Multiscale Simulations on the Catalytic Plasticity of CYP76AH1

QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis

Natural products and their derivatives are widely used across various industries, particularly pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing and meeting the growing need for diverse natural products. Natural enzymes, on the other hand, often exhibit unsatisfactory catalytic characteristics and necessitate further enzyme engineering modifications. QM/MM, as a powerful and extensively used computational tool in the field of enzyme catalysis, has been increasingly applied in rational enzyme engineering over the past decade. In this review, we summarize recent advances in QM/MM computational investigation on enzyme catalysis and enzyme engineering for natural product biosynthesis. The challenges and perspectives for future QM/MM applications aided enzyme engineering in natural product biosynthesis will also be discussed.

Tandemly duplicated CYP82Ds catalyze 14-hydroxylation in triptolide biosynthesis and precursor production in Saccharomyces cerevisiae

Triptolide is a valuable multipotent antitumor diterpenoid in Tripterygium wilfordii, and its C-14 hydroxyl group is often selected for modification to enhance both the bioavailability and antitumor efficacy. However, the mechanism for 14-hydroxylation formation remains unknown. Here, we discover 133 kb of tandem duplicated CYP82Ds encoding 11 genes on chromosome 12 and characterize CYP82D274 and CYP82D263 as 14-hydroxylases that catalyze the metabolic grid in triptolide biosynthesis. The two CYP82Ds catalyze the aromatization of miltiradiene, which has been repeatedly reported to be a spontaneous process. In vivo assays and evaluations of the kinetic parameters of CYP82Ds indicate the most significant affinity to dehydroabietic acid among multiple intermediates. The precursor 14-hydroxy-dehydroabietic acid is successfully produced by engineered Saccharomyces cerevisiae. Our study provides genetic elements for further elucidation of the downstream biosynthetic pathways and heterologous production of triptolide and of the currently intractable biosynthesis of other 14-hydroxyl labdane-type secondary metabolites.

Cytochrome P450s in plant terpenoid biosynthesis: discovery, characterization and metabolic engineering

As the largest family of natural products, terpenoids play valuable roles in medicine, agriculture, cosmetics and food. However, the traditional methods that rely on direct extraction from the original plants not only produce low yields, but also result in waste of resources, and are not applicable at all to endangered species. Modern heterologous biosynthesis is considered a promising, efficient, and sustainable production method, but it relies on the premise of a complete analysis of the biosynthetic pathway of terpenoids, especially the functionalization processes involving downstream cytochrome P450s. In this review, we systematically introduce the biotech approaches used to discover and characterize plant terpenoid-related P450s in recent years. In addition, we propose corresponding metabolic engineering approaches to increase the effective expression of P450 and improve the yield of terpenoids, and also elaborate on metabolic engineering strategies and examples of heterologous biosynthesis of terpenoids in Saccharomyces cerevisiae and plant hosts. Finally, we provide perspectives for the biotech approaches to be developed for future research on terpenoid-related P450.

Molecular Insights into the Heterotropic Allosteric Mechanism in Cytochrome P450 3A4-Mediated Midazolam Metabolism

Cytochrome P450 3A4 (CYP3A4) is the main P450 enzyme for drug metabolism and drug-drug interactions (DDIs), as it is involved in the metabolic process of approximately 50% of drugs. A detailed mechanistic elucidation of DDIs mediated by CYP3A4 is commonly believed to be critical for drug optimization and rational use. Here, two typical probes, midazolam (MDZ, substrate) and testosterone (TST, allosteric effector), are used to investigate the molecular mechanism of CYP3A4-mediated heterotropic allosteric interactions, through conventional molecular dynamics (cMD) and well-tempered metadynamics (WT-MTD) simulations. Distance monitoring shows that TST can stably bind in two potential peripheral sites (Site 1 and Site 2) of CYP3A4. The binding of TST at these two sites can induce conformational changes in CYP3A4 flexible loops on the basis of conformational analysis, thereby promoting the transition of the MDZ binding mode and affecting the ratio of MDZ metabolites. According to the results of the residue interaction network, multiple allosteric communication pathways are identified that can provide vivid and applicable insights into the heterotropic allostery of TST on MDZ metabolism. Comparing the regulatory effects and the communication pathways, the allosteric effect caused by TST binding in Site 2 seems to be more pronounced than in Site 1. Our findings could provide a deeper understanding of CYP3A4-mediated heterotropic allostery at the atomic level and would be helpful for rational drug use as well as the design of new allosteric modulators.

Chemotaxonomic investigation of plant terpenoids with an established database (TeroMOL)

Terpenoids constitute the biggest class of plant-derived natural products with diverse chemical structures and extensive biological activities. Interpreting enzyme functions and mining new structures of terpenoids could be inspired by the cheminformatic and chemotaxonomic analysis, whereas it is hampered by the incompleteness of available data for terpenoids. Here a dedicated terpenoids database, TeroMOL, is developed to collect more than 170 000 terpenoids and their derivatives annotated with reported biological sources, along with a user-friendly and freely accessible webserver to visualise and analyse the terpenoids skeletons and organism sources. The quantitative distributions as well as the qualitative trends between terpenoid skeletons and organism sources in plant kingdom are revealed from a chemotaxonomic view, while no comparisons are attempted due to the inherent data biases. Nevertheless, the terpenoid chemomarkers in several organisms are discussed based on the available data with highly enriched and exclusive carbon skeletons. We believe that the TeroMOL database and its accessory computational tools will be very promising for exploring the chemical space and biological sources of terpenoids, and assisting the terpenoid research community in the future.