QM/MM free energy simulations of the reaction catalysed by (4S)-limonene synthase involving linalyl diphosphate (LPP) substrate

Chemical diversity in angiosperms - monoterpene synthases control complex reactions that provide the precursors for ecologically and commercially important monoterpenoids

Monoterpene synthases (MTSs) catalyze the first committed step in the biosynthesis of monoterpenoids, a class of specialized metabolites with particularly high chemical diversity in angiosperms. In addition to accomplishing a rate enhancement, these enzymes manage the formation and turnover of highly reactive carbocation intermediates formed from a prenyl diphosphate substrate. At each step along the reaction path, a cationic intermediate can be subject to cyclization, migration of a proton, hydride, or alkyl group, or quenching to terminate the sequence. However, enzymatic control of ligand folding, stabilization of specific intermediates, and defined quenching chemistry can maintain the specificity for forming a signature product. This review article will discuss our current understanding of how angiosperm MTSs control the reaction environment. Such knowledge allows inferences about the origin and regulation of chemical diversity, which is pertinent for appreciating the role of monoterpenoids in plant ecology but also for aiding commercial efforts that harness the accumulation of these specialized metabolites for the food, cosmetic, and pharmaceutical industries.

Regiodivergent biosynthesis of bridged bicyclononanes

Medicinal compounds from plants include bicyclo[3.3.1]nonane derivatives, the majority of which are polycyclic polyprenylated acylphloroglucinols (PPAPs). Prototype molecules are hyperforin, the antidepressant constituent of St. John's wort, and garcinol, a potential anticancer compound. Their complex structures have inspired innovative chemical syntheses, however, their biosynthesis in plants is still enigmatic. PPAPs are divided into two subclasses, named type A and B. Here we identify both types in Hypericum sampsonii plants and isolate two enzymes that regiodivergently convert a common precursor to pivotal type A and B products. Molecular modelling and substrate docking studies reveal inverted substrate binding modes in the two active site cavities. We identify amino acids that stabilize these alternative binding scenarios and use reciprocal mutagenesis to interconvert the enzymatic activities. Our studies elucidate the unique biochemistry that yields type A and B bicyclo[3.3.1]nonane cores in plants, thereby providing key building blocks for biotechnological efforts to sustainably produce these complex compounds for preclinical development.

Cyclization mechanism of monoterpenes catalyzed by monoterpene synthases in dipterocarpaceae

Monoterpenoids are typically present in the secretory tissues of higher plants, and their biosynthesis is catalyzed by the action of monoterpene synthases (MTSs). However, the knowledge about these enzymes is restricted in a few plant species. MTSs are responsible for the complex cyclization of monoterpene precursors, resulting in the production of diverse monoterpene products. These enzymatic reactions are considered exceptionally complex in nature. Therefore, it is crucial to understand the catalytic mechanism of MTSs to elucidate their ability to produce diverse or specific monoterpenoid products. In our study, we analyzed thirteen genomes of Dipterocarpaceae and identified 38 MTSs that generate a variety of monoterpene products. By focusing on four MTSs with different product spectra and analyzing the formation mechanism of acyclic, monocyclic and bicyclic products in MTSs, we observed that even a single amino acid mutation can change the specificity and diversity of MTS products, which is due to the synergistic effect between the shape of the active cavity and the stabilization of carbon-positive intermediates that the mutation changing. Notably, residues N340, I448, and phosphoric acid groups were found to be significant contributors to the stabilization of intermediate terpinyl and pinene cations. Alterations in these residues, either directly or indirectly, can impact the synthesis of single monoterpenes or their mixtures. By revealing the role of key residues in the catalytic process and establishing the interaction model between specific residues and complex monoterpenes in MTSs, it will be possible to reasonably design and engineer different catalytic activities into existing MTSs, laying a foundation for the artificial design and industrial application of MTSs.

Heterocyclic and Alkyne Terpenoids by Terpene Synthase-Mediated Biotransformation of Non-Natural Prenyl Diphosphates: Access to New Fragrances and Probes

Two terpene cyclases were used as biocatalytic tool, namely, limonene synthase from Cannabis sativa (CLS) and 5-epi-aristolochene synthase (TEAS) from Nicotiana tabacum. They showed significant substrate flexibility towards non-natural prenyl diphosphates to form novel terpenoids, including core oxa- and thia-heterocycles and alkyne-modified terpenoids. We elucidated the structures of five novel monoterpene-analogues and a known sesquiterpene-analogue. These results reflected the terpene synthases' ability and promiscuity to broaden the pool of terpenoids with structurally complex analogues. Docking studies highlight an on-off conversion of the unnatural substrates.

A Benchmark Study of Quantum Mechanics and Quantum Mechanics-Molecular Mechanics Methods for Carbocation Chemistry

Carbocations play key roles in classical organic reactions and have also been implicated in several enzyme families. A hallmark of carbocation chemistry is multitudes of competing reaction pathways, and to be able to distinguish between pathways with quantum chemical calculations, it is necessary to approach chemical accuracy for relative energies between carbocations. Here, we present an extensive study of the performance of selected density functional theory (DFT) methods in describing the thermochemistry and kinetics of carbocations and their corresponding neutral alkenes both in the gas-phase and within a hybrid quantum mechanics-molecular mechanics (QM/MM) framework. The density functionals are benchmarked against accurate ab initio methods such as CBS-QB3 and DLPNO-CCSD(T). Based on the findings in the gas-phase calculations of carbocations and alkenes, the best functionals are chosen and tested further for non-covalent interactions in model systems using QM and QM/MM methods. We compute the interaction energies between a model carbocation/alkane and model π, dipole, and hydrophobic systems using DFT and QM(DFT)/MM and compare with DLPNO-CCSD(T). These latter model systems are representative of side chains of amino acids such as phenylalanine/tyrosine, tryptophan, asparagine/glutamine, serine/threonine, methionine, and other hydrophobic groups. The Lennard-Jones parameters of the QM atoms in QM(DFT)/MM calculations are modified to obtain an optimal fit with the QM energies. Finally, a selected carbocation reaction is studied in the gas phase and in implicit chloroform solvent using QM and in explicit chloroform solvent using QM/MM and umbrella sampling simulations. This study highlights the highest accuracy possible with selected density functionals and QM/MM methods but also some limitations in using QM/MM methods for carbocation systems.

One- and Two-Proton Transfer Mechanisms Coexist in One Active Site

Acibenzolar-S-methyl (ASM) is one of the most successfully commercialized plant activators of the systemic acquired resistance (SAR). However, its activation (hydrolysis) mechanism catalyzed by the salicylic acid binding protein 2 (SABP2) remains elusive. The fundamental catalytic mechanism of the SABP2-catalyzed hydrolysis of the ASM had been investigated by extensive computational and experimental studies, including QM/MM simulations, charge transfer analysis, small-molecule synthesis, and biochemical assays. Here we report that the promiscuous SABP2 shows different catalytic mechanisms toward different substrates. To catalyze the ASM hydrolysis, the SABP2 uses a two-proton transfer mechanism, and the key intermediate is stabilized by the charge transfer effect; to catalyze the ethyl 1,2,3-benzothiadiazole-7-carboxylate (BTM, an ASM analogue) hydrolysis, the SABP2 applies the one-proton transfer mechanism, and the classic tetrahedral intermediate is stabilized by the electrostatic effect. The HPLC analyses of the SABP2 esterase activities toward the ASM and the BTM show comparable results with our computaional results, suggesting that the obtained computational mechanism insights are reasonable. The obtained mechanism is not only an important supplement to the theory of enzymes' catalytic promiscuity, but it also contributes a possible strategy for the design of next generation plant SAR activators.

Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations

In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and biomimetic synthetic routes to natural and unnatural terpenes.

Human Acetyl-CoA Carboxylase 1 Is an Isomerase: Carboxyl Transfer Is Activated by Catalytic Effect of Isomerization

Obesity and its related diseases such as cancer and diabetes are leading life-threatening issues in the modern world. Thus, new drugs toward obesity and obesity-caused diseases are highly desired. Human acetyl-CoA carboxylase 1 (hACC1) in charge of the rate-limiting step of the human fatty acid synthesis was recognized as an attractive target for rational drug design. The fundamental reaction mechanism and nature of the transition state of hACC1 remain unclear. In this study, combined quantum mechanics and molecular mechanics (QM/MM), molecular dynamics (MD), and free-energy simulations were performed to investigate the catalytic mechanism of the hACC1-catalyzed carboxyl-transfer reaction. Our computational results show a three-step mechanism for carboxyl transferase (CT)-catalyzed reaction, including isomerization of carboxybiotin, proton-transfer from acetyl-CoA to carboxybiotin, and carboxylation of acetyl-CoA enolate. Interestingly, isomerization of carboxybiotin is the rate-limiting step of the entire reaction pathway, indicating hACC1 has the catalytic effect of isomerization and thus might be an isomerase also. The activation free-energy barrier of carboxyl-transfer catalyzed by hACC1 was calculated to be 16.4 kcal/mol, in excellent agreement with the experimental result (16.7 kcal/mol). The obtained reaction mechanism together with the nature of the transition state provides helpful knowledge not only for future investigation of other ACCs but also for rational design of hACC1 inhibitors, such as TS analogue. The catalytic effect of hACC1 isomerization is discussed.

The catalytic mechanism of S-acyltransferases: acylation is triggered on by a loose transition state and deacylation is turned off by a tight transition state

The reaction of S-acyltransferase is characterized by a loose transition state.