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Ashraf RA, Bureik M, Marchisio MA. Design and engineering of logic genetic-enzymatic gates based on the activity of the human CYP2C9 enzyme in permeabilized Saccharomyces cerevisiae cells. Synth Syst Biotechnol 2024; 9:406-415. [PMID: 38590712 PMCID: PMC10999488 DOI: 10.1016/j.synbio.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/10/2024] [Accepted: 03/17/2024] [Indexed: 04/10/2024] Open
Abstract
Gene circuits allow cells to carry out complex functions such as the precise regulation of biological metabolic processes. In this study, we combined, in the yeast S. cerevisiae, genetic regulatory elements with the enzymatic reactions of the human CYP2C9 and its redox partner CPR on luciferin substrates and diclofenac. S. cerevisiae cells were permeabilized and used as enzyme bags in order to host these metabolic reactions. We engineered three different (genetic)-enzymatic basic Boolean gates (YES, NOT, and N-IMPLY). In the YES and N-IMPLY gates, human CYP2C9 was expressed under the galactose-inducible GAL1 promoter. The carbon monoxide releasing molecule CORM-401 was used as an input in the NOT and N-IMPLY gates to impair CYP2C9 activity through inhibition of the Fe+2- heme prosthetic group in the active site of the human enzyme. Our study provides a new approach in designing synthetic bio-circuits and optimizing experimental conditions to favor the heterologous expression of human drug metabolic enzymes over their endogenous counterparts. This new approach will help study precise metabolic attributes of human P450s.
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Affiliation(s)
- Rana Azeem Ashraf
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, Tianjin, China
| | - Matthias Bureik
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, Tianjin, China
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Iori S, D'Onofrio C, Laham-Karam N, Mushimiyimana I, Lucatello L, Montanucci L, Lopparelli RM, Bonsembiante F, Capolongo F, Pauletto M, Dacasto M, Giantin M. Generation and characterization of cytochrome P450 3A74 CRISPR/Cas9 knockout bovine foetal hepatocyte cell line (BFH12). Biochem Pharmacol 2024; 224:116231. [PMID: 38648904 DOI: 10.1016/j.bcp.2024.116231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/04/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
In human, the cytochrome P450 3A (CYP3A) subfamily of drug-metabolizing enzymes (DMEs) is responsible for a significant number of phase I reactions, with the CYP3A4 isoform superintending the hepatic and intestinal metabolism of diverse endobiotic and xenobiotic compounds. The CYP3A4-dependent bioactivation of chemicals may result in hepatotoxicity and trigger carcinogenesis. In cattle, four CYP3A genes (CYP3A74, CYP3A76, CYP3A28 and CYP3A24) have been identified. Despite cattle being daily exposed to xenobiotics (e.g., mycotoxins, food additives, drugs and pesticides), the existing knowledge about the contribution of CYP3A in bovine hepatic metabolism is still incomplete. Nowadays, CRISPR/Cas9 mediated knockout (KO) is a valuable method to generate in vivo and in vitro models for studying the metabolism of xenobiotics. In the present study, we successfully performed CRISPR/Cas9-mediated KO of bovine CYP3A74, human CYP3A4-like, in a bovine foetal hepatocyte cell line (BFH12). After clonal expansion and selection, CYP3A74 ablation was confirmed at the DNA, mRNA, and protein level. The subsequent characterization of the CYP3A74 KO clone highlighted significant transcriptomic changes (RNA-sequencing) associated with the regulation of cell cycle and proliferation, immune and inflammatory response, as well as metabolic processes. Overall, this study successfully developed a new CYP3A74 KO in vitro model by using CRISPR/Cas9 technology, which represents a novel resource for xenobiotic metabolism studies in cattle. Furthermore, the transcriptomic analysis suggests a key role of CYP3A74 in bovine hepatocyte cell cycle regulation and metabolic homeostasis.
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Affiliation(s)
- Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Caterina D'Onofrio
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Nihay Laham-Karam
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211 Kuopio, Finland
| | - Isidore Mushimiyimana
- University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Neulaniementie 2, 70211 Kuopio, Finland
| | - Lorena Lucatello
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Ludovica Montanucci
- Department of Neurology, University of Texas Health Science Center, 6431 Fannin Street, Houston, TX, OH 44106, USA
| | - Rosa Maria Lopparelli
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Federico Bonsembiante
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Francesca Capolongo
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell'Università 16, Legnaro, 35020 Padua, Italy.
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Zhao J, Zhang X, Wang Y, Huang H, Sharma S, Sharma SS, Wolf CA, Liu S, Wolber G, Sorensen EJ, Bureik M. Exploring the Chemical Space of Proluciferins as Probe Substrates for Human Cytochrome P450 Enzymes. Appl Biochem Biotechnol 2023; 195:1042-1058. [PMID: 36287330 DOI: 10.1007/s12010-022-04184-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
We report the synthesis of 21 new proluciferin compounds that bear a small aliphatic ether group connected to the 6' hydroxy function of firefly luciferin and either contain an acid or methyl ester function at the dihydrothiazole ring. Each of these compounds was found to be a substrate for some members of the human CYP1 and CYP3 families; a total of 92 new enzyme-substrate pairs were identified. In a screen of the whole human P450 complement (CYPome) with three selected proluciferin acid substrates, another 13 enzyme-substrate pairs were detected, which involve enzymes belonging to the CYP2, CYP4, CYP7, CYP21, and CYP27 families. All in all, we identified new probe substrates for members of seven out of 18 human CYP families.
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Affiliation(s)
- Jie Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Xue Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yueyin Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Huimin Huang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Shishir Sharma
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | | | - Clemens Alexander Wolf
- Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Institute of Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Sijie Liu
- Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Institute of Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Institute of Pharmacy, Freie Universität Berlin, 14195, Berlin, Germany
| | - Erik J Sorensen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Matthias Bureik
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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Sharma SS, Sharma S, Zhao J, Bureik M. Mutual Influence of Human Cytochrome P450 Enzymes and UDP-Glucuronosyltransferases on Their Respective Activities in Recombinant Fission Yeast. Biomedicines 2023; 11:biomedicines11020281. [PMID: 36830817 PMCID: PMC9953201 DOI: 10.3390/biomedicines11020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Cytochromes P450 (CYPs) and UDP-glucuronosyltransferases (UGTs) are the most important human drug metabolizing enzymes, but their mutual interactions are poorly understood. In this study, we recombinantly co-expressed of each one of the 19 human members of the UGT families 1 and 2 with either CYP2C9, CYP2D6, or CYP4Z1 in fission yeast. Using these strains, we monitored a total of 72 interactions: 57 cases where we tested the influence of UGT co-expression on CYP activity and 15 cases of the opposite approach. In the majority of cases (88%), UGT co-expression had a statistically significant (p < 0.05) effect on P450 activity (58% positive and 30% negative). Strong changes were observed in nine cases, including one case with an activity increase by a factor of 23 (CYP2C9 activity in the presence of UGT2A3) but also four cases with a complete loss of activity. When monitoring the effect of CYP co-expression on the activity of five UGTs, activity changes were generally not so pronounced and, if observed, always detrimental. UGT2B7 activity was not influenced by CYP co-expression, while the other UGTs were affected to varying degrees. These data suggest the notion that mutual influence of CYPs and UGTs on each other's activity is a widespread phenomenon.
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Zhao J, Machalz D, Liu S, Wolf CA, Wolber G, Parr MK, Bureik M. Metabolism of the antipsychotic drug olanzapine by CYP3A43. Xenobiotica 2022; 52:413-425. [PMID: 35582917 DOI: 10.1080/00498254.2022.2078751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
1. Olanzapine is an atypical antipsychotic primarily used to treat schizophrenia and bipolar disorder. An intronic single nucleotide polymorphism (SNP) that highly significantly predicts increased olanzapine clearance (rs472660) was previously identified in the CYP3A43 gene, which encodes a cytochrome P450 enzyme. But until now there was no experimental evidence for the metabolism of olanzapine by the CYP3A43 enzyme.2. In the present study we provide this evidence, together with a thorough analysis of olanzapine metabolism by all human CYP3A enzymes. We also rationalize our findings by molecular docking experiments. Moreover, we describe the activities of several CYP3A43 mutants and present the first enzymatic activity data for the CYP3A43.3 variant; with respect to prostate cancer, this polymorphic variant is associated with both increased risk and increased mortality. The catalytic properties of the wild type enzyme and the tumor mutant were analyzed by molecular dynamics simulations, which fit very well with the observed experimental results.3. Our finding suggests that the SNP rs472660 likely causes an increased CYP3A43 expression level and demonstrate that, depending on the substrate under study, the tumor mutant CYP3A43.3 can have increased activity in comparison to the wild type enzyme CYP3A43.1.
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Affiliation(s)
- Jie Zhao
- Tianjin University, School of Pharmaceutical Science and Technology, 92 Weijin Road, Nankai District, Tianjin, 300072, China.,Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Pharmaceutical Analysis), Koenigin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - David Machalz
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Koenigin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - Sijie Liu
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Koenigin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - Clemens Alexander Wolf
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Koenigin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - Gerhard Wolber
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Koenigin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - Maria Kristina Parr
- Freie Universitaet Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry (Pharmaceutical Analysis), Koenigin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - Matthias Bureik
- Tianjin University, School of Pharmaceutical Science and Technology, 92 Weijin Road, Nankai District, Tianjin, 300072, China
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