Protein engineering of oxidosqualene-lanosterol cyclase into triterpene monocyclase

Tryptophan Stabilization of a Biochemical Carbocation Evaluated by Analysis of π Complexes of 3-Ethylindole with the t-Butyl Cation

Understanding how the highly unstable carbocation intermediates in terpenoid biosynthesis are stabilized and protected during their transient existence in enzyme active sites is an intriguing challenge which has to be addressed computationally. Our efforts have focused on evaluating the stabilization afforded via carbocation-π complexation between a biochemical carbocation and an aromatic amino acid residue. This has involved making measurements on an X-ray structure of an enzyme active site that shows a π donor proximate to a putative carbocation site and using these to build models which are analyzed computationally to provide an estimated stabilization energy (SE). Previously, we reported estimated SEs for several such carbocation-π complexes involving phenylalanine. Herein, we report the first such estimate involving tryptophan as the π donor. Because there was almost no published information about indole as a π-complexation donor, we first located computationally equilibrium π and σ complexes of 3-ethylindole with the t-butyl cation as relevant background information. Then, measurements on the X-ray structure of the enzyme CotB2 complexed with geranylgeranyl thiodiphosphate (GGSPP), specifically on the geometric relationship of the putative carbocation at C15 of GGSPP to W186, were used to build a model that afforded a computed SE of -15.3 kcal/mol.

Engineering Critical Amino Acid Residues of Lanosterol Synthase to Improve the Production of Triterpenoids in Saccharomyces cerevisiae

Triterpenoids are a subgroup of terpenoids and have wide applications in the food, cosmetics, and pharmaceutical industries. The heterologous production of various triterpenoids in Saccharomyces cerevisiae, as well as other microbes, has been successfully implemented as these production hosts not only produce the precursor of triterpenoids 2,3-oxidosqualene by the mevalonate pathway but also allow simple expression of plant membrane-anchored enzymes. Nevertheless, 2,3-oxidosqualene is natively converted to lanosterol catalyzed by the endogenous lanosterol synthase (Erg7p), causing low production of recombinant triterpenoids. While simple deletion of ERG7 was not effective, in this study, the critical amino acid residues of Erg7p were engineered to lower this critical enzyme activity. The engineered S. cerevisiae indeed accumulated 2,3-oxidosqualene up to 180 mg/L. Engineering triterpenoid synthesis into the ERG7-modified strain resulted in 7.3- and 3-fold increases in the titers of dammarane-type and lupane-type triterpenoids, respectively. This study presents an efficient inducer-free strategy for lowering Erg7p activity, thereby providing 2,3-oxidosqualene for the enhanced production of various triterpenoids.

Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-π interaction

Polyamines influence medically relevant processes in the opportunistic pathogen Pseudomonas aeruginosa, including virulence, biofilm formation and susceptibility to antibiotics. Although homospermidine synthase (HSS) is part of the polyamine metabolism in various strains of P. aeruginosa, neither its role nor its structure has been examined so far. The reaction mechanism of the nicotinamide adenine dinucleotide (NAD+)-dependent bacterial HSS has previously been characterized based on crystal structures of Blastochloris viridis HSS (BvHSS). This study presents the crystal structure of P. aeruginosa HSS (PaHSS) in complex with its substrate putrescine. A high structural similarity between PaHSS and BvHSS with conservation of the catalytically relevant residues is demonstrated, qualifying BvHSS as a model for mechanistic studies of PaHSS. Following this strategy, crystal structures of single-residue variants of BvHSS are presented together with activity assays of PaHSS, BvHSS and BvHSS variants. For efficient homospermidine production, acidic residues are required at the entrance to the binding pocket (`ionic slide') and near the active site (`inner amino site') to attract and bind the substrate putrescine via salt bridges. The tryptophan residue at the active site stabilizes cationic reaction components by cation-π interaction, as inferred from the interaction geometry between putrescine and the indole ring plane. Exchange of this tryptophan for other amino acids suggests a distinct catalytic requirement for an aromatic interaction partner with a highly negative electrostatic potential. These findings substantiate the structural and mechanistic knowledge on bacterial HSS, a potential target for antibiotic design.

A simpler method affords evaluation of π stabilization by phenylalanine of several biochemical carbocations

Carbocations are important intermediates in the biosynthesis of terpenes and steroids, and it is challenging to try to understand how these relatively unstable species survive even transiently during biochemical reactions. Carbocation-π interaction with aromatic amino acid residues is an important factor in helping to stabilize these positively charged species. However, the short lifetimes of these active site carbocations makes experimental evaluation of the stabilization afforded by such interaction impossible. Computational studies, however, have provided some insight into this phenomenon. Herein we report a simple, computationally efficient method to estimate such stabilization energies afforded by phenylalanine to biochemical carbocation intermediates. A model is constructed in which the biochemical carbocation is replaced by an appropriate carbocation mimic (t-butyl or dimethylallyl). This substitute carbocation is then aligned with an ethylbenzene serving as a surrogate for each proximate phenylalanine in a geometry that replicates as closely as possible the orientation of that phenylalanine using measurements made on an X-ray structure of an enzyme active site in which a carbocation surrogate is bound. Density functional theory computations on such models were then used to yield estimates of stabilization energies. Application of this method to the tertiary carbocation formed in the reaction catalyzed by geranyl diphosphate C-methyl transferase gave a stabilization energy (-12.3 kcal mol-1) that was essentially identical to that obtained previously by analysis of a much more computationally demanding model of the active site. As a check on the accuracy of the simpler method, it was applied with similar success to the farnesyl cation formed in the reaction catalyzed by aristolochene synthase that is stabilized by cation-π interaction with two phenylalanines. Application of this method is also described to estimate carbocation-π stabilization, by the same two phenylalanines, of the final carbocation intermediate leading to aristolochene through analysis of the X-ray structure of an inhibitor of that carbocation bound in the active site of aristolochene synthase. Finally, the stabilization, by either of two phenylalanines, of six carbocation intermediates in the oxidosqualene cyclase-catalyzed formation of lanosterol is estimated by comparable analysis of an X-ray structure of that reaction product bound in the enzyme active site.

Identification of oxidosqualene cyclases from the medicinal legume tree Bauhinia forficata: a step toward discovering preponderant α-amyrin-producing activity

Triterpenoids are widely distributed among plants of the legume family. However, most studies have focused on triterpenoids and their biosynthetic enzymes in model legumes. We evaluated the triterpenoid aglycones profile of the medicinal legume tree Bauhinia forficata by gas chromatography-mass spectrometry. Through transcriptome analyses, homology-based cloning, and heterologous expression, we discovered four oxidosqualene cyclases (OSCs) which are responsible for the diversity of triterpenols in B. forficata. We also investigated the effects of the unique motif TLCYCR on α-amyrin synthase activity. B. forficata highly accumulated α-amyrin. We discovered an OSC with a preponderant α-amyrin-producing activity, which accounted for at least 95% of the total triterpenols. We also discovered three other functional OSCs (BfOSC1, BfOSC2, and BfOSC4) that produce β-amyrin, germanicol, and cycloartenol. Furthermore, by replacing the unique motif TLCYCR from BfOSC3 with the MWCYCR motif, we altered the function of BfOSC3 such that it no longer produced α-amyrin. Our results provide new insights into OSC cyclization, which is responsible for the diversity of triterpenoid metabolites in B. forficata, a non-model legume plant.

Molecular Docking and Molecular Dynamics Studies on Selective Synthesis of α-Amyrin and β-Amyrin by Oxidosqualene Cyclases from Ilex Asprella

Amyrins are the immediate precursors of many pharmaceutically important pentacyclic triterpenoids. Although various amyrin synthases have been identified, little is known about the relationship between protein structures and the constituent and content of the products. IaAS1 and IaAS2 identified from Ilex asprella in our previous work belong to multifunctional oxidosqualene cyclases and can produce α-amyrin and β-amyrin at different ratios. More than 80% of total production of IaAS1 is α-amyrin; while IaAS2 mainly produces β-amyrin with a yield of 95%. Here, we present a molecular modeling approach to explore the underlying mechanism for selective synthesis. The structures of IaAS1 and IaAS2 were constructed by homology modeling, and were evaluated by Ramachandran Plot and Verify 3D program. The enzyme-product conformations generated by molecular docking indicated that ASP484 residue plays an important role in the catalytic process; and TRP611 residue of IaAS2 had interaction with β-amyrin through π–σ interaction. MM/GBSA binding free energy calculations and free energy decomposition after 50 ns molecular dynamics simulations were performed. The binding affinity between the main product and corresponding enzyme was higher than that of the by-product. Conserved amino acid residues such as TRP257; TYR259; PHE47; TRP534; TRP612; and TYR728 for IaAS1 (TRP257; TYR259; PHE473; TRP533; TRP611; and TYR727 for IaAS2) had strong interactions with both products. GLN450 and LYS372 had negative contribution to binding affinity between α-amyrin or β-amyrin and IaAS1. LYS372 and ARG261 had strong repulsive effects for the binding of α-amyrin with IaAS2. The importance of Lys372 and TRP612 of IaAS1, and Lys372 and TRP611 of IaAS2, for synthesizing amyrins were confirmed by site-directed mutagenesis. The different patterns of residue–product interactions is the cause for the difference in the yields of two products.

A Protonated Quinone Methide Stabilized by a Combination of Partial Aromatization and π-Interaction: Spectroscopic and Crystallographic Analysis

We have expanded the repertoire of cation-π interactions to include a carbocation-π system resulting from the protonation of a π-stacked para-quinone methide (p-QM). This unusual carbocation is stabilized by a combination of partial aromatization of the QM moiety and through-space interaction with the π-system of the adjacent aromatic ring. Single crystal X-ray analysis of the protonated form reveals a structure consisting of a hydrogen-bound complex involving two molecules of the precursor and one proton.

Mutated variants of squalene-hopene cyclase: enzymatic syntheses of triterpenes bearing oxygen-bridged monocycles and a new 6,6,6,6,6-fusded pentacyclic scaffold, named neogammacerane, from 2,3-oxidosqualene

Squalene-hopene cyclase (SHC) catalyzes the conversion of acyclic squalene molecule into a 6,6,6,6,5-fused pentacyclic hopene and hopanol. SHC is also able to convert (3S)-2,3-oxidosqualene into 3β-hydroxyhopene and 3β-hydroxyhopanol and can generate 3α-hydroxyhopene and 3α-hydroxyhopanol from (3R)-2,3-oxidosqualene. Functional analyses of active site residues toward the squalene cyclization reaction have been extensively reported, but investigations of the cyclization reactions of (3R,S)-oxidosqualene by SHC have rarely been reported. The cyclization reactions of oxidosqualene with W169X, G600F/F601G and F601G/P602F were examined. The variants of the W169L generated new triterpene skeletons possessing a 7-oxabicyclo[2.2.1]heptane moiety (oxygen-bridged monocycle) with (1S,2S,4R)- and (1R,2S,4S)-stereochemistry, which were produced from (3R)- and (3S)-oxidosqualenes, respectively. The F601G/P602F double mutant also furnished a novel triterpene, named neogammacer-21(22)-en-3β-ol, consisting of a 6,6,6,6,6-fused pentacyclic system, in which Me-29 at C-22 of the gammacerane skeleton migrated to C-21. We propose to name this novel scaffold neogammacerane. The formation mechanisms of the enzymatic products from 2,3-oxidosqualene are discussed.

Identification of Key Amino Acid Residues Determining Product Specificity of 2,3-Oxidosqualene Cyclase in Siraitia grosvenorii

Sterols and triterpenes are structurally diverse bioactive molecules generated through cyclization of linear 2,3-oxidosqualene. Based on carbocationic intermediates generated during the initial substrate preorganization step, oxidosqualene cyclases (OSCs) are roughly segregated into a dammarenyl cation group that predominantly catalyzes triterpenoid precursor products and a protosteryl cation group which mostly generates sterol precursor products. The mechanism of conversion between two scaffolds is not well understood. Previously, we have characterized a promiscuous OSC from Siraitia grosvenorii (SgCS) that synthesizes a novel cucurbitane-type triterpene cucurbitadienol as its main product. By integration of homology modeling, molecular docking and site-directed mutagenesis, we discover that five key amino acid residues (Asp486, Cys487, Cys565, Tyr535, and His260) may be responsible for interconversions between chair–boat–chair and chair–chair–chair conformations. The discovery of euphol, dihydrolanosterol, dihydroxyeuphol and tirucallenol unlocks a new path to triterpene diversity in nature. Our findings also reveal mechanistic insights into the cyclization of oxidosqualene into cucurbitane-type and lanostane-type skeletons, and provide a new strategy to identify key residues determining OSC specificity.

β-Amyrin biosynthesis: catalytic mechanism and substrate recognition

In the past five years, there have been remarkable advances in the study of β-amyrin synthase. This review outlines the catalytic mechanism and substrate recognition in β-amyrin biosynthesis, which have been attained by the site-directed mutagenesis and substrate analog experiments.

β-Amyrin synthase from Euphorbia tirucalli L. functional analyses of the highly conserved aromatic residues Phe413, Tyr259 and Trp257 disclose the importance of the appropriate steric bulk, and cation-π and CH-π interactions for the efficient catalytic action of the polyolefin cyclization cascade

Many of the functions of the active site residues in β-amyrin synthase and its catalytic mechanism remain unclear. Herein, we examined the functions of the highly conserved Phe413, Tyr259, and Trp257 residues in the β-amyrin synthase of Euphorbia tirucalli. The site-specific mutants F413V and F413M [corrected] showed nearly the same enzymatic activities as the wild type, indicating that π-electrons are not needed for the catalytic reaction. However, the F413A [corrected] mutant yielded a large amount of the tetracyclic dammarane skeleton, with decreased production of β-amyrin. This indicates that the Phe413 [corrected] residue is located near the D-ring formation site and works to position the oxidosqualene substrate correctly within the reaction cavity. On the other hand, the major catalysis-related function of the Tyr259 and Trp257 residues is to yield their π-electrons to the cationic intermediates. The Y259F variant showed nearly equivalent activity to that of the wild type, but aliphatic mutants such as the Ala, Val, and Leu variants showed significantly decreased the activity and yielded the tetracyclic dammarane scaffold, strongly demonstrating that the Tyr259 residue stabilizes the baccharenyl secondary cation via cation-π interaction. The aliphatic variants of Trp257 exhibited remarkably decreased enzymatic activity, and lupeol was produced in a high production ratio, indicating that Trp257 stabilizes the oleanyl cation via cation-π interaction. The aromatic Phe and Tyr mutants exhibited high activities owing to their more increased π-electron density relative to that of the aliphatic mutants, but lupeol was produced in a significantly high yield besides β-amyrin. The Trp residue is likely to be responsible for the robust binding of Me-30 through CH-π interaction. The decreased π-electron density of the Phe and Tyr mutants compared to that of Trp would have resulted in the high production of lupeol.

Friedelin Synthase from Maytenus ilicifolia: Leucine 482 Plays an Essential Role in the Production of the Most Rearranged Pentacyclic Triterpene

Among the biologically active triterpenes, friedelin has the most-rearranged structure produced by the oxidosqualene cyclases and is the only one containing a cetonic group. In this study, we cloned and functionally characterized friedelin synthase and one cycloartenol synthase from Maytenus ilicifolia (Celastraceae). The complete coding sequences of these 2 genes were cloned from leaf mRNA, and their functions were characterized by heterologous expression in yeast. The cycloartenol synthase sequence is very similar to other known OSCs of this type (approximately 80% identity), although the M. ilicifolia friedelin synthase amino acid sequence is more related to β-amyrin synthases (65-74% identity), which is similar to the friedelin synthase cloned from Kalanchoe daigremontiana. Multiple sequence alignments demonstrated the presence of a leucine residue two positions upstream of the friedelin synthase Asp-Cys-Thr-Ala-Glu (DCTAE) active site motif, while the vast majority of OSCs identified so far have a valine or isoleucine residue at the same position. The substitution of the leucine residue with valine, threonine or isoleucine in M. ilicifolia friedelin synthase interfered with substrate recognition and lead to the production of different pentacyclic triterpenes. Hence, our data indicate a key role for the leucine residue in the structure and function of this oxidosqualene cyclase.

A conserved amino acid residue critical for product and substrate specificity in plant triterpene synthases

Triterpenes are structurally complex plant natural products with numerous medicinal applications. They are synthesized through an origami-like process that involves cyclization of the linear 30 carbon precursor 2,3-oxidosqualene into different triterpene scaffolds. Here, through a forward genetic screen in planta, we identify a conserved amino acid residue that determines product specificity in triterpene synthases from diverse plant species. Mutation of this residue results in a major change in triterpene cyclization, with production of tetracyclic rather than pentacyclic products. The mutated enzymes also use the more highly oxygenated substrate dioxidosqualene in preference to 2,3-oxidosqualene when expressed in yeast. Our discoveries provide new insights into triterpene cyclization, revealing hidden functional diversity within triterpene synthases. They further open up opportunities to engineer novel oxygenated triterpene scaffolds by manipulating the precursor supply.

Carbocation–π interaction: evaluation of the stabilization by phenylalanine of a biochemical carbocation intermediate

Computational analyses, using primarily density functional theory, have been used to determine the stabilization associated with the carbocation–π interaction of a biochemical carbocation intermediate binding to a phenylalanine residue in an enzyme active site.

Traversing the fungal terpenome

Fungi (Ascomycota and Basidiomycota) are prolific producers of structurally diverse terpenoid compounds. Classes of terpenoids identified in fungi include the sesqui-, di- and triterpenoids. Biosynthetic pathways and enzymes to terpenoids from each of these classes have been described. These typically involve the scaffold generating terpene synthases and cyclases, and scaffold tailoring enzymes such as e.g. cytochrome P450 monoxygenases, NAD(P)+ and flavin dependent oxidoreductases, and various group transferases that generate the final bioactive structures. The biosynthesis of several sesquiterpenoid mycotoxins and bioactive diterpenoids has been well-studied in Ascomycota (e.g. filamentous fungi). Little is known about the terpenoid biosynthetic pathways in Basidiomycota (e.g. mushroom forming fungi), although they produce a huge diversity of terpenoid natural products. Specifically, many trans-humulyl cation derived sesquiterpenoid natural products with potent bioactivities have been isolated. Biosynthetic gene clusters responsible for the production of trans-humulyl cation derived protoilludanes, and other sesquiterpenoids, can be rapidly identified by genome sequencing and bioinformatic methods. Genome mining combined with heterologous biosynthetic pathway refactoring has the potential to facilitate discovery and production of pharmaceutically relevant fungal terpenoids.

β-Amyrin synthase from Euphorbia tirucalli. Steric bulk, not the π-electrons of Phe, at position 474 has a key role in affording the correct folding of the substrate to complete the normal polycyclization cascade

The importance of the steric bulk at 474 residue is described for completion of the cyclization cascade, but not the π-electrons of the Phe residue.