Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign

Regioselective aromatic O-demethylation with an artificial P450BM3/sugar alcohol oxidase peroxygenase system

The enzymatic demethylation of aromatic compounds presents a major challenge in the valorization of lignin. The main goal was to develop an efficient artificial peroxygenase system combining engineered P450BM3 with AldO (sugar alcohol oxidase) and DFSM (dual function small molecule) for the regioselective O-demethylation of lignin-derived aromatic ethers. P450BM3 serves as a versatile biocatalyst, and its engineered variants demonstrate expanded substrate promiscuity toward non-native substrates. AldO, served as the H2O2 in situ generation system. The DFSM, a rationally designed catalytic auxiliary, facilitates precise control of enzymatic reactions and enhances the efficiency of O-demethylation. We hypothesize that by combining P450BM3 with AldO and DFSM, we can better control the generation of H2O2 and direct the enzymatic system toward efficient O-demethylation. The engineered P450BM3 F87A/V78A/T268D/A328F mutant achieved a TON of 1895 ± 4 for guaiacol, more than double that of the native P450BM3/H2O2 system (TON = 872 ± 7). Moreover, the F87A/T268D mutant efficiently catalyzed double-demethylation of syringol, achieving the highest turnover number (TON) of 483 ± 7. This DFSM-assisted P450BM3/AldO system represents a significant advancement in the biocatalytic degradation of lignin and offers a cost-effective and scalable alternative to traditional NADPH-dependent P450 monooxygenases. Our findings open new pathways for sustainable biotechnological applications in lignin valorization and aromatic compound catabolism.

Engineering Regioselectivity of P450 BM3 Enables the Biosynthesis of Murideoxycholic Acid by 6β-Hydroxylation of Lithocholic Acid

Murideoxycholic acid (MDCA), as a significant secondary bile acid derived from the metabolism of α/β-muricholic acid in rodents, is an important component in maintaining the bile acid homeostasis. However, the biosynthesis of MDCA remains a challenging task. Here, we present the development of cytochrome P450 monooxygenase CYP102A1 (P450 BM3) from Bacillus megaterium, employing semi-rational protein engineering technique. Following three rounds of mutagenesis, a triple variant (T260G/G328A/L82V) has been discovered that proficiently catalyzes the 6β-hydroxylation of lithocholic acid (LCA), thereby generating MDCA with an impressive 8.5-fold increase in yield compared to the template P450 BM3 mutant. The MDCA selectivity has been also promoted from 62.0% to 96.3%. This biocatalyst introduces a novel approach for the biosynthesis of MDCA from LCA. Furthermore, molecular docking and dynamics simulations have been employed to unravel the molecular mechanisms underlying the enhanced LCA conversion and MDCA selectivity.

A General Method to Screen Nanobodies for Cytochrome P450 Enzymes from a Yeast Surface Display Library

The availability of yeast surface display nanobody (Nb) libraries offers a convenient way to acquire antigen-specific nanobodies that may be useful for protein structure-function studies and/or therapeutic applications, complementary to the conventional method of acquiring nanobodies through immunization in camelids. In this study, we developed a general approach to select nanobodies for cytochrome P450 enzymes from a highly diverse yeast display library. We tested our method on three P450 enzymes including CYP102A1, neuronal nitric oxide synthase (nNOS), and the complex of CYP2B4:POR, using a novel streamlined approach where biotinylated P450s were bound to fluorescent-labeled streptavidin for Nb screening. The Nb-antigen binders were selectively enriched using magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS). After two rounds of MACS, the population of positive binders was enriched by >5-fold compared to the naïve library. The subsequent FACS selection, with a gating of 0.1%, identified 634, 270, and 215 positive binders for CYP102A1, nNOS, and CYP2B4:POR, respectively. The positive binders for CYP102A1 were further triaged based on EC50 determined at various antigen concentrations. DNA sequencing of the top 30 binders of CYP102A1 resulted in 26 unique clones, 8 of which were selected for over-expression and characterization. They were found to inhibit CYP102A1-catalyzed oxidation of omeprazole with IC50 values in the range of 0.16-2.8 µM. These results validate our approach and may be applied to other protein targets for the effective selection of specific nanobodies.

Evolving ω-amine transaminase AtATA guided by substrate-enzyme binding free energy for enhancing activity and stability against non-natural substrates

In the field of chiral amine synthesis, ω-amine transaminase (ω-ATA) is one of the most established enzymes capable of asymmetric amination under optimal conditions. However, the applicability of ω-ATA toward more non-natural complex molecules remains limited due to its low transamination activity, thermostability, and narrow substrate scope. Here, by employing a combined approach of computational virtual screening strategy and combinatorial active-site saturation test/iterative saturation mutagenesis strategy, we have constructed the best variant M14C3-V5 (M14C3-V62A-V116S-E117I-L118I-V147F) with improved ω-ATA from Aspergillus terreus (AtATA) activity and thermostability toward non-natural substrate 1-acetylnaphthalene, which is the ketone precursor for producing the intermediate (R)-(+)-1-(1-naphthyl)ethylamine [(R)-NEA] of cinacalcet hydrochloride, showing activity enhancement of up to 3.4-fold compared to parent enzyme M14C3 (AtATA-F115L-M150C-H210N-M280C-V149A-L182F-L187F). The computational tools YASARA, Discovery Studio, Amber, and FoldX were applied for predicting mutation hotspots based on substrate-enzyme binding free energies and to show the possible mechanism with features related to AtATA structure, catalytic activity, and stability in silico analyses. M14C3-V5 achieved 71.8% conversion toward 50 mM 1-acetylnaphthalene in a 50 mL preparative-scale reaction for preparing (R)-NEA. Moreover, M14C3-V5 expanded the substrate scope toward aromatic ketone compounds. The generated virtual screening strategy based on the changes in binding free energies has successfully predicted the AtATA activity toward 1-acetylnaphthalene and related substrates. Together with experimental data, these approaches can serve as a gateway to explore desirable performances, expand enzyme-substrate scope, and accelerate biocatalysis.IMPORTANCEChiral amine is a crucial compound with many valuable applications. Their asymmetric synthesis employing ω-amine transaminases (ω-ATAs) is considered an attractive method. However, most ω-ATAs exhibit low activity and stability toward various non-natural substrates, which limits their industrial application. In this work, protein engineering strategy and computer-aided design are performed to evolve the activity and stability of ω-ATA from Aspergillus terreus toward non-natural substrates. After five rounds of mutations, the best variant, M14C3-V5, is obtained, showing better catalytic efficiency toward 1-acetylnaphthalene and higher thermostability than the original enzyme, M14C3. The robust combinational variant acquired displayed significant application value for pushing the asymmetric synthesis of aromatic chiral amines to a higher level.

The Impact of Inorganic Systems and Photoactive Metal Compounds on Cytochrome P450 Enzymes and Metabolism: From Induction to Inhibition

While cytochrome P450 (CYP; P450) enzymes are commonly associated with the metabolism of organic xenobiotics and drugs or the biosynthesis of organic signaling molecules, they are also impacted by a variety of inorganic species. Metallic nanoparticles, clusters, ions, and complexes can alter CYP expression, modify enzyme interactions with reductase partners, and serve as direct inhibitors. This commonly overlooked topic is reviewed here, with an emphasis on understanding the structural and physiochemical basis for these interactions. Intriguingly, while both organometallic and coordination compounds can act as potent CYP inhibitors, there is little evidence for the metabolism of inorganic compounds by CYPs, suggesting a potential alternative approach to evading issues associated with rapid modification and elimination of medically useful compounds.

Production of Mono-Hydroxylated Derivatives of Terpinen-4-ol by Bacterial CYP102A1 Enzymes

CYP102A1 from Bacillus megaterium is an important enzyme in biotechnology, because engineered CYP102A1 enzymes can react with diverse substrates and produce human cytochrome P450-like metabolites. Therefore, CYP102A1 can be applied to drug metabolite production. Terpinen-4-ol is a cyclic monoterpene and the primary component of essential tea tree oil. Terpinen-4-ol was known for therapeutic effects, including antibacterial, antifungal, antiviral, and anti-inflammatory. Because terpenes are natural compounds, examining novel terpenes and investigating the therapeutic effects of terpenes represent responses to social demands for eco-friendly compounds. In this study, we investigated the catalytic activity of engineered CYP102A1 on terpinen-4-ol. Among CYP102A1 mutants tested here, the R47L/F81I/F87V/E143G/L188Q/N213S/E267V mutant showed the highest activity to terpinen-4-ol. Two major metabolites of terpinen-4-ol were generated by engineered CYP102A1. Characterization of major metabolites was confirmed by liquid chromatography-mass spectrometry (LC-MS), gas chromatography-MS, and nuclear magnetic resonance spectroscopy (NMR). Based on the LC-MS results, the difference in mass-to-charge ratio of an ion (m/z) between terpinen-4-ol and its major metabolites was 16. One major metabolite was defined as 1,4-dihydroxy-p-menth-2-ene by NMR. Given these results, we speculate that another major metabolite is also a mono-hydroxylated product. Taken together, we suggest that CYP102A1 can be applied to make novel terpene derivatives.