Seven-Membered Ring Formation in Triterpene Biosynthesis: A Key Cyclopropane Rearrangement in Ilelic Acid Biosynthesis

Triterpenes represent a crucial class of natural compounds with diverse biological activities and structural complexity. Among the various skeletal modifications in triterpene biosynthesis, the formation of seven-membered rings through ring expansion reactions significantly contributes to their structural diversity and, consequently, their functional versatility. This study elucidates the detailed reaction mechanism of a key seven-membered ring formation via cyclopropane rearrangement in the biosynthesis of ilelic acid. Using density functional theory (DFT) calculations, we thoroughly investigated the biosynthetic pathway of ilelic acid, focusing on the critical ring expansion step. Our computational analysis reveals that the seven-membered ring formation proceeds through a cationic mechanism rather than a radical-mediated process. Notably, we found that the inherent instability of the secondary carbocation intermediate drives a concerted reaction pathway, avoiding the formation of high-energy intermediates. This mechanistic understanding not only sheds light on the biosynthesis of ilelic acid but also offers broader implications for comprehending similar transformations in other triterpene biosynthetic pathways. Our findings contribute to the fundamental understanding of triterpene skeletal diversity and pave the way for potential biomimetic approaches in the synthesis of complex seven-membered ring-containing terpenes. Furthermore, this work underscores the power of computational methods in unraveling intricate biosynthetic mechanisms.

Vibrationally Assisted Tunneling through the Bread of a Proton Sandwich─Connections to Dynamic Matching

Proton sandwiches are unusual nonclassical carbocations characterized by a five-center, four-electron bonding array which rapidly isomerize to lower energy isomers with three-center, two-electron bonding arrays via hydrogen migration transition states. These reactions are suspected to involve significant contributions from tunneling, even at relatively high temperatures, where tunneling effects are usually minimal. Machine-learning-accelerated ring-polymer, quasiclassical, and classical ab initio molecular dynamics simulations were used to investigate the effects of a flavor of dynamic matching that involves coupling of vibrational modes of the reactant to the transition structure mode with an imaginary frequency, and how quantum mechanical tunneling affects this coupling. These nonstatistical dynamic effects were quantified by analysis of momentum in the molecular dynamics simulations. We show the importance of momentum for reactivity with and without tunneling, how tunneling amplifies these benefits, and that vibrational modes can be leveraged to generate beneficial momentum.

Molecular Insight into the Catalytic Mechanism of the Sesquiterpene Cyclase BcABA3

BcABA3 is an unusual sesquiterpene synthase that lacks the conserved DDxxD and DTE/NSE motifs. Despite this, it can catalyze the conversion of farnesyl diphosphate to 2Z,4E-α-ionylideneethane. We used structure prediction, multiscale simulations, and site-directed mutagenesis experiments to investigate BcABA3 and its catalytic mechanism. BcABA3 has structural similarity to typical class I terpenoid cyclases in its active site. Based on simulation results, we identified two discontinuous glutamate residues, E124 and E88, which compensate for the absence of the aspartate-rich DDxxD motif. Quantum chemical calculations show that BcABA3 adopts a direct rotation mechanism for allyl cation isomerization rather than via the nerolidyl diphosphate. Then, it can achieve a successive proton transfer reaction, which is difficult to achieve by intramolecular rearrangement via the protruding outward carbonyl oxygen of A206. This reaction is then directed forward by two relatively stable intermediates containing a cation-conjugated double-bond structure. E124 is also proposed as the proton receptor in the final deprotonation to couple this step with 2Z,4E-α-ionylideneethane release. These findings provide valuable insight into the catalytic mechanisms of BcABA3 and can aid in its engineering, which will facilitate studies of abscisic acid biosynthesis.

Sativene-Related Sesquiterpenoids with Phytotoxic and Plant-Promoting Activities from the Plant Pathogenic Fungus Bipolaris sorokiniana Based on a Molecular Networking Strategy

Sativene-related sesquiterpenoids including seco-sativene analogs are a large member of fungal secondary metabolites with phytotoxic and growth-promoting effects on different plants. In this report, a series of sativene-related sesquiterpenoids with diverse carbon skeletons (1-9, sativene/isosativene/seco-sativene/cyclosativene/seco-isosativene ring systems) were isolated from the plant pathogenic fungus Bipolaris sorokiniana based on a molecular networking strategy. The undescribed structures were elucidated based on NMR spectra, X-ray diffraction analysis, chemical derivation, and calculated electronic circular dichroism calculations. Bipolaric acid (1) has a bicyclo[3.2.1] nonane skeleton (seco-sativene), bipolarone (2) is a unique cage-like cyclosativene sesquiterpenoid first isolated from fungi, and bipolariols A (3) and B (4) contain a novel octahydro-1,4-ethano isobenzofuran ring system (seco-isosativene). The possible biosynthetic pathways of these sesquiterpenoids (1-9) were proposed based on their structural features. Drechslerine B (8) exhibited phytotoxic activities to green foxtails, and compounds 5-7 and 9 showed growth-promoting effects with varying degrees on seedling growth of Arabidopsis thaliana.

Conformational Sampling in Computational Studies of Natural Products: Why Is It Important?

Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.

DFT Study on Retigerane-Type Sesterterpenoid Biosynthesis: Initial Conformation of GFPP Regulates Biosynthetic Pathway, Ring-Construction Order and Stereochemistry

Retigerane-type sesterterpenoids, which feature a unique 5/6/5/5/5 fused pentacyclic structure with an angular-type triquinane moiety, are biosynthesized via successive carbocation-mediated reactions triggered by terpene cyclases. However, the precise biosynthetic pathways/mechanisms, wherein steric inversion of the carbon skeleton occurs at least once, remain elusive. Two plausible reaction pathways have been proposed, which differ in the order of ring cyclization: A → B/C → D/E-ring(s) (Route 1) and A → E → B → C/D-ring(s) (Route 2). Since the reaction intermediates of these complicated domino-type reaction sequences are experimentally inaccessible, we employed comprehensive density functional theory (DFT) calculations to evaluate these routes. The results indicate that retigeranin biosynthesis proceeds via Route 2 involving a multistep carbocation cascade, in which the order of ring cyclization (A → E → B → C/D) is the key to constructing the angular 5/5/5 triquinane structure with the correct stereochemistry at C3. The result also suggests that slight differences in the initial conformation have a significant effect on the order of cyclization and steric inversion. The computed pathway/mechanism also provides a rational basis for the formation of various related terpenes/terpenoids.

Electrophile-Arene Affinity: An Energy Scale for Evaluating the Thermodynamics of Electrophilic Dearomatization Reactions

Rational design and development of organic reactions are lofty goals in synthetic chemistry. Quantitative description of the properties of molecules and reactions by physical organic parameters plays an important role in this regard. In this Article, we report an energy scale, namely, electrophile-arene affinity (EAA), for evaluating the thermodynamics of electrophilic dearomatization reactions, a class of important transformations that can rapidly build up molecular complexity and structural diversity by converting planar aromatic compounds into three-dimensional cyclic molecules. The acquisition of EAA data can be readily achieved by theoretically calculating the enthalpy changes (ΔH) of the hypothetical reactions of various (cationic) electrophiles with aromatic systems (taking the 1-methylnaphthalen-2-olate ion as an example in this study). Linear correlations are found between the calculated ΔH values and established physical organic parameters such as the percentage of buried volume %VBur (steric effect), Hammett's σ or Brown's σ+ (electronic effect), and Mayr's E (reaction kinetics). Careful analysis of the ΔH values leads to the rational design of a dearomative alkynylation reaction using alkynyl hypervalent iodonium reagents as the electrophiles.

Quantum Chemical Interrogation of Reactions Promoted by Dirhodium Tetracarboxylate Catalysts─Mechanism, Selectivity, and Nonstatistical Dynamic Effects

ConspectusRh2L4 catalysts have risen in popularity in the world of organic synthesis, being used to accomplish a variety of reactions, including C-H insertion and cyclopropanation, and often doing so with high levels of stereocontrol. While the mechanisms and origins of selectivity for such reactions have been examined with computational quantum chemistry for decades, only recently have detailed pictures of the dynamic behavior of reacting Rh2L4-complexed molecules become accessible. Our computational studies on Rh2L4 catalyzed reactions are described here, with a focus on C-H insertion reactions of Rh2L4-carbenes. Several issues complicate the modeling of these reactions, each providing an opportunity for greater understanding and each revealing issues that should be incorporated into future rational design efforts. First, the fundamental mechanism of C-H insertion is discussed. While early quantum chemical studies pointed to transition structures with 3-center [C-H-C] substructures and asynchronous hydride transfer/C-C bond formation, recent examples of reactions with particularly flat potential energy surfaces and even discrete zwitterionic intermediates have been found. These reactions are associated with systems bearing π-donating groups at the site of hydride transfer, allowing for an intermediate with a carbocation substructure at that site to be selectively stabilized. Second, the possible importance of solvent coordination at the Rh atom distal to the carbene is discussed. While effects on reactivity and selectivity were found to be small, they turn out not to be negligible in some cases. Third, it is shown that, in contrast to many other transition metal promoted reactions, many Rh2L4 catalyzed reactions likely involve dissociation of the Rh2L4 catalyst before key chemical steps leading to products. When to expect dissociation is associated with specific features of substrates and the product-forming reactions in question. Often, dissociation precedes transition structures for pericyclic reactions that involve electrons that would otherwise bind to Rh2L4. Finally, the importance of nonstatistical dynamic effects, characterized through ab initio molecular dynamics studies, in some Rh2L4 catalyzed reactions is discussed. These are reactions where transition structures are shown to be followed by flat regions, very shallow minima, and/or pathways that bifurcate, all allowing for trajectories from a single transition state to form multiple different products. The likelihood of encountering such a situation is shown to be associated again with the likelihood of formation of zwitterionic structures along reaction paths, but ones for which pathways to multiple products are expected to be associated with very low or no barriers. The connection between these features and reduced yields of desired products are highlighted, as are the means by which some Rh2L4 catalysts modulate dynamic behavior to produce particular products in high yield.

Discovery of a Formal Dyotropic Rearrangement during Acid-Mediated Dioxabicyclo[4.2.1]nonanone Formation

A new reaction mechanism for the construction of dioxabicyclo[4.2.1]nonanone skeletons via a cation cascade has been proposed and examined by DFT and ab initio computations. This mechanism features the following steps: (1) intramolecular Friedel-Crafts-type cyclization with a methyl oxocarbenium cation formed by carboxylate disconnection, (2) electron-rich aromatic ring assisted methoxide loss followed by lactone formation, and (3) stepwise dyotropic rearrangement resulting in skeletal isomerization from a dioxabicyclo[3.2.2]nonanone to the dioxabicyclo[4.2.1]nonanone product observed experimentally. The high regioselectivity and driving force for the overall rearrangement were rationalized, and Lewis and Brønsted acid mediated reactivities were compared.

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

Eunicellane diterpenoids are a unique family of natural products containing a foundational 6/10-bicyclic framework and can be divided into two main classes, cis and trans, based on the configurations of their ring fusion at C1 and C10. Previous studies on two bacterial diterpene synthases, Bnd4 and AlbS, revealed that these enzymes form cis- and trans-eunicellane skeletons, respectively. Although the structures of these diterpenes only differed in their configuration at a single position, C1, they displayed distinct chemical and thermal reactivities. Here, we used a combination of quantum chemical calculations and chemical transformations to probe their intrinsic properties, which result in protonation-initiated cyclization, Cope rearrangement, and atropisomerism. Finally, we exploited the reactivity of the trans-eunicellane skeleton to generate a series of 6/6/6 gersemiane-type diterpenes via electrophilic cyclization.

Controlling Monoterpene Isomerization by Guiding Challenging Carbocation Rearrangement Reactions in Engineered Squalene-Hopene Cyclases

The interconversion of monoterpenes is facilitated by a complex network of carbocation rearrangement pathways. Controlling these isomerization pathways is challenging when using common Brønsted and Lewis acid catalysts, which often produce product mixtures that are difficult to separate. In contrast, natural monoterpene cyclases exhibit high control over the carbocation rearrangement reactions but are reliant on phosphorylated substrates. In this study, we present engineered squalene-hopene cyclases from Alicyclobacillus acidocaldarius (AacSHC) that catalyze the challenging isomerization of monoterpenes with unprecedented precision. Starting from a promiscuous isomerization of (+)-β-pinene, we first demonstrate noticeable shifts in the product distribution solely by introducing single point mutations. Furthermore, we showcase the tuneable cation steering by enhancing (+)-borneol selectivity from 1 % to >90 % (>99 % de) aided by iterative saturation mutagenesis. Our combined experimental and computational data suggest that the reorganization of key aromatic residues leads to the restructuring of the water network that facilitates the selective termination of the secondary isobornyl cation. This work expands our mechanistic understanding of carbocation rearrangements and sets the stage for target-oriented skeletal reorganization of broadly abundant terpenes.

Unified Synthesis of 2-Isocyanoallopupukeanane and 9-Isocyanopupukeanane through a "Contra-biosynthetic" Rearrangement

Herein, we describe our synthetic efforts toward the pupukeanane natural products, in which we have completed the first enantiospecific route to 2-isocyanoallopupukeanane in 10 steps (formal synthesis), enabled by a key Pd-mediated cyclization cascade. This subsequently facilitated an unprecedented bio-inspired "contra-biosynthetic" rearrangement, providing divergent access to 9-isocyanopupukeanane in 15 steps (formal synthesis). Computational studies provide insight into the nature of this rearrangement.

Theoretical Study of Natural Product Biosynthesis Using Computational Chemistry

The biosynthetic pathways of natural products are complicated, and it is difficult to fully elucidate their details using experimental chemistry alone. In recent years, efforts have been made to elucidate the biosynthetic reaction mechanisms by combining computational and experimental methods. In this review, we will discuss the biosynthetic studies using computational chemistry for various terpene compounds such as cyclooctatin, sesterfisherol, quiannulatene, trichobrasilenol, asperterpenol, preasperterpenoid, spiroviolene, and mangicol.

Molecular Dynamics of the Norbornyl Cation in Solution and Its Generation in Winstein-Trifan Solvolysis: The Timing of Sigma Bridging

Molecular dynamics simulations were performed on the solvolyses of exo- and endo-norbornyl brosylate and for the "nonclassical" σ-bridged norbornyl cation in an acetic acid solution. This computational modeling of the original Winstein-Trifan experiment confirms that exo-solvolysis is accompanied by σ-bridging in the transition state, while endo-solvolysis is not; σ-bridging eventually occurs in a dynamically stepwise fashion. Simulations of the norbornyl cation in solution show typical vibrations due to zero-point and thermal vibrations but no tendency to sample localized "classical cation" geometries.

Subrutilane-A Hexacyclic Sesterterpene from Streptomyces subrutilus

Mining of a terpene synthase from Streptomyces subrutilus resulted in the identification of the hexacyclic sesterterpene subrutilane, besides eight pentacyclic side products. Subrutilane represents the first case of a saturated sesterterpene hydrocarbon. Its structure, including the absolute configuration, was unambiguously determined through X-ray crystallographic analysis and stereoselective deuteration. The cyclisation mechanism to subrutilane and its side products was investigated in all detail by isotopic labelling experiments and DFT calculations. The subrutilane synthase (SrS) also converted (2Z)-GFPP into one major product. Additional compounds were obtained from the substrate analogues (7R)-6,7-dihydro-GFPP and (2Z,7R)-6,7-dihydro-GFPP with blocked reactivity at the C6-C7 bond. Interestingly, the early steps of the cyclisation cascade with (2Z)-GFPP and the saturated substrate analogues were analogous to those of GFPP, but then deviations from the natural cyclisation mode occur.

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

Terpene cyclization reactions involve a number of carbocation intermediates. In some cases, these carbocations are stabilized by through-space interactions with π orbitals. Several terpene/terpenoids, such as sativene, santalene, bergamotene, ophiobolin and mangicol, possess prenyl side chains that do not participate in the cyclization reaction. The role of these prenyl side chains has been partially investigated, but remains elusive in the cyclization cascade. In this study, we focus on variexenol B that is synthesized from iso-GGPP, as recently reported by Dickschat and co-workers, and investigate the possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation-π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner.

S-Adenosylmethionine: more than just a methyl donor

Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.

Functional Characterization and Cyclization Mechanism of a Diterpene Synthase Catalyzing the Skeleton Formation of Cephalotane-Type Diterpenoids

CsCTS, a new diterpene synthase from Cephalotaxus sinensis responsible for forming cephalotene, the core skeleton of cephalotane-type diterpenoids with a highly rigid 6/6/5/7 tetracyclic ring system, was functionally characterized. The stepwise cyclization mechanism is proposed mainly based on structural investigation of its derailment products, and further demonstrated through isotopic labeling experiments and density functional theory calculations. Homology modeling and molecular dynamics simulation combined with site-directed mutagenesis revealed the critical amino acid residues for the unique carbocation-driven cascade cyclization mechanism of CsCTS. Altogether, this study reports the discovery of the diterpene synthase that catalyzes the first committed step of cephalotane-type diterpenoid biosynthesis and delineates its cyclization mechanism, laying the foundation to decipher and artificially construct the complete biosynthetic pathway of this type diterpenoids.

Dual-Hydrogen-Bond Donor and Brønsted Acid Cocatalysis Enables Highly Enantioselective Protio-Semipinacol Rearrangement Reactions

A catalytic protio-semipinacol ring-expansion reaction has been developed for the highly enantioselective conversion of tertiary vinylic cyclopropyl alcohols into cyclobutanone products bearing α-quaternary stereogenic centers. The method relies on the cocatalytic effect of a chiral dual-hydrogen-bond donor (HBD) with hydrogen chloride. Experimental evidence is provided for a stepwise mechanism where protonation of the alkene generates a short-lived, high-energy carbocation, which is followed by C-C bond migration to deliver the enantioenriched product. This research applies strong acid/chiral HBD cocatalysis to weakly basic olefinic substrates and lays the foundation for further investigations of enantioselective reactions involving high-energy cationic intermediates.

Concertedness and Activation Energy Control by Distal Methyl Group during Ring Contraction/Expansion in Scalarane-Type Sesterterpenoid Biosynthesis

Salmahyritisol A, similan A, and hippospongide A, which are scalarane-type sesterterpenoids, feature 6/6/5/7/5 pentacyclic skeletons. Although their biosyntheses have been previously proposed to involve a unique skeletal rearrangement reaction, the detailed reaction mechanism remains unclear as none of the corresponding biosynthetic enzymes for this reaction have been reported. Herein, this skeletal rearrangement reaction was investigated using computational techniques, which revealed the following four key features: (i) the distal 24-Me substituent controls both the concertedness and activation energy of this transformation, (ii) enzymes are not responsible for the observed regioselectivity of C12-C20 bond formation, (iii) stereoselectivity is enzyme-regulated, and (iv) protonation is a key step in this skeletal rearrangement process. These new findings provide insight into the C-ring-contraction and D-ring-expansion mechanisms in scalarane-type sesterterpenoid biosyntheses.

Generation of Alternate Indole Diterpene Architectures in Two Species of Aspergilli

The significant structural diversity and potent bioactivity of the fungal indole diterpenes (IDTs) has attracted considerable interest in their biosynthesis. Although substantial skeletal diversity is generated by the action of noncanonical terpene cyclases, comparatively little is known about these enzymes, particularly those involved in the generation of the subgroup containing emindole SA and DA, which show alternate terpenoid skeletons. Here, we describe the IDT biosynthetic machinery generating these unusual IDT architectures from Aspergillus striatus and Aspergillus desertorum. The function of four putative cyclases was interrogated via heterologous expression. Two specific cyclases were identified that catalyze the formation of epimers emindole SA and DA from A. striatus and A. desertorum, respectively. These cyclases are both clustered along with all the elements required for basic IDT biosynthesis yet catalyze an unusual Markovnikov-like cyclization cascade with alternate stereochemical control. Their identification reveals that these alternate architectures are not generated by mechanistically sloppy or promiscuous enzymes, but by cyclases capable of delivering precise regio- and stereospecificities.

Catalysis-Enabled 13-Step Total Synthesis of (-)-Peyssonnoside A

We report a 13-step enantioselective and stereoselective total synthesis of (-)-peyssonnoside A, a unique diterpene glucoside with a rare and highly congested pentasubstituted cyclopropane and promising antimicrobial activity. Among the 10 steps to synthesize (-)-peyssonnosol, the aglycone of (-)-peyssonnoside A, eight transition-metal-catalyzed transformations enabled the construction of all new C-C bonds and stereocenters without involving any protecting groups. Notably, a palladium-catalyzed dearomative cyclization was used to build the C-6 spiro all-carbon quaternary center, and a counterintuitive hydrogen atom transfer (HAT)-initiated reductive olefin cross-coupling was realized to forge the pentasubstituted cyclopropane ring with excellent stereoselectivity.

Cyclopropylmethyldiphosphates are substrates for sesquiterpene synthases: experimental and theoretical results

New homo-sesquiterpenes are accessible after conversion of presilphiperfolan-8β-ol synthase (BcBOT2) with cyclopropylmethyl analogs of farnesyl diphosphate, and this biotransformation is dependent on subtle structural refinements. Two of the three cyclisation products are homo variants of germacrene D and germacrene D-4-ol while the third product reported contains a new bicyclic backbone for which no analogue in nature has been described so far. The findings on diphosphate activation are discussed and rationalised by relaxed force constants and dissociation energies computed at the DFT level of theory.

Combinatorial Biosynthesis of Terpenoids through Mixing-and-Matching Sesquiterpene Cyclase and Cytochrome P450 Pairs

Terpenoids are an important class of natural products with diverse structures and bioactivities. Their hydrocarbon scaffolds are mainly derived from the terpenes produced by terpene cyclases (TCs). Otherwise, new hydrocarbon scaffolds can be achieved through oxidative rearrangement catalyzed by oxygenases such as P450s. Herein, we report the functional characterization of α/β-trans-bergamotene-producing TCs and their multifunctional P450 partners mined from different fungal species. In addition, novel sesquiterpenoids with hydrocarbon scaffolds different from bergamotenes were generated by combinatorial biosynthesis through mixing-and-matching these TC and P450 pairs. Our results provide a successful example of expanding the chemical diversity of terpenoids by combining genome mining and synthetic biology.

Bio-inspired chemical space exploration of terpenoids

Many computational methods are devoted to rapidly generating pseudo-natural products to expand the open-ended border of chemical spaces for natural products. However, the accessibility and chemical interpretation were often ignored or underestimated in conventional library/fragment-based or rule-based strategies, thus hampering experimental synthesis. Herein, a bio-inspired strategy (named TeroGen) is developed to mimic the two key biosynthetic stages (cyclization and decoration) of terpenoid natural products, by utilizing physically based simulations and deep learning models, respectively. The precision and efficiency are validated for different categories of terpenoids, and in practice, more than 30 000 sesterterpenoids (10 times as many as the known sesterterpenoids) are predicted to be linked in a reaction network, and their synthetic accessibility and chemical interpretation are estimated by thermodynamics and kinetics. Since it could not only greatly expand the chemical space of terpenoids but also numerate plausible biosynthetic routes, TeroGen is promising for accelerating heterologous biosynthesis, bio-mimic and chemical synthesis of complicated terpenoids and derivatives.

DFT Study on the Biosynthesis of Asperterpenol and Preasperterpenoid Sesterterpenoids: Exclusion of Secondary Carbocation Intermediates and Origin of Structural Diversification

The biosynthetic pathway to asperterpenol, a sesterterpenoid featuring a 6/6/8/5 tetracyclic ring system, was proposed to involve three secondary (2°) carbocation intermediates (B, D, and I), but it remains controversial whether or not these are viable. Further, the proposed 11/6/5 tricyclic intermediate C has the same "ChemDraw" structure as an intermediate in the biosynthesis of preasperterpenoid, which has a very different 5/7/(3)6/5 pentacyclic skeleton. Here, we present a detailed scrutiny of the asperterpenol/preasperterpenoid biosynthetic pathways based on comprehensive DFT calculations.

Computational Prediction and Experimental Validation of a Bridged Cation Intermediate in Akanthomycin Biosynthesis

Here we report a computation-driven chemoenzymatic synthesis and biosynthesis of the natural product deoxyakanthomycin, an atropisomeric pyridone natural product that features a 7-membered carbocycle with five stereocenters, one of which a quaternary center. The one-step synthesis from a biosynthetic precursor is based on computational analysis that predicted a σ-bridged cation mediated cyclization mechanism to form deoxyakanthomycin. The σ-bridged cation rationalizes the observed substrate-controlled selectivity; diastereoselectivity arises from attack of water anti to the σ-bridging, as is generally found for σ-bridged cations. Our studies also reveal a unifying biosynthetic strategy for 2-pyridone natural products that derive from a common o-quinone methide to create diverse structures.

Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories

Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working conditions, and environmental pollutions. Microbial cell factories come as a suitable replacement. However, designing efficient microbial platforms for isoprenoid synthesis is often a challenging task. This has to do with the cytotoxic effects of pathway intermediates and some end products, instability of expressed pathways, as well as high enzyme promiscuity. Also, the low enzymatic activity of some terpene synthases and prenyltransferases, and the lack of an efficient throughput system to screen improved high-performing strains are bottlenecks in strain development. Metabolic engineering and synthetic biology seek to overcome these issues through the provision of effective synthetic tools. This review sought to provide an in-depth description of novel strategies for improving cell factory performance. We focused on improving transcriptional and translational efficiencies through static and dynamic regulatory elements, enzyme engineering and high-throughput screening strategies, cellular function enhancement through chromosomal integration, metabolite tolerance, and modularization of pathways.

Stability of alkyl carbocations

The traditional and widespread rationale behind the stability trend of alkyl-substituted carbocations is incomplete.

Mechanistic Insights into the Formation of the 6,10-Bicyclic Eunicellane Skeleton by the Bacterial Diterpene Synthase Bnd4

The eunicellane diterpenoids are a unique family of natural products seen in marine organisms, plants, and bacteria. We used a series of biochemical, bioinformatics, and theoretical experiments to investigate the mechanism of the first diterpene synthase known to form the eunicellane skeleton. Deuterium labeling studies and quantum chemical calculations support that Bnd4, from Streptomyces sp. (CL12-4), forms the 6,10-bicyclic skeleton through a 1,10-cyclization, 1,3-hydride shift, and 1,14-cyclization cascade. Bnd4 also demonstrated sesquiterpene cyclase activity and the ability to prenylate small molecules. Bnd4 possesses a unique D94 NxxxD motif and mutation experiments confirmed an absolute requirement for D94 as well as E169.

DFT Study on the Biosynthesis of Verrucosane Diterpenoids and Mangicol Sesterterpenoids: Involvement of Secondary-Carbocation-Free Reaction Cascades

Some experimental observations indicate that a sequential formation of secondary (2°) carbocations might be involved in some biosynthetic pathways, including those of verrucosane-type diterpenoids and mangicol-type sesterterpenoids, but it remains controversial whether or not such 2° cations are viable intermediates. Here, we performed comprehensive density functional theory calculations of these biosynthetic pathways. The results do not support previously proposed pathways/mechanisms: in particular, we find that none of the putative 2° carbocation intermediates is involved in either of the biosynthetic pathways. In verrucosane biosynthesis, the proposed 2° carbocations (II and IV) in the early stage are bypassed by the formation of the adjacent 3° carbocations and by unusual skeletal rearrangement reactions, and in the later stage, the putative 2° carbocation intermediates (VI, VII, and VIII) are not present as the proposed forms but as nonclassical structures between homoallyl and cyclopropylcarbinyl cations. In the mangicol biosynthesis, one of the two proposed 2° carbocations (X) is bypassed by a C-C bond-breaking reaction to generate a 3° carbocation with a C=C bond, while the other (XI) is bypassed by a strong hyperconjugative interaction leading to a nonclassical carbocation. We propose new biosynthetic pathways/mechanisms for the verrucosane-type diterpenoids and mangicol-type sesterterpenoids. These pathways are in good agreement with the findings of previous biosynthetic studies, including isotope-labeling experiments and byproducts analysis, and moreover can account for the biosynthesis of related terpenes.

Recent advances in the synthesis of ent-kaurane diterpenoids

Covering: 2015 to 2020The ent-kaurane diterpenoids are integral parts of tetracyclic natural products that are widely distributed in terrestrial plants. These compounds have been found to possess interesting bioactivities, ranging from antitumor, antifungal and antibacterial to anti-inflammatory activities. Structurally, the different tetracyclic moieties of ent-kauranes can be seen as the results of intramolecular cyclizations, oxidations, C-C bond cleavages, degradation, or rearrangements, starting from their parent skeleton. During the past decade, great efforts have been made to develop novel strategies for synthesizing these natural products. The purpose of this review is to describe the recent advances in the total synthesis of ent-kaurane diterpenoids covering the period from 2015 to date.

An invocation for computational evaluation of isomerization transforms: cationic skeletal reorganizations as a case study

Covering: 2010 to 2020This review article describes how cationic rearrangement reactions have been used in natural product total synthesis over the last decade as a case study for the many productive ways by which isomerization reactions are enabling for synthesis. This review argues that isomerization reactions in particular are well suited for computational evaluation, as relatively simple calculations can provide significant insight.

Dynamic Effects on Migratory Aptitudes in Carbocation Reactions

Carbocation rearrangement reactions are of great significance to synthetic and biosynthetic chemistry. In pursuit of a scale of inherent migratory aptitude that takes into account dynamic effects, both uphill and downhill ab initio molecular dynamics (AIMD) simulations were used to examine competing migration events in a model system designed to remove steric and electronic biases. The results of these simulations were combined with detailed investigations of potential energy surface topography and variational transition state theory calculations to reveal the importance of nonstatistical dynamic effects on migratory aptitude.

Syntheses of Skeletally Diverse Tetracyclic Isodon Diterpenoid Scaffolds Guided by Dienyne Radical Cyclization Logic

We report herein the diversity-oriented synthesis of various tetracyclic Isodon diterpenoid scaffolds guided by radical cyclization logic. Our substrate-based dienyne radical cyclization approach is distinctive from reagent-based rearrangement approaches that are generally applied in biosynthesis or previous synthetic studies. An unprecedented cyclization at C₁₄ via 1,5-radical translocation/5-exo-trig cyclization is observed, which enriches our radical cyclization pattern. Furthermore, biological evaluations revealed that several new natural product-like compounds showed promising anticancer activities against various cancer cell lines.

Catalytic enantiocontrol over a non-classical carbocation

Carbocations can be categorized into classical carbenium ions and non-classical carbonium ions. These intermediates are ubiquitous in reactions of both fundamental and practical relevance, finding application in the petroleum industry as well as the discovery of new drugs and materials. Conveying stereochemical information to carbocations is therefore of interest to a range of chemical fields. While previous studies targeted systems proceeding through classical ions, enantiocontrol over their non-classical counterparts has remained unprecedented. Here we show that strong and confined chiral acids catalyse enantioselective reactions via the non-classical 2-norbornyl cation. This reactive intermediate is generated from structurally different precursors by leveraging the reactivity of various functional groups to ultimately deliver the same enantioenriched product. Our work demonstrates that tailored catalysts can act as suitable hosts for simple, non-functionalized carbocations via a network of non-covalent interactions. We anticipate that the methods described herein will provide catalytic accessibility to valuable carbocation systems.

Naturally Occurring seco-Sativene Sesquiterpenoid: Chemistry and Biology

seco-Sativenes are a small group of sesquiterpenoids with a unique bicyclo[3.2.1]octane core carbon skeleton, which implies the unusual biosynthetic pathway. Up to date, there are 40 seco-sativene analogues with diverse post-modifications isolated from different fungi. Interestingly, some seco-sativene analogues display strong phytotoxic effects, whereas others possess plant-growth-promoting biological activities. The possible mechanism of actions about phytotoxic or growth-promoting activities are partly elucidated, but structure-activity relationships are still not clear. This review provides a comprehensive overview on the structures, ¹H nuclear magnetic resonance features, bioactivities, and biosynthesis of seco-sativene sesquiterpenoids from 1956 to 2020.

Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase

Most terpene synthase reactions follow Markovnikov rules for formation of high-energy carbenium ion intermediates. However, there are notable exceptions. For example, pentalenene synthase (PS) undergoes an initial anti-Markovnikov cyclization reaction followed by a 1,2-hydride shift to form an intermediate humulyl cation with positive charge on the secondary carbon C9 atom of the farnesyl diphosphate substrate. The mechanism by which these enzymes stabilize and guide the regioselectivity of secondary carbocations has not heretofore been elucidated. In an effort to better understand these reactions, we grew crystals of apo-PS, soaked them with the nonreactive substrate analogue 12,13-difluorofarnesyl diphosphate, and determined the X-ray structure of the resulting complex at 2.2 Å resolution. The most striking feature of the active site structure is that C9 is perfectly positioned to make a C-H···π interaction with the side chain benzene ring of residue F76; this would enhance hyperconjugation to stabilize a developing cation at C10 and thus support the anti-Markovnikov regioselectivity of the cyclization. The benzene ring is also positioned to catalyze the migration of H to C10 and stabilize a C9 carbocation. On the opposite face of C9, further cation stabilization is possible via interactions with the main chain carbonyl of I177 and the neighboring intramolecular C6═C7 bond. Mutagenesis experiments also support a role for residue 76 in these interactions, but most interesting is the F76W mutant, whose crystal structure clearly shows C9 and C10 centered above the fused benzene and pyrrole rings of the indole side chain, respectively, such that a carbocation at either position could be stabilized in this complex, and two anti-Markovnikov products, pentalenene and humulene, are formed. Finally, we show that there is a rough correlation (although not absolute) of an aromatic side chain (F or Y) at position 76 in related terpene synthases from Streptomyces that catalyze similar anti-Markovnikov addition reactions.

Late-Stage Diversification of Natural Products

Late-stage diversification of natural products is an efficient way to generate natural product derivatives for drug discovery and chemical biology. Benefiting from the development of site-selective synthetic methodologies, late-stage diversification of natural products has achieved notable success. This outlook will outline selected examples of novel methodologies for site-selective transformations of reactive functional groups and inert C-H bonds that enable late-stage diversification of complex natural products. Accordingly, late-stage diversification provides an opportunity to rapidly access various derivatives for modifying lead compounds, identifying cellular targets, probing protein-protein interactions, and elucidating natural product biosynthetic relationships.

DFT Study on the Biosynthesis of Preasperterpenoid A: Role of Secondary Carbocations in the Carbocation Cascade

Preasperterpenoid A, featuring a 5/7/(3)6/5 pentacyclic structure, is a C₂₅ sesterterpenoid produced by Penicillium verruculosum. The results of density functional calculations on putative biosynthetic carbocation cyclization/rearrangements leading to preasperterpenoid A revealed a highly concerted four-step cyclization mechanism. Interestingly, two secondary carbocation structures were obtained as minima, but appeared almost as shoulders in the energy profile, and may represent essentially transient structures during the highly concerted reaction.

Enantioselective Tail-to-Head Cyclizations Catalyzed by Dual-Hydrogen-Bond Donors

Chiral urea derivatives are shown to catalyze enantioselective tail-to-head cyclization reactions of neryl chloride analogues. Experimental data are consistent with a mechanism in which π-participation by the nucleophilic olefin facilitates chloride ionization and thereby circumvents simple elimination pathways. Kinetic and computational studies support a cooperative mode of catalysis wherein two molecules of the urea catalyst engage the substrate and induce enantioselectivity through selective transition state stabilization.

Predicting Rearrangement-Competent Terpenoid Oxidation Levels

Results of density functional theory calculations on rearrangements of potential biosynthetic precursors to the sesquiterpenoid illisimonin A reveal that only some possible precursors, those with certain specific oxidation patterns, are rearrangement-competent.

Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases

Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.

Nonclassical ammonium ions as intermediates in cinchona alkaloid rearrangements?

The classical/nonclassical nature of cationic ammonium intermediates proposed to be involved in cinchona alkaloid solvolysis and related reactions is investigated. While these intermediates are found to possess highly distorted geometries in which the central nitrogen atom and three of the attached groups are essentially coplanar, we do not find evidence of a nonclassical bonding array. Instead, we find evidence that the intermediate resembles a classical, albeit strained, aziridinium structure, which is still able to account for experimental observations.

Nature-driven approaches to non-natural terpene analogues

The reactions catalysed by terpene synthases belong to the most complex and fascinating cascade-type transformations in Nature.