Modular Oxime Formation by a trans-AT Polyketide Synthase

Modular trans-acyltransferase polyketide synthases (trans-AT PKSs) are enzymatic assembly lines that biosynthesize complex polyketide natural products. Relative to their better studied cis-AT counterparts, the trans-AT PKSs introduce remarkable chemical diversity into their polyketide products. A notable example is the lobatamide A PKS, which incorporates a methylated oxime. Here we demonstrate biochemically that this functionality is installed on-line by an unusual oxygenase-containing bimodule. Furthermore, analysis of the oxygenase crystal structure coupled with site-directed mutagenesis allows us to propose a model for catalysis, as well as identifying key protein-protein interactions that support this chemistry. Overall, our work adds oxime-forming machinery to the biomolecular toolbox available for trans-AT PKS engineering, opening the way to introducing such masked aldehyde functionalities into diverse polyketides.     

Genome Mining of Oxidation Modules in trans-Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides

Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are multimodular megaenzymes that biosynthesize many bioactive natural products. They contain a remarkable range of domains and module types that introduce different substituents into growing polyketide chains. As one such modification, we recently reported Baeyer–Villiger-type oxygen insertion into nascent polyketide backbones, thereby generating malonyl thioester intermediates. In this work, genome mining focusing on architecturally diverse oxidation modules in trans-AT PKSs led us to the culturable plant symbiont Gynuella sunshinyii, which harbors two distinct modules in one orphan PKS. The PKS product was revealed to be lobatamide A, a potent cytotoxin previously only known from a marine tunicate. Biochemical studies show that one module generates glycolyl thioester intermediates, while the other is proposed to be involved in oxime formation. The data suggest varied roles of oxygenation modules in the biosynthesis of polyketide scaffolds and support the importance of trans-AT PKSs in the specialized metabolism of symbiotic bacteria.     

Molecular basis for acyl carrier protein–ketoreductase interaction in trans-acyltransferase polyketide synthases

The biosynthesis of polyketides by type I modular polyketide synthases (PKS) relies on co-ordinated interactions between acyl carrier protein (ACP) domains and catalytic domains within the megasynthase. Despite the importance of these interactions, and their implications for biosynthetic engineering efforts, they remain poorly understood. Here, we report the molecular details of the interaction interface between an ACP domain and a ketoreductase (KR) domain from a trans-acyltransferase (trans-AT) PKS. Using a high-throughput mass spectrometry (MS)-based assay in combination with scanning alanine mutagenesis, residues contributing to the KR-binding epitope of the ACP domain were identified. Application of carbene footprinting revealed the ACP-binding site on the KR domain surface, and molecular docking simulations driven by experimental data allowed production of an accurate model of the complex. Interactions between ACP and KR domains from trans-AT PKSs were found to be specific for their cognate partner, indicating highly optimised interaction interfaces driven by evolutionary processes. Using detailed knowledge of the ACP:KR interaction epitope, an ACP domain was engineered to interact with a non-cognate KR domain partner. The results provide novel, high resolution insights into the ACP:KR interface and offer valuable rules for future engineering efforts of biosynthetic assembly lines.

The interaction epitope between a cognate KR–ACP domain pairing from a trans-AT polyketide synthase is elucidated in molecular detail, providing unique insights into recognition and specificity of the interface.     

Genome Mining of Oxidation Modules in trans‐Acyltransferase Polyketide Synthases Reveals a Culturable Source for Lobatamides

Bacterial trans‐acyltransferase polyketide synthases (trans‐AT PKSs) are multimodular megaenzymes that biosynthesize many bioactive natural products. They contain a remarkable range of domains and module types that introduce different substituents into growing polyketide chains. As one such modification, we recently reported Baeyer–Villiger‐type oxygen insertion into nascent polyketide backbones, thereby generating malonyl thioester intermediates. In this work, genome mining focusing on architecturally diverse oxidation modules in trans‐AT PKSs led us to the culturable plant symbiont Gynuella sunshinyii, which harbors two distinct modules in one orphan PKS. The PKS product was revealed to be lobatamide A, a potent cytotoxin previously only known from a marine tunicate. Biochemical studies show that one module generates glycolyl thioester intermediates, while the other is proposed to be involved in oxime formation. The data suggest varied roles of oxygenation modules in the biosynthesis of polyketide scaffolds and support the importance of trans‐AT PKSs in the specialized metabolism of symbiotic bacteria.     

Mechanistic insights into the cis-trans isomerization of ruthenium complexes relevant to catalysis of olefin metathesis

The mechanism of the trans to cis isomerization in Ru complexes with a chelating alkylidene group has been investigated by using a combined theoretical and experimental approach. Static DFT calculations suggest that a concerted single‐step mechanism is slightly favored over a multistep mechanism, which would require dissociation of one of the ligands from the Ru center. This hypothesis is supported by analysis of the experimental kinetics of isomerization, as followed by ¹H NMR spectroscopy. DFT molecular dynamics simulations revealed that the variation of geometrical parameters around the Ru center in the concerted mechanism is highly uncorrelated; the mechanism actually begins with the transformation of the square‐pyramidal trans isomer, with the Ru?CHR bond in the apical position, into a transition state that resembles a metastable square pyramidal complex with a Cl atom in the apical position. This high‐energy structure collapses into the cis isomer. Then, the influence of the N‐heterocyclic carbene ligand, the halogen, and the chelating alkylidene group on the relative stability of the cis and trans isomers, as well as on the energy barrier separating them, was investigated with static calculations. Finally, we investigated the interconversion between cis and trans isomers of the species involved in the catalytic cycle of olefin metathesis; we characterized an unprecedented square‐pyramidal metallacycle with the N‐heterocyclic carbene ligand in the apical position. Our analysis, which is relevant to the exchange of equatorial ligands in other square pyramidal complexes, presents evidence for a remarkable flexibility well beyond the simple cis–trans isomerization of these Ru complexes.     

Increasing the Bioavailability of RuIII Anticancer Complexes through Hydrophobic Albumin Interactions

A series of pyridine‐based derivatives of the clinically successful Ru^III‐based complexes indazolium [trans‐RuCl₄(1 H‐indazole)₂] (KP1019) and sodium [trans‐RuCl₄(1 H‐indazole)₂] (KP1339) have been synthesized to probe the effect of hydrophobic interactions with human serum albumin (hsA) on anticancer activity. The solution behavior and protein interactions of the new compounds were characterized by using electron paramagnetic resonance (EPR) and UV/Vis spectroscopy. These studies have revealed that incorporation of hydrophobic substituents at the 4′‐position of the axial pyridine ligand stabilizes non‐coordinate interactions with hsA. As a consequence, direct coordination to the protein is inhibited, which is expected to increase the bioavailability of the complexes, thus potentially leading to improved anticancer activity. By using this approach, the lifetimes of hydrophobic protein interactions were extended from 2 h for the unsubstituted pyridine complex, to more than 24 h for several derivatives. Free complexes were tested for their anticancer activity against the SW480 human colon carcinoma cell line, exhibiting low cytotoxicity. Pre‐treatment with hsA improved the solubility of every compound and led to some changes in activity. Particularly notable was the difference in activity between the methyl‐ and dibenzyl‐functionalized complexes. The former shows reduced activity after incubation with hsA, indicating reduced bioavailability due to protein coordination. The latter exhibits little activity on its own but, following treatment with hsA, exhibited significant cytotoxicity, which is consistent with its ability to form non‐coordinate interactions with the protein. Overall, our studies demonstrate that non‐coordinate interactions with hsA are a viable target for enhancing the activity of Ru^III‐based complexes in vivo.     

Structure and Function of the α-Hydroxylation Bimodule of the Mupirocin Polyketide Synthase

Mupirocin is a clinically important antibiotic produced by a trans-AT Type I polyketide synthase (PKS) in Pseudomonas fluorescens. The major bioactive metabolite, pseudomonic acid A (PA−A), is assembled on a tetrasubstituted tetrahydropyran (THP) core incorporating a 6-hydroxy group proposed to be introduced by α-hydroxylation of the thioester of the acyl carrier protein (ACP) bound polyketide chain. Herein, we describe an in vitro approach combining purified enzyme components, chemical synthesis, isotopic labelling, mass spectrometry and NMR in conjunction with in vivo studies leading to the first characterisation of the α-hydroxylation bimodule of the mupirocin biosynthetic pathway. These studies reveal the precise timing of hydroxylation by MupA, substrate specificity and the ACP dependency of the enzyme components that comprise this α-hydroxylation bimodule. Furthermore, using purified enzyme, it is shown that the MmpA KS⁰ shows relaxed substrate specificity, suggesting precise spatiotemporal control of in trans MupA recruitment in the context of the PKS. Finally, the detection of multiple intermodular MupA/ACP interactions suggests these bimodules may integrate MupA into their assembly.     

Toblerols: Cyclopropanol‐Containing Polyketide Modulators of Antibiosis in Methylobacteria

Trans‐AT polyketide synthases (PKSs) are a family of biosynthetically versatile modular type I PKSs that generate bioactive polyketides of impressive structural diversity. In this study, we detected, in the genome of several bacteria a cryptic, architecturally unusual trans‐AT PKS gene cluster which eluded automated PKS prediction. Genomic mining of one of these strains, the model methylotroph Methylobacterium extorquens AM1, revealed unique epoxide‐ and cyclopropanol‐containing polyketides named toblerols. Relative and absolute stereochemistry were determined by NMR experiments, chemical derivatization, and the comparison of CD data between the derivatized natural product and a synthesized model compound. Biosynthetic data suggest that the cyclopropanol moiety is generated by carbon–carbon shortening of a more extended precursor. Surprisingly, a knock‐out strain impaired in polyketide production showed strong inhibitory activity against other methylobacteria in contrast to the wild‐type producer. The activity was inhibited by complementation with toblerols, thus suggesting that these compounds modulate an as‐yet unknown methylobacterial antibiotic.     

A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones

Enzymatic core components from trans‐acyltransferase polyketide synthases (trans‐AT PKSs) catalyze exceptionally diverse biosynthetic transformations to generate structurally complex bioactive compounds. Here we focus on a group of oxygenases identified in various trans‐AT PKS pathways, including those for pederin, oocydins, and toblerols. Using the oocydin pathway homologue (OocK) from Serratia plymuthica 4Rx13 and N‐acetylcysteamine (SNAC) thioesters as test surrogates for acyl carrier protein (ACP)‐tethered intermediates, we show that the enzyme inserts oxygen into β‐ketoacyl moieties to yield malonyl ester SNAC products. Based on these data and the identification of a non‐hydrolyzed oocydin congener with retained ester moiety, we propose a unified biosynthetic pathway of oocydins, haterumalides, and biselides. By providing access to internal ester, carboxylate pseudostarter, and terminal hydroxyl functions, oxygen insertion into polyketide backbones greatly expands the biosynthetic scope of PKSs.     

Insight into How Telomeric G‐Quadruplexes Enhance the Peroxidase Activity of Cellular Hemin

The toxic oxidative damage of G‐quadruplexes (G4), linked to neurodegenerative diseases, may arise from their ability to bind and oxidatively activate cellular hemin. However, there have been no precise studies on how telomeric G4 enhances the low intrinsic peroxidase activity of hemin. Herein, a label‐free and nanopore‐based strategy was developed to explore the enhancement mechanism of peroxidase activity of hemin induced by telomeric G4 (d(TTAGGG)_n). The nanopore‐based strategy demonstrated that there were simultaneously two different binding modes of telomere G4 to hemin. At the single‐molecule level, it was found that the hybrid structural telomeric G4 directly binds to hemin (the affinity constant (K_a)≈10⁶ m ^?1) to form a tight complex, and some of them underwent a topological change to a parallel structure with an enhancement of K_a to approximately 10⁷ m ^?1. Through detailed analysis of the topology and peroxidase activity and molecular modeling investigations, the parallel telomere G4/hemin DNAzyme structure was proven to be preferable for high peroxidase activity. Upon strong π–π stacking, the parallel structural telomere G4 supplied a key axial ligand to the hemin iron, which accelerated the intermediate compound formation with H₂O₂ in the catalytic cycle. Our studies developed a label‐free and single‐molecule strategy to fundamentally understand the catalytic activity and mechanism of telomeric DNAzyme, which provides some support for utilizing the toxic, oxidative‐damage property in cellular oxidative disease and anticancer therapeutics.     

Novel Symmetrical trans‐Bis‐Schiff Bases of N‐Substituted‐4‐ piperidones: Synthesis,Characterization, and Preliminary Antileukemia Activity Mensurations

A series of novel symmetrical trans‐bis‐Schiff bases ( 11a , 11b , 11c , 11d , 11e , 11f , 11g , 11h , 11i , 11j , 11k , 11l , 11m ) were designed and prepared as novel anticancer analogues, with the trans‐configuration confirmed by X‐ray diffraction. Preliminary inhibitory effects of these compounds on CML K562 cell growth were investigated, and the potential analogue 11e showed an excellent anti‐leukemia activity (IC₅₀=6.35 μg/mL), which is higher than that of the clinical drug 5‐fluorouracil (IC₅₀=8.48 μg/mL). Complete assignments had been achieved for the title compounds by spectroscopic techniques, and their structure–activity relationships have been studied.     

Reconstitution of a Type II Polyketide Synthase that Catalyzes Polyene Formation

While type II polyketide synthases (PKSs) are known for producing aromatic compounds, a phylogenetically new subfamily of type II PKSs have been recently proposed to synthesize polyene structures. Here we report in vitro analysis of such a type II PKS, IgaPKS for ishigamide biosynthesis. The ketoreductase (Iga13) and dehydratase (Iga16) were shown to catalyze the reduction of a β‐keto group and dehydration of a β‐hydroxy group, respectively, to form a trans double bond. Incubation of the acyl carrier protein (Iga10), the ketosynthase/chain length factor complex (Iga11–Iga12), Iga13 and Iga16 with malonyl and hexanoyl‐CoAs and NADPH followed by KOH hydrolysis resulted in the formation of four unsaturated carboxylic acids (C₈, C₁₀, C₁₂, and C₁₄), indicating that IgaPKS catalyzes tetraene formation by repeating the cycle of condensation, keto‐reduction and dehydration with strict stereo‐specificity. We propose “highly reducing type II PKS subfamily” for the polyene‐producing type II PKSs.     

Acyl‐Chain Elongation Drives Ketosynthase Substrate Selectivity in trans‐Acyltransferase Polyketide Synthases

Type I modular polyketide synthases (PKSs), which are responsible for the biosynthesis of many biologically active agents, possess a ketosynthase (KS) domain within each module to catalyze chain elongation. Acylation of the KS active site Cys residue is followed by transfer to malonyl‐ACP to yield an extended β‐ketoacyl chain (ACP=acyl carrier protein). To date, the precise contribution of KS selectivity in controlling product fidelity has been unclear. Six KS domains from trans‐acyltransferase (trans‐AT) PKSs were subjected to a mass spectrometry based elongation assay, and higher substrate selectivity was identified for the elongating step than in preceding acylation. A close correspondence between the observed KS selectivity and that predicted by phylogenetic analysis was seen. These findings provide insights into the mechanism of KS selectivity in this important group of PKSs, can serve as guidance for engineering, and show that targeted mutagenesis can be used to expand the repertoire of acceptable substrates.     

Conductivity of I2‐Doped High trans‐1,4‐Polybutadiene

High trans‐l,4‐polybutadiene ( ?96% (trans)) was prepared by lanthanum naphthenate catalytic system. The conductivity of obtained polybutadiene doped with iodine reaches about ?100 s/cm, which is 2 orders of magnitude higher than the value reported.^4,5 During the I₂‐doping, the conjugated sequence was formed through double bond shifting reaction. According to the relationship between conductivity and temperature, conducting mechanism of doped high trans‐l,4‐polybutadiene is fit on variable range hoping (VRH) model.     

Imine‐N‐Heterocyclic Carbenes as Versatile Ligands in Ruthenium(II) p‐Cymene Anticancer Complexes: A Structure–Activity Relationship Study

A family of novel imine‐N‐heterocyclic carbene ruthenium(II) complexes of the general formula [(η⁶‐p‐cymene)Ru(C^N)Cl]PF₆⁻ (where C^N is an imine‐N‐heterocyclic carbene chelating ligand with varying substituents) have been prepared and characterized. In this imine‐N‐heterocyclic carbene chelating ligand framework, there are three potential sites that can be modified, which distinguishes this class of ligand and provides a body of flexibilities and opportunities to tune the cytotoxicity of these ruthenium(II) complexes. The influence of substituent effects of three tunable domains on the anticancer activity and catalytic ability in converting coenzyme NADH to NAD⁺ is investigated. This family of complexes displays an exceedingly distinct anticancer activity against A549 cancer cells, despite their close structural similarity. Complex 9 shows the highest anticancer activity in this series against A549 cancer cells (IC₅₀=14.36 μm ), with an approximately 1.5‐fold better activity than the clinical platinum drug cisplatin (IC₅₀=21.30 μm ) in A549 cancer cells. Mechanistic studies reveal that complex 9 mediates cell death mainly through cell stress, including cell cycle arrest, inducing apoptosis, increasing intracellular reactive oxygen species (ROS) levels, and depolarization of the mitochondrial membrane potential (MMP). Furthermore, lysosomal damage is also detected by confocal microscopy.     

Catalytic activity of cycloaurated complexes in the addition of 2‐methylfuran to methyl vinyl ketone

Cycloaurated gold(III) complexes derived from cycloaurated iminophosphorane, triphenylphosphine sulfide or selenide, or pyridylsulfonamide ligands have been assessed for their catalytic activity in the addition of 2‐methylfuran to methyl vinyl ketone. Addition of AgBF₄ was generally needed for high activity, although those with coordinated atoms of high trans influence showed some activity in the absence of added Ag⁺. Copyright © 2011 John Wiley & Sons, Ltd.     

Versatile and mild HCl-catalyzed cationic imino Diels-Alder reaction for the synthesis of new tetrahydroquinoline derivatives

A simple, inexpensive, and mild one-pot methodology for the synthesis of novel 4-aryl-3-methyl-1,2,3,4-tetrahydroquinolines derivatives using aqueous HCl as catalyst has been developed. The key step involves the formal inverse-electron-demand [4π⁺ + 2π] cycloaddition reaction of in situ–generated cationic 2-azadienes with arylpropenes (isoeugenol and trans-anethole). Iminium ion intermediates are generated through the condensation between N-benzylanilines and formalin. The products are obtained with good to excellent yields and high trans-diastereoselectivity. Further catalytic hydrogenation (Pd/C) allowed debenzylation to successfully obtain the respective 4-aryl-3-methyl-N-H-tetrahydroquinolines of interest. Recent reports suggest that these compounds could serve as interesting models in pharmacological studies against parasites that cause the most common tropical diseases.     

Design and Theoretical Study of Nickel Catalysts for Syndiotactic Polyolefins

A nickel catalyst was nodeled with ligand L^2,[NH=CH-CH=CH-0]^-,which should have potential use as a syndiotactic plyolefin catalyst,and the reaction mechanism was studied by theoretical calculations using the density functinal method at the B3LYP/LANL2MB level.The mechanism involves the formation of the intermediate [NiL^2Me]^ ,in which the metal occupies a T-shaped geometry.This intermediate has two possible structures with the methyl group trans either to the oxygen or to the nitrogen atom of L^2.The results show that both structures can lead to the desired product via similar reaction paths,A and B.Thus,the polymerization could be considered as taking place either with the alkyl group occupying the position trans to the Ni-0 or trans to the Ni-N bond in the catalyst.The polymerization process thus favors the catalysis of syndiotactic polyolefins.The syndiotactic synthesis effects could also be enhanced by varations in the ligand substituents.From energy considerations,we can conclude that it is more favorable for the methyl ttrans-O position to form a complex than to occupy the trans-N position.From bond length considerations,it is also more favoured for ethene to occupy the trans-O position than to occupy the trans-N position.     

Studies on PNPP Hydrolysis Catalyzed by Schiff Base Cobalt（Ⅱ） Complexes Containing Benzoaza-15-crown-5

Three novel Schiff base cobalt（Ⅱ） complexes containing benzoaza-15-crown-5, CoL^1, CoL^2 and CoL^3 were synthesized and characterized, and these complexes were used in catalytic hydrolysis of carboxylic ester （PNPP, p-nitrophenyl picolinate） as mimic hydrolytic metalloenzyme. The analysis of specific absorption spectra of the hydrolytic reaction systems indicated that the catalytic hydrolysis involved the key intermediates formed by PNPP with cobalt（Ⅱ） complexes. The CoL^3 bearing the electron withdrawing group shows better catalytic activity due to its stabilization effect on active species MLS^-. The catalytic mechanism of PNPP hydrolysis was also proposed. The kinetic parameter of PNPP catalytic hydrolysis has been calculated and the activation energy for the catalytic hydrolysis is 43.69, 39.76 and 35.44 kJ·mol^-1, respectively.     

Divergent Mechanistic Routes for the Formation of gem‐Dimethyl Groups in the Biosynthesis of Complex Polyketides

The gem‐dimethyl groups in polyketide‐derived natural products add steric bulk and, accordingly, lend increased stability to medicinal compounds, however, our ability to rationally incorporate this functional group in modified natural products is limited. In order to characterize the mechanism of gem‐dimethyl group formation, with a goal toward engineering of novel compounds containing this moiety, the gem‐dimethyl group producing polyketide synthase (PKS) modules of yersiniabactin and epothilone were characterized using mass spectrometry. The work demonstrated, contrary to the canonical understanding of reaction order in PKSs, that methylation can precede condensation in gem‐dimethyl group producing PKS modules. Experiments showed that both PKSs are able to use dimethylmalonyl acyl carrier protein (ACP) as an extender unit. Interestingly, for epothilone module 8, use of dimethylmalonyl‐ACP appeared to be the sole route to form a gem‐dimethylated product, while the yersiniabactin PKS could methylate before or after ketosynthase condensation.