Catalytic promiscuity, as a modern and imperfect understanding concept in enzyme catalysis community, is prevailing in plant-derived sesquiterpene cyclases (FPPC) and highly related to the chemical diversity of sesquiterpenoid natural products. Both the Nicotiana tabacum 5-epi-aristolochene synthase (TEAS) and Aspergillus terreus aristolochene synthase (ATAS) belong to FPPC, involve the same reaction pathway, and yield their ultimate main product (aristolochene) with different stereochemistries. The catalytic promiscuity of TEAS and fidelity of ATAS have been observed in previous experimental studies, but the detailed catalytic mechanism is still not clear. Herein, by employing the quantum classical multiscale molecular dynamics simulations and site-directed mutagenesis experiments, the complete enzyme catalytic pathways from the substrate to aristolochene and various side products (in TEAS) are investigated and the important mechanism insights are included: (1) the PPi moiety (diphosphate group, released from the substrate) would further act as the general acid/base in both TEAS and ATAS enzyme catalysis, which likely plays a general role in FPPC. (2) The Asp444−Tyr520 dyad acts as an additional general acid/base residue pair to increase promiscuity in TEAS. (3) The enriched aromatic residues are essential for the catalytic fidelity of ATAS. Finally, we further discuss the three critical chemical control factors which are proposed to be responsible for the catalytic promiscuity and fidelity in most FPPC, that is, substrate folding mode, intermediate flexibility, and key residue, owing to the more or less plasticity of the active pocket in various FPPC.

The TEAS, one of the sesquiterpene cyclases (FPPC), shows enzyme promiscuity that can effectively catalyze both the natural substrate (trans,trans)-FPP and the non-native (cis,trans)-FPP substrate to generate diverse products/byproducts. So far, the catalytic mechanism of the promiscuous substrate is still unclear. In this work, QM(DFT)/MM MD simulations were employed to illuminate the predominant 1,6-closure pathway reaction mechanism for the non-native substrate (cis,trans)-FPP, while the 1,10-closure pathway is the major reaction for the native substrate. It has been revealed that the catalytic promiscuity of TEAS is mostly attributable to the notable conformational dynamics of the branching intermediate bisabolyl cation. The comparative studies to FSTS (another widely studied FPPC) further indicate that the intrinsic intermediate flexibility in TEAS is highly correlated to the plasticity of the enzyme active site pocket contour. Finally, we propose a general picture for controlling the promiscuity and fidelity in FPPC catalysis, including substrate folding, intermediate flexibility and key residues.

Enzymatic plasticity, as a modern term referring to the functional conversion of an enzyme, is significant for enzymatic activity redesign. The bacterial diterpene cyclase CotB2 is a typical plastic enzyme by which its native form precisely conducts a chemical reaction while its mutants diversify the catalytic functions drastically. Many efforts have been made to disclose the mysteries of CotB2 enzyme catalysis. However, the catalytic details and regulatory mechanism toward the precise chemo- and stereoselectivity are still elusive. In this work, multiscale simulations are employed to illuminate the biocyclization mechanisms of the linear substrate into the final product cyclooctat-9-en-7-ol with a 5–8–5 fused ring scaffold, and the derailment products arising from the premature quenching of reactive carbocation intermediates are also discussed. The two major regulatory factors, local electrostatic stabilization effects from aromatic residues or polar residue in pocket and global features of active site including pocket-contour and pocket-hydrophobicity, are responsible for the enzymatic plasticity of CotB2. Further comparative studies of representative Euphorbiaceae and fungal diterpene cyclase (RcCS and PaFS) show a correlation between pocket plasticity and product diversity, which inspires a tentative enzyme product prediction and the rational diterpene cyclases’ reengineering in the future.

Natural products are the major resource of drug discovery, and terpenoids represent the largest family of natural products. Terpenome is defined as all terpenoid-like and terpenoidderived natural compounds, including the terpenoids, steroids, and their derivatives. Herein, aiming to navigate the chemical and biological space of terpenome, the first comprehensive database dedicated to terpenome research has been developed by collecting over 110 000 terpenome molecules from various resources, distributed in 14 351 species, belonging to 1109 families, and showing activity against 1366 biological targets. Much of the publically available information or computationally predicted properties for each terpenome molecule is annotated and integrated into TeroKit (http://terokit.qmclab.com/), serving as free Web server for academic use. Moreover, several practical toolkits, such as target profiling and conformer generation modules, are also implemented to facilitate the drug discovery of terpenome.

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An unprecedented protocol for the efficient and highly chemoselective alkylation of unprotected arylamines using alcohols catalyzed by B­(C6F5)3 has been developed. The reaction gives N-alkylated products and ortho C-alkylated products in different solvents in good chemoselectivities and yields. Control experiments and DFT calculations indicated that the borane underwent alcohol/arylamine exchange to ensure catalytic activity, and a possible mechanism involving a carbocation is proposed.

Tyrosinase is a key enzyme in melanin biosynthesis, and is also involved in the enzymatic browning of plant-derived foods. Tyrosinase inhibitors are very important in medicine, cosmetics and agriculture. In order to develop more active and safer tyrosinase inhibitors, an efficient approach is to modify natural product scaffolds. In this work, two series of novel tyrosinase inhibitors were designed and synthesized by the esterification of cinnamic acid derivatives with paeonol or thymol. Their inhibitory effects on mushroom tyrosinase were evaluated. Most of these compounds (IC: 2.0 to 163.8 μM) are found to be better inhibitors than their parent compounds (IC: 121.4 to 5925.0 μM). Among them, ()-2-acetyl-5-methoxyphenyl-3-(4-hydroxyphenyl)acrylate (), ()-2-acetyl-5-methoxyphenyl-3-(4-methoxyphenyl)acrylate () and ()-2-isopropyl-5-methylphenyl-3-(4-hydroxyphenyl)acrylate () showed strong inhibitory activities; the IC values were 2.0 μM, 8.3 μM and 10.6 μM, respectively, compared to the positive control, kojic acid (IC: 32.2 μM). Analysis of the inhibition mechanism of , and demonstrated that their inhibitory effects on tyrosinase are reversible. The inhibition kinetics, analyzed by Lineweaver-Burk plots, revealed that acts as a non-competitive inhibitor while and are mixed-type inhibitors. Furthermore, docking experiments were carried out to study the interactions between and mushroom tyrosinase.

Terpenoids represent the largest family of natural products (NPs) with dramatically chemical and structural diversity, which makes terpenoids the important compound resources of drug discovery. However, comprehensive understanding on the structure− function features for terpenoid NPs is limited. In this work, we have systematically explored the chemical and biological space of terpenoid NPs, including their distribution, physicochemical properties, scaffold features, and functional applications, by utilizing various cheminformatics and bioinformatics approaches. We have not only confirmed that terpenoid NPs have good drug-likeness and great potential for drug discovery but, more importantly, illuminated the uniqueness of cyclic scaffold diversity in different species (plants, fungi, bacteria, and animals) and the specificity of biological function for the dominant fused-ring scaffolds of terpenoids. The present work supplies a valuable reference for identifying the new structure and unknown function of terpenoid NPs.