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Hu K, Tu H, Xie J, Yang Z, Li Z, Chen Y, Liu Y. Phenylalanine Residues in the Active Site of CYP2E1 Participate in Determining the Binding Orientation and Metabolism-Dependent Genotoxicity of Aromatic Compounds. TOXICS 2023; 11:495. [PMID: 37368596 DOI: 10.3390/toxics11060495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023]
Abstract
The composition of amino acids forming the active site of a CYP enzyme is impactful in its substrate selectivity. For CYP2E1, the role of PHE residues in the formation of effective binding orientations for its aromatic substrates remains unclear. In this study, molecular docking and molecular dynamics analysis were performed to reflect the interactions between PHEs in the active site of human CYP2E1 and various aromatic compounds known as its substrates. The results indicated that the orientation of 1-methylpyrene (1-MP) in the active site was highly determined by the presence of PHEs, PHE478 contributing to the binding free energy most significantly. Moreover, by building a random forest model the relationship between each of 19 molecular descriptors of polychlorinated biphenyl (PCB) compounds (from molecular docking, quantum mechanics, and physicochemical properties) and their human CYP2E1-dependent mutagenicityas established mostly in our lab, was investigated. The presence of PHEs did not appear to significantly modify the electronic or structural feature of each bound ligand (PCB), instead, the flexibility of the conformation of PHEs contributed substantially to the effective binding energy and orientation. It is supposed that PHE residues adjust their own conformation to permit a suitablly shaped cavity for holding the ligand and forming its orientation as favorable for a biochemical reaction. This study has provided some insights into the role of PHEs in guiding the interactive adaptation of the active site of human CYP2E1 for the binding and metabolism of aromatic substrates.
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Affiliation(s)
- Keqi Hu
- Department of Science and Education, Guangdong Second Provincial General Hospital, 466 Xingang Middle Road, Guangzhou 510317, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Hongwei Tu
- Guangdong Provincial Center for Disease Control and Prevention, Qunxian Road, Panyu District, Guangzhou 511430, China
| | - Jiayi Xie
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zongying Yang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zihuan Li
- Department of Science and Education, Guangdong Second Provincial General Hospital, 466 Xingang Middle Road, Guangzhou 510317, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Yijing Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Yungang Liu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou 510515, China
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Virtual Screening of Novel 24-Dehydroxysterol Reductase (DHCR24) Inhibitors and the Biological Evaluation of Irbesartan in Cholesterol-Lowering Effect. Molecules 2023; 28:molecules28062643. [PMID: 36985615 PMCID: PMC10053925 DOI: 10.3390/molecules28062643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023] Open
Abstract
Hyperlipidemia is a risk factor for the development of fatty liver and cardiovascular diseases such as atherosclerosis and coronary heart disease, and hence, cholesterol-lowering drugs are considered important and effective in preventing cardiovascular diseases. Thus, researchers in the field of new drug development are endeavoring to identify new types of cholesterol-lowering drugs. 3β-hydroxysterol-Δ(24)-reductase (DHCR24) catalyzes the conversion of desmosterol to cholesterol, which is the last step in the cholesterol biosynthesis pathway. We speculated that blocking the catalytic activity of DHCR24 could be a novel therapeutic strategy for treating hyperlipidemia. In the present study, by virtually screening the DrugBank database and performing molecular dynamics simulation analysis, we selected four potential DHCR24 inhibitor candidates: irbesartan, risperidone, tolvaptan, and conivaptan. All four candidates showed significant cholesterol-lowering activity in HepG2 cells. The experimental mouse model of hyperlipidemia demonstrated that all four candidates improved high blood lipid levels and fat vacuolation in the livers of mice fed with a high-fat diet. In addition, Western blot analysis results suggested that irbesartan reduced cholesterol levels by downregulating the expression of the low-density lipoprotein receptor. Finally, the immune complex activity assay confirmed the inhibitory effect of irbesartan on the enzymatic activity of DHCR24 with its half-maximal inhibitory concentration (IC50) value of 602 nM. Thus, to the best of our knowledge, this is the first study to report that blocking the enzymatic activity of DHCR24 via competitive inhibition is a potential strategy for developing new cholesterol-lowering drugs against hyperlipidemia or multiple cancers. Furthermore, considering that irbesartan is currently used to treat hypertension combined with type 2 diabetes, we believe that irbesartan should be a suitable choice for patients with both hypertension and hyperlipidemia.
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Rodrigues Tanamachi A, Fernandes FH, de Souza Vendemiatti JA, Prediger P, Camparotto NG, Sousa Rocha N, Aragão Umbuzeiro G, Fávero Salvadori DM. Mutagenicity of a novel 2-phenylbenzotriazole (non-chlorinated 2-phenylbenzotriazole-9) in mice. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:471-477. [PMID: 34459030 DOI: 10.1002/em.22463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Dinitrophenylazo dyes can form 2-phenylbenzotriazoles (PBTAs) in the textile dyeing process upon the addition of chemical reducing agents. Some dinitrophenylazo dyes, as well as their respective reduced (non-chlorinated) and chlorinated PBTAs, are now found in rivers owing to wastewater from textile plants. This study aimed to investigate the genotoxicity of a new PBTA derived from C.I. Disperse Violet 93 azo dye, namely non-Cl PBTA-9. Primary DNA damage in the blood, liver, and colon cells, micronucleated cells in the bone marrow, and gene expression (NAT2, CYP1A1, TRP53, and CDKN1A) in liver cells were observed in mice, at acute oral exposure (gavage) doses of 5, 50, and 500 μg/kg body weight (b.w.). The non-chlorinated PBTA-9 caused DNA damage in the blood and liver (at 500 μg/kg b.w.) and in colon cells (at 5, 50, and 500 μg/kg), and increased the frequency of micronucleated cells in the bone marrow (at 5 and 50 μg/kg). No histological alterations or gene expression changes were observed. In conclusion, in vivo exposure to non-chlorinated PBTA-9 induced genetic damage in various rodent tissues, corroborating results previously obtained from the Ames test. Because this compound has been detected in rivers, exposure to humans and biota is a major concern.
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Affiliation(s)
- Amanda Rodrigues Tanamachi
- Department of Pathology, Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- National Institute for Alternative Technologies of Detection, Toxicological Evaluation and Removal of Micropollutants and Radioactives (INCT-DATREM), Institute of Chemistry, Araraquara, São Paulo, Brazil
| | - Fábio Henrique Fernandes
- Department of Pathology, Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- National Institute for Alternative Technologies of Detection, Toxicological Evaluation and Removal of Micropollutants and Radioactives (INCT-DATREM), Institute of Chemistry, Araraquara, São Paulo, Brazil
| | | | - Patrícia Prediger
- School of Technology, State University of Campinas (UNICAMP), Limeira, São Paulo, Brazil
| | | | - Noeme Sousa Rocha
- School of Veterinary and Zootechnics, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | - Daisy Maria Fávero Salvadori
- Department of Pathology, Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- National Institute for Alternative Technologies of Detection, Toxicological Evaluation and Removal of Micropollutants and Radioactives (INCT-DATREM), Institute of Chemistry, Araraquara, São Paulo, Brazil
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Lamazares E, MacLeod-Carey D, Miranda FP, Mena-Ulecia K. Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents. Molecules 2021; 26:E386. [PMID: 33451037 PMCID: PMC7828527 DOI: 10.3390/molecules26020386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 01/29/2023] Open
Abstract
The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which is the main virulence factor of these bacteria. In this work, we used the previous results of a computational biochemistry protocol of a series of ligands designed in silico using thermolysin as a model for the search of antihypertensive agents. Here, thermolysin from Bacillus thermoproteolyticus, a metalloprotein of the M4 family, was used to determine the most promising candidate as an antibacterial agent. Our results from docking, molecular dynamics simulation, molecular mechanics Poisson-Boltzmann (MM-PBSA) method, ligand efficiency, and ADME-Tox properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity) indicate that the designed ligands were adequately oriented in the thermolysin active site. The Lig783, Lig2177, and Lig3444 compounds showed the best dynamic behavior; however, from the ADME-Tox calculated properties, Lig783 was selected as the unique antibacterial agent candidate amongst the designed ligands.
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Affiliation(s)
- Emilio Lamazares
- Pathophysiology Department, Biotechnology and Biopharmaceutical Laboratory, School of Biological Sciences, Universidad de Concepción, Victor Lamas 1290, P.O. Box 160-C, Concepción 4079386, Chile;
| | - Desmond MacLeod-Carey
- Inorganic Chemistry and Molecular Materials Center, Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, San Miguel, Santiago 8900000, Chile;
| | - Fernando P. Miranda
- Instituto de Fisiología, Facultad de Medicina, Universidad Austral de Chile, Valdivia 5090000, Chile;
| | - Karel Mena-Ulecia
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Ave. Rudecindo Ortega 02950, Temuco 4780000, Chile
- Núcleo de Investigación en Bioproductos y Materiales Avanzados (BIOMA), Facultad de Ingeniería, Universidad Católica de Temuco, Ave. Rudecindo Ortega 02950, Temuco 4780000, Chile
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Bitencourt-Ferreira G, de Azevedo WF. Molecular Dynamics Simulations with NAMD2. Methods Mol Biol 2020; 2053:109-124. [PMID: 31452102 DOI: 10.1007/978-1-4939-9752-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
X-ray diffraction crystallography is the primary technique to determine the three-dimensional structures of biomolecules. Although a robust method, X-ray crystallography is not able to access the dynamical behavior of macromolecules. To do so, we have to carry out molecular dynamics simulations taking as an initial system the three-dimensional structure obtained from experimental techniques or generated using homology modeling. In this chapter, we describe in detail a tutorial to carry out molecular dynamics simulations using the program NAMD2. We chose as a molecular system to simulate the structure of human cyclin-dependent kinase 2.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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The Multifarious Link between Cytochrome P450s and Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3028387. [PMID: 31998435 PMCID: PMC6964729 DOI: 10.1155/2020/3028387] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/08/2019] [Accepted: 12/18/2019] [Indexed: 02/07/2023]
Abstract
Cancer is a leading cause of death worldwide. Cytochrome P450s (P450s) play an important role in the metabolism of endogenous as well as exogenous substances, especially drugs. Moreover, many P450s can serve as targets for disease therapy. Increasing reports of epidemiological, diagnostic, and clinical research indicate that P450s are enzymes that play a major part in the formation of cancer, prevention, and metastasis. The purposes of this review are to shed light on the current state of knowledge about the cancer molecular mechanism involving P450s and to summarize the link between the cancer effects and the participation of P450s.
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Santes-Palacios R, Camacho-Carranza R, Espinosa-Aguirre JJ. Bacterial mutagenicity of selected procarcinogens in the presence of recombinant human or rat cytochrome P4501A1. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 835:25-31. [DOI: 10.1016/j.mrgentox.2018.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/30/2022]
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