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Costa GJ, Egbemhenghe A, Liang R. Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. J Phys Chem B 2023; 127:10987-10999. [PMID: 38096487 DOI: 10.1021/acs.jpcb.3c06311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.
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Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Abel Egbemhenghe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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Qin ZY, Gao S, Zou Y, Liu Z, Wang JB, Houk KN, Arnold FH. Biocatalytic Construction of Chiral Pyrrolidines and Indolines via Intramolecular C(sp 3)-H Amination. ACS CENTRAL SCIENCE 2023; 9:2333-2338. [PMID: 38161360 PMCID: PMC10755850 DOI: 10.1021/acscentsci.3c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024]
Abstract
Nature harnesses exquisite enzymatic cascades to construct N-heterocycles and further uses these building blocks to assemble the molecules of life. Here we report an enzymatic platform to construct important chiral N-heterocyclic products, pyrrolidines and indolines, via abiological intramolecular C(sp3)-H amination of organic azides. Directed evolution of cytochrome P411 (a P450 enzyme with serine as the heme-ligating residue) yielded variant P411-PYS-5149, capable of catalyzing the insertion of alkyl nitrene into C(sp3)-H bonds to build pyrrolidine derivatives with good enantioselectivity and catalytic efficiency. Further evolution of activity on aryl azide substrates yielded variant P411-INS-5151 that catalyzes intramolecular C(sp3)-H amination to afford chiral indolines. In addition, we show that these enzymatic aminations can be coupled with a P411-based carbene transferase or a tryptophan synthase to generate an α-amino lactone or a noncanonical amino acid, respectively, underscoring the power of new-to-nature biocatalysis in complexity-building chemical synthesis.
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Affiliation(s)
- Zi-Yang Qin
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Shilong Gao
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Yike Zou
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - Zhen Liu
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - James B. Wang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Kendall N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095, United States
| | - Frances H. Arnold
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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Meyer ST, Fernandes S, Anderson RE, Pacherille A, Toms B, Kerr WG, Chisholm JD. Structure-Activity Studies on Bis-Sulfonamide SHIP1 Activators. Molecules 2023; 28:8048. [PMID: 38138538 PMCID: PMC10745928 DOI: 10.3390/molecules28248048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
The SH2-containing inositol polyphosphate 5-phosphatase 1 (SHIP1) enzyme opposes the activity of PI3K and therefore is of interest in the treatment of inflammatory disorders. Recent results also indicate that SHIP1 promotes phagolysosomal degradation of lipids by microglia, suggesting that the enzyme may be a target for the treatment of Alzheimer's disease. Therefore, small molecules that increase SHIP1 activity may have benefits in these areas. Recently we discovered a bis-sulfonamide that increases the enzymatic activity of SHIP1. A series of similar SHIP1 activators have been synthesized and evaluated to determine structure-activity relationships and improve in vivo stability. Some new analogs have now been found with improved potency. In addition, both the thiophene and the thiomorpholine in the parent structure can be replaced by groups without a low valent sulfur atom, which provides a way to access activators that are less prone to oxidative degradation.
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Affiliation(s)
- Shea T. Meyer
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Sandra Fernandes
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | | | - Angela Pacherille
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Bonnie Toms
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - William G. Kerr
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - John D. Chisholm
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
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Yang H, Yu F, Qian Z, Huang T, Peng T, Hu Z. Cytochrome P450 for environmental remediation: catalytic mechanism, engineering strategies and future prospects. World J Microbiol Biotechnol 2023; 40:33. [PMID: 38057619 DOI: 10.1007/s11274-023-03823-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/29/2023] [Indexed: 12/08/2023]
Abstract
Environmental pollution is a global concern. Various organic compounds are released into the environment through wastewater, waste gas, and waste residue, ultimately accumulating in the environment and the food chain. This poses a significant threat to both human health and ecology. Currently, a growing body of research has demonstrated that microorganisms employ their Cytochrome P450 (CYP450) system for biodegradation, offering a crucial approach for eliminating these pollutants in environmental remediation. CYP450, a ubiquitous catalyst in nature, includes a vast array of family members distributed widely across various organisms, including bacteria, fungi, and mammals. These enzymes participate in the metabolism of diverse organic compounds. Furthermore, the rapid advancements in enzyme and protein engineering have led to increased utilization of engineered CYP450s in environmental remediation, enhancing their efficiency in pollutant removal. This article presents an overview of the current understanding of various members of the CYP450 superfamily involved in transforming organic pollutants and the engineering of biodegrading CYP450s. Additionally, it explores the catalytic mechanisms, current practical applications of CYP450-based systems, their potential applications, and the prospects in bioremediation.
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Affiliation(s)
- Haichen Yang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Fei Yu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
- Guangdong Research Center of Offshore Environmental Pollution Control Engineering, Shantou University, Shantou, 515063, Guangdong, People's Republic of China.
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55
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [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: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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56
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Wang Z, Wang Z, Wang G, Zhang Q, Wang Q, Wang W. New insight into biodegradation mechanism of phenylurea herbicides by cytochrome P450 enzymes: Successive N-demethylation mechanism. ENVIRONMENT INTERNATIONAL 2023; 182:108332. [PMID: 37988774 DOI: 10.1016/j.envint.2023.108332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
Phenylurea herbicides (PUHs) present one of the most important herbicides, which have cause serious effects on ecological environment and humans. Nowadays enzyme strategy shows great advantages in degradation of PUHs. Here density functional theory (DFT), quantitative structure - activity relationship (QSAR) and quantum mechanics/molecular mechanics (QM/MM) approaches are used to investigate the degradation mechanism of PUHs catalyzed by P450 enzymes. Two successive N-demethylation pathways are identified and two hydrogen abstraction (H-abstraction) reaction pathways are identified as the rate-determining step through high-throughput DFT calculations. The Boltzmann-weighted average energy barrier of the second H-abstraction pathway (19.95 kcal/mol) is higher than that of the first H-abstraction pathway (16.80 kcal/mol). Two QSAR models are established to predict the energy barriers of the two H-abstraction pathways based on the quantum chemical descriptors and mordred molecular descriptors. The determination coefficient (R2) values of QSAR models are > 0.9, which reveal that the established QSAR models have great predictive capability. QM/MM calculations indicate that human P450 enzymes are more efficient in degradation of PUHs than crop and weed P450 enzymes. Correlations between energy barriers and key structural/charge parameters are revealed and key parameters that have influence on degradation efficiency of PUHs are identified. This study provides lateral insights into the biodegradation strategy and removal method of PUHs and valuable information for designing or engineering of highly efficient degradation enzymes and genetically modified crops.
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Affiliation(s)
- Zijian Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Zhong Wang
- Shandong Nuclear and Radiation Safety Monitoring Center, Jinan 250117, PR China
| | - Guoqiang Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Qiao Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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57
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Zhang Y, Yuan M, Wu X, Zhang Q, Wang Y, Zheng L, Chiu T, Zhang H, Lan L, Wang F, Liao Y, Gong X, Yan S, Wang Y, Shen Y, Fu X. The construction and optimization of engineered yeast chassis for efficient biosynthesis of 8-hydroxygeraniol. MLIFE 2023; 2:438-449. [PMID: 38818263 PMCID: PMC10989129 DOI: 10.1002/mlf2.12099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/26/2023] [Accepted: 11/29/2023] [Indexed: 06/01/2024]
Abstract
Microbial production of monoterpenoid indole alkaloids (MIAs) provides a sustainable and eco-friendly means to obtain compounds with high pharmaceutical values. However, efficient biosynthesis of MIAs in heterologous microorganisms is hindered due to low supply of key precursors such as geraniol and its derivative 8-hydroxygeraniol catalyzed by geraniol 8-hydroxylase (G8H). In this study, we developed a facile evolution platform to screen strains with improved yield of geraniol by using the SCRaMbLE system embedded in the Sc2.0 synthetic yeast and confirmed the causal role of relevant genomic targets. Through genome mining, we identified several G8H enzymes that perform much better than the commonly used CrG8H for 8-hydroxygeraniol production in vivo. We further showed that the N-terminus of these G8H enzymes plays an important role in cellular activity by swapping experiments. Finally, the combination of the engineered chassis, optimized biosynthesis pathway, and utilization of G8H led to the final strain with more than 30-fold improvement in producing 8-hydroxygeraniol compared with the starting strain. Overall, this study will provide insights into the construction and optimization of yeast cells for efficient biosynthesis of 8-hydroxygeraniol and its derivatives.
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Affiliation(s)
- Yu Zhang
- BGI ResearchShenzhenChina
- BGI ResearchHangzhouChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
| | | | | | | | | | | | | | | | | | | | | | - Xuemei Gong
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
| | - Shirui Yan
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
| | - Yun Wang
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
| | - Yue Shen
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
| | - Xian Fu
- BGI ResearchShenzhenChina
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI ResearchShenzhenChina
- BGI ResearchChangzhouChina
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58
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Wang S, Sun D, Wu Z, Zhao Y, Wang Y. The elusive reaction mechanism of Mn(II)-mediated benzylic oxidation of alkylarene by H 2O 2: a gem-diol mechanism or a dual hydrogen abstraction mechanism? Dalton Trans 2023. [PMID: 37997638 DOI: 10.1039/d3dt02943c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The direct oxygenation of alkylarenes at the benzylic position employing bioinspired nonheme catalysts has emerged as a promising strategy for the production of bioactive arene ketone scaffolds in drugs. However, the structure-activity relationship of the active species and the mechanism of these reactions remain elusive. Herein, the reaction mechanism of the Mn(II)-mediated benzylic oxygenation of phenylbutanoic acid (PBA) to 4-oxo-4-phenylbutyric acid (4-oxo-PBA) by H2O2 was investigated using density functional theory calculations. The calculated results demonstrated that the MnIII-OOH species (1) is a sluggish oxidant and needs to be converted to a high-valent manganese-oxo species (2). The conversion of PBA to 4-oxo-PBA by 2 occurs via the consecutive hydroxylation of PBA to 4-hydroxyl-4-phenylbutyric acid (4-OH-PBA) and the alcohol oxidation of 4-OH-PBA to 4-oxo-PBA. The hydroxylation of PBA proceeds via a novel hydride transfer/hydroxyl-rebound mechanism and the alcohol oxidation of 4-OH-PBA occurs via three pathways (gem-diol, dual hydrogen abstraction (DHA), and reversed-DHA pathways). The regio-selectivity of benzylic oxidations was caused by a strong π-π stacking interaction between the pyridine ring of the nonheme ligand and the phenyl ring of the substrate. These mechanistic findings enrich the knowledge of biomimetic alcohol oxidations and play a positive role in the rational design of new non-heme catalysts.
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Affiliation(s)
- Shoujun Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China.
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China.
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Zhimin Wu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China.
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China.
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China.
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
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59
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Di Q, Dong L, Jiang L, Liu X, Cheng P, Liu B, Yu G. Genome-wide association study and RNA-seq identifies GmWRI1-like transcription factor related to the seed weight in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1268511. [PMID: 38046612 PMCID: PMC10691256 DOI: 10.3389/fpls.2023.1268511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
The cultivated soybean (Glycine max (L.) Merrill) is domesticated from wild soybean (Glycine soja) and has heavier seeds with a higher oil content than the wild soybean. In this study, we identified a novel candidate gene associated with SW using a genome-wide association study (GWAS). The candidate gene GmWRI14-like was detected by GWAS analysis in three consecutive years. By constructing transgenic soybeans overexpressing the GmWRI14-like gene and gmwri14-like soybean mutants, we found that overexpression of GmWRI14-like increased the SW and increased total fatty acid content. We then used RNA-seq and qRT-PCR to identify the target genes directly or indirectly regulated by GmWRI14-like. Transgenic soyabeans overexpressing GmWRI14-like showed increased accumulation of GmCYP78A50 and GmCYP78A69 than non-transgenic soybean lines. Interestingly, we also found that GmWRI14-like proteins could interact with GmCYP78A69/GmCYP78A50 using yeast two-hybrid and bimolecular fluorescence complementation. Our results not only shed light on the genetic architecture of cultivated soybean SW, but also lays a theoretical foundation for improving the SW and oil content of soybeans.
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Affiliation(s)
- Qin Di
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Li Jiang
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Xiaoyi Liu
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, College of Life Sciences, Guangzhou University, Guangzhou, Guangdong, China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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Qunies AM, Spitznagel BD, Du Y, David Weaver C, Emmitte KA. Design, synthesis, and biological evaluation of a novel series of 1,2,4-oxadiazole inhibitors of SLACK potassium channels: Identification of in vitro tool VU0935685. Bioorg Med Chem 2023; 95:117487. [PMID: 37812884 PMCID: PMC10842602 DOI: 10.1016/j.bmc.2023.117487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Abstract
Malignant migrating partial seizure of infancy (MMPSI) is a devastating and pharmacoresistant form of infantile epilepsy. MMPSI has been linked to multiple gain-of-function (GOF) mutations in the KCNT1 gene, which encodes for a potassium channel often referred to as SLACK. SLACK channels are sodium-activated potassium channels distributed throughout the central nervous system (CNS) and the periphery. The investigation described here aims to discover SLACK channel inhibitor tool compounds and profile their pharmacokinetic and pharmacodynamic properties. A SLACK channel inhibitor VU0531245 (VU245) was identified via a high-throughput screen (HTS) campaign. Structure-activity relationship (SAR) studies were conducted in five distinct regions of the hit VU245. VU245 analogs were evaluated for their ability to affect SLACK channel activity using a thallium flux assay in HEK-293 cells stably expressing wild-type (WT) human SLACK. Selected analogs were tested for metabolic stability in mouse liver microsomes and plasma-protein binding in mouse plasma. The same set of analogs was tested via thallium flux for activity versus human A934T SLACK and other structurally related potassium channels, including SLICK and Maxi-K. In addition, potencies for selected VU245 analogs were obtained using whole-cell electrophysiology (EP) assays in CHO cells stably expressing WT human SLACK through an automated patch clamp system. Results revealed that this scaffold tolerates structural changes in some regions, with some analogs demonstrating improved SLACK inhibitory activity, good selectivity against the other channels tested, and modest improvements in metabolic clearance. Analog VU0935685 represents a new, structurally distinct small-molecule inhibitor of SLACK channels that can serve as an in vitro tool for studying this target.
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Affiliation(s)
- Alshaima'a M Qunies
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | | | - Yu Du
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - C David Weaver
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Kyle A Emmitte
- Department of Pharmaceutical Sciences, UNT System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
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61
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Yildiz I. Computational insights on the hydride and proton transfer mechanisms of L-proline dehydrogenase. PLoS One 2023; 18:e0290901. [PMID: 37967056 PMCID: PMC10651016 DOI: 10.1371/journal.pone.0290901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/18/2023] [Indexed: 11/17/2023] Open
Abstract
L-Proline dehydrogenase (ProDH) is a flavin-dependent oxidoreductase, which catalyzes the oxidation of L-proline to (S)-1-pyrroline-5-carboxylate. Based on the experimental studies, a stepwise proton and hydride transfer mechanism is supported. According to this mechanism, the amino group of L-proline is deprotonated by a nearby Lys residue, which is followed by the hydride transfer process from C5 position of L-proline to N5 position of isoalloxazine ring of FAD. It was concluded that the hydride transfer step is rate limiting in the reductive half-reaction, however, in the overall reaction, the oxidation of FAD is the rate limiting step. In this study, we performed a computational mechanistic investigation based on ONIOM method to elucidate the mechanism of the reductive half-reaction corresponding to the oxidation of L-proline into iminoproline. Our calculations support the stepwise mechanism in which the deprotonation occurs initially as a fast step as result of a proton transfer from L-proline to the Lys residue. Subsequently, a hydride ion transfers from L-proline to FAD with a higher activation barrier. The enzyme-product complex showed a strong interaction between reduced FAD and iminoproline, which might help to explain why a step in the oxidative half-reaction is rate-limiting.
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Affiliation(s)
- Ibrahim Yildiz
- Chemistry Department and Applied Material Chemistry Center (AMCC), Khalifa University, Abu Dhabi, UAE
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62
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Yamaguchi K, Miyagawa K, Shoji M, Kawakami T, Isobe H, Yamanaka S, Nakajima T. Theoretical elucidation of the structure, bonding, and reactivity of the CaMn 4O x clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01053-7. [PMID: 37945776 DOI: 10.1007/s11120-023-01053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.
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Affiliation(s)
- Kizashi Yamaguchi
- Center for Quantum Information and Quantum Biology, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan.
- SANKEN, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
| | - Koichi Miyagawa
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Mitsuo Shoji
- Center of Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takashi Kawakami
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Takahito Nakajima
- RIKEN Center for Computational Science, Kobe, Hyogo, 650-0047, Japan
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63
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Kardam V, Dubey KD. Tyr 118-Mediated Electron Transfer is Key to the Chlorite Decomposition in Heme-Dependent Chlorite Dismutase. Inorg Chem 2023; 62:18322-18330. [PMID: 37885054 DOI: 10.1021/acs.inorgchem.3c03334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Chlorite dismutase (Cld) is a crucial enzyme that catalyzes the decomposition of chlorite ions into chloride ions (Cl-) and molecular oxygen (O2). Despite playing an important role in the detoxification of toxic chlorite ions, the mechanism of cleavage of the Cl-O bond by Cld remains highly debatable. The present study highlights the mechanism of such Cl-O bond cleavage in Cld using sophisticated computational tools such as hybrid quantum mechanical/molecular mechanical calculations and long-time scale molecular dynamics simulations. Here, we show that Cld forms a high spin ferric hexacoordinated substrate adduct in the presence of a chlorite ion, which subsequently reduces to a ferrous state. Our study shows a stepwise pathway with the homolytic cleavage of the Cl-O bond that produces a high spin Fe(III)-OH species and a diradicaloid species formed by the combination of a chlorine-based ClO• radical and a protein-based tyrosine118• radical. The findings provide significant insights into Cl-O bond cleavage and O2 formation which shows a crucial role of the tyrosine118 during the electron transfer process.
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Affiliation(s)
- Vandana Kardam
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence Delhi NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence Delhi NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
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64
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Yildiz I. Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase. Chemphyschem 2023; 24:e202300431. [PMID: 37540527 DOI: 10.1002/cphc.202300431] [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: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/05/2023]
Abstract
D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.
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Affiliation(s)
- Ibrahim Yildiz
- Khalifa University, Chemistry Department and Applied Material Chemistry Center (AMCC), PO Box, 127788, Abu Dhabi, UAE
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65
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Yamaguchi K, Isobe H, Shoji M, Kawakami T, Miyagawa K. The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations. Molecules 2023; 28:7119. [PMID: 37894598 PMCID: PMC10609222 DOI: 10.3390/molecules28207119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).
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Affiliation(s)
- Kizashi Yamaguchi
- SANKEN, Osaka University, Ibaraki 567-0047, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka 560-0043, Osaka, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Okayama, Japan;
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan;
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
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66
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Zhang Y, Mokkawes T, de Visser SP. Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides. Angew Chem Int Ed Engl 2023; 62:e202310785. [PMID: 37641517 DOI: 10.1002/anie.202310785] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through a 1,2-fluorine shift in an electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, in the absence of a proton donor a strong Fe-F bond can be obtained as shown from the calculations.
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Affiliation(s)
- Yi Zhang
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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67
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Mori T, Abe I. Functional analysis of a fungal P450 enzyme. Methods Enzymol 2023; 693:171-190. [PMID: 37977730 DOI: 10.1016/bs.mie.2023.09.003] [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] [Indexed: 11/19/2023]
Abstract
Fungal cytochrome P450s participate in various physiological reactions, including the synthesis of internal cellular components, metabolic detoxification of xenobiotic compounds, and oxidative modification of natural products. Although functional analysis reports of fungal P450s continue to grow, there are still some difficulties as compared to prokaryotic P450s, because most of these fungal enzymes are transmembrane proteins. In this chapter, we will describe the methods for heterologous expression, in vivo analysis, enzyme preparation, and in vitro enzyme assays of the fungal P450 enzyme Trt6 and isomerase Trt14, which play important roles in the divergence of the biosynthetic pathway of terretonins, as a model for the functional analysis of fungal P450 enzymes.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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68
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Stout CN, Renata H. Self-sufficient P450-reductase chimeras for biocatalysis. Methods Enzymol 2023; 693:51-71. [PMID: 37977738 DOI: 10.1016/bs.mie.2023.09.010] [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] [Indexed: 11/19/2023]
Abstract
In recent years, cytochromes P450 have emerged as powerful, versatile biocatalysts for the site-selective functionalization of small molecules. Catalyzing an impressive range of chemical transformations, these enzymes have been widely used to effect C-H oxidation, biaryl coupling, and carbon-heteroatom bond formation, among many other reactions. However, the majority of P450s are multi-protein systems that employ secondary redox partners in key steps of the catalytic cycle, which limits their broader applicability. In response, the discovery of self-sufficient P450s, such as P450BM3 and P450RhF, has provided a template for the construction of artificial, self-sufficient P450-reductase fusions. In this chapter, we describe a procedure for the design, assembly, and application of two engineered, self-sufficient P450s of Streptomyces origin via fusion with an exogenous reductase domain. In particular, we generated artificial chimeras of P450s PtmO5 and TleB by linking them covalently with the reductase domain of P450RhF. Upon verification of their activities, both enzymes were employed in preparative-scale biocatalytic reactions. This approach can feasibly be applied to any P450 of interest, thereby laying the groundwork for the production of self-sufficient P450s for diverse chemical applications.
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Affiliation(s)
- Carter N Stout
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, CA, United States
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, TX, United States.
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69
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Chen H, Fu W, Yang Y. P450-catalyzed atom transfer radical cyclization. Methods Enzymol 2023; 693:31-49. [PMID: 37977735 PMCID: PMC11289761 DOI: 10.1016/bs.mie.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Cytochromes P450 have been extensively studied for both fundamental enzymology and biotechnological applications. Over the past decade, by taking inspiration from synthetic organic chemistry, new classes of P450-catalyzed reactions that were not previously encountered in the biological world have been developed to address challenging problems in organic chemistry and asymmetric catalysis. In particular, by repurposing and evolving P450 enzymes, stereoselective biocatalytic atom transfer radical cyclization (ATRC) was developed as a new means to impose stereocontrol over transient free radical intermediates. In this chapter, we describe the detailed experimental protocol for the directed evolution of P450 atom transfer radical cyclases. We also delineate protocols for analytical and preparative scale biocatalytic atom transfer radical cyclization processes. These methods will find application in the development of new P450-catalyzed radical reactions, as well as other synthetically useful processes.
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Affiliation(s)
- Heyu Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States
| | - Wenzhen Fu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States; Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, CA, United States.
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70
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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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71
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Liu S, Zheng Q, Bai F. Differences of Atomic-Level Interactions between Midazolam and Two CYP Isoforms 3A4 and 3A5. Molecules 2023; 28:6900. [PMID: 37836743 PMCID: PMC10574787 DOI: 10.3390/molecules28196900] [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: 07/16/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
CYP 3A4 and CYP 3A5 are two important members of the human cytochrome P450 family. Although their overall structures are similar, the local structures of the active site are different, which directly leads to obvious individual differences in drug metabolic efficacy and toxicity. In this work, midazolam (MDZ) was selected as the probe substrate, and its interaction with two proteins, CYP 3A4 and CYP 3A5, was studied by molecular dynamics simulation (MD) along with the calculation of the binding free energy. The results show that two protein-substrate complexes have some similarities in enzyme-substrate binding; that is, in both complexes, Ser119 forms a high occupancy hydrogen bond with MDZ, which plays a key role in the stability of the interaction between MDZ and the enzymes. However, the complex formed by CYP 3A4 and MDZ is more stable, which may be attributed to the sandwich structure formed by the fluorophenyl group of the substrate with Leu216 and Leu482. Our study interprets the binding differences between two isoform-substrate complexes and reveals a structure-function relationship from the atomic perspective, which is expected to provide a theoretical basis for accurately measuring the effectiveness and toxicity of drugs for individuals in the era of precision medicine.
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Affiliation(s)
- Shuhui Liu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China;
- School and Hospital of Stomatology, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China;
| | - Fuquan Bai
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China;
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72
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Park J, Lee HH, Moon H, Lee N, Kim S, Kim JE, Lee Y, Min K, Kim H, Choi GJ, Lee YW, Seo YS, Son H. A combined transcriptomic and physiological approach to understanding the adaptive mechanisms to cope with oxidative stress in Fusarium graminearum. Microbiol Spectr 2023; 11:e0148523. [PMID: 37671872 PMCID: PMC10581207 DOI: 10.1128/spectrum.01485-23] [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: 04/07/2023] [Accepted: 07/04/2023] [Indexed: 09/07/2023] Open
Abstract
In plant-pathogen interactions, oxidative bursts are crucial for plants to defend themselves against pathogen infections. Rapid production and accumulation of reactive oxygen species kill pathogens directly and cause local cell death, preventing pathogens from spreading to adjacent cells. Meanwhile, the pathogens have developed several mechanisms to tolerate oxidative stress and successfully colonize plant tissues. In this study, we investigated the mechanisms responsible for resistance to oxidative stress by analyzing the transcriptomes of six oxidative stress-sensitive strains of the plant pathogenic fungus Fusarium graminearum. Weighted gene co-expression network analysis identified several pathways related to oxidative stress responses, including the DNA repair system, autophagy, and ubiquitin-mediated proteolysis. We also identified hub genes with high intramodular connectivity in key modules and generated deletion or conditional suppression mutants. Phenotypic characterization of those mutants showed that the deletion of FgHGG4, FgHGG10, and FgHGG13 caused sensitivity to oxidative stress, and further investigation on those genes revealed that transcriptional elongation and DNA damage responses play roles in oxidative stress response and pathogenicity. The suppression of FgHGL7 also led to hypersensitivity to oxidative stress, and we demonstrated that FgHGL7 plays a crucial role in heme biosynthesis and is essential for peroxidase activity. This study increases the understanding of the adaptive mechanisms to cope with oxidative stress in plant pathogenic fungi. IMPORTANCE Fungal pathogens have evolved various mechanisms to overcome host-derived stresses for successful infection. Oxidative stress is a representative defense system induced by the host plant, and fungi have complex response systems to cope with it. Fusarium graminearum is one of the devastating plant pathogenic fungi, and understanding its pathosystem is crucial for disease control. In this study, we investigated adaptive mechanisms for coping with oxidative stress at the transcriptome level using oxidative stress-sensitive strains. In addition, by introducing genetic modification technique such as CRISPR-Cas9 and the conditional gene expression system, we identified pathways/genes required for resistance to oxidative stress and also for virulence. Overall, this study advances the understanding of the oxidative stress response and related mechanisms in plant pathogenic fungi.
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Affiliation(s)
- Jiyeun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Heeji Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Nahyun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sieun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jung-Eun Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Jeju, Republic of Korea
| | - Yoonji Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Kyunghun Min
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Hun Kim
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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73
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Podgorski MN, Keto AB, Coleman T, Bruning JB, De Voss JJ, Krenske EH, Bell SG. The Oxidation of Oxygen and Sulfur-Containing Heterocycles by Cytochrome P450 Enzymes. Chemistry 2023; 29:e202301371. [PMID: 37338048 DOI: 10.1002/chem.202301371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The cytochrome P450 (CYP) superfamily of monooxygenase enzymes play important roles in the metabolism of molecules which contain heterocyclic, aromatic functional groups. Here we study how oxygen- and sulfur-containing heterocyclic groups interact with and are oxidized using the bacterial enzyme CYP199A4. This enzyme oxidized both 4-(thiophen-2-yl)benzoic acid and 4-(thiophen-3-yl)benzoic acid almost exclusively via sulfoxidation. The thiophene oxides produced were activated towards Diels-Alder dimerization after sulfoxidation, forming dimeric metabolites. Despite X-ray crystal structures demonstrating that the aromatic carbon atoms of the thiophene ring were located closer to the heme than the sulfur, sulfoxidation was still favoured with 4-(thiophen-3-yl)benzoic acid. These results highlight a preference of this cytochrome P450 enzyme for sulfoxidation over aromatic hydroxylation. Calculations predict a strong preference for homodimerization of the enantiomers of the thiophene oxides and the formation of a single major product, in broad agreement with the experimental data. 4-(Furan-2-yl)benzoic acid was oxidized to 4-(4'-hydroxybutanoyl)benzoic acid using a whole-cell system. This reaction proceeded via a γ-keto-α,β-unsaturated aldehyde species which could be trapped in vitro using semicarbazide to generate a pyridazine species. The combination of the enzyme structures, the biochemical data and theoretical calculations provides detailed insight into the formation of the metabolites formed from these heterocyclic compounds.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Angus B Keto
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Tom Coleman
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld, 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
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74
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Wu Z, Zhang X, Gao L, Sun D, Zhao Y, Nam W, Wang Y. Elusive Active Intermediates and Reaction Mechanisms of ortho-/ ipso-Hydroxylation of Benzoic Acid by Hydrogen Peroxide Mediated by Bioinspired Iron(II) Catalysts. Inorg Chem 2023; 62:14261-14278. [PMID: 37604675 DOI: 10.1021/acs.inorgchem.3c01576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Aromatic hydroxylation of benzoic acids (BzOH) to salicylates and phenolates is fundamentally interesting in industrial chemistry. However, key mechanistic uncertainties and dichotomies remain after decades of effort. Herein, the elusive mechanism of the competitive ortho-/ipso-hydroxylation of BzOH by H2O2 mediated by a nonheme iron(II) catalyst was comprehensively investigated using density functional theory calculations. Results revealed that the long-postulated FeV(O)(anti-BzO) oxidant is an FeIV(O)(anti-BzO•) species 2 (anti- and syn- are defined by the orientation of the carboxyl oxygen of BzO to the oxo), which rules out the noted two-oxidant mechanism proposed previously. We propose a new mechanism in which, following the formation of an FeV(O)(syn-BzO) species (3) and its electromer FeIV(O)(syn-BzO•) (3'), 3/3' either converts to salicylate and phenolate via intramolecular self-hydroxylation (route A) or acts as an oxidant to oxygenate another BzOH to generate the same products (route B). In route A, the rotation of the BzO group along the C-O bond forms 2, in which the BzO group is orientated by π-π stacking interactions. An electrophilic ipso-addition forms a phenolate by concomitant decarboxylation or an ortho-attack forms a cationic complex, which readily undergoes an NIH shift and a BzOH-assisted proton shift to form a salicylate. In route B, 3 oxidizes an additional BzOH molecule directed by hydrogen bonding and π-π stacking interactions. In both routes, selectivity is determined by the chemical property of the BzO ring. These mechanistic findings provide a clear mechanistic scenario and enrich the knowledge of hydroxylation of aromatic acids.
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Affiliation(s)
- Zhimin Wu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Xuan Zhang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Lanping Gao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
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75
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Zhao Y, Hansen NL, Duan YT, Prasad M, Motawia MS, Møller BL, Pateraki I, Staerk D, Bak S, Miettinen K, Kampranis SC. Biosynthesis and biotechnological production of the anti-obesity agent celastrol. Nat Chem 2023; 15:1236-1246. [PMID: 37365337 DOI: 10.1038/s41557-023-01245-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 05/19/2023] [Indexed: 06/28/2023]
Abstract
Obesity is a major health risk still lacking effective pharmacological treatment. A potent anti-obesity agent, celastrol, has been identified in the roots of Tripterygium wilfordii. However, an efficient synthetic method is required to better explore its biological utility. Here we elucidate the 11 missing steps for the celastrol biosynthetic route to enable its de novo biosynthesis in yeast. First, we reveal the cytochrome P450 enzymes that catalyse the four oxidation steps that produce the key intermediate celastrogenic acid. Subsequently, we show that non-enzymatic decarboxylation-triggered activation of celastrogenic acid leads to a cascade of tandem catechol oxidation-driven double-bond extension events that generate the characteristic quinone methide moiety of celastrol. Using this acquired knowledge, we have developed a method for producing celastrol starting from table sugar. This work highlights the effectiveness of combining plant biochemistry with metabolic engineering and chemistry for the scalable synthesis of complex specialized metabolites.
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Affiliation(s)
- Yong Zhao
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Nikolaj L Hansen
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Yao-Tao Duan
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Meera Prasad
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Mohammed S Motawia
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Birger L Møller
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Irini Pateraki
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Bak
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
| | - Karel Miettinen
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
| | - Sotirios C Kampranis
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark.
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76
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Zhang Y, Chu JM. Computational Mechanistic Investigations of Biocatalytic Nitrenoid C-H Functionalizations via Engineered Heme Proteins. Chembiochem 2023; 24:e202300260. [PMID: 37134298 DOI: 10.1002/cbic.202300260] [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: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/05/2023]
Abstract
Engineered heme proteins were developed to possess numerous excellent biocatalytic nitrenoid C-H functionalizations. Computational approaches such as density functional theory (DFT), hybrid quantum mechanics/molecular mechanics (QM/MM), and molecular dynamics (MD) calculations were employed to help understand some important mechanistic aspects of these heme nitrene transfer reactions. This review summarizes advances of computational reaction pathway results of these biocatalytic intramolecular and intermolecular C-H aminations/amidations, focusing on mechanistic origins of reactivity, regioselectivity, enantioselectivity, diastereoselectivity as well as effects of substrate substituent, axial ligand, metal center, and protein environment. Some important common and distinctive mechanistic features of these reactions were also described with brief outlook of future development.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
| | - Jia-Min Chu
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
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77
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Ye L, Jiang S, Hu J, Wang M, Weng T, Wu F, Cai L, Sun Z, Ma L. Induction of Metabolic Reprogramming in Kidney by Singlet Diradical Nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2301338. [PMID: 37295411 DOI: 10.1002/adma.202301338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/05/2023] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic compounds with an open-shell singlet diradical ground state, namely singlet diradicals, have recently gained attention in the fields of organic electronics, photovoltaics, and spintronics owing to their unique electronic structures and properties. Notably, singlet diradicals exhibit tunable redox amphoterism, which makes them excellent redox-active materials for biomedical applications. However, the safety and therapeutic efficacy of singlet diradicals in biological systems have not yet been explored. Herein, the study presents a newly designed singlet diradical nanomaterial, diphenyl-substituted biolympicenylidene (BO-Ph), exhibiting low cytotoxicity in vitro, non-significant acute nephrotoxicity in vivo, and the ability to induce metabolic reprogramming in kidney organoids. Integrated transcriptome and metabolome analyses reveal that the metabolism of BO-Ph stimulates glutathione (GSH) synthesis and fatty acid degradation, increases the levels of intermediates in the tricarboxylic acid (TCA) and carnitine cycles, and eventually boosts oxidative phosphorylation (OXPHOS) under redox homeostasis. Benefits of BO-Ph-induce metabolic reprogramming in kidney organoids include enhancing cellular antioxidant capacity and promoting mitochondrial function. The results of this study can facilitate the application of singlet diradical materials in the treatment of clinical conditions induced by mitochondrial abnormalities in kidney.
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Affiliation(s)
- Lei Ye
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Shengwei Jiang
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, 518055, China
| | - Jinlian Hu
- Institute of Molecular Plus, Department of Chemistry and Haihe Laboratory of Sustainable Chemical Transformations, Tianjin University, Tianjin, 300072, China
| | - Mingzhe Wang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Taoyu Weng
- Institute of Molecular Plus, Department of Chemistry and Haihe Laboratory of Sustainable Chemical Transformations, Tianjin University, Tianjin, 300072, China
| | - Feng Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Liangyu Cai
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhe Sun
- Institute of Molecular Plus, Department of Chemistry and Haihe Laboratory of Sustainable Chemical Transformations, Tianjin University, Tianjin, 300072, China
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, 518055, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, 518132, China
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78
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Majumder P, Basak A, Kuiry H, Sasmal HS, Karak S, Saha P, Chandra B, Sen Gupta S, Banerjee R. Proximity-Enabled Photochemical C-H Functionalization using a Covalent Organic Framework-Confined Fe 2IV-μ-oxo Species in Water. J Am Chem Soc 2023; 145:18855-18864. [PMID: 37587434 DOI: 10.1021/jacs.3c04409] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Water has been recognized as an excellent solvent for maneuvering both the catalytic activity and selectivity, especially in the case of heterogeneous catalysis. However, maintaining the active catalytic species in their higher oxidation states (IV/V) while retaining the catalytic activity and recyclability in water is an enormous challenge. Herein, we have developed a solution to this problem using covalent organic frameworks (COFs) to immobilize the (Et4N)2[FeIII(Cl)bTAML] molecules, taking advantage of the COF's morphology and surface charge. By using the visible light and [CoIII(NH3)5Cl]Cl2 as a sacrificial electron acceptor within the COF, we have successfully generated and stabilized the [(bTAML)FeIV-O-FeIV(bTAML)]- species in water. The COF backbone simultaneously acts as a porous host and a photosensitizer. This is the first time that the photochemically generated Fe2IV-μ-oxo radical cation species has demonstrated high catalytic activity with moderate to high yield for the selective oxidation of the unactivated C-H bonds, even in water. To enhance the catalytic activity and achieve good recyclability, we have developed a TpDPP COF film by transforming the TpDPP COF nanospheres. We have achieved the regio- and stereoselective functionalization of unactivated C-H bonds of alkanes and alkenes (3°:2° = 102:1 for adamantane with the COF film), which is improbable in homogeneous conditions. The film exhibits C-H bond oxidation with higher catalytic yield (32-98%) and a higher degree of selectivity (cis/trans = 74:1; 3°:2° = 100:1 for cis-decalin).
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Affiliation(s)
- Poulami Majumder
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Ananda Basak
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Himangshu Kuiry
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Himadri Sekhar Sasmal
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Suvendu Karak
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Paramita Saha
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, West Bengal, India
| | - Bittu Chandra
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Sayam Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
| | - Rahul Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741246, India
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79
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Mattioli S, Moretti E, Castellini C, Signorini C, Corsaro R, Angelucci E, Collodel G. Can Dietary n-3 Polyunsaturated Fatty Acids Affect Apelin and Resolvin in Testis and Sperm of Male Rabbits? Molecules 2023; 28:6188. [PMID: 37687017 PMCID: PMC10488499 DOI: 10.3390/molecules28176188] [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: 07/17/2023] [Revised: 08/12/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Apelin and other novel adipokines have been associated with normal and pathological reproductive conditions in humans and animals. In this paper, we used a rabbit model to investigate if apelin and resolvin (RvD1) in testis and sperm are associated with the oxidative status of semen and serum testosterone of rabbits fed different diets enriched with flaxseed (alpha-linolenic acid, ALA) or with fish oil (eicosapentaenoic acid, EPA, docosapentaenoic acid, DPAn-3, and docosahexaenoic acid, DHA). Apelin and RvD1 were detected by ELISA and apelin and the apelin receptor by immunofluorescence. Increased levels of apelin in testes from both enriched diets were shown, particularly in the interstitial tissue of the FLAX group. The FLAX diet enhanced serum testosterone, and both enriched diets showed higher levels of malondialdehyde and RvD1 in the testis. In ejaculated sperm, apelin and its receptor were localized in the entire tail of the control and both treated groups. The ryanodine receptor was investigated in rabbit testis; the fluorescent signal was increased in mature elongated spermatids of the FLAX group. In conclusion, this data seems to indicate that FLAX increases the amount of apelin in testis, suggesting an involvement of this adipokine in male reproduction and probably a role in the resolution of the inflammatory status.
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Affiliation(s)
- Simona Mattioli
- Department of Agricultural, Environmental, and Food Science, University of Perugia, Borgo XX Giugno 74, 06123 Perugia, Italy; (S.M.); (C.C.); (E.A.)
| | - Elena Moretti
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (R.C.); (G.C.)
| | - Cesare Castellini
- Department of Agricultural, Environmental, and Food Science, University of Perugia, Borgo XX Giugno 74, 06123 Perugia, Italy; (S.M.); (C.C.); (E.A.)
| | - Cinzia Signorini
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (R.C.); (G.C.)
| | - Roberta Corsaro
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (R.C.); (G.C.)
| | - Elisa Angelucci
- Department of Agricultural, Environmental, and Food Science, University of Perugia, Borgo XX Giugno 74, 06123 Perugia, Italy; (S.M.); (C.C.); (E.A.)
| | - Giulia Collodel
- Department of Molecular and Developmental Medicine, University of Siena, Policlinico Santa Maria alle Scotte, Viale Bracci 14, 53100 Siena, Italy; (C.S.); (R.C.); (G.C.)
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80
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Zhang X, Liu Y. Direct Electrophilic Attack of Compound I on the Indole Ring in the Peroxygenase Mechanism of Dehaloperoxidase DHP B in Degrading Haloindole: Electron Transfer Promotes the Reaction. Inorg Chem 2023; 62:13230-13240. [PMID: 37561650 DOI: 10.1021/acs.inorgchem.3c01425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The H2O2-dependent degradation of haloindole catalyzed by the dehaloperoxidase (DHP) from Amphitrite ornate has been reported to employ the peroxygenase mechanism, and the two oxidized products 5-halo-2-oxindole and 5-halo-3-oxindole have a similar amount. According to a previous experimental study, compound I (Cpd I) was suggested to be responsible for triggering the reaction, and the reaction may undergo three possible intermediates; however, the reaction details are still unclear. To clarify the reaction mechanism of DHP, the computational model was constructed on the basis of the high-resolution crystal structure, and a series of the quantum mechanical/molecular mechanical calculations were performed. Based on our calculation results, it is confirmed that the reaction starts from the direct electrophilic attack of Cpd I on the indole ring of the substrate, and the resulted intermediate contains both a carbocation and an oxygen anion, whereas the common hydrogen abstraction by Cpd I was calculated to correspond to a relatively higher barrier. In addition, a net electron transfer from the substrate to the iron center is observed during the attack of Cpd I on the indole ring; therefore, the carbocation/oxygen anion intermediate can easily undergo an intramolecular hydride transfer to form the product 5-halo-2-oxindole or isomerize to the epoxide intermediate which finally generates another product 5-halo-3-oxindole. It is the zwitterionic characteristic of the intermediate that makes the intermolecular hydride transfer quite easy, and it is the high electron affinity of the iron center that promotes the single-electron oxidation of the reaction intermediate. Our calculations well explain the formation of two oxidized products 5-halo-2-oxindole and 5-halo-3-oxindole.
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Affiliation(s)
- Xianghui Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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81
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Carter S, Tao W, Majumder R, Sokolov AY, Zhang S. Two-State Hydrogen Atom Transfer Reactivity of Unsymmetric [Cu 2(O)(NO)] 2+ Complexes. J Am Chem Soc 2023; 145:17779-17785. [PMID: 37540110 DOI: 10.1021/jacs.3c04510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
We report the temperature-dependent spin switching of dicopper oxo nitrosyl [Cu2(O)(NO)]2+ complexes and their influence on hydrogen atom transfer (HAT) reactivity. Electron paramagnetic resonance (EPR) and Evans method analysis suggest that [Cu2(O)(NO)]2+ complexes transition from the S = 1/2 to the S = 3/2 state around ca. 202 K. At low temperatures (198 K) where S = 3/2 dominates, a strong correlation between the rate of HAT (kHAT) and the population of the S = 1/2 state was identified (R2 = 0.988), suggesting that the HAT by [Cu2(O)(NO)]2+ complexes proceeds by the S = 1/2 isomer. Installation of functional groups that introduce an unsymmetric secondary coordination environment accelerates the HAT rates through perturbation of the spin equilibria. Given the often unsymmetric coordination sphere of bimetallic active sites in natural proteins, we anticipate that similar strategies could be employed by metalloenzymes to control HAT reactions.
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Affiliation(s)
- Samantha Carter
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Wenjie Tao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Rajat Majumder
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Alexander Yu Sokolov
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiyu Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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82
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Nemoto DT, Bian KJ, Kao SC, West JG. Radical ligand transfer: a general strategy for radical functionalization. Beilstein J Org Chem 2023; 19:1225-1233. [PMID: 37614927 PMCID: PMC10442530 DOI: 10.3762/bjoc.19.90] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023] Open
Abstract
The place of alkyl radicals in organic chemistry has changed markedly over the last several decades, evolving from challenging-to-generate "uncontrollable" species prone to side reactions to versatile reactive intermediates enabling construction of myriad C-C and C-X bonds. This maturation of free radical chemistry has been enabled by several advances, including the proliferation of efficient radical generation methods, such as hydrogen atom transfer (HAT), alkene addition, and decarboxylation. At least as important has been innovation in radical functionalization methods, including radical-polar crossover (RPC), enabling these intermediates to be engaged in productive and efficient bond-forming steps. However, direct engagement of alkyl radicals remains challenging. Among these functionalization approaches, a bio-inspired mechanistic paradigm known as radical ligand transfer (RLT) has emerged as a particularly promising and versatile means of forming new bonds catalytically to alkyl radicals. This development has been driven by several key features of RLT catalysis, including the ability to form diverse bonds (including C-X, C-N, and C-S), the use of simple earth abundant element catalysts, and the intrinsic compatibility of this approach with varied radical generation methods, including HAT, radical addition, and decarboxylation. Here, we provide an overview of the evolution of RLT catalysis from initial studies to recent advances and provide a conceptual framework we hope will inspire and enable future work using this versatile elementary step.
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Affiliation(s)
- David T Nemoto
- Department of Chemistry, Rice University, 6100 Main St MS 602, Houston, TX 77005, USA
| | - Kang-Jie Bian
- Department of Chemistry, Rice University, 6100 Main St MS 602, Houston, TX 77005, USA
| | - Shih-Chieh Kao
- Department of Chemistry, Rice University, 6100 Main St MS 602, Houston, TX 77005, USA
| | - Julian G West
- Department of Chemistry, Rice University, 6100 Main St MS 602, Houston, TX 77005, USA
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83
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Gagliardi A, Bajraktari-Sylejmani G, Barocelli E, Weiss J, Rigalli JP. Extracellular Vesicles as Surrogates for Drug Metabolism and Clearance: Promise vs. Reality. Life (Basel) 2023; 13:1745. [PMID: 37629602 PMCID: PMC10455864 DOI: 10.3390/life13081745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Drug-metabolizing enzymes (DMEs) and transporters play a major role in drug efficacy and safety. They are regulated at multiple levels and by multiple factors. Estimating their expression and activity could contribute to predicting drug pharmacokinetics and their regulation by drugs or pathophysiological situations. Determining the expression of these proteins in the liver, intestine, and kidney requires the collection of biopsy specimens. Instead, the isolation of extracellular vesicles (EVs), which are nanovesicles released by most cells and present in biological fluids, could deliver this information in a less invasive way. In this article, we review the use of EVs as surrogates for the expression and activity of DMEs, uptake, and efflux transporters. Preliminary evidence has been provided for a correlation between the expression of some enzymes and transporters in EVs and the tissue of origin. In some cases, data obtained in EVs reflect the induction of phase I-DMEs in the tissues. Further studies are required to elucidate to what extent the regulation of other DMEs and transporters in the tissues reflects in the EV cargo. If an association between tissues and their EVs is firmly established, EVs may represent a significant advancement toward precision therapy based on the biotransformation and excretion capacity of each individual.
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Affiliation(s)
- Anna Gagliardi
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Gzona Bajraktari-Sylejmani
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Elisabetta Barocelli
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Johanna Weiss
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Juan Pablo Rigalli
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
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84
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Guo YY, Tian ZH, Han YC, Ma D, Shao T, Jiang Z. Hantzsch Ester as Efficient and Economical NAD(P)H Mimic for In Vitro Bioredox Reactions. Chemistry 2023; 29:e202301180. [PMID: 37263982 DOI: 10.1002/chem.202301180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/03/2023]
Abstract
Biocatalysis has emerged as a valuable and reliable tool for industrial and academic societies, particularly in fields related to bioredox reactions. The cost of cofactors, especially those needed to be replenished at stoichiometric amounts or more, is the chief economic concern for bioredox reactions. In this study, a readily accessible, inexpensive, and bench-stable Hantzsch ester is verified as the viable and efficient NAD(P)H mimic by four enzymatic redox transformations, including two non-heme diiron N-oxygenases and two flavin-dependent reductases. This finding provides the potential to significantly reduce the costs of NAD(P)H-relying bioredox reactions.
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Affiliation(s)
- Yuan-Yang Guo
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Ze-Hua Tian
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Yu-Chen Han
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Dandan Ma
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Tianju Shao
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Zhiyong Jiang
- Collaborative Innovation Centre of Henan Province for Green Manufacturing of Fine Chemicals Key Laboratory of Green Chemical Media and Reactions Ministry of Education NMPA Key Laboratory for Research and Evaluation of Innovative Drug Henan Key Laboratory of Organic Functional Molecule and Drug Innovation School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, 453007, China
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85
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Kumar N, He J, Rusling JF. Electrochemical transformations catalyzed by cytochrome P450s and peroxidases. Chem Soc Rev 2023; 52:5135-5171. [PMID: 37458261 DOI: 10.1039/d3cs00461a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Cytochrome P450s (Cyt P450s) and peroxidases are enzymes featuring iron heme cofactors that have wide applicability as biocatalysts in chemical syntheses. Cyt P450s are a family of monooxygenases that oxidize fatty acids, steroids, and xenobiotics, synthesize hormones, and convert drugs and other chemicals to metabolites. Peroxidases are involved in breaking down hydrogen peroxide and can oxidize organic compounds during this process. Both heme-containing enzymes utilize active FeIVO intermediates to oxidize reactants. By incorporating these enzymes in stable thin films on electrodes, Cyt P450s and peroxidases can accept electrons from an electrode, albeit by different mechanisms, and catalyze organic transformations in a feasible and cost-effective way. This is an advantageous approach, often called bioelectrocatalysis, compared to their biological pathways in solution that require expensive biochemical reductants such as NADPH or additional enzymes to recycle NADPH for Cyt P450s. Bioelectrocatalysis also serves as an ex situ platform to investigate metabolism of drugs and bio-relevant chemicals. In this paper we review biocatalytic electrochemical reactions using Cyt P450s including C-H activation, S-oxidation, epoxidation, N-hydroxylation, and oxidative N-, and O-dealkylation; as well as reactions catalyzed by peroxidases including synthetically important oxidations of organic compounds. Design aspects of these bioelectrocatalytic reactions are presented and discussed, including enzyme film formation on electrodes, temperature, pH, solvents, and activation of the enzymes. Finally, we discuss challenges and future perspective of these two important bioelectrocatalytic systems.
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Affiliation(s)
- Neeraj Kumar
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
| | - Jie He
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
| | - James F Rusling
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3136, USA.
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
- Department of Surgery and Neag Cancer Center, Uconn Health, Farmington, CT 06030, USA
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
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86
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Mao R, Wackelin DJ, Jamieson CS, Rogge T, Gao S, Das A, Taylor DM, Houk KN, Arnold FH. Enantio- and Diastereoenriched Enzymatic Synthesis of 1,2,3-Polysubstituted Cyclopropanes from ( Z/ E)-Trisubstituted Enol Acetates. J Am Chem Soc 2023; 145:16176-16185. [PMID: 37433085 PMCID: PMC10528827 DOI: 10.1021/jacs.3c04870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
In nature and synthetic chemistry, stereoselective [2 + 1] cyclopropanation is the most prevalent strategy for the synthesis of chiral cyclopropanes, a class of key pharmacophores in pharmaceuticals and bioactive natural products. One of the most extensively studied reactions in the organic chemist's arsenal, stereoselective [2 + 1] cyclopropanation, largely relies on the use of stereodefined olefins, which can require elaborate laboratory synthesis or tedious separation to ensure high stereoselectivity. Here, we report engineered hemoproteins derived from a bacterial cytochrome P450 that catalyze the synthesis of chiral 1,2,3-polysubstituted cyclopropanes, regardless of the stereopurity of the olefin substrates used. Cytochrome P450BM3 variant P411-INC-5185 exclusively converts (Z)-enol acetates to enantio- and diastereoenriched cyclopropanes and in the model reaction delivers a leftover (E)-enol acetate with 98% stereopurity, using whole Escherichia coli cells. P411-INC-5185 was further engineered with a single mutation to enable the biotransformation of (E)-enol acetates to α-branched ketones with high levels of enantioselectivity while simultaneously catalyzing the cyclopropanation of (Z)-enol acetates with excellent activities and selectivities. We conducted docking studies and molecular dynamics simulations to understand how active-site residues distinguish between the substrate isomers and enable the enzyme to perform these distinct transformations with such high selectivities. Computational studies suggest the observed enantio- and diastereoselectivities are achieved through a stepwise pathway. These biotransformations streamline the synthesis of chiral 1,2,3-polysubstituted cyclopropanes from readily available mixtures of (Z/E)-olefins, adding a new dimension to classical cyclopropanation methods.
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Affiliation(s)
- Runze Mao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Daniel J. Wackelin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Cooper S. Jamieson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Torben Rogge
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Shilong Gao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Anuvab Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Doris Mia Taylor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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87
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Fu R, Ma Z, Zhao H, Jin H, Tang Y, He T, Ding Y, Zhang J, Ye D. Research Progress in Iron-Based Nanozymes: Catalytic Mechanisms, Classification, and Biomedical Applications. Anal Chem 2023. [PMID: 37438259 DOI: 10.1021/acs.analchem.3c01005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Natural enzymes are crucial in biological systems and widely used in biology and medicine, but their disadvantages, such as insufficient stability and high-cost, have limited their wide application. Since Fe3O4 nanoparticles were found to show peroxidase-like activity, researchers have designed and developed a growing number of nanozymes that mimic the activity of natural enzymes. Nanozymes can compensate for the defects of natural enzymes and show higher stability with lower cost. Iron, a nontoxic and low-cost transition metal, has been used to synthesize a variety of iron-based nanozymes with unique structural and physicochemical properties to obtain different enzymes mimicking catalytic properties. In this perspective, catalytic mechanisms, activity modulation, and their recent research progress in sensing, tumor therapy, and antibacterial and anti-inflammatory applications are systematically presented. The challenges and perspectives on the development of iron-based nanozymes are also analyzed and discussed.
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Affiliation(s)
- Ruixue Fu
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Zijian Ma
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Hongbin Zhao
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Huan Jin
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Ya Tang
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Ting He
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yaping Ding
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Jiujun Zhang
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Daixin Ye
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
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88
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Jia W, Chen S, Wei R, Yang X, Zhang M, Qian Y, Liu H, Lei D. CYP4F12 is a potential biomarker and inhibits cell migration of head and neck squamous cell carcinoma via EMT pathway. Sci Rep 2023; 13:10956. [PMID: 37414830 PMCID: PMC10326030 DOI: 10.1038/s41598-023-37950-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSC) is the most common malignant tumor of head and neck. Due to the insidious nature of HNSC and the lack of effective early diagnostic indicators, the development of novel biomarkers to improve patient prognosis is particularly urgent. In this study, we explored and validated the correlation between cytochrome P450 family 4 subfamily F member 12 (CYP4F12) expression levels and HNSC progression using data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) datasets and collected patient samples. We analyzed the association of CYP4F12 expression with clinicopathological features, immune correlation and prognosis. Finally, we analyzed the correlation between CYP4F12 and pathways, and verified by experiments. The results showed that CYP4F12 was low expressed in tumor tissues, participated in a variety of phenotypic changes of HNSC and affected immune cell infiltration. Pathway analysis indicated that CYP4F12 may play a key role in tumor cell migration and apoptosis. Experimental results showed that over-expression of CYP4F12 inhibited cell migration and enhanced the adhesion between cells and matrix by inhibiting epithelial-mesenchymal transition (EMT) pathway in HNSC cells. In conclusion, our study provided insights into the role of CYP4F12 in HNSC and revealed that CYP4F12 may be a potential therapeutic target for HNSC.
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Affiliation(s)
- Wenming Jia
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission (NHC) Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, China
| | - Shuai Chen
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission (NHC) Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, China
| | - Ran Wei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission (NHC) Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, China
| | - Xiaoqi Yang
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission (NHC) Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, China
| | - Minfa Zhang
- Department of Otolaryngology/Head and Neck Surgery, Institute of Otolaryngology, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - Ye Qian
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission (NHC) Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, China
| | - Heng Liu
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission (NHC) Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, China.
| | - Dapeng Lei
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission (NHC) Key Laboratory of Otorhinolaryngology (Shandong University), Jinan, China.
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89
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Wu H, Xu S, Du P, Liu Y, Li H, Yang H, Wang T, Wang ZG. A nucleotide-copper(II) complex possessing a monooxygenase-like catalytic function. J Mater Chem B 2023. [PMID: 37409588 DOI: 10.1039/d3tb00780d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The de novo design of artificial biocatalysts with enzyme-like active sites and catalytic functions has long been an attractive yet challenging goal. In this study, we present a nucleotide-Cu2+ complex, synthesized through a one-pot approach, capable of catalyzing ortho-hydroxylation reactions resembling those of minimalist monooxygenases. Both experimental and theoretical findings demonstrate that the catalyst, in which Cu2+ coordinates with both the nucleobase and phosphate moieties, forms a ternary-complex intermediate with H2O2 and tyramine substrates through multiple weak interactions. The subsequent electron transfer and hydrogen (or proton) transfer steps lead to the ortho-hydroxylation of tyramine, where the single copper center exhibits a similar function to natural dicopper sites. Moreover, Cu2+ bound to nucleotides or oligonucleotides exhibits thermophilic catalytic properties within the temperature range of 25 °C to 75 °C, while native enzymes are fully deactivated above 35 °C. This study may provide insights for the future design of oxidase-mimetic catalysts and serve as a guide for the design of primitive metallocentre-dependent enzymes.
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Affiliation(s)
- Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Haijun Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ting Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
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90
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Rebilly JN, Herrero C, Sénéchal-David K, Guillot R, Banse F. Catalytic oxidation properties of an acid-resistant cross-bridged cyclen Fe(II) complex. Influence of the rigid donor backbone and protonation on the reactivity. Dalton Trans 2023. [PMID: 37334566 DOI: 10.1039/d3dt00393k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The catalytic properties of an iron complex bearing a pentadentate cross-bridged ligand backbone are reported. With H2O2 as an oxidant, it displays moderate conversions in epoxidation and alkane hydroxylation and satisfactory ones in aromatic hydroxylation. Upon addition of an acid to the reaction medium, a significant enhancement in aromatic and alkene oxidation is observed. Spectroscopic analyses showed that accumulation of the expected FeIII(OOH) intermediate is limited under these conditions, unless an acid is added to the mixture. This is ascribed to the inertness induced by the cross-bridged ligand backbone, which is partly reduced under acidic conditions.
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Affiliation(s)
- Jean-Noël Rebilly
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), 91405 Orsay cedex, France.
| | - Christian Herrero
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), 91405 Orsay cedex, France.
| | - Katell Sénéchal-David
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), 91405 Orsay cedex, France.
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), 91405 Orsay cedex, France.
| | - Frédéric Banse
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), 91405 Orsay cedex, France.
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91
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Hou Z, Li Y, Zheng M, Liu X, Zhang Q, Wang W. Regioselective oxidation of heterocyclic aromatic hydrocarbons catalyzed by cytochrome P450: A case study of carbazole. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 258:114964. [PMID: 37121081 DOI: 10.1016/j.ecoenv.2023.114964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/22/2023]
Abstract
Recently there are increasing interests in accurately evaluating the health effects of heterocyclic PAHs. However, the activation mechanism and possible metabolites of heterocyclic PAHs catalyzed by human CYP1A1 is still elusive to a great extent. Here, leveraged to high level QM/MM calculations, the corresponding activation pathways of a representative heterocyclic PAHs, carbazole, were systematically explored. The first stage is electrophilic addition or hydrogen abstraction from N-H group. Electrophilic addition was evidenced to be more feasible and regioselectivity at C3 and C4 sites were identified. Correlations between energy barriers and key structural/electrostatic parameters reveal that O-Cα distance and Fe-O-Cα angle are the main origin for the catalytic regioselectivity. Electrophilic addition was determined as the rate-determining step and the subsequent possible reactions include epoxidation, NIH shift (the hydrogen migration from the site of hydroxylation to the adjacent carbon) and proton shuttle. The corresponding products are epoxides, ketones and hydroxylated carbazoles, respectively. The main metabolites (hydroxylated carbazoles) are estimated to be more toxic than carbazole. The regioselectivity of carbazole activated by CYP1A1 is different from the environmental processes (gas and aqueous phase). Collectively, these results will inform the in-depth understanding the metabolic processes of heterocyclic PAHs and aid the accurate evaluation of their health effects.
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Affiliation(s)
- Zexi Hou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; Shenzhen Research Institute, Shandong University, Shenzhen 518057, PR China.
| | - Mingna Zheng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Xinning Liu
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
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92
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Zhao Z, Yang D, Guo J, Liu X, Li Q, Su P, Wang J, Ma Y, Huang L. Functional Study and Efficient Catalytic Element Mining of CYP76AHs in Salvia Plants. Molecules 2023; 28:4711. [PMID: 37375266 DOI: 10.3390/molecules28124711] [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: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Salvia is a large genus with hundreds of species used in traditional Chinese medicine. Tanshinones are a highly representative class of exclusive compounds found in the Salvia genus that exhibit significant biological activity. Tanshinone components have been identified in 16 Salvia species. The CYP76AH subfamily (P450) is crucial for the synthesis of tanshinone due to its catalytic generation of polyhydroxy structures. In this study, a total of 420 CYP76AH genes were obtained, and phylogenetic analysis showed their clear clustering relationships. Fifteen CYP76AH genes from 10 Salvia species were cloned and studied from the perspectives of evolution and catalytic efficiency. Three CYP76AHs with significantly improved catalytic efficiency compared to SmCYP76AH3 were identified, providing efficient catalytic elements for the synthetic biological production of tanshinones. A structure-function relationship study revealed several conserved residues that might be related to the function of CYP76AHs and provided a new mutation direction for the study of the directed evolution of plant P450.
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Affiliation(s)
- Zhenyu Zhao
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Dongfeng Yang
- Key Laboratory of Plant Secondary Metabolism and Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Juan Guo
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiuyu Liu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450008, China
| | - Qishuang Li
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Ping Su
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jian Wang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ying Ma
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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93
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Yildiz I. Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method. ACS OMEGA 2023; 8:19963-19968. [PMID: 37305300 PMCID: PMC10249383 DOI: 10.1021/acsomega.3c01949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023]
Abstract
l-Aspartate oxidase (Laspo) is responsible for the oxidation of l-aspartate into iminoaspartate using flavin as a cofactor. During this process flavin is reduced, and it can be reoxidized by either molecular oxygen or fumarate. The overall fold and the catalytic residues of Laspo are similar to succinate dehydrogenase and fumarate reductase. On the basis of deuterium kinetic isotope effects as well as other kinetic and structural data, it is proposed that the enzyme can catalyze the oxidation of l-aspartate through a mechanism similar to amino acid oxidases. It is suggested that a proton is removed from the α-amino group, while a hydride is transferred from C2 to flavin. It is also suggested that the hydride transfer is a rate-limiting step. However, there is still an ambiguity about the stepwise or concerted mechanism of hydride- and proton-transfer steps. In this study, we formulated some computational models to study the hydride-transfer mechanism using the crystal structure of Escherichia colil-aspartate oxidase in complexes with succinate. The calculations involved our own N-layered integrated molecular orbital and molecular mechanics method, and we evaluated the geometry and energetics of the hydride/proton-transfer processes while probing the roles of active site residues. Based on the calculations, it is concluded that proton- and hydride-transfer steps are decoupled, and a stepwise mechanism might be operative as opposed to the concerted one.
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94
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Maciuk S, Wood SH, Patel VK, Shapland PDP, Tomkinson NCO. Peracid Oxidation of Unactivated sp 3 C-H Bonds: An Important Solvent Effect. Chemistry 2023; 29:e202204007. [PMID: 36888902 PMCID: PMC10946557 DOI: 10.1002/chem.202204007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/10/2023]
Abstract
The peracid oxidation of hydrocarbons in chlorinated solvents is a low yielding and poorly selective process. Through a combination of DFT calculations, spectroscopic studies, and kinetic measurement it is shown that the origin of this is electronic in nature and can be influenced through the addition of hydrogen bond donors (HBD) and hydrogen bond acceptors (HBA). Performing the reaction of a cycloalkane with mCPBA in a fluorinated alcohol solvent such as nonafluoro-tert-butanol (NFTB) or hexafluoroisopropanol (HFIP), which act as strong HBD and poor HBA, leads to significantly higher yields and selectivities being observed for the alcohol product. Application of the optimised reaction conditions allows for the selective oxidation of both cyclic and linear alkane substrates delivering the corresponding alcohol in up to 86 % yield. The transformation shows selectivity for tertiary centres over secondary centres and the oxidation of secondary centres is strongly influenced by stereoelectronic effects. Primary centres are not oxidised by this method. A simple computational model developed to understand this transformation provides a powerful tool to reliably predict the influence of substitution and functionality on reaction outcome.
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Affiliation(s)
- Sergej Maciuk
- Department Pure and Applied Chemistry Thomas Graham BuildingUniversity of StrathclydeGlasgowG1 1XLUK
| | - Susanna H. Wood
- Department Pure and Applied Chemistry Thomas Graham BuildingUniversity of StrathclydeGlasgowG1 1XLUK
| | | | | | - Nicholas C. O. Tomkinson
- Department Pure and Applied Chemistry Thomas Graham BuildingUniversity of StrathclydeGlasgowG1 1XLUK
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95
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Liu L, Wang A, Hu J, Hou H, Liang S, Yang J. Peroxymonosulfate activated by natural porphyrin derivatives for rapid degradation of organic pollutants via singlet oxygen and high-valent iron-oxo species. CHEMOSPHERE 2023; 331:138783. [PMID: 37119928 DOI: 10.1016/j.chemosphere.2023.138783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/31/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
The activation of peroxymonosulfate (PMS) by sodium ferric chlorophyllin (SFC), a natural porphyrin derivative extracted from chlorophyll-rich substances, was systematically investigated for facile degradation of bisphenol A (BPA). SFC/PMS is capable of degrading 97.5% of BPA in the first 10 min with the initial BPA concentration of 20 mg/L and pH = 3, whereas conventional Fe2+/PMS could only remove 22.6% of BPA under identical conditions. It demonstrates a prominent flexibility to a broad pH range of 3-11 with complete pollutant degradation. A remarkable tolerance toward concomitant high concentration of inorganic anions (100 mM) was also observed, among which (bi)carbonates can even accelerate the degradation. The nonradical oxidation species, including high-valent iron-oxo porphyrin species and 1O2, are identified as dominant species. Particularly, the generation and participation of 1O2 in the reaction is evidenced by experimental and theoretical methods, which is vastly different from the previous study. The specific activation mechanism is unveiled by density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations. The results shed light on effective PMS activation by iron (III) porphyrin and the proposed natural porphyrin derivative would be a promising candidate for efficient abatement of recalcitrant pollutants toward complicated aqueous media in wastewater treatment.
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Affiliation(s)
- Lu Liu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Technology Research Center of Water Supply Safety and Pollution Control, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
| | - Anqi Wang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Technology Research Center of Water Supply Safety and Pollution Control, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
| | - Jingping Hu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Technology Research Center of Water Supply Safety and Pollution Control, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China.
| | - Huijie Hou
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Technology Research Center of Water Supply Safety and Pollution Control, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
| | - Sha Liang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Technology Research Center of Water Supply Safety and Pollution Control, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
| | - Jiakuan Yang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; Hubei Provincial Engineering Technology Research Center of Water Supply Safety and Pollution Control, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China; State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology (HUST), Wuhan, Hubei, 430074, PR China
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96
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Coleman T, Podgorski MN, Doyle ML, Scaffidi-Muta JM, Campbell EC, Bruning JB, De Voss JJ, Bell SG. Cytochrome P450-catalyzed oxidation of halogen-containing substrates. J Inorg Biochem 2023; 244:112234. [PMID: 37116269 DOI: 10.1016/j.jinorgbio.2023.112234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/15/2023] [Accepted: 04/15/2023] [Indexed: 04/30/2023]
Abstract
Cytochrome P450 (CYP) enzymes are heme-thiolate monooxygenases which catalyze the oxidation of aliphatic and aromatic C-H bonds and other reactions. The oxidation of halogens by cytochrome P450 enzymes has also been reported. Here we use CYP199A4, from the bacterium Rhodopseudomonas palustris strain HaA2, with a range of para-substituted benzoic acid ligands, which contain halogens, to assess if this enzyme can oxidize these species or if the presence of these electronegative atoms can alter the outcome of P450-catalyzed reactions. Despite binding to the enzyme, there was no detectable oxidation of any of the 4-halobenzoic acids. CYP199A4 was, however, able to efficiently catalyze the oxidation of both 4-chloromethyl- and 4-bromomethyl-benzoic acid to 4-formylbenzoic acid via hydroxylation of the α‑carbon. The 4-chloromethyl substrate bound in the enzyme active site in a similar manner to 4-ethylbenzoic acid. This places the benzylic α‑carbon hydrogens in an unfavorable position for abstraction indicating a degree of substrate mobility must be possible within the active site. CYP199A4 catalyzed oxidations of 4-(2'-haloethyl)benzoic acids yielding α-hydroxylation and desaturation metabolites. The α-hydroxylation product was the major metabolite. The desaturation pathway is significantly disfavored compared to 4-ethylbenzoic acid. This may be due to the electron-withdrawing halogen atom or a different positioning of the substrate within the active site. The latter was demonstrated by the X-ray crystal structures of CYP199A4 with these substrates. Overall, the presence of a halogen atom positioned close to the heme iron can alter the binding orientation and outcomes of enzyme-catalyzed oxidation.
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Affiliation(s)
- Tom Coleman
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | | | - Maya L Doyle
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | | | - Eleanor C Campbell
- Australian Synchrotron, 800 Blackburn Rd, Clayton, Melbourne, VIC 3168. Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Stephen G Bell
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia.
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97
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Morgante P, Peverati R. Comparison of the Performance of Density Functional Methods for the Description of Spin States and Binding Energies of Porphyrins. Molecules 2023; 28:molecules28083487. [PMID: 37110720 PMCID: PMC10146789 DOI: 10.3390/molecules28083487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
This work analyzes the performance of 250 electronic structure theory methods (including 240 density functional approximations) for the description of spin states and the binding properties of iron, manganese, and cobalt porphyrins. The assessment employs the Por21 database of high-level computational data (CASPT2 reference energies taken from the literature). Results show that current approximations fail to achieve the "chemical accuracy" target of 1.0 kcal/mol by a long margin. The best-performing methods achieve a mean unsigned error (MUE) <15.0 kcal/mol, but the errors are at least twice as large for most methods. Semilocal functionals and global hybrid functionals with a low percentage of exact exchange are found to be the least problematic for spin states and binding energies, in agreement with the general knowledge in transition metal computational chemistry. Approximations with high percentages of exact exchange (including range-separated and double-hybrid functionals) can lead to catastrophic failures. More modern approximations usually perform better than older functionals. An accurate statistical analysis of the results also casts doubts on some of the reference energies calculated using multireference methods. Suggestions and general guidelines for users are provided in the conclusions. These results hopefully stimulate advances for both the wave function and the density functional side of electronic structure calculations.
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Affiliation(s)
- Pierpaolo Morgante
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Roberto Peverati
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
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98
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Xiang J, Pan Y, Liu LL, Wang LX, Yang H, Cheng SC, Yiu SM, Leung CF, Ko CC, Lau KC, Lau TC. Visible Light-Induced Oxidation of Alcohols by a Luminescent Osmium(VI) Nitrido Complex: Evidence for the Generation of PhIO + as a Highly Active Oxidant in the Presence of PhIO. J Am Chem Soc 2023; 145:9129-9135. [PMID: 37053567 DOI: 10.1021/jacs.3c00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Although alcohols are readily oxidized by a variety of oxidants, their oxidation by metal nitrido complexes is yet to be studied. We report herein visible-light-induced oxidation of primary and secondary alcohols to carbonyl compounds by a strongly luminescent osmium(VI) nitrido complex (OsN). The proposed mechanism involves initial rate-limiting hydrogen-atom transfer (HAT) from the α-carbon of the alcohol to OsN*. Attempts to develop catalytic oxidation of alcohols by OsN* using PhIO as the terminal oxidant resulted in the formation of novel osmium(IV) iminato complexes in which the nitrido ligand is bonded to a δ-carbon of the alcohol. Experimental and theoretical studies suggest that OsN* is reductively quenched by PhIO to generate PhIO+, which is a highly active oxidant that readily undergoes α- and δ-C-H activation of alcohols.
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Affiliation(s)
- Jing Xiang
- Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434020, China
| | - Yi Pan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China
| | - Lu-Lu Liu
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434020, China
| | - Li-Xin Wang
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434020, China
| | - Huan Yang
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434020, China
| | - Shun-Cheung Cheng
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China
| | - Shek-Man Yiu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China
| | - Chi-Fai Leung
- Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po N. T., Hong Kong 00000, China
| | - Chi-Chiu Ko
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China
| | - Kai-Chung Lau
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China
| | - Tai-Chu Lau
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, Guangdong 523808, China
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China
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99
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Gao Y, Hu X, Deng C, Wang M, Niu X, Luo N, Ji Y, Li G, An T. New insight into molecular mechanism of P450-Catalyzed metabolism of emerging contaminants and its consequence for human health: A case study of preservative methylparaben. ENVIRONMENT INTERNATIONAL 2023; 174:107890. [PMID: 37001212 DOI: 10.1016/j.envint.2023.107890] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Hydroxylated metabolites in the living body are considered as a potential biomarker of exposure to emerging contaminations (ECs) and breast cancer, but their formation mechanism has not received enough attention. Besides, the adverse impacts of metabolites during the metabolic transformation of ECs largely remain unknown. In this study, we employed a density functional calculation combing with in-vitro incubation of human liver microsomes to explore the bio-transformation of preservative methylparaben (MPB) in human bodies. Our results showed that hydroxylated metabolites of MPB (OH-MPB) were observed experimentally, while a formation mechanism was revealed at the molecular level. That is, hydroxylated metabolite was exclusively formed via the hydrogen abstraction from the phenolic hydroxyl group of MPB followed by the OH-rebound pathway, rather than the direct hydroxylation on the benzene ring. The increasing of hydroxyl groups on ECs could improve the metabolisms. This was confirmed in the metabolism of ECs without hydroxyl group and with multiple-hydroxyl groups, respectively. Furthermore, toxicity assessments show that compared to parent MPB, the hydroxylated metabolites have increased negative impacts on the gastrointestinal system and liver. A semiquinone product exhibits potential damage in the cardiovascular system and epoxides are toxic to the blood and gastrointestinal system. The findings deepen our insight into the biotransformation of parabens in human health, especially by providing health warnings about the potential impacts caused by semiquinone and epoxides.
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Affiliation(s)
- Yanpeng Gao
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Xinyi Hu
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Chuyue Deng
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Mei Wang
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaolin Niu
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Na Luo
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yuemeng Ji
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Guiying Li
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Taicheng An
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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100
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Williford EE, DeAngelo CM, Blake KS, Kumar H, Lam KK, Jones KV, Tolia NH, Dantas G, Wencewicz TA. Structure-Based Design of Bisubstrate Tetracycline Destructase Inhibitors That Block Flavin Redox Cycling. J Med Chem 2023; 66:3917-3933. [PMID: 36877173 PMCID: PMC10099279 DOI: 10.1021/acs.jmedchem.2c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Tetracyclines (TCs) are an important class of antibiotics threatened by an emerging new resistance mechanism─enzymatic inactivation. These TC-inactivating enzymes, also known as tetracycline destructases (TDases), inactivate all known TC antibiotics, including drugs of last resort. Combination therapies consisting of a TDase inhibitor and a TC antibiotic represent an attractive strategy for overcoming this type of antibiotic resistance. Here, we report the structure-based design, synthesis, and evaluation of bifunctional TDase inhibitors derived from anhydrotetracycline (aTC). By appending a nicotinamide isostere to the C9 position of the aTC D-ring, we generated bisubstrate TDase inhibitors. The bisubstrate inhibitors have extended interactions with TDases by spanning both the TC and presumed NADPH binding pockets. This simultaneously blocks TC binding and the reduction of FAD by NADPH while "locking" TDases in an unproductive FAD "out" conformation.
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Affiliation(s)
- Emily E. Williford
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Caitlin M. DeAngelo
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Kevin S. Blake
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., St. Louis, MO, 63108, USA
| | - Hirdesh Kumar
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institute of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, MD, 20814, USA
| | - Kendrick K. Lam
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Katherine V. Jones
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Niraj H. Tolia
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institute of Health, 9000 Rockville Pike, BG 29B Rm 4NN08, Bethesda, MD, 20814, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4513 Clayton Ave., St. Louis, MO, 63108, USA
- Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, 4515 McKinley Ave., St. Louis, MO, 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Timothy A. Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO, 63130, USA
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