Structural and Mechanistic Insights into the C-C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase

Recently discovered heteromeric enzymes in natural product biosynthesis

The abundant diversity and elegant complexity in the chemical structures of natural products have attracted vigorous investigations of the chemistry and enzymology underlying their biosynthetic processes over the past few decades. Among the biochemical events, the formation of complexes of heteromeric enzymes has been observed in the biosynthesis of several natural products and metabolic pathways. In this review, we aim to consolidate the recently discovered cases of heteromeric enzymes in natural product biosynthesis and metabolism, in order to clarify the genetic and structural bases leading to the formation of these heteromeric complexes and provide insights for the rational redesign of proteins in biosynthetic machineries.

What Factors Determine the Brevione B Desaturation Mechanism in the Nonheme Iron Dioxygenase BrvJ?

The natural product synthesis of brevione J undergoes a cascade of reactions including an oxidative desaturation and a ring-expansion. The C1-C2 desaturation of brevione B is catalyzed by the nonheme iron dioxygenase BrvJ using one molecule of O2 and α-ketoglutarate (αKG). However, whether the subsequent oxidative ring expansion reaction is also catalyzed by the same enzyme is unknown and remains controversial. To gain insight into the mechanism of brevione J biosynthesis a computational study is reported here using molecular dynamics and density functional theory approaches. The work predicts that both cycles can proceed in the same protein structure on an iron center with O2 and αKG for each cycle. The rate-determining step is a hydrogen atom abstraction step in both reaction cycles. Interestingly, the OH rebound barriers are high in energy in cycle 1 due to stereochemical interactions and substrate positioning that enable an efficient desaturation reaction.

Biosynthesis of unique natural product scaffolds by Fe(II)/αKG-dependent oxygenases

Fe(II)/αKG-dependent oxygenases are multifunctional oxidases responsible for the formation of unique natural product skeletons. Studies of these enzymes are important because the knowledge of their catalytic functions, enzyme structures, and reaction mechanisms can be used to create non-natural enzymes through mutation and synthesize non-natural compounds. In this review, I will introduce the research we have conducted on two fungal Fe(II)/αKG-dependent oxygenases, TlxI-J and TqaL. TlxI-J is the first Fe(II)/αKG-dependent oxygenase type enzyme heterodimer that catalyzes consecutive oxidation reactions, hydroxylation followed by retro-aldol or ketal formation, to form the complex skeletons of meroterpenoids. TqaL is the first naturally occurring aziridine synthase, and I will discuss the mechanism of its unique C-N bond formation in nonproteinogenic amino acid biosynthesis. This review will advance research on the discovery of new enzymes and the analysis of their functions by reviewing the structures and functions of these extraordinary Fe(II)/αKG-dependent oxygenases, and promote their use in the synthesis of new natural medicines.

Implications of non-native metal substitution in carbonic anhydrase - engineered enzymes and models

The enzyme carbonic anhydrase has been intensely studied over decades as a means to understand the role of zinc in hydrating CO2. The naturally occurring enzyme has also been immobilized on distinct heterogeneous platforms, which results in a different hybrid class of catalysts that are useful for the adsorption and hydration of CO2. However, the reusability and robustness of such natural and immobilized systems are substantially affected when tested under industrial conditions, such as high temperature and high flow rate. This led to the generation of model systems in the form of metal-coordination complexes, metal-organic frameworks, metallo-peptide self-assembled supramolecules and nanomaterials that mimic the primary, and, to some extent, secondary coordination sphere of the active site of the natural carbonic anhydrase enzymes. Furthermore, the effects of zinc-substitution by other relevant transition metals in both the naturally occurring enzymes and model systems has been reported. It has been observed that some other transition metal ions in the active site of carbonic anhydrase and its models can also accomplish similar activity, established by various reaction probes and ideas. Herein, we present a comprehensive highlight about substituting zinc in the active site of the modified enzymes and its biomimetic model systems with non-native metal ions and review how they affect the structural orientation and reactivity towards CO2 hydration. In addition, the utility of artificially engineered carbonic anhydrases towards a number of non-natural reactions is also discussed.

Tutorial Review on the Set-Up and Running of Quantum Mechanical Cluster Models for Enzymatic Reaction Mechanisms

Enzymes turnover substrates into products with amazing efficiency and selectivity and as such have great potential for use in biotechnology and pharmaceutical applications. However, details of their catalytic cycles and the origins surrounding the regio- and chemoselectivity of enzymatic reaction processes remain unknown, which makes the engineering of enzymes and their use in biotechnology challenging. Computational modelling can assist experimental work in the field and establish the factors that influence the reaction rates and the product distributions. A popular approach in modelling is the use of quantum mechanical cluster models of enzymes that take the first- and second coordination sphere of the enzyme active site into consideration. These QM cluster models are widely applied but often the results obtained are dependent on model choice and model selection. Herein, we show that QM cluster models can give highly accurate results that reproduce experimental product distributions and free energies of activation within several kcal mol-1, regarded that large cluster models with >300 atoms are used that include key hydrogen bonding interactions and charged residues. In this tutorial review, we give general guidelines on the set-up and applications of the QM cluster method and discuss its accuracy and reproducibility. Finally, several representative QM cluster model examples on metal-containing enzymes are presented, which highlight the strength of the approach.

Enantioselective Allylboration of Acetylene: A Versatile Tool for the Stereodivergent Synthesis of Natural Products

Efficient catalytic methods that allow the use of simple and abundant chemical feedstocks for the preparation of synthetically versatile compounds are central to modern synthetic chemistry. Acetylene is a basic feedstock with a remarkable production over one million tons per year, although it is underutilized in the stereoselective synthesis of fine chemicals. Here we report a facile catalytic multicomponent reaction that allows for the enantio- and diastereoselective allylboration of acetylene gas. This process is catalyzed by a chiral copper catalyst, operates without specialized equipment or pressurization, and provides chiral skipped dienes bearing stereodefined and orthogonally functionalized olefins with excellent levels of chemo-, regio-, enantio- and diastereoselectivity. The combined stereochemical features and orthogonal functionalization make the products privileged structural scaffolds to access the complete set of stereoisomers of the chiral skipped diene core through simple enantio- and diastereodivergent pathways. The utility of the method is demonstrated with the enantioselective synthesis of three bioactive natural skipped diene products, namely (+)-Nyasol, (+)-Hinokiresinol and Phorbasin C, and other related synthetically relevant chiral molecules.

Functions and mechanisms of enzymes assembling lignans and norlignans

Lignans and norlignans are distributed throughout the plant kingdom and exhibit diverse chemical structures and biological properties that offer potential for therapeutic use. Originating from the phenylpropanoid biosynthesis pathway, their characteristic carbon architectures are formed through unique enzyme catalysis, featuring regio- and stereoselective C-C bond forming processes. Despite extensive research on these plant natural products, their biosynthetic pathways, and enzyme mechanisms remain enigmatic. This review highlights recent advancements in elucidating the functions and mechanisms of the biosynthetic enzymes responsible for constructing the distinct carbon frameworks of lignans and norlignans.

QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase

The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.

Unusual Enzymatic C-C Bond Formation and Cleavage Reactions during Natural Product Biosynthesis

Natural products from plants and microorganisms provide a valuable reservoir of pharmaceutical compounds. C-C bond formation and cleavage are crucial events during natural product biosynthesis, playing pivotal roles in generating diverse and intricate chemical structures that are essential for biological functions. This review summarizes our recent findings regarding biosynthetic enzymes that catalyze unconventional C-C bond formation and cleavage reactions during natural product biosynthesis.

Rare 7,9'-dinorlignans with neuroprotective activity from the roots of Lindera aggregata (Sims) Kosterm

Linderagatins C-F (1-4), the first examples of naturally occurring diaryltetrahydrofuran-type 7,9'-dinorlignans, were characterized from the roots of Lindera aggregata (Sims) Kosterm. The structures of these dinorlignans were elucidated by extensive spectroscopic analysis. The absolute configurations were determined based on calculated and experimental ECD data. A biosynthetic pathway for these dinorlignans was hypothetically proposed. Compounds 2 and 3 showed significant neuroprotective effects on erastin-induced ferroptosis in HT-22 cells with EC50 values of 23.4 and 21.8 μM, respectively.

Hot off the Press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as alscholarine A from Alstonia scholaris.