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Terpene synthases often catalyze complex carbocation cascade reactions. It has been previously shown that single residue switches involving replacement of a key aliphatic residue with serine or threonine can "short-circuit" such reactions, presumed to act indirectly via dipole stabilization of intermediate carbocations. Here a similar switch was found in the structurally characterized ent-kaurene synthase from Bradyrhizobium japonicum. Application of a recently developed computational approach to terpene synthases, TerDockin, surprisingly indicates direct action of the introduced serine hydroxyl as a catalytic base. Notably, this model suggests alternative interpretation of previous results, and potential routes towards reengineering terpene synthase activity more generally.

Sclareol synthase from Salvia sclarea (SsSS) naturally acts on 8α-hydroxy-copalyl diphosphate (1), stereoselectively adding water to produce (13R)-sclareol (2a), and similarly yields hydroxylated products with manifold other such bicyclic diterpene precursors. Here a key residue for this addition of water was identified. Strikingly, substitution with glutamine switches stereochemical outcome with 1, leading to selective production of (13S)-sclareol (2b). Moreover, changes to the stereospecificity of water addition with the structurally closely-related substrate copalyl diphosphate (4) could be accomplished with alternative substitutions. Thus, this approach is expected to provide biosynthetic access to both epimers of 13-hydroxylated derivatives of manifold labdane-related diterpenes.

Meroterpenes derived from dimethylorsellinic acid (DMOA) and farnesyl pyrophosphate have attracted much biosynthetic attention, yet only recently have synthetic solutions to any family members appeared. A key point of divergence in DMOA-derived meroterpene biosynthesis is the protoaustinoid A carbocation, which can be diverted to either the berkeleyone, andrastin, or terretonin structural classes by cyclase-controlled rearrangement pathways. Shown herein is that the protoaustinoid bicyclo[3.3.1]nonane nucleus can be reverted to either andrastin or terretonin ring systems under abiotic reaction conditions. The first total syntheses of members of these natural product families are reported as their racemates.

Substitution of a histidine, comprising part of the catalytic base group in the ent-copalyl diphosphate synthases found in all seed plants for gibberellin phytohormone metabolism, by a larger aromatic residue leads to rearrangements. Through a series of 1,2-hydride and methyl shifts of the initially formed bicycle predominant formation of (-)-kolavenyl diphosphate is observed. Further mutational analysis and quantum chemical calculations provide mechanistic insight into the basis for this profound effect on product outcome.

Computational chemistry approaches for studying the formation of terpenes/terpenoids in wines are presented, using five particular terpenes/terpenoids (1,8-cineole, α-ylangene, botrydial, rotundone, and the wine lactone), volatile compounds (or their precursors) found in wine and/or wine grapes, as representative examples. Through these examples, we show how modern computational quantum chemistry can be employed as an effective tool for assessing the validity of proposed mechanisms for terpene/terpenoid formation.

Summary: Bioactive triterpenes feature complex fused‐ring structures, primarily shaped by the first‐committed enzyme, 2,3‐oxidosqualene cyclases (OSCs) in plant triterpene biosynthesis. Triterpenes with B,C‐ring‐opened skeletons are extremely rare with unknown formation mechanisms, harbouring unchartered chemistry and biology.Here, through mining the genome of Chenopodium quinoa followed by functional characterization, we identified a stress‐responsive and neofunctionalized OSC capable of generating B,C‐ring‐opened triterpenes, including camelliol A and B and the novel (−)‐quinoxide A as wax components of the specialized epidermal bladder cells, namely the quinoxide synthase (CqQS).Protein structure analysis followed by site‐directed mutagenesis identified key variable amino acid sites underlying functional interconversion between pentacyclic β‐amyrin synthase (CqbAS1) and B,C‐ring‐opened triterpene synthase CqQS. Mutation of one key residue (N612K) in even evolutionarily distant Arabidopsis β‐amyrin synthase could generate quinoxides, indicating a conserved mechanism for B,C‐ring‐opened triterpene formation in plants. Quantum computation combined with docking experiments further suggests that conformations of conserved W613 and F413 of CqQS might be key to selectively stabilizing intermediate carbocations towards B,C‐ring‐opened triterpene formation.Our findings shed light on quinoa triterpene skeletal diversity and mechanisms underlying B,C‐ring‐opened triterpene biosynthesis, opening avenues towards accessing their chemistry and biology and paving the way for quinoa trait engineering and quality improvement. [ABSTRACT FROM AUTHOR]

Terpene cyclization, one of the most complex chemical reactions in nature, is generally catalyzed by two classes of terpene cyclases (TCs). Cytochrome P450s that act as unexpected TC‐like enzymes are known but are very rare. In this study, we genome‐mined a cryptic bacterial terpenoid gene cluster, named ari, from the thermophilic actinomycete strain Amycolatopsis arida. By employing a heterologous production system, we isolated and characterized three highly oxidized eunicellane derived diterpenoids, aridacins A−C (1–3), that possess a 6/7/5‐fused tricyclic scaffold. In vivo and in vitro experiments systematically established a noncanonical two‐step biosynthetic pathway for diterpene skeleton formation. First, a class I TC (AriE) cyclizes geranylgeranyl diphosphate (GGPP) into a 6/10‐fused bicyclic cis‐eunicellane skeleton. Next, a cytochrome P450 (AriF) catalyzes cyclization of the eunicellane skeleton into the 6/7/5‐fused tricyclic scaffold through C2−C6 bond formation. Based on the results of quantum chemical computations, hydrogen abstraction followed by electron transfer coupled to barrierless carbocation ring closure is shown to be a viable mechanism for AriF‐mediated cyclization. The biosynthetic logic of skeleton construction in the aridacins is unprecedented, expanding the catalytic capacity and diversity of P450s and setting the stage to investigate the inherent principles of carbocation generation by P450s in the biosynthesis of terpenoids. [ABSTRACT FROM AUTHOR]

[Display omitted] Both concerted [4 + 2] cycloadditions and stepwise carbocation-alkene cyclizations have been proposed as means to construct the complex polycyclic cores of the artatrovirenols and daphenoid natural products during their biosyntheses. Here the energetic feasibility of each of these reactions is assessed using density functional theory calculations. While none of the previously proposed processes can be ruled out, an alternative process with a lower barrier is proposed. This process would allow for formation of a key C C bond during the cyclase phase of terpenoid biosynthesis. [ABSTRACT FROM AUTHOR]

Quantum chemical methods are useful for probing the energetic viability of chemical mechanisms involved in natural product biosynthesis. Typical computational approaches are described and representative examples of mechanistic studies on radical, pericyclic, and carbocation rearrangement reactions that lead to polycyclic skeletons of complex natural products showcase the utility of such methods in providing understanding and shaping future experimental studies. The importance of inherent substrate reactivity is highlighted and cautions for interpreting computational results are discussed. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and CatalysisTheoretical and Physical Chemistry > Reaction Dynamics and KineticsStructure and Mechanism > Computational Biochemistry and Biophysics [ABSTRACT FROM AUTHOR]

Abstract: Sesterterpenoids are a relatively rare class of plant terpenes. Sesterterpene synthase (STS)‐mediated cyclization of the linear C25 isoprenoid precursor geranylfarnesyl diphosphate (GFPP) defines sesterterpene scaffolds. So far only a very limited number of STSs have been characterized. The discovery of three new plant STSs is reported that produce a suite of sesterterpenes with unprecedented 6/11/5 and 6/6/7/5 fused ring systems when transiently co‐expressed with a GFPP synthase in Nicotiana benthamiana. Structural elucidation, feeding experiments, and quantum chemical calculations suggest that these STSs catalyze an unusual cyclization path involving reprotonation, intramolecular 1,6 proton transfer, and concerted but asynchronous bicyclization events. The cyclization is diverted from those catalyzed by the characterized plant STSs by forming unified 15/5 bicyclic sesterterpene intermediates. Mutagenesis further revealed a conserved amino acid residue implicated in reprotonation. [ABSTRACT FROM AUTHOR]

Sesterterpenoids are a rare terpene class harboring untapped chemodiversity and bioactivities. Their structural diversity originates primarily from the scaffold-generating sesterterpene synthases (STSs). In fungi, all six known STSs are bifunctional, containing C-terminal trans-prenyltransferase (PT) and N-terminal terpene synthase (TPS) domains. In plants, two colocalized PT and TPS gene pairs from Arabidopsis thaliana were recently reported to synthesize sesterterpenes. However, the landscape of PT and TPS genes in plant genomes is unclear. Here, using a customized algorithm for systematically searching plant genomes, we reveal a suite of physically colocalized pairs of PT and TPS genes for the biosynthesis of a large sesterterpene repertoire in the wider Brassicaceae. Transient expression of seven TPSs from A. thaliana, Capsella rubella, and Brassica oleracea in Nicotiana benthamiana yielded fungal-type sesterterpenes with tri-, tetra-, and pentacyclic scaffolds, and notably (-)-ent-quiannulatene, an enantiomer of the fungal metabolite (+)-quiannulatene. Protein and structural modeling analysis identified an amino acid site implicated in structural diversification. Mutation of this site in one STS (AtTPS19) resulted in premature termination of carbocation intermediates and accumulation of bi-, tri-, and tetracyclic sesterterpenes, revealing the cyclization path for the pentacyclic sesterterpene (-)-retigeranin B. These structural and mechanistic insights, together with phylogenetic analysis, suggest convergent evolution of plant and fungal STSs, and also indicate that the colocalized PT-TPS gene pairs in the Brassicaceae may have originated from a common ancestral gene pair present before speciation. Our findings further provide opportunities for rapid discovery and production of sesterterpenes through metabolic and protein engineering. [ABSTRACT FROM AUTHOR]

A biomimetic total synthesis of santalin Y, a structurally complex but racemic natural product, is described. The key step is proposed to be a (3+2) cycloaddition of a benzylstyrene to a 'vinylogous oxidopyrylium', which is followed by an intramolecular Friedel-Crafts reaction. This cascade generates the unique oxafenestrane framework of the target molecule and sets its five stereocenters in one operation. Our work provides rapid access to santalin Y and clarifies its biosynthetic relationship with other colorants isolated from red sandalwood. [ABSTRACT FROM AUTHOR]

On the basis of results from quantum chemical calculations, the feasibility of an extensive series of intramolecular proton-transfer reactions postulated to occur during terpene biosynthesis is assessed and guiding principles are proposed. [ABSTRACT FROM AUTHOR]

The results of quantum-chemical calculations aimed at assessing the viability of nonclassical carbocations proposed to be involved in the biosynthesis of atiserne, beyerene, kaurene, and trachylobane diterpenes are presented. While the proposed edge-protonated structure is much lower in energy than the proposed face-protonated structure, neither is predicted to be a viable intermediate energetically. [ABSTRACT FROM AUTHOR]

Selectivity in chemical reactions that form complex molecular architectures from simpler precursors is usually rationalized by comparing competing transition-state structures that lead to different possible products. Herein we describe a system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. The reaction network described connects the pimar-15-en-8-yl cation to miltiradiene, a tricyclic diterpene natural product, and isomers via cyclizations and/or rearrangements. The results suggest that the selectivity of the reaction is controlled by (post-transition-state) dynamic effects, that is, how the carbocation structure changes in response to the distribution of energy in its vibrational modes. The inherent dynamical effects revealed herein (characterized through quasiclassical direct dynamics calculations using density functional theory) have implications not only for the general principles of selectivity prediction in systems with complex potential energy surfaces, but also for the mechanisms of terpene synthase enzymes and their evolution. These findings redefine the challenges faced by nature in controlling the biosynthesis of complex natural products. [ABSTRACT FROM AUTHOR]

An Escherichia coli ( E. coli) strain was engineered to synthesize 2-butanone from glucose by extending the 2,3-butanediol synthesis reaction sequence catalyzed by exogenous enzymes. To convert 2,3-butanediol to 2-butanone, B12-dependent glycerol dehydratase from Klebsiella pneumoniae was introduced into E. coli. It has been proposed that the enzyme has a weak activity toward 2,3-butanediol. The activity in E. coli is confirmed in this study. Furthermore, co-expressing coenzyme B12 reactivators increased the 2-butanone titer. This demonstration of 2-butanone production by extending the 2,3-butanediol biosynthetic pathway provides the possibility to produce this valuable chemical renewably. [ABSTRACT FROM AUTHOR]

Terpene synthases, as key enzymes of terpene biosynthesis, have garnered the attention of chemists and biologists for many years. Their carbocationic reaction mechanisms are responsible for the huge variety of terpene structures in nature. These mechanisms are amenable to study by using classical biochemical approaches as well as computational analysis, and in this study we combine quantum-chemical calculations and deuterium-labeling experiments to elucidate the reaction mechanism of a triquinane forming sesquiterpene synthase from chamomile. Our results suggest that the reaction from farnesyl diphosphate to triquinanes proceeds through caryophyllyl and presilphiperfolanyl cations and involves the protonation of a stable (−)-( E)-β-caryophyllene intermediate. A tyrosine residue was identified that appears to be involved in the proton-transfer process. [ABSTRACT FROM AUTHOR]

A survey of computational studies on the mechanisms of dyotropic, Schmidt, and related reactions is presented. Connections between synthetically applied versions of these processes and those predicted to occur during biosynthetic terpeneforming carbocation cascades are highlighted. [ABSTRACT FROM AUTHOR]

Terpenes comprise a class of natural products that includes molecules with thousands of distinct structurally and stereochemically complex molecular architectures. The core hydrocarbon frameworks of these molecules are constructed via carbocation rearrangements promoted by terpene synthase (cyclase) enzymes. Although many mechanistic details for such reactions have been uncovered, the factors that control which carbocation intermediates and transition-state structures form are not well understood. Here we show that rearrangement pathways that pass through particular transition-state structures can bifurcate after the transition state. The resulting pathways lead to terpenes with distinctly different skeletons from each other. Although these types of bifurcating pathways have been described previously for some small molecules, the possibility that they may have an important role in the production of complex molecules in nature has, to our knowledge, not previously been considered. [ABSTRACT FROM AUTHOR]

Recent theoretical studies on concerted carbocation rearrangements that involve multiple asynchronous chemical events are described. The relevance of such rearrangements to natural products biosynthesis is highlighted. Copyright © 2008 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Herein we describe quantum chemical calculations (B3LYP) on the intramolecular oxidopyrylium-alkene cycloadditions used in two recently reported total syntheses of (+)-intricarene, and possibly also occurring during its biosynthesis. Using theory, we address (1) the necessity of enzyme intervention if this reaction occurs in Nature and (2) the effects of substituents attached to the oxidopyrylium and alkene groups on the activation barriers for cycloaddition. [ABSTRACT FROM AUTHOR]

Review: [103 refs. [ABSTRACT FROM AUTHOR]

Theoretical investigation of cyclopropane-to-cyclopropane rearrangements of sterols indicates a role for highly delocalized bicyclobutonium ions in biosynthesis. [ABSTRACT FROM AUTHOR]

Thetheoretical investigation of concerted and stepwise Cope rearrangementsof natural products led to the prediction that some concerted Coperearrangements can be promoted by noncovalent association of theirtransition state structures with ammonium cations. [ABSTRACT FROM AUTHOR]

Abstract: The results of quantum chemical calculations on a previously proposed biosynthetic pathway for the formation of calophyline A from rhazimol, which features formally forbidden 4-electron [1,2] and [1,3] sigmatropic shifts, are discussed. The proposed pathway was not found to be energetically viable, despite a surprisingly low predicted barrier for the [1,3] shift, but an alternative route involving a series of tautomerizations and carbonyl addition reactions is shown to be more energetically feasible. [Copyright &y& Elsevier]

Abstract: Quantum chemical calculations (B3LYP/6-31G(d)) on carbocation rearrangements that are proposed to occur in the biosynthesis of aspernomine are described. Based on these calculations, a pathway involving a concerted but asynchronous [4+2] cycloaddition that avoids the formation of a secondary carbocation is proposed for small model systems. [Copyright &y& Elsevier]

In this paper, we describe theoretical studies, using gas-phase quantum chemical calculations, on carbocationic rearrangement pathways leading to the sesquiterpenes sativene, cyclosativene, α-ylangene, and β-ylangene. For all four sesquiterpene natural products, viable pathways are presented, and these are compared both to mechanistic proposals found in the literature, and in certain cases to alternative stereochemical and rearrangement possibilities, thus providing a basis for comparison to experimental results. We find that these four sesquiterpenes likely arise from a common bicyclic intermediate and, furthermore, that the computed pathways are mostly in agreement with previous mechanistic proposals, although the few differences that we have uncovered are significant. Additionally, the potential energy profiles of the pathways are found to be very flat, supporting the notion that following the initial ionization of farnesyl diphosphate, minimal enzymatic intervention may be required for the generation of such sesquiterpenes. [ABSTRACT FROM AUTHOR]

Viridicatumtoxin (1) is a tetracycline-like fungal meroterpenoid with a unique, fused spirobicyclic ring system. Puzzlingly, no dedicated terpene cyclase is found in the gene cluster identified in Penicillium aethiopicum. Cytochrome P450 enzymes VrtE and VrtK in the vrt gene cluster were shown to catalyze C5-hydroxylation and spirobicyclic ring formation, respectively. Feeding acyclic previridicatumtoxin to Saccharomyces cerevisiae expressing VrtK confirmed that VrtK is the sole enzyme required for cyclizing the geranyl moiety. Thus, VrtK is the first example of a P450 that can catalyze terpene cyclization, most likely via initial oxidation of C17 to an allylic carbocation. Quantum chemical modeling revealed a possible new tertiary carbocation intermediate E that forms after allylic carbocation formation. Intermediate E can readily undergo concerted 1,2-alkyl shift/1,3-hydride shift, either spontaneously or further aided by VrtK, followed by C7 Friedel-Crafts alkylation to afford 1. The most likely stereochemical course of the reaction was proposed on the basis of the results of our computations. [ABSTRACT FROM AUTHOR]

Abietic acid, a constituent of pine resin, is naturally derived from abietadiene - a process that requires four enzymes: one (abietadiene synthase) for conversion of the acyclic, achiral geranylgeranyl diphosphate to the polycydic, chiral abietadiene (a complex process involving the copalyl diphosphate intermediate) and then three to oxidize a single methyl group of abietadiene to the corresponding carboxylic acid. In previous work (Nature Chem. 2009, 1, 384), electronic structure calculations on carbocation rearrangements leading to abietadienyl cation revealed an interesting potential enerysurface with a bifurcating reaction pathway (two transition-state structures connected directly with no intervening minimum), which links two products - one natural and one not yet isolated from Nature. Herein we describe direct dynamics simulations of the key step in the formation of abietadiene (in the gas phase and in the absence of the enzyme). The simulations reveal that abietadiene synthase must intervene in order to produce abietadiene selectively, in essence steering this reaction to avoid the generation of byproducts with different molecular architectures. [ABSTRACT FROM AUTHOR]

Terpenoid natural products are generally derived from isoprenyl diphosphate precursors with trans double-bond configuration, and no diterpenoid derived from the cisoid precursor (Z,Z,Z)-nerylneryl diphosphate (1) has yet been identified. Here further investigation of a terpenoid biosynthetic gene cluster from tomato is reported, which resulted in identification of a biosynthetic pathway from 1, in a pathway featuring a number of interesting transformations. Compound 1 is first cyclized to a tricyclene core ring structure analogous to that found in α-santalene, with the resulting diterpene termed here lycosantalene (2). Quantum chemical calculations indicate a role for the diphosphate anion coproduct in this cyclization reaction. Subsequently, the internal cis double bond of the neryl side chain in 2 is then further transformed to an α-hydroxy ketone moiety via an epoxide intermediate (3). Oxygen labeling studies indicate 3 undergoes oxidative conversion to lycosantalonol (4). Thus, in addition to elucidating the cisoid origins of 4, this work has further provided mechanistic insight into the interesting transformations required for its production. [ABSTRACT FROM AUTHOR]