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Pisoni LA, Semple SJ, Liu S, Sykes MJ, Venter H. Combined Structure- and Ligand-Based Approach for the Identification of Inhibitors of AcrAB-TolC in Escherichia coli. ACS Infect Dis 2023; 9:2504-2522. [PMID: 37888944 DOI: 10.1021/acsinfecdis.3c00350] [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: 10/28/2023]
Abstract
The inhibition of efflux pumps is a promising approach to combating multidrug-resistant bacteria. We have developed a combined structure- and ligand-based model, using OpenEye software, for the identification of inhibitors of AcrB, the inner membrane protein component of the AcrAB-TolC efflux pump in Escherichia coli. From a database of 1391 FDA-approved drugs, 23 compounds were selected to test for efflux inhibition in E. coli. Seven compounds, including ivacaftor (25), butenafine (19), naftifine (27), pimozide (30), thioridazine (35), trifluoperazine (37), and meloxicam (26), enhanced the activity of at least one antimicrobial substrate and inhibited the efflux pump-mediated removal of the substrate Nile Red from cells. Ivacaftor (25) inhibited efflux dose dependently, had no effect on an E. coli strain with genomic deletion of the gene encoding AcrB, and did not damage the bacterial outer membrane. In the presence of a sub-minimum inhibitory concentration (MIC) of the outer membrane permeabilizer colistin, ivacaftor at 1 μg/mL reduced the MICs of erythromycin and minocycline by 4- to 8-fold. The identification of seven potential AcrB inhibitors shows the merits of a combined structure- and ligand-based approach to virtual screening.
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Affiliation(s)
- Lily A Pisoni
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Susan J Semple
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Sida Liu
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Matthew J Sykes
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
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2
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Chu Y, Zhang C, Wang R, Chen X, Ren N, Ho SH. Biotransformation of sulfamethoxazole by microalgae: Removal efficiency, pathways, and mechanisms. WATER RESEARCH 2022; 221:118834. [PMID: 35839594 DOI: 10.1016/j.watres.2022.118834] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/01/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Recently, the biotransformation of sulfamethoxazole (SMX) by microalgae has attracted increasing interest. In particular, cytochrome P450 (CYP450) has been suggested to be the main enzymatic contributor to this biodegradation. However, the molecular evidence of CYP450 enzymes being involved in SMX biodegradation remains relatively unclear, hindering its applicability. Herein, the biodegradation of SMX by Chlorella sorokiniana (C. sorokiniana) was investigated, and comprehensively elucidated the reaction mechanism underlying CYP450-mediated SMX metabolism. C. sorokiniana was able to efficiently remove over 80% of SMX mainly through biodegradation, in which CYP450 enzymes responded substantially to metabolize SMX in cells. Additionally, screening of transformation products (TPs) revealed that N4-hydroxylation-SMX (TP270) was the main TP in the SMX biodegradation pathway of microalgae. Molecular dynamics (MD) simulation suggested that the aniline of SMX was the most prone to undergo metabolism, while density functional theory (DFT) indicated that SMX was metabolized by CYP450 enzymes through H-abstraction-OH-rebound reaction. Collectively, this work reveals key details of the hydroxylamine group of SMX, elucidates the SMX biodegradation pathway involving CYP450 in microalgae in detail, and accelerates the development of using microalgae-mediated CYP450 to eliminate antibiotics.
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Affiliation(s)
- Yuhao Chu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chaofan Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Rupeng Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xi Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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3
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Zhang H, Sanidad KZ, Zhu L, Parsonnet J, Haggerty TD, Zhang G, Cai Z. Frequent occurrence of triclosan hydroxylation in mammals: A combined theoretical and experimental investigation. JOURNAL OF HAZARDOUS MATERIALS 2021; 407:124803. [PMID: 33338815 DOI: 10.1016/j.jhazmat.2020.124803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/07/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Triclosan (TCS) is a widespread antimicrobial agent with many adverse health risks. Its hepatoxicity invariably points to the activation of constitutive androstane receptor (CAR), which regulates cytochrome P450 (CYP) genes that are critical for oxidative metabolism. Here, we provide the theoretical and experimental evidences showing that metabolic activation of TCS frequently occurs through aromatic hydroxylation in mammals. CYP-mediated oxidation was predicted to take place at each aromatic C‒H bond. Molecular docking and in vitro approaches reveal oxidative reaction could be efficiently catalyzed by CAR-regulated CYP2B6 enzyme. Parallel reaction monitoring (PRM) high-resolution mass spectrometry was utilized to identify and profile TCS oxidative metabolites in paired mouse liver, bile, feces, plasma and urine. We found multiple hydroxylated isomers including the products generated via the NIH shift of chlorine, as well as their subsequent conjugates. These metabolites showed isomer-specific retention in mice. Glucuronide conjugates are more readily excreted than the sulfates. Moreover, for the first time, isomeric hydroxylated metabolites were detected in the urine and stool of human subjects used TCS-contained household and personal care products. Collectively, these findings suggest that hydroxylation is an important, yet often underestimated element that worth considering to fully evaluate the biological fates and health risks of TCS.
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Affiliation(s)
- Hongna Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077 Hong Kong, China
| | - Katherine Z Sanidad
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077 Hong Kong, China
| | - Julie Parsonnet
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA
| | - Thomas D Haggerty
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA 94305, USA
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA; Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 999077 Hong Kong, China.
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Li L, Wang Z, Gao Y, Yu J, Kaziem AE, Shi H, Wang M. Stereoselective environmental behavior and biological effects of the chiral bitertanol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138867. [PMID: 32570326 DOI: 10.1016/j.scitotenv.2020.138867] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/19/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Bitertanol is a widely used chiral triazole fungicide. The stereoselective environmental behavior and biological effects of bitertanol are not clear. The present study evaluated the stereoselectivity of bitertanol, including its degradation in five typical soils (under laboratory controlled aerobic, anaerobic and sterilization conditions), metabolism in rat liver microsomes (RLM; in vitro), and the endocrine disruption effects on the estrogen receptor (ER) and thyroid hormone receptor (TR) using reporter gene assays. The results indicated that (1S,2R)-bitertanol and (1R,2S)-bitertanol had faster degradation rates in soil than the other stereoisomers. The half-lives of four bitertanol stereoisomers ranged from 9.1 d to 86.6 d in different soils under different conditions. (1S,2R)-bitertanol was preferentially metabolized in RLM. The molecular docking results confirmed the in vitro experiments that (1S,2R)-bitertanol had shortest binding distances and lowest energies with cytochrome P450 enzymes (CYPs). Four bitertanol stereoisomers showed stereoselective antagonistic effects on ER. Additionally, (1S,2R)-bitertanol and (1R,2S)-bitertanol exhibited antagonistic effects on TR. These results suggest that the use of pure (1S,2R)-bitertanol instead of the commercial stereoisomer mix, may help reduce environmental pollution and biological toxicity.
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Affiliation(s)
- Lianshan Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Zhen Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Yingying Gao
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Jie Yu
- SCIEX Analytical Instrument Trading Co., Shanghai 200335, China
| | - Amir E Kaziem
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Haiyan Shi
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Minghua Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China.
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Kaziem AE, Gao B, Li L, Zhang Z, He Z, Wen Y, Wang MH. Enantioselective bioactivity, toxicity, and degradation in different environmental mediums of chiral fungicide epoxiconazole. JOURNAL OF HAZARDOUS MATERIALS 2020; 386:121951. [PMID: 31895998 DOI: 10.1016/j.jhazmat.2019.121951] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/13/2019] [Accepted: 12/21/2019] [Indexed: 06/10/2023]
Abstract
To clarify the environmental behaviour and bioactivity of epoxiconazole enantiomers, an integrated assessment has been done. The degradation in soil, water, and river-sediments were studied. The toxicity to Chlorella vulgaris and Daphnia magna was also examined. The bioactivity to plant-pathogens and molecular docking to CYP51 were investigated. The obtained results showed that the half-lives of R,S-(+)- and S,R-(-)-epoxiconazole were 38.8 and 21.2 days in Jiangsu soil, 43.2 and 22.7 days in Jiangxi soil, 29.1 and 21.3 days in Jilin soil, 43.5 and 32.7 days in anaerobic Jilin soil, 12.3 and 10.1 days in river sediments, and 33.2 and 9.3 days in river water, respectively. Maximum EF was 0.36 in Yangzi-river water. No enantioselective degradation was found in sterilized conditions. The EC50 to C. vulgaris after 48 h was 27.78 mg L-1, and 18.93 mg L-1 for R,S-(+)-, and S,R-(-)-epoxiconazole, respectively. The LC50 to D. magna was 4.16 mg L-1, and 8.49 mg L-1 for R,S-(+)-, and S,R-(-)-epoxiconazole, respectively. R,S-(+)-epoxiconazole bioactivity was 1.3-7.25 times higher than S,R-(-)-epoxiconazole. In conclusion, R,S-(+)- has higher bioactivity and higher environmental toxicity. In opposite, S,R-(-)- has lower environmental toxicity and lower bioactivity. R,S-(+)-epoxiconazole use is recommended with lower concentrations, which is appropriate for environment safety.
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Affiliation(s)
- Amir E Kaziem
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China; Department of Environmental Agricultural Sciences, Institute of Environmental Studies and Research, Ain Shams University, Cairo 11566, Egypt
| | - Beibei Gao
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Lianshan Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Zhaoxian Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Zongzhe He
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Yong Wen
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Ming-Hua Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China.
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6
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Zhang Z, Gao B, He Z, Li L, Zhang Q, Kaziem AE, Wang M. Stereoselective bioactivity of the chiral triazole fungicide prothioconazole and its metabolite. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 160:112-118. [PMID: 31519245 DOI: 10.1016/j.pestbp.2019.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Chiral triazole fungicides have played a significant role in plant pathogen control. Although their enantiomers often exhibit different bioactivity, the mechanism of the stereoselectivity has not been well studied. The stereoselective bioactivity and mechanisms of prothioconazole and its chiral metabolite against plant pathogenic fungi were investigated. The results indicated that the metabolite exerted more fungicidal activities than the activities of the parent compound. R-Prothioconazole and R-prothioconazole-desthio were 6-262 and 19-954 times more potent against pathogenic fungi than the S-enantiomers, respectively. The R-enantiomers were more effective than in inhibiting the biosynthesis of ergosterol and deoxynivalenol the S-enantiomer. Homology modeling and molecular docking suggested that the R-enantiomers of prothioconazole and prothioconazole-desthio possessed better binding modes than S-enantiomers to CYP51B. Moreover, exposure to prothioconazole and its metabolite enantiomers significantly changed the transcription levels of the CYP51 (CYP 51A, CYP51B, CYP 51C) and Tri (Tri5, Tri6, Tri12) genes. The results showed that application of the R-prothioconazole could require a smaller application amount to eliminate the carcinogenic mycotoxins and any environmental risks.
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Affiliation(s)
- Zhaoxian Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Beibei Gao
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Zongzhe He
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Lianshan Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Qing Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Amir E Kaziem
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China; Department of Environmental Agricultural Science, Institute of Environmental Studies and Research, Ain Shams University, Cairo 11566, Egypt
| | - Minghua Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China.
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7
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Zhang Z, Gao B, He Z, Li L, Shi H, Wang M. Enantioselective metabolism of four chiral triazole fungicides in rat liver microsomes. CHEMOSPHERE 2019; 224:77-84. [PMID: 30818197 DOI: 10.1016/j.chemosphere.2019.02.119] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Triazole fungicides with one or two chiral centers are widely used worldwide. The liver microsomes plays a major role in the metabolism and systemic elimination of chiral pesticides after exposure. In this present work, enantioselective metabolism of four representative chiral triazole fungicides (prothioconazole, flutriafol, triticonazole, and epoxiconazole) in rat liver microsomes (RLM) was investigated using LC-MS/MS. Baseline separation of the four chiral fungicides and prothioconazole-desthio was achieved on Lux-cellulose-1. The results demonstrated that the R-enantiomers of flutriafol and triticonazole were preferentially metabolized with half-life ranged from 17.33 min to 99.00 min. The R,S-epoxiconazole accumulated with a half-life of 173.25 min. There was no stereoselectivity for prothioconazole. However, remarkable stereoselective metabolism was observed for prothioconazole-desthio. The results of enzyme kinetic revealed different affinities between the enantiomers and metabolic enzymes. In addition, homologous modeling and molecular docking results indicated that enantioselectivity were partially to enantiospecific binding affinities with CYP enzymes. This study highlights a new quantitative approach for stereoselective metabolism of chiral agrochemicals and provides more accurate data on risk assessment of triazole fungicides.
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Affiliation(s)
- Zhaoxian Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Ministry of Education, Nanjing, 210095, PR China
| | - Beibei Gao
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Ministry of Education, Nanjing, 210095, PR China
| | - Zongzhe He
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Ministry of Education, Nanjing, 210095, PR China
| | - Lianshan Li
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Ministry of Education, Nanjing, 210095, PR China
| | - Haiyan Shi
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Ministry of Education, Nanjing, 210095, PR China
| | - Minghua Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Ministry of Education, Nanjing, 210095, PR China.
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Nair PC, McKinnon RA, Miners JO. Computational Prediction of the Site(s) of Metabolism and Binding Modes of Protein Kinase Inhibitors Metabolized by CYP3A4. Drug Metab Dispos 2019; 47:616-631. [DOI: 10.1124/dmd.118.085167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/18/2019] [Indexed: 01/13/2023] Open
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Huang H, Wang D, Wen B, Lv J, Zhang S. Roles of maize cytochrome P450 (CYP) enzymes in stereo-selective metabolism of hexabromocyclododecanes (HBCDs) as evidenced by in vitro degradation, biological response and in silico studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:364-372. [PMID: 30513427 DOI: 10.1016/j.scitotenv.2018.11.351] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
In vitro biotransformation of HBCDs by maize cytochrome P450 (CYP) enzymes, responses of CYPs to HBCDs at protein and transcription levels, and in silico simulation of interactions between CYPs and HBCDs were investigated in order to elucidate the roles of CYPs in the metabolism of HBCDs in maize. The results showed that degradation reactions of HBCDs by maize microsomal CYPs followed the first-order kinetics and were stereo-selective, with the metabolic rates following the order (-)γ- > (+)γ- > (+)α- > (-)α-HBCD. The hydroxylated metabolites OH-HBCDs, OH-PBCDs and OH-TBCDs were detected. (+)/(-)-α-HBCDs significantly decreased maize CYP protein content and inhibited CYP enzyme activity, whereas (+)/(-)-γ-HBCDs had obvious effects on the induction of CYPs. HBCDs selectively mediated the gene expression of maize CYPs, including the isoforms of CYP71C3v2, CYP71C1, CYP81A1, CYP92A1 and CYP97A16. Molecular docking results suggested that HBCDs could bind with these five CYPs, with binding affinity following the order CYP71C3v2 < CYP81A1 < CYP97A16 < CYP92A1 < CYP71C1. The shortest distances between the Br-unsubstituted C atom of HBCD isomers and the iron atom of heme in CYPs were 4.18-11.7 Å, with only the distances for CYP71C3v2 being shorter than 6 Å (4.61-5.38 Å). These results suggested that CYP71C3v2 was an efficient catalyst for degradation of HBCDs. For (+)α- and (-)γ-HBCDs, their binding affinities to CYPs were lower and the distances to the iron atom of heme in CYPs were shorter than their corresponding antipodes, consistent with the in vitro experimental results showing that they had shorter half-lives and were more easily hydroxylated. This study provides solid evidence for the roles of maize CYPs in the metabolism of HBCDs, and gives insight into the molecular mechanisms of the enantio-selective metabolism of HBCDs by plant CYPs.
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Affiliation(s)
- Honglin Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
| | - Dan Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bei Wen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
| | - Jitao Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
| | - Shuzhen Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Chemometric studies of thymol binding with bovine serum albumin: A developing strategy for the successful investigation of pharmacological activity. Bioelectrochemistry 2018; 124:172-184. [DOI: 10.1016/j.bioelechem.2018.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/21/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022]
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11
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Goto E, Haga Y, Kubo M, Itoh T, Kasai C, Shoji O, Yamamoto K, Matsumura C, Nakano T, Inui H. Metabolic enhancement of 2,3',4,4',5-pentachlorobiphenyl (CB118) using cytochrome P450 monooxygenase isolated from soil bacterium under the presence of perfluorocarboxylic acids (PFCAs) and the structural basis of its metabolism. CHEMOSPHERE 2018; 210:376-383. [PMID: 30015128 DOI: 10.1016/j.chemosphere.2018.07.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
2,3',4,4',5-Pentachlorobiphenyl (CB118) is one of the most abundant polychlorinated biphenyl (PCB) congeners in the environment, and perfluoroalkyl acids, including perfluorocarboxylic acids (PFCAs), are widely distributed in the environment. Although CB118 and perfluoroalkyl acids are present in all humans and biota, effects in the metabolic fate of CB118 leading to toxicity change are unclear. P450BM3, which is isolated from the soil bacterium Bacillus megaterium, metabolized CB118 to three different hydroxylated pentachlorobiphenyls (M1-M3). M2 was identified as 4'-OH-2,3',4,5,5'-pentachlorobiphenyl. These reactions were promoted by the presence of PFCAs, and perfluorooctanoic acid (PFCA-C8) was the most effective for accelerating these reactions among PFCAs with different carbon chain length. The production rate of M2 was accelerated by 25-times using PFCA-C8. Furthermore, the docking models of P450BM3 with CB118 and PFCAs revealed that the conformational changes of the substrate-binding cavity of P450BM3 after binding of PFCAs to P450BM3 were important for selective production of CB118 metabolites. This study leads to the clarification of the different metabolic fates of PCBs under complex contamination with PFCAs.
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Affiliation(s)
- Erika Goto
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Yuki Haga
- Hyogo Prefectural Institute of Environmental Sciences, 3-1-18 Yukihira-cho, Suma-ku, Kobe, Hyogo, 657-0037, Japan
| | - Makoto Kubo
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashitamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashitamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Chie Kasai
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Osami Shoji
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashitamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Chisato Matsumura
- Hyogo Prefectural Institute of Environmental Sciences, 3-1-18 Yukihira-cho, Suma-ku, Kobe, Hyogo, 657-0037, Japan
| | - Takeshi Nakano
- Research Center for Environmental Preservation, Osaka University, 2-4 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hideyuki Inui
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan; Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
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12
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Hirakawa S, Miyawaki T, Hori T, Kajiwara J, Katsuki S, Hirano M, Yoshinouchi Y, Iwata H, Mitoma C, Furue M. Accumulation properties of polychlorinated biphenyl congeners in Yusho patients and prediction of their cytochrome P450-dependent metabolism by in silico analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:16455-16463. [PMID: 28639016 PMCID: PMC6301142 DOI: 10.1007/s11356-017-9498-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/08/2017] [Indexed: 06/10/2023]
Abstract
In what has become known as the Yusho incident, thousands of people in western Japan were poisoned by the accidental ingestion of rice bran oil contaminated with polychlorinated biphenyls (PCBs) and various dioxins and dioxin-like compounds. In this study, we investigated the accumulation patterns of 69 PCB congeners in the blood of Yusho patients in comparison with those of non-exposed controls. The blood samples were collected at medical check-ups in 2004 and 2005. To compare the patterns of PCB congeners, we calculated the concentration ratio of each congener relative to the 2,2',4,4',5,5'-hexaCB (CB153) concentration. The concentration ratios of tetra- and penta-chlorinated congeners in the blood of Yusho patients were significantly lower than those of controls. To examine the cytochrome P450 (CYP)-dependent metabolic potential of the 2,3',4,4'5-pentaCB (CB118), CB153, and 2,3,3',4,4'5-hexaCB (CB156) congeners, we conducted PCB-CYP (CYP1A1, CYP1A2, CYP2A6, and CYP2B6) docking simulation by in silico analysis. The docking models showed that human CYP1A1, CYP2A6, and CYP2B6 isozymes have the potential to metabolize CB118 and CB153. On the other hand, it was inferred that CB156 is difficult to be metabolized by these four CYP isozymes. These results indicate that CYP1 and CYP2 isozymes may be involved in the characteristic accumulation patterns of PCB congeners in the blood of Yusho patients.
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Affiliation(s)
- Shusaku Hirakawa
- Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka, 818-0135, Japan.
| | - Takashi Miyawaki
- Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka, 818-0135, Japan
| | - Tsuguhide Hori
- Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka, 818-0135, Japan
| | - Jumboku Kajiwara
- Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka, 818-0135, Japan
| | - Susumu Katsuki
- Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka, 818-0135, Japan
| | - Masashi Hirano
- Kumamoto College, National Institute of Technology, 2627 Hirayamashin-Machi, Yatsushiro, Kumamoto, 866-8501, Japan
| | - Yuka Yoshinouchi
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama, 790-8577, Japan
| | - Hisato Iwata
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 2-5, Matsuyama, 790-8577, Japan
| | - Chikage Mitoma
- Research and Clinical Center for Yusho and Dioxin, Kyusyu University Hospital, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masutaka Furue
- Research and Clinical Center for Yusho and Dioxin, Kyusyu University Hospital, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
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13
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Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M. Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem 2018; 183:117-136. [DOI: 10.1016/j.jinorgbio.2018.03.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/16/2018] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
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14
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Daly AK, Rettie AE, Fowler DM, Miners JO. Pharmacogenomics of CYP2C9: Functional and Clinical Considerations. J Pers Med 2017; 8:E1. [PMID: 29283396 PMCID: PMC5872075 DOI: 10.3390/jpm8010001] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023] Open
Abstract
CYP2C9 is the most abundant CYP2C subfamily enzyme in human liver and the most important contributor from this subfamily to drug metabolism. Polymorphisms resulting in decreased enzyme activity are common in the CYP2C9 gene and this, combined with narrow therapeutic indices for several key drug substrates, results in some important issues relating to drug safety and efficacy. CYP2C9 substrate selectivity is detailed and, based on crystal structures for the enzyme, we describe how CYP2C9 catalyzes these reactions. Factors relevant to clinical response to CYP2C9 substrates including inhibition, induction and genetic polymorphism are discussed in detail. In particular, we consider the issue of ethnic variation in pattern and frequency of genetic polymorphisms and clinical implications. Warfarin is the most well studied CYP2C9 substrate; recent work on use of dosing algorithms that include CYP2C9 genotype to improve patient safety during initiation of warfarin dosing are reviewed and prospects for their clinical implementation considered. Finally, we discuss a novel approach to cataloging the functional capabilities of rare 'variants of uncertain significance', which are increasingly detected as more exome and genome sequencing of diverse populations is conducted.
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Affiliation(s)
- Ann K Daly
- Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Douglas M Fowler
- Department of Genome Sciences and Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - John O Miners
- Department of Clinical Pharmacology, Flinders University School of Medicine, Adelaide 5042, Australia.
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15
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de Bruyn Kops C, Friedrich NO, Kirchmair J. Alignment-Based Prediction of Sites of Metabolism. J Chem Inf Model 2017; 57:1258-1264. [PMID: 28520411 DOI: 10.1021/acs.jcim.7b00165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Prediction of metabolically labile atom positions in a molecule (sites of metabolism) is a key component of the simulation of xenobiotic metabolism as a whole, providing crucial information for the development of safe and effective drugs. In 2008, an exploratory study was published in which sites of metabolism were derived based on molecular shape- and chemical feature-based alignment to a molecule whose site of metabolism (SoM) had been determined by experiments. We present a detailed analysis of the breadth of applicability of alignment-based SoM prediction, including transfer of the approach from a structure- to ligand-based method and extension of the applicability of the models from cytochrome P450 2C9 to all cytochrome P450 isozymes involved in drug metabolism. We evaluate the effect of molecular similarity of the query and reference molecules on the ability of this approach to accurately predict SoMs. In addition, we combine the alignment-based method with a leading chemical reactivity model to take reactivity into account. The combined model yielded superior performance in comparison to the alignment-based approach and the reactivity models with an average area under the receiver operating characteristic curve of 0.85 in cross-validation experiments. In particular, early enrichment was improved, as evidenced by higher BEDROC scores (mean BEDROC = 0.59 for α = 20.0, mean BEDROC = 0.73 for α = 80.5).
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Affiliation(s)
- Christina de Bruyn Kops
- Faculty of Mathematics, Informatics and Natural Sciences, Department of Computer Science, Center for Bioinformatics, Universität Hamburg , Hamburg 20146, Germany
| | - Nils-Ole Friedrich
- Faculty of Mathematics, Informatics and Natural Sciences, Department of Computer Science, Center for Bioinformatics, Universität Hamburg , Hamburg 20146, Germany
| | - Johannes Kirchmair
- Faculty of Mathematics, Informatics and Natural Sciences, Department of Computer Science, Center for Bioinformatics, Universität Hamburg , Hamburg 20146, Germany
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16
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Advances in drug metabolism and pharmacogenetics research in Australia. Pharmacol Res 2017; 116:7-19. [DOI: 10.1016/j.phrs.2016.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 01/04/2023]
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17
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Dixit VA, Deshpande S. Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s. ChemistrySelect 2016. [DOI: 10.1002/slct.201601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
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18
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Mukherjee G, Lal Gupta P, Jayaram B. Predicting the binding modes and sites of metabolism of xenobiotics. MOLECULAR BIOSYSTEMS 2016; 11:1914-24. [PMID: 25913019 DOI: 10.1039/c5mb00118h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metabolism studies are an essential integral part of ADMET profiling of drug candidates to evaluate their safety and efficacy. Cytochrome P-450 (CYP) metabolizes a wide variety of xenobiotics/drugs. The binding modes of these compounds with CYP and their intrinsic reactivities decide the metabolic products. We report here a novel computational protocol, which comprises docking of ligands to heme-containing CYPs and prediction of binding energies through a newly developed scoring function, followed by analyses of the docked structures and molecular orbitals of the ligand molecules, for predicting the sites of metabolism (SOM) of ligands. The calculated binding free energies of 121 heme-containing protein-ligand docked complexes yielded a correlation coefficient of 0.84 against experiment. Molecular orbital analyses of the resultant top three unique poses of the docked complexes provided a success rate of 87% in identifying the experimentally known sites of metabolism of the xenobiotics. The SOM prediction methodology is freely accessible at .
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Affiliation(s)
- Goutam Mukherjee
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, India.
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19
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Yoo J, Hirano M, Mizukawa H, Nomiyama K, Agusa T, Kim EY, Tanabe S, Iwata H. In Vitro and in Silico Analyses for Predicting Hepatic Cytochrome P450-Dependent Metabolic Potencies of Polychlorinated Biphenyls in the Baikal Seal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:14588-14596. [PMID: 26579933 DOI: 10.1021/acs.est.5b03890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this study was to understand the cytochrome P450 (CYP)-dependent metabolic pathway and potency of polychlorinated biphenyls (PCBs) in the Baikal seal (Pusa sibirica). In vitro metabolism of 62 PCB congener mixtures was investigated by using liver microsomes of this species. A decreased ratio of over 20% was observed for CB3, CB4, CB8, CB15, CB19, CB22, CB37, CB54, CB77, and CB105, suggesting the preferential metabolism of low-chlorinated PCBs by CYPs. The highly activated metabolic pathways in Baikal seals that were predicted from the decreased PCBs and detected hydroxylated PCBs (OH-PCBs) were CB22 to 4'OH-CB20 and CB77 to 4'OH-CB79. The total amount of OH-PCBs detected as identified and unidentified congeners accounted for only a 3.8 ± 1.7 mol % of loaded PCBs, indicating many unknown PCB metabolic pathways. To explore factors involved in CYP-dependent PCB metabolism, we examined the relationships among the structural and physicochemical properties of PCBs, the in silico PCB-CYP docking parameters, and the in vitro PCB decreased ratios by principal component analysis. Statistical analysis showed that the decreased PCB ratio was at least partly accounted for by the substituted chlorine number of PCBs and the distance from the Cl-unsubstituted carbon of docked PCBs to the heme Fe in CYP2A and 2B.
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Affiliation(s)
- Jean Yoo
- Center for Marine Environmental Studies (CMES), Ehime University , Bunkyo-cho 2-5, Matsuyama 790-8577, Japan
| | - Masashi Hirano
- Center for Marine Environmental Studies (CMES), Ehime University , Bunkyo-cho 2-5, Matsuyama 790-8577, Japan
| | - Hazuki Mizukawa
- Center for Marine Environmental Studies (CMES), Ehime University , Bunkyo-cho 2-5, Matsuyama 790-8577, Japan
| | - Kei Nomiyama
- Center for Marine Environmental Studies (CMES), Ehime University , Bunkyo-cho 2-5, Matsuyama 790-8577, Japan
| | - Tetsuro Agusa
- Center for Marine Environmental Studies (CMES), Ehime University , Bunkyo-cho 2-5, Matsuyama 790-8577, Japan
| | - Eun-Young Kim
- Department of Life and Nanopharmaceutical Science and Department of Biology, Kyung Hee University , Hoegi-Dong, Dongdaemun-Gu, Seoul 130-701, Korea
| | - Shinsuke Tanabe
- Center for Marine Environmental Studies (CMES), Ehime University , Bunkyo-cho 2-5, Matsuyama 790-8577, Japan
| | - Hisato Iwata
- Center for Marine Environmental Studies (CMES), Ehime University , Bunkyo-cho 2-5, Matsuyama 790-8577, Japan
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20
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An integrated approach for discovery of highly potent and selective Mnk inhibitors: Screening, synthesis and SAR analysis. Eur J Med Chem 2015; 103:539-50. [DOI: 10.1016/j.ejmech.2015.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/07/2014] [Accepted: 09/05/2015] [Indexed: 02/02/2023]
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21
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Abstract
Drug metabolism can produce metabolites with physicochemical and pharmacological properties that differ substantially from those of the parent drug, and consequently has important implications for both drug safety and efficacy. To reduce the risk of costly clinical-stage attrition due to the metabolic characteristics of drug candidates, there is a need for efficient and reliable ways to predict drug metabolism in vitro, in silico and in vivo. In this Perspective, we provide an overview of the state of the art of experimental and computational approaches for investigating drug metabolism. We highlight the scope and limitations of these methods, and indicate strategies to harvest the synergies that result from combining measurement and prediction of drug metabolism.
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22
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Sheng Y, Chen Y, Wang L, Liu G, Li W, Tang Y. Effects of protein flexibility on the site of metabolism prediction for CYP2A6 substrates. J Mol Graph Model 2014; 54:90-9. [DOI: 10.1016/j.jmgm.2014.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 12/01/2022]
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23
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Combining structure- and ligand-based approaches to improve site of metabolism prediction in CYP2C9 substrates. Pharm Res 2014; 32:986-1001. [PMID: 25208877 DOI: 10.1007/s11095-014-1511-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/03/2014] [Indexed: 10/24/2022]
Abstract
PURPOSE Predicting atoms in a potential drug compound that are susceptible to oxidation by cytochrome P450 (CYP) enzymes is of great interest to the pharmaceutical community. We aimed to develop a computational approach combining ligand- and structure-based design principles to accurately predict sites of metabolism (SoMs) in a series of CYP2C9 substrates. METHODS We employed the reactivity model, SMARTCyp, ensemble docking, and pseudo-receptor modeling based on quantitative structure-activity relationships (QSAR) to account for influences of both the inherent reactivity of each atom and the physical structure of the CYP2C9 binding site. RESULTS We tested ligand-based prediction alone (i.e. SMARTCyp), structure-based prediction alone (i.e. AutoDock Vina docking), the linear combination of the SMARTCYP and docking scores, and finally a pseudo-receptor QSAR model based on the docked compounds in combination with SMARTCyp. We found that by using the latter combined approach we were able to accurately predict 88% and 96% of the true SoMs, within the top-1 and top-2 predictions, respectively. CONCLUSIONS We have outlined a novel combination approach for accurately predicting SoMs in CYP2C9 ligands. We believe that this method may be applied to other CYP2C9 ligands as well as to other CYP systems.
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24
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Belka M, Hewelt-Belka W, Sławiński J, Bączek T. Mass spectrometry based identification of geometric isomers during metabolic stability study of a new cytotoxic sulfonamide derivatives supported by quantitative structure-retention relationships. PLoS One 2014; 9:e98096. [PMID: 24893169 PMCID: PMC4043666 DOI: 10.1371/journal.pone.0098096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/29/2014] [Indexed: 12/24/2022] Open
Abstract
A set of 15 new sulphonamide derivatives, presenting antitumor activity have been subjected to a metabolic stability study. The results showed that besides products of biotransformation, some additional peaks occurred in chromatograms. Tandem mass spectrometry revealed the same mass and fragmentation pathway, suggesting that geometric isomerization occurred. Thus, to support this hypothesis, quantitative structure-retention relationships were applied. Human liver microsomes were used as an in vitro model of metabolism. The biotransformation reactions were tracked by liquid chromatography assay and additionally, fragmentation mass spectra were recorded. In silico molecular modeling at a semi-empirical level was conducted as a starting point for molecular descriptor calculations. A quantitative structure-retention relationship model was built applying multiple linear regression based on selected three-dimensional descriptors. The studied compounds revealed high metabolic stability, with a tendency to form hydroxylated biotransformation products. However, significant chemical instability in conditions simulating human body fluids was noticed. According to literature and MS data geometrical isomerization was suggested. The developed in sillico model was able to describe the relationship between the geometry of isomer pairs and their chromatographic retention properties, thus it supported the hypothesis that the observed pairs of peaks are most likely geometric isomers. However, extensive structural investigations are needed to fully identify isomers' geometry. An effort to describe MS fragmentation pathways of novel chemical structures is often not enough to propose structures of potent metabolites and products of other chemical reactions that can be observed in compound solutions at early drug discovery studies. The results indicate that the relatively non-expensive and not time- and labor-consuming in sillico approach could be a good supportive tool assisting the identification of cis-trans isomers based on retention data. This methodology can be helpful during the structural identification of biotransformation and degradation products of new chemical entities--potential new drugs.
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Affiliation(s)
- Mariusz Belka
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Weronika Hewelt-Belka
- Department of Analytical Chemistry, Chemical Faculty, Gdańsk University of Technology, Gdańsk, Poland
- Mass Spectrometry and Chromatography Laboratory, Pomeranian Science and Technology Park, Gdynia, Poland
| | - Jarosław Sławiński
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Tomasz Bączek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
- * E-mail:
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25
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Bello M, Mendieta-Wejebe JE, Correa-Basurto J. Structural and energetic analysis to provide insight residues of CYP2C9, 2C11 and 2E1 involved in valproic acid dehydrogenation selectivity. Biochem Pharmacol 2014; 90:145-58. [PMID: 24794636 DOI: 10.1016/j.bcp.2014.04.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 11/17/2022]
Abstract
Docking and molecular dynamics (MD) simulation have been two computational techniques used to gain insight about the substrate orientation within protein active sites, allowing to identify potential residues involved in the binding and catalytic mechanisms. In this study, both methods were combined to predict the regioselectivity in the binding mode of valproic acid (VPA) on three cytochrome P-450 (CYP) isoforms CYP2C9, CYP2C11, and CYP2E1, which are involved in the biotransformation of VPA yielding reactive hepatotoxic intermediate 2-n-propyl-4-pentenoic acid (4nVPA). There are experimental data about hydrogen atom abstraction of the C4-position of VPA to yield 4nVPA, however, there are not structural evidence about the binding mode of VPA and 4nVPA on CYPs. Therefore, the complexes between these CYP isoforms and VPA or 4nVPA were studied to explore their differences in binding and energetic stabilization. Docking results showed that VPA and 4nVPA are coupled into CYPs binding site in a similar conformation, but it does not explain the VPA hydrogen atom abstraction. On the other hand, MD simulations showed a set of energetic states that reorient VPA at the first ns, then making it susceptible to a dehydrogenation reaction. For 4nVPA, multiple binding modes were observed in which the different states could favor either undergo other reaction mechanism or ligand expulsion from the binding site. Otherwise, the energetic and entropic contribution point out a similar behavior for the three CYP complexes, showing as expected a more energetically favorable binding free energy for the complexes between CYPs and VPA than with 4nVPA.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, México, Distrito Federal 11340, Mexico.
| | - Jessica E Mendieta-Wejebe
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, México, Distrito Federal 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, México, Distrito Federal 11340, Mexico.
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Brändén G, Sjögren T, Schnecke V, Xue Y. Structure-based ligand design to overcome CYP inhibition in drug discovery projects. Drug Discov Today 2014; 19:905-11. [PMID: 24642031 DOI: 10.1016/j.drudis.2014.03.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/26/2014] [Accepted: 03/11/2014] [Indexed: 01/01/2023]
Abstract
Cytochrome P450 (CYP) enzymes are key players in xenobiotic metabolism, and inhibition of CYPs can therefore result in unwanted drug-drug interactions. Within drug discovery, CYP inhibition can cause delays in the progression of candidate drugs, or even premature closure of projects. During the past decade, a massive effort in the pharmaceutical industry and academic research has produced a wealth of structural information in the CYP field. In this short review, we will describe how structure-based approaches can be used in the pharmaceutical industry to work away from CYP inhibition, with a focus on the opportunities and challenges. We will show two examples from our own work where structural information on CYP2C9 and CYP3A4 inhibitor complexes have been successfully exploited in ongoing drug discovery projects.
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Affiliation(s)
- Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg S-405 30, Sweden.
| | - Tove Sjögren
- Discovery Sciences, AstraZeneca R&D Mölndal, Mölndal S-431 83, Sweden
| | - Volker Schnecke
- CVMD iMed, AstraZeneca R&D Mölndal, Mölndal S-431 83, Sweden
| | - Yafeng Xue
- Discovery Sciences, AstraZeneca R&D Mölndal, Mölndal S-431 83, Sweden
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27
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Rudik AV, Dmitriev AV, Lagunin AA, Filimonov DA, Poroikov VV. Metabolism site prediction based on xenobiotic structural formulas and PASS prediction algorithm. J Chem Inf Model 2014; 54:498-507. [PMID: 24417355 DOI: 10.1021/ci400472j] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A new ligand-based method for the prediction of sites of metabolism (SOMs) for xenobiotics has been developed on the basis of the LMNA (labeled multilevel neighborhoods of atom) descriptors and the PASS (prediction of activity spectra for substances) algorithm and applied to predict the SOMs of the 1A2, 2C9, 2C19, 2D6, and 3A4 isoforms of cytochrome P450. An average IAP (invariant accuracy of prediction) of SOMs calculated by the leave-one-out cross-validation procedure was 0.89 for the developed method. The external validation was made with evaluation sets containing data on biotransformations for 57 cardiovascular drugs. An average IAP of regioselectivity for evaluation sets was 0.83. It was shown that the proposed method exceeds accuracy of SOM prediction by RS-Predictor for CYP 1A2, 2D6, 2C9, 2C19, and 3A4 and is comparable to or better than SMARTCyp for CYP 2C9 and 2D6.
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Affiliation(s)
- Anastasia V Rudik
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences , Building 10/8, Pogodinskaya Str., Moscow, 119121, Russia
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28
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Ramesh M, Bharatam PV. Importance of hydrophobic parameters in identifying appropriate pose of CYP substrates in cytochromes. Eur J Med Chem 2014; 71:15-23. [DOI: 10.1016/j.ejmech.2013.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 10/07/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
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29
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Huang TW, Zaretzki J, Bergeron C, Bennett KP, Breneman CM. DR-predictor: incorporating flexible docking with specialized electronic reactivity and machine learning techniques to predict CYP-mediated sites of metabolism. J Chem Inf Model 2013; 53:3352-66. [PMID: 24261543 DOI: 10.1021/ci4004688] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational methods that can identify CYP-mediated sites of metabolism (SOMs) of drug-like compounds have become required tools for early stage lead optimization. In recent years, methods that combine CYP binding site features with CYP/ligand binding information have been sought in order to increase the prediction accuracy of such hybrid models over those that use only one representation. Two challenges that any hybrid ligand/structure-based method must overcome are (1) identification of the best binding pose for a specific ligand with a given CYP and (2) appropriately incorporating the results of docking with ligand reactivity. To address these challenges we have created Docking-Regioselectivity-Predictor (DR-Predictor)--a method that incorporates flexible docking-derived information with specialized electronic reactivity and multiple-instance-learning methods to predict CYP-mediated SOMs. In this study, the hybrid ligand-structure-based DR-Predictor method was tested on substrate sets for CYP 1A2 and CYP 2A6. For these data, the DR-Predictor model was found to identify the experimentally observed SOM within the top two predicted rank-positions for 86% of the 261 1A2 substrates and 83% of the 100 2A6 substrates. Given the accuracy and extendibility of the DR-Predictor method, we anticipate that it will further facilitate the prediction of CYP metabolism liabilities and aid in in-silico ADMET assessment of novel structures.
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Affiliation(s)
- Tao-wei Huang
- Department of Chemistry and Chemical Biology and §Department of Mathematics, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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Sousa MC, Braga RC, Cintra BA, de Oliveira V, Andrade CH. In silico metabolism studies of dietary flavonoids by CYP1A2 and CYP2C9. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.09.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Liu R, Liu J, Tawa G, Wallqvist A. 2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes. J Chem Inf Model 2012; 52:1698-712. [DOI: 10.1021/ci3001524] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruifeng Liu
- DoD Biotechnology High Performance
Computing Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Material Command, Fort Detrick, Maryland 21702,
United States
| | - Jin Liu
- DoD Biotechnology High Performance
Computing Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Material Command, Fort Detrick, Maryland 21702,
United States
| | - Greg Tawa
- DoD Biotechnology High Performance
Computing Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Material Command, Fort Detrick, Maryland 21702,
United States
| | - Anders Wallqvist
- DoD Biotechnology High Performance
Computing Software Applications Institute, Telemedicine and Advanced
Technology Research Center, U.S. Army Medical Research and Material Command, Fort Detrick, Maryland 21702,
United States
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Zaretzki J, Rydberg P, Bergeron C, Bennett KP, Olsen L, Breneman CM. RS-Predictor models augmented with SMARTCyp reactivities: robust metabolic regioselectivity predictions for nine CYP isozymes. J Chem Inf Model 2012; 52:1637-59. [PMID: 22524152 DOI: 10.1021/ci300009z] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RS-Predictor is a tool for creating pathway-independent, isozyme-specific, site of metabolism (SOM) prediction models using any set of known cytochrome P450 (CYP) substrates and metabolites. Until now, the RS-Predictor method was only trained and validated on CYP 3A4 data, but in the present study, we report on the versatility the RS-Predictor modeling paradigm by creating and testing regioselectivity models for substrates of the nine most important CYP isozymes. Through curation of source literature, we have assembled 680 substrates distributed among CYPs 1A2, 2A6, 2B6, 2C19, 2C8, 2C9, 2D6, 2E1, and 3A4, the largest publicly accessible collection of P450 ligands and metabolites released to date. A comprehensive investigation into the importance of different descriptor classes for identifying the regioselectivity mediated by each isozyme is made through the generation of multiple independent RS-Predictor models for each set of isozyme substrates. Two of these models include a density functional theory (DFT) reactivity descriptor derived from SMARTCyp. Optimal combinations of RS-Predictor and SMARTCyp are shown to have stronger performance than either method alone, while also exceeding the accuracy of the commercial regioselectivity prediction methods distributed by Optibrium and Schrödinger, correctly identifying a large proportion of the metabolites in each substrate set within the top two rank-positions: 1A2 (83.0%), 2A6 (85.7%), 2B6 (82.1%), 2C19 (86.2%), 2C8 (83.8%), 2C9 (84.5%), 2D6 (85.9%), 2E1 (82.8%), 3A4 (82.3%), and merged (86.0%). Comprehensive datamining of each substrate set and careful statistical analyses of the predictions made by the different models revealed new insights into molecular features that control metabolic regioselectivity and enable accurate prospective prediction of likely SOMs.
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Affiliation(s)
- Jed Zaretzki
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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Rydberg P, Olsen L. Predicting drug metabolism by cytochrome P450 2C9: comparison with the 2D6 and 3A4 isoforms. ChemMedChem 2012; 7:1202-9. [PMID: 22593031 DOI: 10.1002/cmdc.201200160] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 04/23/2012] [Indexed: 11/10/2022]
Abstract
By the use of knowledge gained through modeling of drug metabolism mediated by the cytochrome P450 2D6 and 3A4 isoforms, we constructed a 2D-based model for site-of-metabolism prediction for the cytochrome P450 2C9 isoform. The similarities and differences between the models for the 2C9 and 2D6 isoforms are discussed through structural knowledge from the X-ray crystal structures and trends in experimental data. The final model was validated on an independent test set, resulting in an area under the curve value of 0.92, and a site of metabolism was found among the top two ranked atoms for 77% of the compounds.
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Affiliation(s)
- Patrik Rydberg
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Denmark.
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Identification of benzoylisoquinolines as potential anti-Chagas agents. Bioorg Med Chem 2012; 20:2587-94. [DOI: 10.1016/j.bmc.2012.02.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/14/2012] [Accepted: 02/20/2012] [Indexed: 12/15/2022]
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Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 2012; 52:617-48. [PMID: 22339582 PMCID: PMC3317594 DOI: 10.1021/ci200542m] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Metabolism of xenobiotics remains a central challenge
for the discovery
and development of drugs, cosmetics, nutritional supplements, and
agrochemicals. Metabolic transformations are frequently related to
the incidence of toxic effects that may result from the emergence
of reactive species, the systemic accumulation of metabolites, or
by induction of metabolic pathways. Experimental investigation of
the metabolism of small organic molecules is particularly resource
demanding; hence, computational methods are of considerable interest
to complement experimental approaches. This review provides a broad
overview of structure- and ligand-based computational methods for
the prediction of xenobiotic metabolism. Current computational approaches
to address xenobiotic metabolism are discussed from three major perspectives:
(i) prediction of sites of metabolism (SOMs), (ii) elucidation of
potential metabolites and their chemical structures, and (iii) prediction
of direct and indirect effects of xenobiotics on metabolizing enzymes,
where the focus is on the cytochrome P450 (CYP) superfamily of enzymes,
the cardinal xenobiotics metabolizing enzymes. For each of these domains,
a variety of approaches and their applications are systematically
reviewed, including expert systems, data mining approaches, quantitative
structure–activity relationships (QSARs), and machine learning-based
methods, pharmacophore-based algorithms, shape-focused techniques,
molecular interaction fields (MIFs), reactivity-focused techniques,
protein–ligand docking, molecular dynamics (MD) simulations,
and combinations of methods. Predictive metabolism is a developing
area, and there is still enormous potential for improvement. However,
it is clear that the combination of rapidly increasing amounts of
available ligand- and structure-related experimental data (in particular,
quantitative data) with novel and diverse simulation and modeling
approaches is accelerating the development of effective tools for
prediction of in vivo metabolism, which is reflected by the diverse
and comprehensive data sources and methods for metabolism prediction
reviewed here. This review attempts to survey the range and scope
of computational methods applied to metabolism prediction and also
to compare and contrast their applicability and performance.
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Affiliation(s)
- Johannes Kirchmair
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
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Yuki H, Honma T, Hata M, Hoshino T. Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4. Bioorg Med Chem 2011; 20:775-83. [PMID: 22197672 DOI: 10.1016/j.bmc.2011.12.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 11/25/2022]
Abstract
In drug discovery process, improvement of ADME/Tox properties of lead compounds including metabolic stability is critically important. Cytochrome P450 (CYP) is one of the major metabolizing enzymes and the prediction of sites of metabolism (SOM) on the given lead compounds is key information to modify the compounds to be more stable against metabolism. There are two factors essentially important in SOM prediction. First is accessibility of each substrate atom to the oxygenated Fe atom of heme in a CYP protein, and the other is the oxidative reactivity of each substrate atom. To predict accessibility of substrate atoms to the heme iron, conventional protein-rigid docking simulations have been applied. However, the docking simulations without consideration of protein flexibility often lead to incorrect answers in the case of very flexible proteins such as CYP3A4. In this study, we demonstrated an approach utilizing molecular dynamics (MD) simulation for SOM prediction in which multiple MD runs were executed using different initial structures. We applied this strategy to CYP3A4 and carbamazepine (CBZ) complex. Through 10 ns MD simulations started from five different CYP3A4-CBZ complex models, our approach correctly predicted SOM observed in experiments. The experimentally known epoxidized sites of CBZ by CYP3A4 were successfully predicted as the most accessible sites to the heme iron that was judged from a numerical analysis of calculated ΔG(binding) and the frequency of appearance. In contrast, the predictions using protein-rigid docking methods hardly provided the correct SOM due to protein flexibility or inaccuracy of the scoring functions. Our strategy using MD simulation with multiple initial structures will be one of the reliable methods for SOM prediction.
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Affiliation(s)
- Hitomi Yuki
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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Braga RC, Alves VM, Fraga CAM, Barreiro EJ, de Oliveira V, Andrade CH. Combination of docking, molecular dynamics and quantum mechanical calculations for metabolism prediction of 3,4-methylenedioxybenzoyl-2-thienylhydrazone. J Mol Model 2011; 18:2065-78. [DOI: 10.1007/s00894-011-1219-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 08/09/2011] [Indexed: 11/29/2022]
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Danielson ML, Desai PV, Mohutsky MA, Wrighton SA, Lill MA. Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures. Eur J Med Chem 2011; 46:3953-63. [PMID: 21703735 DOI: 10.1016/j.ejmech.2011.05.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/24/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
Cytochrome P450 enzymes are responsible for metabolizing many endogenous and xenobiotic molecules encountered by the human body. It has been estimated that 75% of all drugs are metabolized by cytochrome P450 enzymes. Thus, predicting a compound's potential sites of metabolism (SOM) is highly advantageous early in the drug development process. We have combined molecular dynamics, AutoDock Vina docking, the neighboring atom type (NAT) reactivity model, and a solvent-accessible surface-area term to form a reactivity-accessibility model capable of predicting SOM for cytochrome P450 2C9 substrates. To investigate the importance of protein flexibility during the ligand-binding process, the results of SOM prediction using a static protein structure for docking were compared to SOM prediction using multiple protein structures in ensemble docking. The results reported here indicate that ensemble docking increases the number of ligands that can be docked in a bioactive conformation (ensemble: 96%, static: 85%) but only leads to a slight improvement (49% vs. 44%) in predicting an experimentally known SOM in the top-1 position for a ligand library of 75 CYP2C9 substrates. Using ensemble docking, the reactivity-accessibility model accurately predicts SOM in the top-1 ranked position for 49% of the ligand library and considering the top-3 predicted sites increases the prediction success rate to approximately 70% of the ligand library. Further classifying the substrate library according to K(m) values leads to an improvement in SOM prediction for substrates with low K(m) values (57% at top-1). While the current predictive power of the reactivity-accessibility model still leaves significant room for improvement, the results illustrate the usefulness of this method to identify key protein-ligand interactions and guide structural modifications of the ligand to increase its metabolic stability.
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Affiliation(s)
- Matthew L Danielson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
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Wendt B, Mulbaier M, Wawro S, Schultes C, Alonso J, Janssen B, Lewis J. Toluidinesulfonamide hypoxia-induced factor 1 inhibitors: alleviating drug-drug interactions through use of PubChem data and comparative molecular field analysis guided synthesis. J Med Chem 2011; 54:3982-6. [PMID: 21574568 DOI: 10.1021/jm200272h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inhibitors of hypoxia-inducible factor 1 (HIF-1) represent promising anticancer therapeutics. We have identified a series of potent toluidinesulfonamide HIF-1 inhibitors. However, the series was threatened by a potential liability to inhibit CYP2C9 which could cause dangerous drug-drug interactions when being coadministered with other drugs. We used structure-activity data from the PubChem database to develop a topomer CoMFA model that guided the design of novel sulfonamides with high selectivity for HIF-1 over CYP2C9 inhibition.
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Affiliation(s)
- Bernd Wendt
- Elara Pharmaceuticals GmbH , Boxbergring 107, 69127 Heidelberg, Germany
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Tarcsay Á, Keserű GM. In silicosite of metabolism prediction of cytochrome P450-mediated biotransformations. Expert Opin Drug Metab Toxicol 2011; 7:299-312. [DOI: 10.1517/17425255.2011.553599] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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41
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Yamazaki K, Suzuki M, Itoh T, Yamamoto K, Kanemitsu M, Matsumura C, Nakano T, Sakaki T, Fukami Y, Imaishi H, Inui H. Structural basis of species differences between human and experimental animal CYP1A1s in metabolism of 3,3′,4,4′,5-pentachlorobiphenyl. ACTA ACUST UNITED AC 2011; 149:487-94. [DOI: 10.1093/jb/mvr009] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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42
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Pogrebnoi AA, Grishina MA, Potemkin VA, Sysakov DA. Modeling complexes of substrates with cytochrome P450 2C9. Pharm Chem J 2010. [DOI: 10.1007/s11094-010-0438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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43
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Yongye AB, Pinilla C, Medina-Franco JL, Giulianotti MA, Dooley CT, Appel JR, Nefzi A, Scior T, Houghten RA, Martínez-Mayorga K. Integrating computational and mixture-based screening of combinatorial libraries. J Mol Model 2010; 17:1473-82. [DOI: 10.1007/s00894-010-0850-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/06/2010] [Indexed: 11/29/2022]
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Itoh T, Takemura H, Shimoi K, Yamamoto K. A 3D Model of CYP1B1 Explains the Dominant 4-Hydroxylation of Estradiol. J Chem Inf Model 2010; 50:1173-8. [DOI: 10.1021/ci1000554] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshimasa Itoh
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan, Faculty of Human Health Sciences, Matsumoto University, 2095-1 Niimura, Matsumoto 390-1295, Japan, and Institute for Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Hitomi Takemura
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan, Faculty of Human Health Sciences, Matsumoto University, 2095-1 Niimura, Matsumoto 390-1295, Japan, and Institute for Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Kayoko Shimoi
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan, Faculty of Human Health Sciences, Matsumoto University, 2095-1 Niimura, Matsumoto 390-1295, Japan, and Institute for Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
| | - Keiko Yamamoto
- Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan, Faculty of Human Health Sciences, Matsumoto University, 2095-1 Niimura, Matsumoto 390-1295, Japan, and Institute for Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan
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Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach. J Comput Aided Mol Des 2010; 24:399-408. [PMID: 20361237 DOI: 10.1007/s10822-010-9347-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 03/18/2010] [Indexed: 01/21/2023]
Abstract
A novel structure-based approach for site of metabolism prediction has been developed. This knowledge-based method consists of three steps: (1) generation of possible metabolites, (2) docking the predicted metabolites to the CYP binding site and (3) selection of the most probable metabolites based on their complementarity to the binding site. As a proof of concept we evaluated our method by using MetabolExpert for metabolite generation and Glide for docking into the binding site of the CYP2C9 crystal structure. Our method could identify the correct metabolite among the three best-ranked compounds in 69% of the cases. The predictive power of our knowledge-based method was compared to that achieved by substrate docking and two alternative literature approaches.
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46
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AFM study of the interaction of cytochrome P450 2C9 with phospholipid bilayers. Chem Phys Lipids 2010; 163:182-9. [DOI: 10.1016/j.chemphyslip.2009.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 08/07/2009] [Accepted: 11/09/2009] [Indexed: 11/18/2022]
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48
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49
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Kim DN, Cho KH, Oh WS, Lee CJ, Lee SK, Jung J, No KT. EaMEAD: Activation energy prediction of cytochrome P450 mediated metabolism with effective atomic descriptors. J Chem Inf Model 2009; 49:1643-54. [PMID: 19545128 DOI: 10.1021/ci900011g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an effort to improve drug design and predictions for pharmacokinetics (PK), an empirical model was developed to predict the activation energies (Ea) of cytochrome P450 (CYP450) mediated metabolism. The model, EaMEAD (Activation energy of Metabolism reactions with Effective Atomic Descriptors), predicts the Ea of four major metabolic reactions of the CYP450 enzyme: aliphatic hydroxylation, N-dealkylation, O-dealkylation, and aromatic hydroxylation. To build and validate the empirical model, the E(a) values of the substrates with diverse chemical structures (394 metabolic sites for aliphatic hydroxylation, 27 metabolic sites for N-dealkylation, 9 metabolic sites for O-dealkylation, and 85 metabolic sites for aromatic hydroxylation) were calculated by AM1 molecular orbital (MO). Empirical equations, Quantitative Structure Activity Relationship (QSAR) models, were derived using effective atomic charge, effective atomic polarizability, and bond dipole moments of the substrates as descriptors. EaMEAD is shown to accurately predict Ea with a correlation coefficient (R) of 0.94 and root-mean-square error (RMSE, unit is kcal/mol) of 0.70 for aliphatic hydroxylation, N-dealkylation, and O-dealkylation, and R of 0.83 and RMSE of 0.80 for aromatic hydroxylation, respectively. Physical origin and the role of the effective atomic descriptors of the models are presented in detail. With this model, the Ea of the metabolism can be rapidly predicted without any experimental parameters or time-consuming QM calculation. Regioselectivity prediction with our model is presented in the case of CYP3A4 metabolism. The reliability and ease of use of this model will greatly facilitate early stage PK predictions and rational drug design. Moreover, the model can be applied to develop the Ea prediction model of various types of chemical reactions.
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Affiliation(s)
- Doo Nam Kim
- Bioinformatics and Molecular Design Research Center, Seoul 120-749, Korea
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50
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Prusis P, Afzelius L. Reduced vdW Radius Improves Site of Metabolism Predictions Using X-Ray Structure of CYP2D6. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200860181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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