Catalytic performances of engineered and artificial heme peroxygenases

doi:10.1016/S1872-2067(24)60206-8

Chinese Journal of Catalysis ›› 2025, Vol. 69: 35-51.DOI: 10.1016/S1872-2067(24)60206-8

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Catalytic performances of engineered and artificial heme peroxygenases

Yiping Jiang^a^,¹, Zaw Ko Latt^b^,¹, Zhiqi Cong^a^,^*()

^aKey Laboratory of Photoelectric Conversion and Utilization of Solar Energy, Qingdao New Energy Shandong Laboratory, CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
^bBiotechnology Research Department, Ministry of Education, Kyaukse 05151, Myanmar

Received:2024-09-29 Accepted:2024-12-02 Online:2025-02-18 Published:2025-02-10
Contact: *E-mail: congzq@qibebt.ac.cn (Z. Cong).
About author:Prof. Cong Zhiqi (Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences) received his Ph.D. degree in Organic Chemistry from Kumamoto University, Japan, in 2009. From 2009 to 2016, he engaged in scientific research at the Institute for Molecular Science in Japan and Nagoya University. Since 2016, he has been a full professor and group leader at the current institute. He is Qingdao Innovative Leading Talent (2018) and Taishan Scholar of Shandong Province (2024). His research focuses on protein engineering, enzyme catalysis, and synthetic biology. He has firstly proposed the concepts of dual-functional small molecule (DFSM) and H₂O₂ tunnel engineering, successfully converting P450 monooxygenases to peroxizymes with high catalytic efficiencies. He has published over 50 peer-reviewed papers and holds 8 authorized patents.
First author contact:
¹Contributed equally to this work.
Supported by:
National Key Research and Development Program of China(2023YFA0915500);National Natural Science Foundation of China(32371311);National Natural Science Foundation of China(32471325);National Natural Science Foundation of China(22207112);Taishan Scholars Program(tstp20240841);CAS PIFI program(2019PB0167);QIBEBT/SEI/QNESL(S202302)

Abstract

Abstract:

Heme peroxygenases exhibit remarkable catalytic versatility in facilitating a wide array of oxidative reactions under mild conditions, eliminating the need for coenzymes and intricate electron transport systems. This unique character underscores their essentiality and potential as promising tools in synthetic biology. Recent advancements in enzyme engineering have significantly enhanced the catalytic performance of both natural and artificial peroxygenases. Extensive engineering efforts have been directed towards unspecific peroxygenases and fatty acid peroxygenases, aiming to expand their substrate specificities, and enhance reaction selectivities, as well as increase enzyme stability. Furthermore, innovative strategies such as dual-functional small molecule-assisted systems and H₂O₂ tunnel engineering have been harnessed to transform P450 monooxygenases into highly efficient peroxygenases, capable of catalyzing reactions with a variety of unnatural substrates. This review consolidates the latest progress in the engineered and artificial heme peroxygenases, emphasizing their catalytic performances as potent biocatalysts for sustainable organic synthesis.

Key words: Peroxygenases, Hydrogen peroxide, Cytochrome P450 peroxygenases, Unspecific peroxygenases, Protein engineering

Yiping Jiang, Zaw Ko Latt, Zhiqi Cong. Catalytic performances of engineered and artificial heme peroxygenases[J]. Chinese Journal of Catalysis, 2025, 69: 35-51.

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Figures/Tables 21

Fig. 1. Simplified catalytic cycle of natural heme-dependent oxygenases.

Fig. 2. Active sites of UPO from) Agrocybe aegerita (PDB ID: 2YP1) (A and Marasmius rotula (PDB ID: 5FUJ) (B). The hydrogen bonds and measured distances (?) are drawn by dashed lines in yellow and black, respectively. The acid-base pairs and heme are shown as stick models in white and magenta, respectively.

Fig. 3. Calcitriol and typical 25-hydroxy-Grundmann's ketone generated by PaDa-I.

Fig. 4. Enantioenrichment of representative organoperoxides by PaDa-I.

Fig. 5. Halogenation and oxygenation modes of PaDa-I-H are fine-tuned by pH values.

Fig. 6. Peroxygenation of N-heterocycles using the lyophilized PaDa-I-H.

Fig. 7. Representative reactions catalyzed by PaDa-I derived mutants.

Fig. 8. Structural alignment of PaDa-I (PDB ID: 5OXU, colored in white) and Fett (PDB ID: 7PN6, colored in yellow). The heme cavity is narrowed by introducing a bulky leucine residue. The cavities are shown as surface models.

Fig. 9. Representative reactions catalyzed by engineered short UPOs.

Fig. 10. Active sites of P450SPα in complex with Palmitic acid (PDB ID: 3AWM) (A) and (R)-ibuprofen (PDB ID: 3VM4) (B). The hydrogen bonds and measured distances (?) are drawn by dashed lines in yellow and black, respectively. The substrate, decoy molecule, and heme are shown as stick models in green, yellow and magenta, respectively.

Fig. 11. Styrene oxidation catalyzed by P450SPα and P450BSβ with the assistance of decoy molecules.

Fig. 12. Representative reactions of catalytic selectivity modulated by P450BSβ mutants.

Fig. 13. Active sites of P450BSβ mutants in complex with Palmitic acid (PDB ID: 7WYG) (A) and Palmitoleic acid (PDB ID: 8HKD) (B). The hydrogen bonds and measured distances (?) are drawn by dashed lines in yellow and black, respectively. The substrate and heme are shown as stick models in green and magenta, respectively.

Fig. 14. Active site of CYP199A4 in complex with 4-methoxybenzoic acid (PDB ID: 7REH). The hydrogen bonds and measured distances (?) are drawn by dashed lines in yellow and black, respectively. The substrate and heme are shown as stick models in green and magenta, respectively.

Fig. 15. (A) The conceptual graph of DFSM-facilitated P450 peroxygenase. The DFSM is fixed at the specific site of P450 enzyme by the anchoring group, while the catalytic group is responsible for H2O2 activation. (B) The chemical structure of Im-C6-Phe. The anchoring and catalytic groups are labelled as green rectangle and magenta circle, respectively.

Fig. 16. The catalytic performance of (R)-enantioselective epoxidation of styrene and its derivatives.

Fig. 17. Typical demethylation reactions catalysed by P450BM3 mutants with the assistance of Im-C6-Phe/Im-C5-Phe.

Fig. 18. Typical hydroxylation reactions of alkanes (C3?C6) catalysed by P450BM3 mutants with the assistance of Im-C6-Phe.

Fig. 19. Representative long-term hydroxylation reactions of alkylbenzenes catalysed by P450BM3 with the addition of Im-C5-Phe.

Fig. 20. Active site of the P450BM3 mutants in complex with DFSMs. (A) Toluene (PDB ID: 7YDB); (B) ethylbenzene (PDB ID: 7YD9); (C) propylbenzene (PDB ID: 7YDD); (D) indane (PDB ID: 7YFT). DFSMs, heme and alkylbenzenes are shown as stick models in yellow, magenta, and cyan, respectively.

Fig. 21. The evolution of novel DFSMs and their catalytic performances. (A) The idea of evolving dipeptide based novel artificial cofactor. (B) Hydrogen-bonding networks and hydrophobic interactions between the enzyme and Im-C6-Phe-Phe. The hydrophobic binding pocket is denoted as stick and surface models colored in white. The hydrogen bonds and measured distances are shown by dashed lines in yellow and black, respectively. (C) The chemical structures of novel DFSMs. Each DFSM contains a catalytic base (imidazole, amine or pyridine) and a dipeptide-liked anchoring group (R1, R2: side chain of natural or unnatural amino acid). Binding affinity and reaction performance of novel DFSMs. (D) Binding affinity of representative novel DFSMs. (E) Concentration gradient experiments of representative DFSMs for styrene epoxidation reaction.

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Catalytic performances of engineered and artificial heme peroxygenases

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