Lactones or Saturated Esters

N‐Heterocyclic carbenes (NHCs) generated from imidazolium, imidazopyridinium and imidazoquinolinium hydrochlorides in situ using base and microwave irradiation were employed as organocatalysts to yield homoenolates from cinnamaldehyde and its aryl‐substituted analogs. Depending on the catalytic base either γ‐lactones were prepared when the strong base tBuOK was used or the corresponding saturated ethyl 3‐aryl propionates were synthesized with the milder DIPEA base. Novel imidazopyridinium and imidazoquinolinium hydrochlorides were synthesized and were compared to commercially available NHCs IMes and IDip for their catalytic activity. The optimum reaction conditions were established using IMes and the broad scope of both reactions was investigated using the 4 most efficient NHCs.

Arabidopsis thaliana argininosuccinate lyase structure uncovers the role of serine as the catalytic base

Arginine is an important amino acid in plants, as it not only plays a structural role and serves as nitrogen storage but is also a precursor for various molecules, including polyamines and proline. Arginine is produced by argininosuccinate lyase (ASL) which catalyzes the cleavage of argininosuccinate to arginine and fumarate. ASL belongs to the fumarate lyase family and while many members of this family were well-characterized, little is known about plant ASLs. Here we present the first crystal structures of ASL from the model plant, Arabidopsis thaliana (AtASL). One of the structures represents the unliganded form of the AtASL homotetramer. The other structure, obtained from a crystal soaked in argininosuccinate, accommodates the substrate or the reaction products in one of four active sites of the AtASL tetramer. Each active site is located at the interface of three neighboring protomers. The AtASL structure with ligands allowed us to analyze the enzyme-substrate and the enzyme-product interactions in detail. Furthermore, based on our analyses, we describe residues of AtASL crucial for catalysis. The structure of AtASL gives the rationale for the open-to-close transition of the GSS mobile loop and indicates the importance of serine 333 from this loop for the enzymatic action of the enzyme. Finally, we supplemented the structural data with the identification of sequence motifs characteristic for ASLs.

Ene‐Reductase‐Catalyzed Oxidation Reactions

AbstractEne‐reductases from the old yellow enzyme (OYE) family have been traditionally employed in the reduction of conjugated C═C double bonds. This study explores the underutilized oxidative potential of OYEs, demonstrating their capability to catalyze the enantioselective desaturation of carbonyl compounds. Utilizing a deprotonated tyrosine residue as a catalytic base, we developed a method to enable OYE‐catalyzed desaturation at ambient temperature and alkaline pH without the need for high‐temperature conditions. Through screening of various OYE enzymes, we identified several candidates from different genera with enhanced desaturase activity across different substrates. This work broadens the scope of biocatalytic applications for OYEs, introducing a novel approach to the synthesis of chiral α,β‐unsaturated carbonyl compounds.

Development of Organocatalytic Darzens Reactions Exploiting the Cyclopropenimine Superbase.

A truly organocatalytic approach to the Darzens reaction affording α,β-epoxy carbonyl compounds in good yields was developed taking advantage of the high basic strength and low nucleophilicity of cyclopropenimine superbases. The catalytic active free base can easily be generated in situ from its hydrochloride salt and maintained in the active deprotonated form by performing the reactions in a heterogeneous reaction system in the presence of excess potassium carbonate as a sacrificial base.

Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)-Ib From Campylobacter fetus subsp. fetus.

Aminoglycoside antibiotics have played a critical role in the treatment of both Gram-negative and Gram-positive bacterial infections. However, antibiotic resistance has severely compromised the efficacy of aminoglycosides. A leading cause of aminoglycoside resistance is mediated by bacterial enzymes that inactivate these drugs via chemical modification. Aminoglycoside nucleotidyltransferase-6 (ANT(6)) enzymes inactivate streptomycin by transferring an adenyl group from ATP to position 6 on the antibiotic. Despite the clinical significance of this activity, ANT(6) enzymes remain relatively uncharacterized. Here, we report the first high resolution x-ray crystallographic structure of ANT(6)-Ib from Campylobacter fetus subsp. fetus bound with streptomycin. Structural modeling and gel filtration chromatography experiments suggest that the enzyme exists as a dimer in which both subunits contribute to the active site. Moreover, superposition of the ANT(6)-Ib structure with the structurally related enzyme lincosamide nucleotidyltransferase B (LinB) permitted the identification of a putative nucleotide binding site. These data also suggest that residues D44 and D46 coordinate essential divalent metal ions and D102 functions as the catalytic base.

Insights from Structure-Based Simulations into the Persulfidation of Uridine Diphosphate-Glycosyltransferase71c5 Facilitating the Reversible Inactivation of Abscisic Acid.

The action of abscisic acid (ABA) is closely related to its level in plant tissues. Uridine diphosphate-glycosyltransferase71c5 (UGT71C5) was characterized as a major UGT enzyme to catalyze the formation of the ABA-glucose ester (ABA-GE), a reversible inactive form of free ABA in Arabidopsis thaliana (thale cress). UGTs function in a mode where the catalytic base deprotonates an acceptor to allow a nucleophilic attack at the anomeric center of the donor, achieving the transfer of a glucose moiety. The proteomic data revealed that UGT71C5 can be persulfidated. Herein, an experimental method was employed to detect the persulfidation site of UGT71C5, and the computational methods were further used to identify the yet unknown molecular basis of ABA glycosylation as well as the regulatory role of persulfidation in this process. Our results suggest that the linker and the U-shaped loop are regulatory structural elements: the linker is associated with the binding of uridine diphosphate glucose (UPG) and the U-shaped loop is involved in binding both UPG and ABA.It was also found that it is through tuning the dynamics of the U-shaped loop that is accompanied by the movement of tyrosine (Y388) that the persulfidation of cysteine (C311) leads to the catalytic residue histidine (H16) being in place, preparing for the deprotonation of ABA, and then reorientates UPG and deprotonated ABA closer to the 'Michaelis' complex, facilitating the transfer of a glucose moiety. Ultimately, the persulfidation of UGT71C5 is in favor of ABA glycosylation. Our results provide insights into the molecular details of UGT71C5 recognizing substrates and insights concerning persulfidation as a possible mechanism for hydrogen sulfide (H2S) to modulate the content of ABA, which helps us understand how modulating ABA level strengthens plant tolerance.

Novel, tightly structurally related N-myristoyltransferase inhibitors display equally potent yet distinct inhibitory mechanisms

N-myristoyltransferases (NMTs) catalyze essential acylations of N-terminal alpha or epsilon amino groups of glycines or lysines. Here, we reveal that peptides tightly fitting the optimal glycine recognition pattern of human NMTs are potent prodrugs relying on a single-turnover mechanism. Sequence scanning of the inhibitory potency of the series closely reflects NMT glycine substrate specificity rules, with the lead inhibitor blocking myristoylation by NMTs of various species. We further redesigned the series based on the recently recognized lysine-myristoylation mechanism by taking advantage of (1) the optimal peptide chassis and (2) lysine side chain mimicry with unnatural enantiomers. Unlike the lead series, the inhibitory properties of the new compounds rely on the protonated state of the side chain amine, which stabilizes a salt bridge with the catalytic base at the active site. Our study provides the basis for designing first-in-class NMT inhibitors tailored for infectious diseases and alternative active site targeting.

Molecular Mechanism of Double-Displacement Retaining β-Kdo Glycosyltransferase WbbB.

Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining β-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.

Structural basis for expanded substrate specificities of human long chain acyl-CoA dehydrogenase and related acyl-CoA dehydrogenases

Crystal structures of human long-chain acyl-CoA dehydrogenase (LCAD) and the catalytically inactive Glu291Gln mutant, have been determined. These structures suggest that LCAD harbors functions beyond its historically defined role in mitochondrial β-oxidation of long and medium-chain fatty acids. LCAD is a homotetramer containing one FAD per 43 kDa subunit with Glu291 as the catalytic base. The substrate binding cavity of LCAD reveals key differences which makes it specific for longer and branched chain substrates. The presence of Pro132 near the start of the E helix leads to helix unwinding that, together with adjacent smaller residues, permits binding of bulky substrates such as 3α, 7α, l2α-trihydroxy-5β-cholestan-26-oyl-CoA. This structural element is also utilized by ACAD11, a eucaryotic ACAD of unknown function, as well as bacterial ACADs known to metabolize sterol substrates. Sequence comparison suggests that ACAD10, another ACAD of unknown function, may also share this substrate specificity. These results suggest that LCAD, ACAD10, ACAD11 constitute a distinct class of eucaryotic acyl CoA dehydrogenases.

Asymmetric aza-Henry reaction toward trifluoromethyl β-nitroamines and biological investigation of their adamantane-type derivatives.

Amino acid-derived quaternary ammonium salts were successfully applied in the asymmetric aza-Henry reaction of nitromethane to N-Boc trifluoromethyl ketimines. α-Trifluoromethyl β-nitroamines were synthesized in good to excellent yields with moderate to good enantioselectivities. This reaction is distinguished by its mild conditions, low catalyst loading (1mol%), and catalytic base. It also proceeded on a gram scale without loss of enantioselectivity. The products were transformed to a series of adamantane-type compounds containing chiral trifluoromethylamine fragments. The potent anticancer activities of these compounds against liver cancer HepG2 and melanoma B16F10 were evaluated. Six promising compounds with notable efficacy have potential for further development.

Construction of graphdiyne/CoMoO4 type II heterojunction for efficiently enhanced photocatalytic hydrogen evolution

Cost-effective bimetallic oxide catalysts are gradually replacing noble metal catalysts for photocatalytic hydrogen production. This study used a two-step method to synthesize CoMoO4 with a rod-shaped structurea. CuBr is a catalytic base synthesis graphdiyne material. The graphdiyne that serves to anchor CoMoO4 rods through a solvent-thermal synthesis method, thereby enhancing the photocatalytic performance of the resultant composite catalyst. The results show that the 5 h hydrogen evolution capacity of the optimized CoMoO4/graphdiyne composite catalyst is 187.47 μmol, which is 2.9 times higher than that of CoMoO4 monomer and 41.7 times higher than that of graphdiyne monomer. The addition of graphdiyne provides a larger comparison area for CoMoO4, giving composite catalyst more active sites, and enhancing the optical hydrogenation effect of catalysts. Through the Mott-Schottky test, the UV–visible diffuse reflectance test and band gap calculation can be speculated that the CoMoO4 and graphdiyne construct the type II heterojunction which promotes the rapid transfer of photogonic carriers. This work provides a good prospect and opportunity for studying graphdiyne in the application of graphdiyne in the application of dualmetal oxides.

The active site of the SGNH hydrolase-like fold proteins: Nucleophile–oxyanion (Nuc-Oxy) and Acid–Base zones

SGNH hydrolase-like fold proteins are serine proteases with the default Asp-His-Ser catalytic triad. Here, we show that these proteins share two unique conserved structural organizations around the active site: (1) the Nuc-Oxy Zone around the catalytic nucleophile and the oxyanion hole, and (2) the Acid-Base Zone around the catalytic acid and base. The Nuc-Oxy Zone consists of 14 amino acids cross-linked with eight conserved intra- and inter-block hydrogen bonds. The Acid–Base Zone is constructed from a single fragment of the polypeptide chain, which incorporates both the catalytic acid and base, and whose N- and C-terminal residues are linked together by a conserved hydrogen bond. The Nuc-Oxy and Acid-Base Zones are connected by an SHLink, a two-bond conserved interaction from amino acids, adjacent to the catalytic nucleophile and base.

Catalytic Domino Three-Component Synthesis of Functionalized Heterocycles from Carbon Dioxide.

A catalytic domino, three-component reaction has been developed for the transformation of carbon dioxide into functionalized six-membered cyclic carbonates. The catalytic process combines an initial carboxylative cyclization of β-epoxy alcohols followed by an oxa-Michael reaction affording an unparalleled scope of heterocyclic structures. The wide range of functional groups, including free-alcohols, empowers the access to a range of products including C11-oxo-based bicyclic heterocycles. The versatility of these functionalized carbonates is further complemented by a series of synthetic diversifications. Control experiments are consistent with the first step of this domino process being promoted by a binary Lewis acid/base catalyst, while the second stage only requires catalytic base.

Mutational analysis of predicted active site residues of an exoglucanase secreted by Xanthomonas oryzae pv. oryzae to determine their role in catalysis and in virulence on rice

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight disease in rice. As a part of its virulence repertoire, Xoo secretes a cell wall degrading enzyme Cellobiosidase (CbsA), which is a critical virulence factor and also a determinant of tissue specificity. CbsA protein is made up of an N-terminal catalytic domain and a C-terminal fibronectin type III domain. According to the CAZy classification, the catalytic domain of CbsA protein belongs to the glycosyl hydrolase-6 (GH6) family that performs acid–base catalysis. However, the identity of the catalytic acid and the catalytic base of CbsA is not known. Based on the available structural and biochemical data, we identified putative catalytic residues and probed them by site-directed mutagenesis. Intriguingly, the biochemical analysis showed that none of the mutations abolishes the catalytic activity of CbsA, an observation that is contrary to other GH6 family members. All the mutants exhibited altered enzymatic activity and caused significant virulence deficiency in Xoo emphasising the requirement of specific exoglucanase activity of wild-type CbsA for virulence on rice. Our study highlights the need for further studies and the detailed characterisation of bacterial exoglucanases.

“Stepwise or concerted or a hybrid mechanism for berberine bridge enzyme?”: A computational mechanistic study by QM-MM and QM methods

Berberine bridge enzyme (BBE) is a plant-based amine oxidase that catalyzes conversion of (S)-reticuline into (S)-scoulerine using flavin as cofactor in a stereospecific way in an alkaloid biosynthesis pathway. Based on the active site enzyme variants, a concerted mechanism was proposed involving hydride transfer, proton transfer, and substrate cyclization processes in a single step. In this mechanism, Glu417 residue acts as the catalytic base which deprotonates the phenolic proton of the substrate while a hydride ion transfers from the substrate to flavin and the substrate cyclizes. However, based on solvent and substrate deuterium kinetic isotope effect studies, it was proposed that the oxidation process occurs in a stepwise fashion in which a hydride ion transfer from substrate to flavin first, then cyclization of the substrate occurs together with the proton transfer process. In this study, we formulated computational models to elucidate the oxidation mechanism of (S)-reticuline into (S)-scoulerine using the crystal structure of enzyme complexed with (S)-reticuline. Both QM and QM-MM calculations revealed that a hybrid of concerted and stepwise mechanisms might be operative during the catalysis. It was found that a concerted hydride-proton transfer processes occurs forming a reactive intermediate which subsequently cyclize without an energy barrier as a decoupled step.

Synthesis, Antifungal, and Anti-tubercular Activity of some new 7-amino-2- (Substituted aryl)-5-oxo-1,5-dihydro-[1,2,4]Triazolo[1,5- a]Pyridine-6-carbonitrile Derivatives

A series of some 7-amino-2-(substituted aryl)-5-oxo-1,5-dihydro-[1,2,4]triazolo[1,5- a]pyridine-6-carbonitrile derivatives was synthesized by the reaction of cyanoacetohydrazone derivatives with malononitrile in presence of catalytic base piperidine and ethanol as solvent. Comparing the antifungal activity of all the investigated compounds to that of standard Amphotericin-B on Potato- Dextrose-Agar medium, compounds 1a, 1e, and 1i revealed excellent antifungal action against Aspergillus niger and Candida albicans. Using the Microplate-Alamar Blue Assay, the anti-tubercular activity of compounds 1a?1j was assessed against Mycobacterium tuberculosis H37Rv. Compared to the conventional isoniazid and ethambutol minimum inhibitory concentration of 1.6 ?g/mL, 1i and 1j had potent anti-tubercular activity at 1.6 ?g/mL, and 1b possessed moderate activity at 3.12 ?g/mL. Electron-donating groups have better anti-fungal and anti-tubercular efficacy than other substituents.. KEYWORDS :Anti-tubercular activity, Ethylcyanoacetate, Malononitrile, Microplate- Alamar Blue Assay, Potato-Dextrose-Agar medium, Triazolo[1,5-a]pyridines.