1
|
Jing M, Han G, Wan J, Zong W, Liu R. Differential eco-toxicological responses toward Eisenia fetida exposed to soil contaminated with naphthalene and typical metabolites. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:44800-44814. [PMID: 38954347 DOI: 10.1007/s11356-024-34149-1] [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: 12/19/2023] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Naphthalene (NAP) was frequently detected in polycyclic aromatic hydrocarbons (PAHs)-contaminated soil, and its residues may pose an eco-toxicological threat to soil organisms. The toxic effects of NAP were closely tied to phenolic and quinone metabolites in biological metabolism. However, the present knowledge concerning the eco-toxicological impacts of NAP metabolites at the animal level is scanty. Here, we assessed the differences in the eco-toxicological responses of Eisenia fetida (E. fetida) in NAP, 1-naphthol (1-NAO) or 1,4-naphthoquinone (1,4-NQ) contaminated soils. NAP, 1-NAO, and 1,4-NQ exposure triggered the onset of oxidative stress as evidenced by the destruction of the antioxidant enzyme system. The lipid peroxidation and DNA oxidative damage levels induced by 1-NAO and 1,4-NQ were higher than those of NAP. The elevation of DNA damage varied considerably depending on differences in oxidative stress and the direct mode of action of NAP or its metabolites with DNA. All three toxicants induced different degrees of physiological damage to the body wall, but only 1, 4-NQ caused the shedding of intestinal epithelial cells. The integrated biomarker response for different exposure times illustrated that the comprehensive toxicity at the animal level was 1,4-NQ > 1-NAO > NAP, and the time-dependent trends of oxidative stress responses induced by the three toxicants were similar. At the initial stage, the antioxidant system of E. fetida responded positively to the provocation, but the ability of E. fetida to resist stimulation decreased with the prolongation of time resulting in provocation oxidative damage. This study would provide new insights into the toxicological effects and biohazard of PAHs on soil animals.
Collapse
Affiliation(s)
- Mingyang Jing
- Shandong Urban Construction Vocational College, 4657# Tourism Road, Jinan, Shandong, 250100, P.R. China
| | - Guangye Han
- Shandong Academy of Environmental Sciences Co., Ltd, Licheng, 12777# Zhenyuan Road, Jinan, Shandong, 250100, P.R. China
| | - Jingqiang Wan
- School of Environmental Science and Engineering, America CRC for Environment & Health, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, P.R. China
| | - Wansong Zong
- College of Geography and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan, 250014, Shandong, China
| | - Rutao Liu
- School of Environmental Science and Engineering, America CRC for Environment & Health, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, P.R. China.
| |
Collapse
|
2
|
Feng S, Zheng Q. Mechanism of 7H-Dibenzo[c,g]carbazole metabolism in cytochrome P450 1A1: Insights from computational studies. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134933. [PMID: 38925058 DOI: 10.1016/j.jhazmat.2024.134933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
7H-Dibenzo[c,g]carbazole (DBC) is a prevalent environmental contaminant that induces tumorigenesis in several experimental animals. Recently, it has been utilized to develop high-performance solar cells and organic phosphorescent materials. It is imperative to strengthen investigations of DBC metabolism to understand its potential risks to human health. In this study, human CYP1A1 was employed as the metabolic enzyme to investigate the metabolic mechanism of DBC by molecular docking, molecular dynamics (MD) simulation, and quantum mechanical (QM) calculation. The results indicate that DBC binds to CYP1A1 in two modes (mode 1 and mode 2) mainly through nonpolar solvation energies (ΔGnonpolar). The formation of the two binding modes is attributed to the anchoring effect of the hydrogen bond formed by DBC with Asp320 (mode 1) or Ser116 (mode 2). Mode 1 is a "reactive" conformation, while mode 2 is not considered a "reactive" conformation. C5 is identified as the dominant site, and the pyrrole nitrogen cannot participate in the metabolism. DBC is metabolized mainly by a distinct electrophilic addition-rearrangement mechanism, with an energy barrier of 21.74 kcal/mol. The results provide meaningful insights into the biometabolic process of DBC and contribute to understanding its environmental effects and health risks.
Collapse
Affiliation(s)
- Shi Feng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China; Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China.
| |
Collapse
|
3
|
Ditte M, Barborini M, Medrano Sandonas L, Tkatchenko A. Molecules in Environments: Toward Systematic Quantum Embedding of Electrons and Drude Oscillators. PHYSICAL REVIEW LETTERS 2023; 131:228001. [PMID: 38101380 DOI: 10.1103/physrevlett.131.228001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/26/2023] [Accepted: 10/20/2023] [Indexed: 12/17/2023]
Abstract
We develop a quantum embedding method that enables accurate and efficient treatment of interactions between molecules and an environment, while explicitly including many-body correlations. The molecule is composed of classical nuclei and quantum electrons, whereas the environment is modeled via charged quantum harmonic oscillators. We construct a general Hamiltonian and introduce a variational Ansatz for the correlated ground state of the fully interacting molecule-environment system. This wave function is optimized via the variational Monte Carlo method and the ground state energy is subsequently estimated through the diffusion Monte Carlo method. The proposed scheme allows an explicit many-body treatment of electrostatic, polarization, and dispersion interactions between the molecule and the environment. We study solvation energies and excitation energies of benzene derivatives, obtaining excellent agreement with explicit ab initio calculations and experiments.
Collapse
Affiliation(s)
- Matej Ditte
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Matteo Barborini
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| |
Collapse
|
4
|
Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
Collapse
Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Feng S, Li Y, Zhang R, Zhang Q, Wang W. Origin of metabolites diversity and selectivity of P450 catalyzed benzo[a]pyrene metabolic activation. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:129008. [PMID: 35490637 DOI: 10.1016/j.jhazmat.2022.129008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Polycyclic Aromatic Hydrocarbon (PAHs) presents one of the most abundant class of environmental pollutants. Recent study shows a lab-synthesized PAHs derivative, helicenium, can selectively kill cancer cells rather than normal cells, calling for the in-depth understanding of the metabolic process. However, the origin of metabolites diversity and selectivity of P450 catalyzed PAHs metabolic activation is still unclear to a great extent. Here we systematically investigated P450 enzymes catalyzed activation mechanism of a representative PAHs, benzo[a]pyrene (BaP), and found the corresponding activation process mainly involves two elementary steps: electrophilic addition and epoxidation. Electrophilic addition step is evidenced to be rate determining step. Two representative binding modes of BaP with P450 were found, which enables the electrophilic addition of Heme (FeO) to almost all the carbons of BaP. This electrophilic addition was proposed to be accelerated by the P450 enzyme environment when compared with the gas phase and water solvent. To dig deeper on the origin of metabolites diversity, we built several linear regression models to explore the structural-energy relationships. The selectivity was eventually attributed to the integrated effects of structural (e.g. O-C distance and O-C-Fe angle) and electrostatic parameters (e.g. charge of C and O) from both BaP and P450.
Collapse
Affiliation(s)
- Shanshan Feng
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Ruiming Zhang
- 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
| |
Collapse
|
7
|
Zhou J, Zhang X, Li Y, Feng S, Zhang Q, Wang W. Endocrine-disrupting metabolic activation of 2-nitrofluorene catalyzed by human cytochrome P450 1A1: A QM/MM approach. ENVIRONMENT INTERNATIONAL 2022; 166:107355. [PMID: 35751956 DOI: 10.1016/j.envint.2022.107355] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Nitropolycyclic aromatic hydrocarbons (NPAHs) present one of the most important airborne pollutants. Recent studies have shown that one of the most abundant NPAHs, 2-Nitrofluorene (NF), was supposed to be converted to endocrine-disrupting metabolites by cytochrome P450 1A1 (CYP1A1) in human cells. However, the mechanism is still largely unexplored. Here the metabolic activation and transformation mechanism of NF catalyzed by CYP1A1 were systematically studied with the aid of Molecular Dynamics, Density Functional Theory and Quantum Mechanics/Molecular Mechanics techniques. We evidence that CYP1A1 can activate NF through two elementary processes: (i) electrophilic addition (12.4 kcal·mol-1) or hydrogen abstraction (38.2 kcal·mol-1) and (ii) epoxidation (5.9 and 8.7 kcal·mol-1) or NIH shift (12.5 and 14.9 kcal·mol-1) or proton shuttle (12.1 kcal·mol-1). Electrophilic addition was found to be the rate-determining step while epoxidation rather than NIH shift or proton shuttle is the more feasible pathway after electrophilic addition. Metabolites 6,7-epoxide-2-nitrofluorene and 7,8-epoxide-2-nitrofluorene were identified as the major epoxidation products. Epoxides are unstable and easy to react with hydrated hydrogen ions and hydroxyls to produce endocrine disrupter 7-hydroxy-2-nitrofluorene. Toxic analysis shows that some of the metabolites are more toxic to model aquatic organisms (e.g. Green algea) than NF. Binding affinity analysis to human sex hormone binding globulin reveals that NF metabolites all have endocrine-disrupting potential. This study provides a comprehensive understanding on the biotransformation process of NF and may aid future studies on various NPAHs activation catalyzed by human P450 enzyme.
Collapse
Affiliation(s)
- Junhua Zhou
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, PR China
| | - Xin Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, PR China.
| | - Shanshan Feng
- 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
| |
Collapse
|
8
|
Chen C, Min Y, Li X, Chen D, Shen J, Zhang D, Sun H, Bian Q, Yuan H, Wang SL. Mutagenicity risk prediction of PAH and derivative mixtures by in silico simulations oriented from CYP compound I-mediated metabolic activation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147596. [PMID: 33991922 DOI: 10.1016/j.scitotenv.2021.147596] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/26/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
PAHs and their derivatives are the main sources of mutagenicity and carcinogenicity in airborne particular matter and cause serious public health and environmental problems. Risk assessment is challenging due to the mixed nature and deficiency of toxicity data of most PAHs and their derivatives. Cytochrome P450 enzymes (CYPs) play important roles in PAH-induced carcinogenicity via metabolic activation, and CYP conformations with compound I structures strongly influence metabolic sites and metabolite species. In this study, complexes of BaP with CYP1A1, CYP1B1 or CYP2C19 compound I were successfully simulated by QM/MM methods and verified by metabolic clearance, and the mutagenicity of chemicals was then predicted by the BaP-7,8-epoxide-related metabolic conformation fitness (MCF) approach, which was validated by Ames tests, showing satisfying accuracy (R2 = 0.46-0.66). Furthermore, a prediction model of the mutagenicity risk of PAH and derivative mixtures was established based on the relative potential factor (RPF) approach and the RPF calculated from the mathematical relationship between the minimum MCF (MCFmin) and RPF, which was successfully validated by the mutagenesis of PAH and derivative mixture mimic-simulating PM2.5 samples collected in eastern China. This study provides fast reliable tools for assessing risk of the complex components of environmental PAHs and their derivatives.
Collapse
Affiliation(s)
- Chao Chen
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Yue Min
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Xuxu Li
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; School of Nursing, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Dongyin Chen
- School of Pharmacy, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Jiemiao Shen
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Di Zhang
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China
| | - Hong Sun
- Jiangsu Provincial Center for Disease Control and Prevention, 172 Jiangsu Rd., Nanjing 210009, PR China
| | - Qian Bian
- Jiangsu Provincial Center for Disease Control and Prevention, 172 Jiangsu Rd., Nanjing 210009, PR China
| | - Haoliang Yuan
- State Key Laboratory of Natural Medicines and Center of Drug Discovery, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Shou-Lin Wang
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China; School of Nursing, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, PR China.
| |
Collapse
|
9
|
Zhang R, Li P, Shi X, Zhang R, Wang J, Li Y, Zhang Q, Wang W. Insights into the metabolic mechanism of PBDEs catalyzed by cytochrome P450 enzyme 3A4: A QM/MM study. CHEMOSPHERE 2021; 278:130430. [PMID: 33836398 DOI: 10.1016/j.chemosphere.2021.130430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 06/12/2023]
Abstract
Elucidating the metabolic mechanism and the derivatives of polybrominated diphenyl ethers (PBDEs) is significant to risk assessment. This study delineated the metabolic mechanism of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) catalyzed by P450 enzymes using a combination of molecular dynamic (MD), quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT). The calculation results reveal that the electrophilic addition is the main pathway for the biotransformation of BDE-47 catalyzed by P450 enzymes. 6-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (6-OH-BDE-47) is a more kinetically preferable product than 5-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (5-OH-BDE-47). Electrophilic addition reaction can lead to the formation of polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/Fs). The ecotoxicity assessment indicates that the final products of BDE-47 are still toxic to aquatic organisms, but the solubility increase of the hydroxylated products can accelerate their excretion from the body. We expect that the established metabolic mechanism and the derivatives will be used to predict the biotransformation of other PBDE congeners catalyzed by P450 enzymes in human livers.
Collapse
Affiliation(s)
- Ruiming Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Pengfei Li
- Shandong Academy for Environmental Planning, Jinan, 250014, PR China
| | - Xiangli Shi
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Ruiying Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Junjie Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Yanwei Li
- 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
| |
Collapse
|
10
|
Zhang R, Li P, Zhang R, Shi X, Li Y, Zhang Q, Wang W. Computational study on the detoxifying mechanism of DDT metabolized by cytochrome P450 enzymes. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125457. [PMID: 33652222 DOI: 10.1016/j.jhazmat.2021.125457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Predicting the detoxifying mechanism and potential toxic derivatives of xenobiotic substances is significant for risk assessment. The present study delineated the detoxifying mechanism of 1-chloro-4-[2,2,2-trichloro-1-(4-chlorophenyl)ethyl]benzene (DDT) metabolized by human P450 enzymes using a combination of molecular dynamic (MD), quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT). This study highlights that DDT can be metabolized by P450 enzymes through the hydrogen abstraction and electrophilic addition mechanism, and the main derivatives are epoxides (2,3-oxide-DDT and 3,4-oxide-DDT), DDE and dicofol. The epoxides are unstable and the C-O bond cleavage easily occurs by the reaction with hydronium ion or hydroxyl radicals, yielding endocrine disruptor hydroxylated DDT. The eco-toxicity evaluation indicates that the derivatives of DDT are less toxic than DDT, and the solubility increase of the derivatives can accelerate their excretion from the body. The study can provide an understanding of the biotransformation of DDT by the P450 enzymes in human livers.
Collapse
Affiliation(s)
- Ruiming Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Pengfei Li
- Shandong Academy for Environmental Planning, Jinan 250014, PR China
| | - Ruiying Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, PR China
| | - Xiangli Shi
- College of Geography and Environment, Shandong Normal University, Jinan 250014, PR China
| | - Yanwei Li
- 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
| |
Collapse
|
11
|
Qiu Y, Diao H, Zheng Y, Wu R. Multiscale Simulations on the Catalytic Plasticity of CYP76AH1. Front Chem 2021; 9:689731. [PMID: 34150721 PMCID: PMC8207200 DOI: 10.3389/fchem.2021.689731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The catalytic promiscuity and fidelity of cytochrome P450 enzymes are widespread in the skeletal modification of terpenoid natural products and have attracted much attention. CYP76AH1 is involved in key modification reactions in the biosynthetic pathway of tanshinone, a well-known medicinal norditerpenoid. In this work, classical molecular dynamic simulations, metadynamics, and DFT calculations were performed to investigate the protein conformational dynamics, ligand binding poses, and catalytic reaction mechanism in wide-type and mutant CYP76AH1. Our results not only reveal a plausible enzymatic mechanism for mutant CYP76AH1 leading to various products but also provide valuable guidance for rational protein engineering of the CYP76 family.
Collapse
Affiliation(s)
- Yufan Qiu
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongjuan Diao
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Zheng
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruibo Wu
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
12
|
Jones LO, Mosquera MA, Schatz GC, Ratner MA. Embedding Methods for Quantum Chemistry: Applications from Materials to Life Sciences. J Am Chem Soc 2020; 142:3281-3295. [PMID: 31986877 DOI: 10.1021/jacs.9b10780] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Quantum mechanical embedding methods hold the promise to transform not just the way calculations are performed, but to significantly reduce computational costs and improve scaling for macro-molecular systems containing hundreds if not thousands of atoms. The field of embedding has grown increasingly broad with many approaches of different intersecting flavors. In this perspective, we lay out the methods into two streams: QM:MM and QM:QM, showcasing the advantages and disadvantages of both. We provide a review of the literature, the underpinning theories including our contributions, and we highlight current applications with select examples spanning both materials and life sciences. We conclude with prospects and future outlook on embedding, and our view on the use of universal test case scenarios for cross-comparisons of the many available (and future) embedding theories.
Collapse
Affiliation(s)
- Leighton O Jones
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martín A Mosquera
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - George C Schatz
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Mark A Ratner
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| |
Collapse
|
13
|
Sunke R, Kalyani A, Swamy KCK. Cu(I)-Catalyzed Ligand-Free Tandem One-Pot or Sequential Annulation via Knoevenagel Intermediates: An Entry into Multifunctional Naphthalenes, Phenanthrenes, Quinolines, and Benzo[ b]carbazoles. J Org Chem 2020; 85:1073-1086. [PMID: 31823603 DOI: 10.1021/acs.joc.9b02991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A simple but efficient one-pot or sequential copper-catalyzed protocol using 2-bromoaldehydes and active methylene group containing substrates that affords multifunctional naphthalenes, phenanthrenes, quinolines, and benzo[b]carbazoles via Knoevenagel condensation, C-arylation, and decarboxylation, followed by aromatization, is developed. The reaction utilizes the potential of Knoevenagel intermediates and does not require any ancillary ligand. The phenanthrene products thus obtained show moderate fluorescence activity. Structural elaboration of the products to obtain dihydrobenzoquinazolines is also highlighted.
Collapse
Affiliation(s)
- Rajnikanth Sunke
- School of Chemistry , University of Hyderabad , Hyderabad 500046 , Telangana , India
| | - Adula Kalyani
- School of Chemistry , University of Hyderabad , Hyderabad 500046 , Telangana , India
| | - K C Kumara Swamy
- School of Chemistry , University of Hyderabad , Hyderabad 500046 , Telangana , India
| |
Collapse
|