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Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
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Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
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2
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Gasteazoro F, Catucci G, Barbieri L, De Angelis M, Dalla Costa A, Sadeghi SJ, Gilardi G, Valetti F. Cascade reactions with two non-physiological partners for NAD(P)H regeneration via renewable hydrogen. Biotechnol J 2024; 19:e2300567. [PMID: 38581100 DOI: 10.1002/biot.202300567] [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: 10/20/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/08/2024]
Abstract
An attractive application of hydrogenases, combined with the availability of cheap and renewable hydrogen (i.e., from solar and wind powered electrolysis or from recycled wastes), is the production of high-value electron-rich intermediates such as reduced nicotinamide adenine dinucleotides. Here, the capability of a very robust and oxygen-resilient [FeFe]-hydrogenase (CbA5H) from Clostridium beijerinckii SM10, previously identified in our group, combined with a reductase (BMR) from Bacillus megaterium (now reclassified as Priestia megaterium) was tested. The system shows a good stability and it was demonstrated to reach up to 28 ± 2 nmol NADPH regenerated s-1 mg of hydrogenase-1 (i.e., 1.68 ± 0.12 U mg-1, TOF: 126 ± 9 min-1) and 0.46 ± 0.04 nmol NADH regenerated s-1 mg of hydrogenase-1 (i.e., 0.028 ± 0.002 U mg-1, TOF: 2.1 ± 0.2 min-1), meaning up to 74 mg of NADPH and 1.23 mg of NADH produced per hour by a system involving 1 mg of CbA5H. The TOF is comparable with similar systems based on hydrogen as regenerating molecule for NADPH, but the system is first of its kind as for the [FeFe]-hydrogenase and the non-physiological partners used. As a proof of concept a cascade reaction involving CbA5H, BMR and a mutant BVMO from Acinetobacter radioresistens able to oxidize indole is presented. The data show how the cascade can be exploited for indigo production and multiple reaction cycles can be sustained using the regenerated NADPH.
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Affiliation(s)
- Francisco Gasteazoro
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- CICATA Unidad Morelos, Instituto Politécnico Nacional, Mexico D. F., Mexico
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Lisa Barbieri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- University School for Advanced Studies IUSS Pavia, Pavia, Italy
| | - Melissa De Angelis
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | | | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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3
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Mokkawes T, De Visser T, Cao Y, De Visser SP. Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes. Molecules 2023; 28:6961. [PMID: 37836804 PMCID: PMC10574541 DOI: 10.3390/molecules28196961] [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: 08/28/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.
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Affiliation(s)
| | | | | | - Sam P. De Visser
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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4
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Huang X, Sun Y, Osawa Y, Chen YE, Zhang H. Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign. J Biol Chem 2023; 299:105050. [PMID: 37451479 PMCID: PMC10413352 DOI: 10.1016/j.jbc.2023.105050] [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: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/18/2023] Open
Abstract
Cytochrome P450 CYP102A1 is a prototypic biocatalyst that has great potential in chemical synthesis, drug discovery, and biotechnology. CYP102A1 variants engineered by directed evolution and/or rational design are capable of catalyzing the oxidation of a wide range of organic compounds. However, it is difficult to foresee the outcome of engineering CYP102A1 for a compound of interest. Here, we introduce UniDesign as a computational framework for enzyme design and engineering. We tested UniDesign by redesigning CYP102A1 for stereoselective metabolism of omeprazole (OMP), a proton pump inhibitor, starting from an active but nonstereoselective triple mutant (TM: A82F/F87V/L188Q). To shift stereoselectivity toward (R)-OMP, we computationally scanned three active site positions (75, 264, and 328) for mutations that would stabilize the binding of the transition state of (R)-OMP while destabilizing that of (S)-OMP and picked three variants, namely UD1 (TM/L75I), UD2 (TM/A264G), and UD3 (TM/A328V), for experimentation, based on computed energy scores and models. UD1, UD2, and UD3 exhibit high turnover rates of 55 ± 4.7, 84 ± 4.8, and 79 ± 5.7 min-1, respectively, for (R)-OMP hydroxylation, whereas the corresponding rates for (S)-OMP are only 2.2 ± 0.19, 6.0 ± 0.68, and 14 ± 2.8 min-1, yielding an enantiomeric excess value of 92, 87, and 70%, respectively. These results suggest the critical roles of L75I, A264G, and A328V in steering OMP in the optimal orientation for stereoselective oxidation and demonstrate the utility of UniDesign for engineering CYP102A1 to produce drug metabolites of interest. The results are discussed in the context of protein structures.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
| | - Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Y Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA.
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5
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Sun Y, Huang X, Osawa Y, Chen YE, Zhang H. The Versatile Biocatalyst of Cytochrome P450 CYP102A1: Structure, Function, and Engineering. Molecules 2023; 28:5353. [PMID: 37513226 PMCID: PMC10383305 DOI: 10.3390/molecules28145353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Wild-type cytochrome P450 CYP102A1 from Bacillus megaterium is a highly efficient monooxygenase for the oxidation of long-chain fatty acids. The unique features of CYP102A1, such as high catalytic activity, expression yield, regio- and stereoselectivity, and self-sufficiency in electron transfer as a fusion protein, afford the requirements for an ideal biocatalyst. In the past three decades, remarkable progress has been made in engineering CYP102A1 for applications in drug discovery, biosynthesis, and biotechnology. The repertoire of engineered CYP102A1 variants has grown tremendously, whereas the substrate repertoire is avalanched to encompass alkanes, alkenes, aromatics, organic solvents, pharmaceuticals, drugs, and many more. In this article, we highlight the major advances in the past five years in our understanding of the structure and function of CYP102A1 and the methodologies used to engineer CYP102A1 for novel applications. The objective is to provide a succinct review of the latest developments with reference to the body of CYP102A1-related literature.
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Affiliation(s)
- Yudong Sun
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoqiang Huang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuqing Eugene Chen
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Jangjou A, Moqadas M, Mohsenian L, Kamyab H, Chelliapan S, Alshehery S, Ali MA, Dehbozorgi F, Yadav KK, Khorami M, Zarei Jelyani N. Awareness raising and dealing with methanol poisoning based on effective strategies. ENVIRONMENTAL RESEARCH 2023; 228:115886. [PMID: 37072082 DOI: 10.1016/j.envres.2023.115886] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023]
Abstract
Intoxication with methanol most commonly occurs as a consequence of ingesting, inhaling, or coming into contact with formulations that include methanol as a base. Clinical manifestations of methanol poisoning include suppression of the central nervous system, gastrointestinal symptoms, and decompensated metabolic acidosis, which is associated with impaired vision and either early or late blindness within 0.5-4 h after ingestion. After ingestion, methanol concentrations in the blood that are greater than 50 mg/dl should raise some concern. Ingested methanol is typically digested by alcohol dehydrogenase (ADH), and it is subsequently redistributed to the body's water to attain a volume distribution that is about equivalent to 0.77 L/kg. Moreover, it is removed from the body as its natural, unchanged parent molecules. Due to the fact that methanol poisoning is relatively uncommon but frequently involves a large number of victims at the same time, this type of incident occupies a special position in the field of clinical toxicology. The beginning of the COVID-19 pandemic has resulted in an increase in erroneous assumptions regarding the preventative capability of methanol in comparison to viral infection. More than 1000 Iranians fell ill, and more than 300 of them passed away in March of this year after they consumed methanol in the expectation that it would protect them from a new coronavirus. The Atlanta epidemic, which involved 323 individuals and resulted in the deaths of 41, is one example of mass poisoning. Another example is the Kristiansand outbreak, which involved 70 people and resulted in the deaths of three. In 2003, the AAPCC received reports of more than one thousand pediatric exposures. Since methanol poisoning is associated with high mortality rates, it is vital that the condition be addressed seriously and managed as quickly as feasible. The objective of this review was to raise awareness about the mechanism and metabolism of methanol toxicity, the introduction of therapeutic interventions such as gastrointestinal decontamination and methanol metabolism inhibition, the correction of metabolic disturbances, and the establishment of novel diagnostic/screening nanoparticle-based strategies for methanol poisoning such as the discovery of ADH inhibitors as well as the detection of the adulteration of alcoholic drinks by nanoparticles in order to prevent methanol poisoning. In conclusion, increasing warnings and knowledge about clinical manifestations, medical interventions, and novel strategies for methanol poisoning probably results in a decrease in the death load.
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Affiliation(s)
- Ali Jangjou
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Moqadas
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Mohsenian
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hesam Kamyab
- Faculty of Architecture and Urbanism, UTE University, Calle Rumipamba S/N and Bourgeois, Quito, Ecuador; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India; Process Systems Engineering Centre (PROSPECT), Faculty of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.
| | - Shreeshivadasan Chelliapan
- Engineering Department, Razak Faculty of Technology and Informatics, Universiti Teknologi Malaysia, Jln Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia.
| | - Sultan Alshehery
- Department of Mechanical Engineering King Khalid University, zip code - 62217, Saudi Arabia
| | - Mohammed Azam Ali
- Department of Mechanical Engineering King Khalid University, zip code - 62217, Saudi Arabia
| | - Farbod Dehbozorgi
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal, 462044, India; Environmental and Atmospheric Sciences Research Group, Scientific Research Center, Al-Ayen University, Thi-Qar, Nasiriyah, 64001, Iraq
| | - Masoud Khorami
- Department of Civil Engineering, Islamic Azad University, Central Tehran Branch, Tehran, Iran
| | - Najmeh Zarei Jelyani
- Department of Emergency Medicine, School of Medicine, Namazi Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran; Emergency Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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7
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Fabelle NR, Oktavia FARH, Cha GS, Nguyen NA, Choi SK, Yun CH. Production of a major metabolite of niclosamide using bacterial cytochrome P450 enzymes. Enzyme Microb Technol 2023; 165:110210. [PMID: 36764029 DOI: 10.1016/j.enzmictec.2023.110210] [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: 12/09/2022] [Revised: 01/19/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Niclosamide has been proposed as a possible candidate for a Covid-19 drug. However, the metabolites of niclosamide are difficult to investigate because they are usually not available commercially or they are quite expensive in the commercial market. In this study, the major metabolite of niclosamide in human liver microsomes (HLMs) was confirmed to be 3-OH niclosamide. Because the production of 3-OH niclosamide using HLMs has a slow turnover rate, a new method of producing niclosamide metabolite with an easier and highly cost-efficient method was thus conducted. Bacterial CYP102A1 (BM3) is one of the bacterial cytochrome P450s (CYPs) from Bacillus megaterium that structurally show similar activities to human CYPs. Here, the BM3 mutants were used to produce niclosamide metabolites and the metabolites were analyzed using high-performance liquid chromatography and LC-mass spectrometry. Among a set of mutants tested here, BM3 M14 mutant was the most active in producing 3-OH niclosamide, the major metabolite of niclosamide. Comparing BM3 M14 and HLMs, BM3 M14 production of 3-OH niclosamide was 34-fold higher than that of HLMs. Hence, the engineering of BM3 can be a cost-efficient method to produce 3-OH niclosamide.
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Affiliation(s)
- Nabilla Rizkia Fabelle
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | | | - Gun Su Cha
- Namhae Garlic Research Institute, 2465-8 Namdaero, Gyeongsangnamdo 52430, Republic of Korea
| | - Ngoc Anh Nguyen
- School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea
| | - Soo-Keun Choi
- Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-Ro, Yuseong, Daejon 34141, Republic of Korea.
| | - Chul-Ho Yun
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea; School of Biological Sciences and Technology, Chonnam National University, 77 Yongbongro, Gwangju 61186, Republic of Korea.
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8
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Thomson RES, D'Cunha SA, Hayes MA, Gillam EMJ. Use of engineered cytochromes P450 for accelerating drug discovery and development. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:195-252. [PMID: 35953156 DOI: 10.1016/bs.apha.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.
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Affiliation(s)
- Raine E S Thomson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Stephlina A D'Cunha
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, BioPharmaceuticals R&D AstraZeneca, Mölndal, Sweden
| | - Elizabeth M J Gillam
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
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9
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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10
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Production and structural characterization of the cytochrome P450 enzymes in carotene ring hydroxylation. Methods Enzymol 2022; 671:223-241. [DOI: 10.1016/bs.mie.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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A Promiscuous Bacterial P450: The Unparalleled Diversity of BM3 in Pharmaceutical Metabolism. Int J Mol Sci 2021; 22:ijms222111380. [PMID: 34768811 PMCID: PMC8583553 DOI: 10.3390/ijms222111380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
CYP102A1 (BM3) is a catalytically self-sufficient flavocytochrome fusion protein isolated from Bacillus megaterium, which displays similar metabolic capabilities to many drug-metabolizing human P450 isoforms. BM3's high catalytic efficiency, ease of production and malleable active site makes the enzyme a desirable tool in the production of small molecule metabolites, especially for compounds that exhibit drug-like chemical properties. The engineering of select key residues within the BM3 active site vastly expands the catalytic repertoire, generating variants which can perform a range of modifications. This provides an attractive alternative route to the production of valuable compounds that are often laborious to synthesize via traditional organic means. Extensive studies have been conducted with the aim of engineering BM3 to expand metabolite production towards a comprehensive range of drug-like compounds, with many key examples found both in the literature and in the wider industrial bioproduction setting of desirable oxy-metabolite production by both wild-type BM3 and related variants. This review covers the past and current research on the engineering of BM3 to produce drug metabolites and highlights its crucial role in the future of biosynthetic pharmaceutical production.
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12
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Maxel S, Saleh S, King E, Aspacio D, Zhang L, Luo R, Li H. Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst. ACS Synth Biol 2021; 10:2359-2370. [PMID: 34469126 PMCID: PMC10362907 DOI: 10.1021/acssynbio.1c00258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclohexanone monooxygenases (CHMO) consume molecular oxygen and NADPH to catalyze the valuable oxidation of cyclic ketones. However, CHMO usage is restricted by poor stability and stringent specificity for NADPH. Efforts to engineer CHMO have been limited by the sensitivity of the enzyme to perturbations in conformational dynamics and long-range interactions that cannot be predicted. We demonstrate an aerobic, high-throughput growth selection platform in Escherichia coli for oxygenase evolution based on NADH redox balance. We applied this NADH-dependent selection to alter the cofactor specificity of CHMO to accept NADH, a less expensive cofactor than NADPH. We first identified the variant CHMO DTNP (S208D-K326T-K349N-L143P) with a ∼1200-fold relative cofactor specificity switch from NADPH to NADH compared to the wild type through semirational design. Molecular modeling suggests CHMO DTNP activity is driven by cooperative fine-tuning of cofactor contacts. Additional evolution of CHMO DTNP through random mutagenesis yielded the variant CHMO DTNPY with a ∼2900-fold relative specificity switch compared to the wild type afforded by an additional distal mutation, H163Y. These results highlight the difficulty in engineering functionally innovative variants from static models and rational designs, and the need for high throughput selection methods. Our introduced tools for oxygenase engineering accelerate the advancements of characteristics essential for industrial feasibility.
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Affiliation(s)
- Sarah Maxel
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Samer Saleh
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Edward King
- Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Derek Aspacio
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Linyue Zhang
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
| | - Ray Luo
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
- Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - Han Li
- Departments of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
- Biomedical Engineering, University of California, Irvine, California 92697, United States
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13
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Negative catalysis / non-Bell-Evans-Polanyi reactivity by metalloenzymes: Examples from mononuclear heme and non-heme iron oxygenases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213914] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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14
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Felker D, Zhang H, Bo Z, Lau M, Morishima Y, Schnell S, Osawa Y. Mapping protein-protein interactions in homodimeric CYP102A1 by crosslinking and mass spectrometry. Biophys Chem 2021; 274:106590. [PMID: 33894563 DOI: 10.1016/j.bpc.2021.106590] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 11/28/2022]
Abstract
Covalent crosslinking and mass spectrometry techniques hold great potential in the study of multiprotein complexes, but a major challenge is the inability to differentiate intra- and inter- protein crosslinks in homomeric complexes. In the current study we use CYP102A1, a well-characterized homodimeric P450, to examine a subtractive method that utilizes limited crosslinking with disuccinimidyl dibutyric urea (DSBU) and isolation of the monomer, in addition to the crosslinked dimer, to identify inter-monomer crosslinks. The utility of this approach was examined with the use of MS-cleavable crosslinker DSBU and recently published cryo-EM based structures of the CYP102A1 homodimer. Of the 31 unique crosslinks found, 26 could be fit to the reported structures whereas 5 exceeded the spatial constraints. Not only did these crosslinks validate the cryo-EM structure, they point to new conformations of CYP102A1 that bring the flavins in closer proximity to the heme.
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Affiliation(s)
- Dana Felker
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Zhiyuan Bo
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Miranda Lau
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Yoshihiro Morishima
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology, 7744 MS II, 1137 E. Catherine St., Ann Arbor, MI 48109-5622, USA.
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-5632, USA.
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15
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David F, Davis AM, Gossing M, Hayes MA, Romero E, Scott LH, Wigglesworth MJ. A Perspective on Synthetic Biology in Drug Discovery and Development-Current Impact and Future Opportunities. SLAS DISCOVERY 2021; 26:581-603. [PMID: 33834873 DOI: 10.1177/24725552211000669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The global impact of synthetic biology has been accelerating, because of the plummeting cost of DNA synthesis, advances in genetic engineering, growing understanding of genome organization, and explosion in data science. However, much of the discipline's application in the pharmaceutical industry remains enigmatic. In this review, we highlight recent examples of the impact of synthetic biology on target validation, assay development, hit finding, lead optimization, and chemical synthesis, through to the development of cellular therapeutics. We also highlight the availability of tools and technologies driving the discipline. Synthetic biology is certainly impacting all stages of drug discovery and development, and the recognition of the discipline's contribution can further enhance the opportunities for the drug discovery and development value chain.
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Affiliation(s)
- Florian David
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew M Davis
- Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Michael Gossing
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Hayes
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elvira Romero
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Louis H Scott
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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16
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Liu Y, Cong Y, Zhang C, Fang B, Pan Y, Li Q, You C, Gao B, Zhang JZH, Zhu T, Zhang L. Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement. RSC Adv 2021; 11:12036-12042. [PMID: 35423749 PMCID: PMC8696588 DOI: 10.1039/d1ra00352f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 11/21/2022] Open
Abstract
Cytochrome P450 BM3 (BM3) is an important oxidoreductase that is widely used in drug synthesis, chemical synthesis, and other industries. However, as BM3 unquestionably increases costs by consuming a natural cofactor that unstably provides electrons, an alternative biomimetic cofactor with simpler structures represented by nicotinamide mononucleotide (NMNH) has been utilized. Currently, few reports exist on artificially modified BM3 enzymes using NMNH, especially regarding theoretical simulation and calculation. With the cognition of the mechanism in mind, we propose a strategy that optimizes and refines catalytic conformation. Based on constrained molecular dynamics simulation, the distance between N-5 of FAD flavin and C-4 of NMNH is used as a cue for the determination of improved conformation, and the potential positive mutants are subsequently screened virtually in accordance with binding free energy requirements. As a result, the Kcat/KM values of the favorable mutant S848R increased to 205.38% compared to the wild-type BM3 with NMNH. These data indicate that our strategy can be applied for the specific utilization of biomimetic cofactors by oxidoreductases represented by BM3. A rational design strategy was proposed to improve the efficient utilization of alternative biomimetic cofactor by P450 BM3 enzyme.![]()
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Affiliation(s)
- Yao Liu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Chuanxi Zhang
- School of Biotechnology, East China University of Science and Technology Shanghai 200237 China
| | - Bohuan Fang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Yue Pan
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China
| | - Qiangzi Li
- University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Chun You
- University of Chinese Academy of Sciences 19A Yuquan Road, Shijingshan District Beijing 100049 P. R. China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Bei Gao
- School of Biotechnology, East China University of Science and Technology Shanghai 200237 China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China.,Department of Chemistry, New York University New York New York 10003 USA
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 China .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
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17
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Finnigan JD, Young C, Cook DJ, Charnock SJ, Black GW. Cytochromes P450 (P450s): A review of the class system with a focus on prokaryotic P450s. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:289-320. [PMID: 32951814 DOI: 10.1016/bs.apcsb.2020.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 (P450s) are a large superfamily of heme-containing monooxygenases. P450s are found in all Kingdoms of life and exhibit incredible diversity, both at sequence level and also on a biochemical basis. In the majority of cases, P450s can be assigned into one of ten classes based on their associated redox partners, domain architecture and cellular localization. Prokaryotic P450s now represent a large diverse collection of annotated/known enzymes, of which many have great potential biocatalytic potential. The self-sufficient P450 classes (Class VII/VIII) have been explored significantly over the past decade, with many annotated and biochemically characterized members. It is clear that the prokaryotic P450 world is expanding rapidly, as the number of published genomes and metagenome studies increases, and more P450 families are identified and annotated (CYP families).
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Affiliation(s)
| | - Carl Young
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | - Darren J Cook
- Prozomix Limited, Haltwhistle, Northumberland, United Kingdom
| | | | - Gary W Black
- Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
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18
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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19
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Abstract
Two cytochrome P450 enzymes, CYP97A3 and CYP97C1, catalyze hydroxylations of the β- and ε-rings of α-carotene to produce lutein. Chirality is introduced at the C-3 atom of both rings, and the reactions are both pro-3R-stereospecific. We determined the crystal structures of CYP97A3 in substrate-free and complex forms with a nonnatural substrate and the structure of CYP97C1 in a detergent-bound form. The structures of CYP97A3 in different states show the substrate channel and the structure of CYP97C1 bound with octylthioglucoside confirms the binding site for the carotenoid substrate. Biochemical assays confirm that the ferredoxin-NADP+ reductase (FNR)-ferredoxin pair is used as the redox partner. Details of the pro-3R stereospecificity are revealed in the retinal-bound CYP97A3 structure. Further analysis indicates that the CYP97B clan bears similarity to the β-ring-specific CYP97A clan. Overall, our research describes the molecular basis for the last steps of lutein biosynthesis.
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20
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Luirink RA, Verkade‐Vreeker MCA, Commandeur JNM, Geerke DP. A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion. Chembiochem 2020; 21:1461-1472. [PMID: 31919943 PMCID: PMC7318578 DOI: 10.1002/cbic.201900751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Indexed: 12/21/2022]
Abstract
The regio- (and stereo-)selectivity and specific activity of cytochrome P450s are determined by the accessibility of potential sites of metabolism (SOMs) of the bound substrate relative to the heme, and the activation barrier of the regioselective oxidation reaction(s). The accessibility of potential SOMs depends on the relative binding free energy (ΔΔGbind ) of the catalytically active substrate-binding poses, and the probability of the substrate to adopt a transition-state geometry. An established experimental method to measure activation energies of enzymatic reactions is the analysis of reaction rate constants at different temperatures and the construction of Arrhenius plots. This is a challenge for multistep P450-catalyzed processes that involve redox partners. We introduce a modified Arrhenius approach to overcome the limitations in studying P450 selectivity, which can be applied in multiproduct enzyme catalysis. Our approach gives combined information on relative activation energies, ΔΔGbind values, and collision entropies, yielding direct insight into the basis of selectivity in substrate conversion.
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Affiliation(s)
- Rosa A. Luirink
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | | | - Jan N. M. Commandeur
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular ToxicologyVrije UniversiteitDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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21
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Zhou AZ, Chen K, Arnold FH. Enzymatic Lactone-Carbene C–H Insertion to Build Contiguous Chiral Centers. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01349] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrew Z. Zhou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kai Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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22
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Jeffreys LN, Pacholarz KJ, Johannissen LO, Girvan HM, Barran PE, Voice MW, Munro AW. Characterization of the structure and interactions of P450 BM3 using hybrid mass spectrometry approaches. J Biol Chem 2020; 295:7595-7607. [PMID: 32303637 PMCID: PMC7261786 DOI: 10.1074/jbc.ra119.011630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
The cytochrome P450 monooxygenase P450 BM3 (BM3) is a biotechnologically important and versatile enzyme capable of producing important compounds such as the medical drugs pravastatin and artemether, and the steroid hormone testosterone. BM3 is a natural fusion enzyme comprising two major domains: a cytochrome P450 (heme-binding) catalytic domain and a NADPH-cytochrome P450 reductase (CPR) domain containing FAD and FMN cofactors in distinct domains of the CPR. A crystal structure of full-length BM3 enzyme is not available in its monomeric or catalytically active dimeric state. In this study, we provide detailed insights into the protein-protein interactions that occur between domains in the BM3 enzyme and characterize molecular interactions within the BM3 dimer by using several hybrid mass spectrometry (MS) techniques, namely native ion mobility MS (IM-MS), collision-induced unfolding (CIU), and hydrogen-deuterium exchange MS (HDX-MS). These methods enable us to probe the structure, stoichiometry, and domain interactions in the ∼240 kDa BM3 dimeric complex. We obtained high-sequence coverage (88–99%) in the HDX-MS experiments for full-length BM3 and its component domains in both the ligand-free and ligand-bound states. We identified important protein interaction sites, in addition to sites corresponding to heme-CPR domain interactions at the dimeric interface. These findings bring us closer to understanding the structure and catalytic mechanism of P450 BM3.
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Affiliation(s)
- Laura N Jeffreys
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Linus O Johannissen
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Hazel M Girvan
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E Barran
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.,Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee, DD2 1NH, United Kingdom
| | - Andrew W Munro
- The Manchester Institute of Biotechnology, School of Natural Sciences, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom .,Manchester Synthetic Biology Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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23
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Su M, Chakraborty S, Osawa Y, Zhang H. Cryo-EM reveals the architecture of the dimeric cytochrome P450 CYP102A1 enzyme and conformational changes required for redox partner recognition. J Biol Chem 2020; 295:1637-1645. [PMID: 31901079 PMCID: PMC7008367 DOI: 10.1074/jbc.ra119.011305] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/02/2020] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 family 102 subfamily A member 1 (CYP102A1) is a self-sufficient flavohemeprotein and a highly active bacterial enzyme capable of fatty acid hydroxylation at a >3,000 min-1 turnover rate. The CYP102A1 architecture has been postulated to be responsible for its extraordinary catalytic prowess. However, the structure of a functional full-length CYP102A1 enzyme remains to be determined. Herein, we used a cryo-EM single-particle approach, revealing that full-length CYP102A1 forms a homodimer in which both the heme and FAD domains contact each other. The FMN domain of one monomer was located close to the heme domain of the other monomer, exhibiting a trans configuration. Moreover, full-length CYP102A1 is highly dynamic, existing in multiple conformational states, including open and closed states. In the closed state, the FMN domain closely contacts the FAD domain, whereas in the open state, one of the FMN domains rotates away from its FAD domain and traverses to the heme domain of the other monomer. This structural arrangement and conformational dynamics may facilitate rapid intraflavin and trans FMN-to-heme electron transfers (ETs). Results with a variant having a 12-amino-acid deletion in the CYP102A1 linker region, connecting the catalytic heme and the diflavin reductase domains, further highlighted the importance of conformational dynamics in the ET process. Cryo-EM revealed that the Δ12 variant homodimer is conformationally more stable and incapable of FMN-to-heme ET. We conclude that closed-to-open alternation is crucial for redox partner recognition and formation of an active ET complex for CYP102A1 catalysis.
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Affiliation(s)
- Min Su
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.
| | - Sumita Chakraborty
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109
| | - Yoichi Osawa
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109
| | - Haoming Zhang
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109.
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24
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Dey KK, Ghosh M. Determination of chemical shift anisotropy tensor and molecular correlation time of proton pump inhibitor omeprazole by solid state NMR measurements. NEW J CHEM 2020. [DOI: 10.1039/d0nj01827a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The correlation between the structure and dynamics of omeprazole is portrayed by extracting CSA parameters through the 13C 2DPASS CP-MAS SSNMR experiment, site specific spin–lattice relaxation time by Torchia CP experiment, and calculation of the molecular correlation time.
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Affiliation(s)
- Krishna Kishor Dey
- Department of Physics
- Dr. Harisingh Gour Central University
- Sagar-470003
- India
| | - Manasi Ghosh
- Department of Physics (MMV Section)
- Banaras Hindu University
- Varanasi-221005
- India
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25
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Kanoh N, Kawamata-Asano A, Suzuki K, Takahashi Y, Miyazawa T, Nakamura T, Moriya T, Hirano H, Osada H, Iwabuchi Y, Takahashi S. An integrated screening system for the selection of exemplary substrates for natural and engineered cytochrome P450s. Sci Rep 2019; 9:18023. [PMID: 31792277 PMCID: PMC6888865 DOI: 10.1038/s41598-019-54473-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/14/2019] [Indexed: 11/26/2022] Open
Abstract
Information about substrate and product selectivity is critical for understanding the function of cytochrome P450 monooxygenases. In addition, comprehensive understanding of changes in substrate selectivity of P450 upon amino acid mutation would enable the design and creation of engineered P450s with desired selectivities. Therefore, systematic methods for obtaining such information are required. Herein, we developed an integrated P450 substrate screening system for the selection of “exemplary” substrates for a P450 of interest. The established screening system accurately selected the known exemplary substrates and also identified previously unknown exemplary substrates for microbial-derived P450s from a library containing sp3-rich synthetic small molecules. Synthetically potent transformations were also found by analyzing the reactions and oxidation products. The screening system was applied to analyze the substrate selectivity of the P450 BM3 mutants F87A and F87A/A330W, which acquired an ability to hydroxylate non-natural substrate steroids regio- and stereoselectively by two amino acid mutations. The distinct transition of exemplary substrates due to each single amino acid mutation was revealed, demonstrating the utility of the established system.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan. .,Institute of Medicinal Chemistry, Hoshi University, 2-4-1 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Ayano Kawamata-Asano
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Kana Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Yusuke Takahashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takeshi Miyazawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takemichi Nakamura
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takashi Moriya
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Hirano
- Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Chemical Resource Development Research Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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Regioselective hydroxylation pathway of tenatoprazole to produce human metabolites by Bacillus megaterium CYP102A1. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Production of metabolites of the anti-cancer drug noscapine using a P450 BM3 mutant library. ACTA ACUST UNITED AC 2019; 24:e00372. [PMID: 31516852 PMCID: PMC6728265 DOI: 10.1016/j.btre.2019.e00372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 12/27/2022]
Abstract
Mutants of P450BM3 can metabolise noscapine. Noscapine is N-demethylated with high selectivity. The metabolites produced are of interest for drug development. The profile of metabolites generated resembles that of mammalian CYP3A4.
Cytochrome P450 enzymes are a promising tool for the late-stage diversification of lead drug candidates and can provide an alternative route to structural modifications that are difficult to achieve with synthetic chemistry. In this study, a library of P450BM3 mutants was produced using site-directed mutagenesis and the enzymes screened for metabolism of the opium poppy alkaloid noscapine, a drug with anticancer activity. Of the 18 enzyme mutants screened, 12 showed an ability to metabolise noscapine that was not present in the wild-type enzyme. Five noscapine metabolites were detected by LC-MS/MS, with the major metabolite for all mutants being N-demethylated noscapine. The highest observed regioselectivity for N-demethylation was 88%. Two hydroxylated metabolites, a catechol and two C-C cleavage products were also detected. P450-mediated production of hydroxylated and N-demethylated noscapine structures may be useful for the development of noscapine analogues with improved biological activity. The variation in substrate turnover, coupling efficiency and product distribution between the active mutants was considered alongside in silico docking experiments to gain insight into structural and functional effects of the introduced mutations. Selected mutants were identified as targets for further mutagenesis to improve activity and when coupled with an optimised process may provide a route for the preparative-scale production of noscapine metabolites.
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28
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Santos GDA, Dhoke GV, Davari MD, Ruff AJ, Schwaneberg U. Directed Evolution of P450 BM3 towards Functionalization of Aromatic O-Heterocycles. Int J Mol Sci 2019; 20:E3353. [PMID: 31288417 PMCID: PMC6651506 DOI: 10.3390/ijms20133353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 02/04/2023] Open
Abstract
The O-heterocycles, benzo-1,4-dioxane, phthalan, isochroman, 2,3-dihydrobenzofuran, benzofuran, and dibenzofuran are important building blocks with considerable medical application for the production of pharmaceuticals. Cytochrome P450 monooxygenase (P450) Bacillus megaterium 3 (BM3) wild type (WT) from Bacillus megaterium has low to no conversion of the six O-heterocycles. Screening of in-house libraries for active variants yielded P450 BM3 CM1 (R255P/P329H), which was subjected to directed evolution and site saturation mutagenesis of four positions. The latter led to the identification of position R255, which when introduced in the P450 BM3 WT, outperformed all other variants. The initial oxidation rate of nicotinamide adenine dinucleotide phosphate (NADPH) consumption increased ≈140-fold (WT: 8.3 ± 1.3 min-1; R255L: 1168 ± 163 min-1), total turnover number (TTN) increased ≈21-fold (WT: 40 ± 3; R255L: 860 ± 15), and coupling efficiency, ≈2.9-fold (WT: 8.8 ± 0.1%; R255L: 25.7 ± 1.0%). Computational analysis showed that substitution R255L (distant from the heme-cofactor) does not have the salt bridge formed with D217 in WT, which introduces flexibility into the I-helix and leads to a heme rearrangement allowing for efficient hydroxylation.
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Affiliation(s)
| | - Gaurao V Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
- DWI-Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52074 Aachen, Germany.
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29
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Cytochrome P450 Monooxygenases in Biotechnology and Synthetic Biology. Trends Biotechnol 2019; 37:882-897. [PMID: 30739814 DOI: 10.1016/j.tibtech.2019.01.001] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022]
Abstract
Cytochromes P450 (P450 or CYP) are heme-containing enzymes that catalyze the introduction of one atom of molecular oxygen into nonactivated C-H bonds, often in a regio- and stereoselective manner. This ability, combined with a tremendous number of accepted substrates, makes P450s powerful biocatalysts. Sixty years after their discovery, P450 systems are recognized as essential bio-bricks in synthetic biology approaches to enable production of high-value complex molecules in recombinant hosts. Recent impressive results in protein engineering led to P450s with tailored properties that are even able to catalyze abiotic reactions. The introduction of P450s in artificial multi-enzymatic cascades reactions and chemo-enzymatic processes offers exciting future perspectives to access novel compounds that cannot be synthesized by nature or by chemical routes.
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30
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Jeffreys LN, Poddar H, Golovanova M, Levy CW, Girvan HM, McLean KJ, Voice MW, Leys D, Munro AW. Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs. Sci Rep 2019; 9:1577. [PMID: 30733479 PMCID: PMC6367340 DOI: 10.1038/s41598-018-37330-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/14/2018] [Indexed: 11/09/2022] Open
Abstract
Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the ω-1, ω-2 and ω-3 positions. However, protein engineering has led to variants of this enzyme that are able to bind and oxidize diverse compounds, including steroids, terpenes and various human drugs. The wild-type P450 BM3 enzyme binds inefficiently to many azole antifungal drugs. However, we show that the BM3 A82F/F87V double mutant (DM) variant binds substantially tighter to numerous azole drugs than does the wild-type BM3, and that their binding occurs with more extensive heme spectral shifts indicative of complete binding of several azoles to the BM3 DM heme iron. We report here the first crystal structures of P450 BM3 bound to azole antifungal drugs - with the BM3 DM heme domain bound to the imidazole drugs clotrimazole and tioconazole, and to the triazole drugs fluconazole and voriconazole. This is the first report of any protein structure bound to the azole drug tioconazole, as well as the first example of voriconazole heme iron ligation through a pyrimidine nitrogen from its 5-fluoropyrimidine ring.
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Affiliation(s)
- Laura N Jeffreys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Harshwardhan Poddar
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Marina Golovanova
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Colin W Levy
- Manchester Protein Structure Facility (MPSF), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Hazel M Girvan
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Michael W Voice
- Cypex Ltd., 6 Tom McDonald Avenue, Dundee DD2 1NH, Scotland, United Kingdom
| | - David Leys
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom.
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31
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Vickers C, Backfisch G, Oellien F, Piel I, Lange UEW. Enzymatic Late‐Stage Oxidation of Lead Compounds with Solubilizing Biomimetic Docking/Protecting groups. Chemistry 2018; 24:17936-17947. [DOI: 10.1002/chem.201802331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/12/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Clare Vickers
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Gisela Backfisch
- Development Sciences, DMPK and Bioanalytical ResearchAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Frank Oellien
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Isabel Piel
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Udo E. W. Lange
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
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32
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Geronimo I, Denning CA, Heidary DK, Glazer EC, Payne CM. Molecular Determinants of Substrate Affinity and Enzyme Activity of a Cytochrome P450 BM3 Variant. Biophys J 2018; 115:1251-1263. [PMID: 30224054 DOI: 10.1016/j.bpj.2018.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/29/2022] Open
Abstract
Cytochrome P450BM3 catalyzes the hydroxylation and/or epoxidation of fatty acids, fatty amides, and alcohols. Protein engineering has produced P450BM3 variants capable of accepting drug molecules normally metabolized by human P450 enzymes. The enhanced substrate promiscuity has been attributed to the greater flexibility of the lid of the substrate channel. However, it is not well understood how structurally different and highly polar drug molecules can stably bind in the active site nor how the activity and coupling efficiency of the enzyme may be affected by the lack of enzyme-substrate complementarity. To address these important aspects of non-native small molecule binding, this study investigated the binding of drug molecules with different size, charge, polar surface area, and human P450 affinity on the promiscuous R47L/F87V/L188Q/E267V/F81I pentuple mutant of P450BM3. Binding free energy data and energy decomposition analysis showed that pentuple mutant P450BM3 stably binds (i.e., negative ΔGb°) a broad range of substrate and inhibitor types because dispersion interactions with active site residues overcome unfavorable repulsive and electrostatic effects. Molecular dynamics simulations revealed that 1) acidic substrates tend to disrupt the heme propionate A-K69 salt bridge, which may reduce heme oxidizing ability, and 2) the lack of complementarity leads to high substrate mobility and water density in the active site, which may lead to uncoupling. These factors must be considered in future developments of P450BM3 as a biocatalyst in the large-scale production of drug metabolites.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky
| | | | - David K Heidary
- Department of Chemistry, University of Kentucky, Lexington, Kentucky
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky.
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33
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Jeffreys LN, Girvan HM, McLean KJ, Munro AW. Characterization of Cytochrome P450 Enzymes and Their Applications in Synthetic Biology. Methods Enzymol 2018; 608:189-261. [PMID: 30173763 DOI: 10.1016/bs.mie.2018.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The cytochrome P450 monooxygenase enzymes (P450s) catalyze a diverse array of chemical transformations, most originating from the insertion of an oxygen atom into a substrate that binds close to the P450 heme. The oxygen is delivered by a highly reactive heme iron-oxo species (compound I) and, according to the chemical nature of the substrate and its position in the active site, the P450 can catalyze a wide range of reactions including, e.g., hydroxylation, reduction, decarboxylation, sulfoxidation, N- and O-demethylation, epoxidation, deamination, CC bond formation and breakage, nitration, and dehalogenation. In this chapter, we describe the structural, biochemical, and catalytic properties of the P450s, along with spectroscopic and analytical methods used to characterize P450 enzymes and their redox partners. Important uses of P450 enzymes are highlighted, including how various P450s have been exploited for applications in synthetic biology.
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Affiliation(s)
- Laura N Jeffreys
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Hazel M Girvan
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Kirsty J McLean
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Andrew W Munro
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom.
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34
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Zhang H, Yokom AL, Cheng S, Su M, Hollenberg PF, Southworth DR, Osawa Y. The full-length cytochrome P450 enzyme CYP102A1 dimerizes at its reductase domains and has flexible heme domains for efficient catalysis. J Biol Chem 2018; 293:7727-7736. [PMID: 29618513 DOI: 10.1074/jbc.ra117.000600] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/28/2018] [Indexed: 11/06/2022] Open
Abstract
The cytochrome P450 enzyme CYP102A1 from Bacillus megaterium is a highly efficient hydroxylase of fatty acids, and there is a significant interest in using CYP102A1 for biotechnological applications. Here, we used size-exclusion chromatography-multiangle light scattering (SEC-MALS) analysis and negative-stain EM to investigate the molecular architecture of CYP102A1. The SEC-MALS analysis yielded a homogeneous peak with an average molecular mass of 235 ± 5 kDa, consistent with homodimeric CYP102A1. The negative-stain EM of dimeric CYP102A1 revealed four distinct lobes, representing the two heme and two reductase domains. Two of the lobes were in close contact, whereas the other two were often observed apart and at the ends of a U-shaped configuration. The overall dimension of the dimer was ∼130 Å. To determine the identity of the lobes, we FLAG-tagged the N or C terminus of CYP102A1 to visualize additional densities in EM and found that anti-FLAG Fab could bind only the N-tagged P450. Single-particle analysis of this anti-Flag Fab-CYP102A1 complex revealed additional density in the N-terminally tagged heme domains, indicating that the heme domains appear flexible, whereas the reductase domains remain tightly associated. The effects of truncation on CYP102A1 dimerization, identification of cross-linked sites by peptide mapping, and molecular modeling results all were consistent with the dimerization of the reductase domain. We conclude that functional CYP102A1 is a compact globular protein dimerized at its reductase domains, with its heme domains exhibiting multiple conformations that likely contribute to the highly efficient catalysis of CYP102A1.
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Affiliation(s)
| | | | - Shen Cheng
- From the Departments of Pharmacology and
| | - Min Su
- the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
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35
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Acevedo-Rocha CG, Gamble CG, Lonsdale R, Li A, Nett N, Hoebenreich S, Lingnau JB, Wirtz C, Fares C, Hinrichs H, Deege A, Mulholland AJ, Nov Y, Leys D, McLean KJ, Munro AW, Reetz MT. P450-Catalyzed Regio- and Diastereoselective Steroid Hydroxylation: Efficient Directed Evolution Enabled by Mutability Landscaping. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00389] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Charles G. Gamble
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Aitao Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University 368 Youyi Road, Wuchang Wuhan 430062, China
| | - Nathalie Nett
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Sabrina Hoebenreich
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Julia B. Lingnau
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Cornelia Wirtz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Christophe Fares
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Alfred Deege
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa 31905, Israel
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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36
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Li Y, Qin B, Li X, Tang J, Chen Y, Zhou L, You S. Selective Oxidations of Cyperenoic Acid by Slightly Reshaping the Binding Pocket of Cytochrome P450 BM3. ChemCatChem 2018. [DOI: 10.1002/cctc.201701088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuxin Li
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Bin Qin
- Wuya College of Innovation; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Xiaoqin Li
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Jun Tang
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Yu Chen
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Lina Zhou
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
| | - Song You
- School of Life Science and Biopharmaceutics; Shenyang Pharmaceutical University; 103 Wenhua Road, Shenhe District Shenyang 110016 P.R. China
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37
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Abstract
This mini review gives an overview over different design approaches and methodologies applied in rational and semirational enzyme engineering. The underlying principles for engineering novel activities, enantioselectivity, substrate specificity, stability, and pH optimum are summarized.
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Affiliation(s)
- Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA.
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38
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Darimont D, Weissenborn MJ, Nebel BA, Hauer B. Modulating proposed electron transfer pathways in P450 BM3 led to improved activity and coupling efficiency. Bioelectrochemistry 2017; 119:119-123. [PMID: 28965071 DOI: 10.1016/j.bioelechem.2017.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 10/18/2022]
Abstract
Electrochemical in vitro reduction of P450 enzymes is a promising alternative to in vivo applications. Previously we presented three engineered P450BM3 variants for aniline hydroxylation, equipped with a carbon nanotube binding-peptide (CNT-tag) for self-assembly on CNT electrodes. Compared to wildtype P450BM3 the NADPH-dependent activity was enhanced, but the coupling efficiency remained low. For P450BM3 Verma, Schwaneberg and Roccatano (2014, Biopolymers 101, 197-209) calculated putative electron transfer pathways (eTPs) by MD simulations. We hypothesised that knockouts of these transfer pathways would alter the coupling efficiency of the system. The results revealed no improved system for the electrically-driven P450s. For the NADPH-driven P450s, however, the most active eTP-mutant showed a 13-fold increased activity and a 32-fold elevated coupling efficiency using NADPH as reducing equivalent. This suggests an alternative principle of electron transport for the reduction by NADPH and an electrode, respectively. The work presents moreover a tool to improve the coupling and activity of P450s with non-natural substrates.
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Affiliation(s)
- Dominique Darimont
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin J Weissenborn
- Leibniz-Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany; Martin-Luther-University Halle-Wittenberg, Institute of Chemistry, Germany
| | - Bernd A Nebel
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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39
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Baker G, Girvan HM, Matthews S, McLean KJ, Golovanova M, Waltham TN, Rigby SEJ, Nelson DR, Blankley RT, Munro AW. Expression, Purification, and Biochemical Characterization of the Flavocytochrome P450 CYP505A30 from Myceliophthora thermophila. ACS OMEGA 2017; 2:4705-4724. [PMID: 30023729 PMCID: PMC6044835 DOI: 10.1021/acsomega.7b00450] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/26/2017] [Indexed: 05/21/2023]
Abstract
The cytochrome P450/P450 reductase fusion enzyme CYP505A30 from the thermophilic fungus Myceliophthora thermophila and its heme (P450) domain were expressed in Escherichia coli and purified using affinity, ion exchange, and size exclusion chromatography. CYP505A30 binds straight chain fatty acids (from ∼C10 to C20), with highest affinity for tridecanoic acid (KD = 2.7 μM). Reduced nicotinamide adenine dinucleotide phosphate is the preferred reductant for CYP505A30 (KM = 3.1 μM compared to 330 μM for reduced nicotinamide adenine dinucleotide in cytochrome c reduction). Electron paramagnetic resonance confirmed cysteine thiolate coordination of heme iron in CYP505A30 and its heme domain. Redox potentiometry revealed an unusually positive midpoint potential for reduction of the flavin adenine dinucleotide and flavin mononucleotide cofactors (E0' ∼ -118 mV), and a large increase in the CYP505A30 heme domain FeIII/FeII redox couple (ca. 230 mV) on binding arachidonic acid substrate. This switch brings the ferric heme iron potential into the same range as that of the reductase flavins. Multiangle laser light scattering analysis revealed CYP505A30's ability to dimerize, whereas the heme domain is monomeric. These data suggest CYP505A30 may function catalytically as a dimer (as described for Bacillus megaterium P450 BM3), and that binding interactions between CYP505A30 heme domains are not required for dimer formation. CYP505A30 catalyzed hydroxylation of straight chain fatty acids at the ω-1 to ω-3 positions, with a strong preference for ω-1 over ω-3 hydroxylation in the oxidation of dodecanoic and tetradecanoic acids (88 vs 2% products and 63 vs 9% products, respectively). CYP505A30 has important structural and catalytic similarities to P450 BM3 but distinct regioselectivity of lipid substrate oxidation with potential biotechnological applications.
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Affiliation(s)
- George
J. Baker
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Hazel M. Girvan
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Sarah Matthews
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Kirsty J. McLean
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Marina Golovanova
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Timothy N. Waltham
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Stephen E. J. Rigby
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - David R. Nelson
- Department
of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Richard T. Blankley
- Agilent
Technologies U.K. Ltd., Lakeside, Cheadle Royal Business Park, Stockport, Cheshire SK8 3GR, U.K.
| | - Andrew W. Munro
- Centre
for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM),
School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- E-mail: . Phone: 0044-161-306-5151
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40
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Shoji O, Yanagisawa S, Stanfield JK, Suzuki K, Cong Z, Sugimoto H, Shiro Y, Watanabe Y. Direct Hydroxylation of Benzene to Phenol by Cytochrome P450BM3 Triggered by Amino Acid Derivatives. Angew Chem Int Ed Engl 2017; 56:10324-10329. [DOI: 10.1002/anie.201703461] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Osami Shoji
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
- Core Research for Evolutional Science and Technology (Japan) Science and Technology Agency 5 Sanbancho, Chiyoda-ku Tokyo 102-0075 Japan
| | - Sota Yanagisawa
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Kazuto Suzuki
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Zhiqi Cong
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Hiroshi Sugimoto
- Core Research for Evolutional Science and Technology (Japan) Science and Technology Agency 5 Sanbancho, Chiyoda-ku Tokyo 102-0075 Japan
- RIKEN SPring-8 Center Harima Institute 1-1-1 Kouto Sayo Hyogo 679–5148 Japan
| | - Yoshitsugu Shiro
- RIKEN SPring-8 Center Harima Institute 1-1-1 Kouto Sayo Hyogo 679–5148 Japan
| | - Yoshihito Watanabe
- Research Center for Materials Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
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41
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Shoji O, Yanagisawa S, Stanfield JK, Suzuki K, Cong Z, Sugimoto H, Shiro Y, Watanabe Y. Direct Hydroxylation of Benzene to Phenol by Cytochrome P450BM3 Triggered by Amino Acid Derivatives. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Osami Shoji
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
- Core Research for Evolutional Science and Technology (Japan) Science and Technology Agency 5 Sanbancho, Chiyoda-ku Tokyo 102-0075 Japan
| | - Sota Yanagisawa
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Joshua Kyle Stanfield
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Kazuto Suzuki
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Zhiqi Cong
- Department of Chemistry Graduate School of Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
| | - Hiroshi Sugimoto
- Core Research for Evolutional Science and Technology (Japan) Science and Technology Agency 5 Sanbancho, Chiyoda-ku Tokyo 102-0075 Japan
- RIKEN SPring-8 Center Harima Institute 1-1-1 Kouto Sayo Hyogo 679–5148 Japan
| | - Yoshitsugu Shiro
- RIKEN SPring-8 Center Harima Institute 1-1-1 Kouto Sayo Hyogo 679–5148 Japan
| | - Yoshihito Watanabe
- Research Center for Materials Science Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-8602 Japan
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42
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Kavanagh ME, Chenge J, Zoufir A, McLean KJ, Coyne AG, Bender A, Munro AW, Abell C. Fragment Profiling Approach to Inhibitors of the Orphan M. tuberculosis P450 CYP144A1. Biochemistry 2017; 56:1559-1572. [PMID: 28169518 DOI: 10.1021/acs.biochem.6b00954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Similarity between the ligand binding profiles of enzymes may aid functional characterization and be of greater relevance to inhibitor development than sequence similarity or structural homology. Fragment screening is an efficient approach for characterization of the ligand binding profile of an enzyme and has been applied here to study the family of cytochrome P450 enzymes (P450s) expressed by Mycobacterium tuberculosis (Mtb). The Mtb P450s have important roles in bacterial virulence, survival, and pathogenicity. Comparing the fragment profiles of seven of these enzymes revealed that P450s which share a similar biological function have significantly similar fragment profiles, whereas functionally unrelated or orphan P450s exhibit distinct ligand binding properties, despite overall high structural homology. Chemical structures that exhibit promiscuous binding between enzymes have been identified, as have selective fragments that could provide leads for inhibitor development. The similarity between the fragment binding profiles of the orphan enzyme CYP144A1 and CYP121A1, a characterized enzyme that is important for Mtb viability, provides a case study illustrating the subsequent identification of novel CYP144A1 ligands. The different binding modes of these compounds to CYP144A1 provide insight into structural and dynamic aspects of the enzyme, possible biological function, and provide the opportunity to develop inhibitors. Expanding this fragment profiling approach to include a greater number of functionally characterized and orphan proteins may provide a valuable resource for understanding enzyme-ligand interactions.
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Affiliation(s)
- Madeline E Kavanagh
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jude Chenge
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Azedine Zoufir
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Kirsty J McLean
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andreas Bender
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew W Munro
- Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Manchester M1 7DN, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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43
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Matthews S, Tee KL, Rattray NJ, McLean KJ, Leys D, Parker DA, Blankley RT, Munro AW. Production of alkenes and novel secondary products by P450 Ole
T
JE
using novel H
2
O
2
‐generating fusion protein systems. FEBS Lett 2017; 591:737-750. [DOI: 10.1002/1873-3468.12581] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah Matthews
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - Kang Lan Tee
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - Nicholas J. Rattray
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | - David Leys
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
| | | | | | - Andrew W. Munro
- Manchester Institute of Biotechnology Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) School of Chemistry The University of Manchester UK
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44
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Venkatachalam A, Parashar A, Manoj KM. Functioning of drug-metabolizing microsomal cytochrome P450s: In silico probing of proteins suggests that the distal heme 'active site' pocket plays a relatively 'passive role' in some enzyme-substrate interactions. In Silico Pharmacol 2016; 4:2. [PMID: 26894412 PMCID: PMC4760962 DOI: 10.1186/s40203-016-0016-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/05/2016] [Indexed: 01/01/2023] Open
Abstract
PURPOSE The currently held mechanistic understanding of microsomal cytochrome P450s (CYPs) seeks that diverse drug molecules bind within the deep-seated distal heme pocket and subsequently react at the heme centre. To explain a bevy of experimental observations and meta-analyses, we indulge a hypothesis that involves a "diffusible radical mediated" mechanism. This new hypothesis posits that many substrates could also bind at alternate loci on/within the enzyme and be reacted without the pertinent moiety accessing a bonding proximity to the purported catalytic Fe-O enzyme intermediate. METHODS Through blind and heme-distal pocket centered dockings of various substrates and non-substrates (drug molecules of diverse sizes, classes, topographies etc.) of microsomal CYPs, we explored the possibility of access of substrates via the distal channels, its binding energies, docking orientations, distance of reactive moieties (or molecule per se) to/from the heme centre, etc. We investigated specific cases like- (a) large drug molecules as substrates, (b) classical marker drug substrates, (c) class of drugs as substrates (Sartans, Statins etc.), (d) substrate preferences between related and unrelated CYPs, (e) man-made site-directed mutants' and naturally occurring mutants' reactivity and metabolic disposition, (f) drug-drug interactions, (g) overall affinities of drug substrate versus oxidized product, (h) meta-analysis of in silico versus experimental binding constants and reaction/residence times etc. RESULTS It was found that heme-centered dockings of the substrate/modulator drug molecules with the available CYP crystal structures gave poor docking geometries and distances from Fe-heme centre. In conjunction with several other arguments, the findings discount the relevance of erstwhile hypothesis in many CYP systems. Consequently, the newly proposed hypothesis is deemed a viable alternate, as it satisfies Occam's razor. CONCLUSIONS The new proposal affords expanded scope for explaining the mechanism, kinetics and overall phenomenology of CYP mediated drug metabolism. It is now understood that the heme-iron and the hydrophobic distal pocket of CYPs serve primarily to stabilize the reactive intermediate (diffusible radical) and the surface or crypts of the apoprotein bind to the xenobiotic substrate (and in some cases, the heme distal pocket could also serve the latter function). Thus, CYPs enhance reaction rates and selectivity/specificity via a hitherto unrecognized modality.
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Affiliation(s)
- Avanthika Venkatachalam
- Formerly at PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004, India.
| | - Abhinav Parashar
- Formerly at Hemoproteins Lab, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India, 632014.
| | - Kelath Murali Manoj
- Formerly at PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004, India.
- Formerly at Hemoproteins Lab, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India, 632014.
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2 (PO), Kerala, 679122, India.
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45
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P450 BM3 fused to phosphite dehydrogenase allows phosphite-driven selective oxidations. Appl Microbiol Biotechnol 2016; 101:2319-2331. [PMID: 27900443 PMCID: PMC5320008 DOI: 10.1007/s00253-016-7993-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/30/2016] [Accepted: 11/05/2016] [Indexed: 11/24/2022]
Abstract
To facilitate the wider application of the NADPH-dependent P450BM3, we fused the monooxygenase with a phosphite dehydrogenase (PTDH). The resulting monooxygenase-dehydrogenase fusion enzyme acts as a self-sufficient bifunctional catalyst, accepting phosphite as a cheap electron donor for the regeneration of NADPH. The well-expressed fusion enzyme was purified and analyzed in comparison to the parent enzymes. Using lauric acid as substrate for P450BM3, it was found that the fusion enzyme had similar substrate affinity and hydroxylation selectivity while it displayed a significantly higher activity than the non-fused monooxygenase. Phosphite-driven conversions of lauric acid at restricted NADPH concentrations confirmed multiple turnovers of the cofactor. Interestingly, both the fusion enzyme and the native P450BM3 displayed enzyme concentration dependent activity and the fused enzyme reached optimal activity at a lower enzyme concentration. This suggests that the fusion enzyme has an improved tendency to form functional oligomers. To explore the constructed phosphite-driven P450BM3 as a biocatalyst, conversions of the drug compounds omeprazole and rosiglitazone were performed. PTDH-P450BM3 driven by phosphite was found to be more efficient in terms of total turnover when compared with P450BM3 driven by NADPH. The results suggest that PTDH-P450BM3 is an attractive system for use in biocatalytic and drug metabolism studies.
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46
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Jang HH, Ryu SH, Le TK, Doan TTM, Nguyen THH, Park KD, Yim DE, Kim DH, Kang CK, Ahn T, Kang HS, Yun CH. Regioselective C-H hydroxylation of omeprazole sulfide by Bacillus megaterium CYP102A1 to produce a human metabolite. Biotechnol Lett 2016; 39:105-112. [DOI: 10.1007/s10529-016-2211-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/08/2016] [Indexed: 12/24/2022]
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47
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Notonier S, Gricman Ł, Pleiss J, Hauer B. Semirational Protein Engineering of CYP153AM.aq. -CPRBM3 for Efficient Terminal Hydroxylation of Short- to Long-Chain Fatty Acids. Chembiochem 2016; 17:1550-7. [PMID: 27251775 DOI: 10.1002/cbic.201600207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/07/2022]
Abstract
The regioselective terminal hydroxylation of alkanes and fatty acids is of great interest in a variety of industrial applications, such as in cosmetics, in fine chemicals, and in the fragrance industry. The chemically challenging activation and oxidation of non-activated C-H bonds can be achieved with cytochrome P450 enzymes. CYP153AM.aq. -CPRBM3 is an artificial fusion construct consisting of the heme domain from Marinobacter aquaeolei and the reductase domain of CYP102A1 from Bacillus megaterium. It has the ability to hydroxylate medium- and long-chain fatty acids selectively at their terminal positions. However, the activity of this interesting P450 construct needs to be improved for applications in industrial processes. For this purpose, the design of mutant libraries including two consecutive steps of mutagenesis is demonstrated. Targeted positions and residues chosen for substitution were based on semi-rational protein design after creation of a homology model of the heme domain of CYP153AM.aq. , sequence alignments, and docking studies. Site-directed mutagenesis was the preferred method employed to address positions within the binding pocket, whereas diversity was created with the aid of a degenerate codon for amino acids located at the substrate entrance channel. Combining the successful variants led to the identification of a double variant-G307A/S233G-that showed alterations of one position within the binding pocket and one position located in the substrate access channel. This double variant showed twofold increased activity relative to the wild type for the terminal hydroxylation of medium-chain-length fatty acids. This variant furthermore showed improved activity towards short- and long-chain fatty acids and enhanced stability in the presence of higher concentrations of fatty acids.
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Affiliation(s)
- Sandra Notonier
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Łukasz Gricman
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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48
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Geronimo I, Denning CA, Rogers WE, Othman T, Huxford T, Heidary DK, Glazer EC, Payne CM. Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450BM3 Variants. Biochemistry 2016; 55:3594-606. [PMID: 27267136 PMCID: PMC7422958 DOI: 10.1021/acs.biochem.6b00183] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450BM3 is a heme-containing enzyme from Bacillus megaterium that exhibits high monooxygenase activity and has a self-sufficient electron transfer system in the full-length enzyme. Its potential synthetic applications drive protein engineering efforts to produce variants capable of oxidizing nonnative substrates such as pharmaceuticals and aromatic pollutants. However, promiscuous P450BM3 mutants often exhibit lower stability, thereby hindering their industrial application. This study demonstrated that the heme domain R47L/F87V/L188Q/E267V/F81I pentuple mutant (PM) is destabilized because of the disruption of hydrophobic contacts and salt bridge interactions. This was directly observed from crystal structures of PM in the presence and absence of ligands (palmitic acid and metyrapone). The instability of the tertiary structure and heme environment of substrate-free PM was confirmed by pulse proteolysis and circular dichroism, respectively. Binding of the inhibitor, metyrapone, significantly stabilized PM, but the presence of the native substrate, palmitic acid, had no effect. On the basis of high-temperature molecular dynamics simulations, the lid domain, β-sheet 1, and Cys ligand loop (a β-bulge segment connected to the heme) are the most labile regions and, thus, potential sites for stabilizing mutations. Possible approaches to stabilization include improvement of hydrophobic packing interactions in the lid domain and introduction of new salt bridges into β-sheet 1 and the heme region. An understanding of the molecular factors behind the loss of stability of P450BM3 variants therefore expedites site-directed mutagenesis studies aimed at developing thermostability.
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Affiliation(s)
- Inacrist Geronimo
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, United States
| | - Catherine A. Denning
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - W. Eric Rogers
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Thaer Othman
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, California 92182-1030, United States
| | - David K. Heidary
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Edith C. Glazer
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, United States
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49
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Girvan HM, Munro AW. Applications of microbial cytochrome P450 enzymes in biotechnology and synthetic biology. Curr Opin Chem Biol 2016; 31:136-45. [PMID: 27015292 DOI: 10.1016/j.cbpa.2016.02.018] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 12/11/2022]
Abstract
Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenase enzymes with enormous potential for synthetic biology applications. Across Nature, their substrate range is vast and exceeds that of other enzymes. The range of different chemical transformations performed by P450s is also substantial, and continues to expand through interrogation of the properties of novel P450s and by protein engineering studies. The ability of P450s to introduce oxygen atoms at specific positions on complex molecules makes these enzymes particularly valuable for applications in synthetic biology. This review focuses on the enzymatic properties and reaction mechanisms of P450 enzymes, and on recent studies that highlight their broad applications in the production of oxychemicals. For selected soluble bacterial P450s (notably the high-activity P450-cytochrome P450 reductase enzyme P450 BM3), variants with a multitude of diverse substrate selectivities have been generated both rationally and by random mutagenesis/directed evolution approaches. This highlights the robustness and malleability of the P450 fold, and the capacity of these biocatalysts to oxidise a wide range of chemical scaffolds. This article reviews recent research on the application of wild-type and engineered P450s in the production of important chemicals, including pharmaceuticals and drug metabolites, steroids and antibiotics. In addition, the properties of unusual members of the P450 superfamily that do not follow the canonical P450 catalytic pathway are described.
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Affiliation(s)
- Hazel M Girvan
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Andrew W Munro
- Manchester Institute of Biotechnology, Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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50
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Quesne MG, Senthilnathan D, Singh D, Kumar D, Maldivi P, Sorokin AB, de Visser SP. Origin of the Enhanced Reactivity of μ-Nitrido-Bridged Diiron(IV)-Oxo Porphyrinoid Complexes over Cytochrome P450 Compound I. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02720] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Matthew G. Quesne
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Dhurairajan Senthilnathan
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- Center for
Computational Chemistry, CRD, PRIST University, Vallam, Thanjavur, Tamilnadu 613403, India
| | - Devendra Singh
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Devesh Kumar
- Department
of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow, Uttar Pradesh 226025, India
| | - Pascale Maldivi
- Univ. Grenoble Alpes, INAC-SCIB, Reconnaissance
Ionique et Chimie de Coordination, F-38000 Grenoble, France
- CEA, INAC-SCIB, F-38000 Grenoble, France
| | - Alexander B. Sorokin
- Institut
de Recherches sur la Catalyse et l’Environnement de Lyon (IRCELYON),
UMR 5256, CNRS-Université Lyon 1, 2, av. A. Einstein, 69626 Villeurbanne, France
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology and School of Chemical Engineering and
Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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