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Rajan RK, Engels M, Ramanathan M. Predicting phase-I metabolism of piceatannol: an in silico study. In Silico Pharmacol 2024; 12:52. [PMID: 38854674 PMCID: PMC11153392 DOI: 10.1007/s40203-024-00228-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 05/28/2024] [Indexed: 06/11/2024] Open
Abstract
Piceatannol is a natural compound found in plants and can be derived from resveratrol. While resveratrol has been extensively researched for its effects and how the body processes it, there are concerns about its use. These concerns include its limited absorption in the body, the need for specific dosages, potential interactions with other drugs, lack of standardization, and limited clinical evidence to support its benefits. Interestingly, Piceatannol, another compound derived from resveratrol, has received less attention from researchers but appears to offer advantages. It has better bioavailability and seems to have a more favorable therapeutic profile compared to resveratrol. Surprisingly, no previous attempts have been made to explore or predict the metabolites of piceatannol when it interacts with the enzyme cytochrome P450. This study aims to fill that gap by predicting how piceatannol is metabolized by cytochrome P450 and assessing any potential toxicity associated with its metabolites. This research is interesting because it's the first of its kind to investigate the metabolic fate of piceatannol, especially in the context of cytochrome P450. The findings have the potential to significantly contribute to the field of piceatannol research, particularly in the food industry where this compound has applications and implications. Graphical abstract
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Affiliation(s)
- Ravi Kumar Rajan
- Department of Pharmacology, School of Pharmaceutical Sciences, Girijananda Chowdhury University, Tezpur Campus, Tezpur, Assam India
- Present Address: Department of Pharmacology, Himalayan Pharmacy Institute, Majitar, East Sikkim 737136 India
| | - Maida Engels
- Department of Pharmaceutical Chemistry, PSG College of Pharmacy, Coimbatore, Tamil Nadu India
| | - Muthiah Ramanathan
- Department of Pharmacology, PSG College of Pharmacy, Coimbatore, Tamil Nadu India
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Guttman Y, Kerem Z. Computer-Aided (In Silico) Modeling of Cytochrome P450-Mediated Food–Drug Interactions (FDI). Int J Mol Sci 2022; 23:ijms23158498. [PMID: 35955630 PMCID: PMC9369352 DOI: 10.3390/ijms23158498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 02/01/2023] Open
Abstract
Modifications of the activity of Cytochrome 450 (CYP) enzymes by compounds in food might impair medical treatments. These CYP-mediated food–drug interactions (FDI) play a major role in drug clearance in the intestine and liver. Inter-individual variation in both CYP expression and structure is an important determinant of FDI. Traditional targeted approaches have highlighted a limited number of dietary inhibitors and single-nucleotide variations (SNVs), each determining personal CYP activity and inhibition. These approaches are costly in time, money and labor. Here, we review computational tools and databases that are already available and are relevant to predicting CYP-mediated FDIs. Computer-aided approaches such as protein–ligand interaction modeling and the virtual screening of big data narrow down hundreds of thousands of items in databanks to a few putative targets, to which the research resources could be further directed. Structure-based methods are used to explore the structural nature of the interaction between compounds and CYP enzymes. However, while collections of chemical, biochemical and genetic data are available today and call for the implementation of big-data approaches, ligand-based machine-learning approaches for virtual screening are still scarcely used for FDI studies. This review of CYP-mediated FDIs promises to attract scientists and the general public.
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Davydov DR, Dangi B, Yue G, Ahire DS, Prasad B, Zgoda VG. Exploring the Interactome of Cytochrome P450 2E1 in Human Liver Microsomes with Chemical Crosslinking Mass Spectrometry. Biomolecules 2022; 12:biom12020185. [PMID: 35204686 PMCID: PMC8869672 DOI: 10.3390/biom12020185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/05/2022] Open
Abstract
Aiming to elucidate the system-wide effects of the alcohol-induced increase in the content of cytochrome P450 2E1 (CYP2E1) on drug metabolism, we explored the array of its protein-protein interactions (interactome) in human liver microsomes (HLM) with chemical crosslinking mass spectrometry (CXMS). Our strategy employs membrane incorporation of purified CYP2E1 modified with photoreactive crosslinkers benzophenone-4-maleimide and 4-(N-succinimidylcarboxy)benzophenone. Exposure of bait-incorporated HLM samples to light was followed by isolating the His-tagged bait protein and its crosslinked aggregates on Ni-NTA agarose. Analyzing the individual bands of SDS-PAGE slabs of thereby isolated protein with the toolset of untargeted proteomics, we detected the crosslinked dimeric and trimeric complexes of CYP2E1 with other drug-metabolizing enzymes. Among the most extensively crosslinked partners of CYP2E1 are the cytochromes P450 2A6, 2C8, 3A4, 4A11, and 4F2, UDP-glucuronosyltransferases (UGTs) 1A and 2B, fatty aldehyde dehydrogenase (ALDH3A2), epoxide hydrolase 1 (EPHX1), disulfide oxidase 1α (ERO1L), and ribophorin II (RPN2). These results demonstrate the exploratory power of the proposed CXMS strategy and corroborate the concept of tight functional integration in the human drug-metabolizing ensemble through protein-protein interactions of the constituting enzymes.
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Affiliation(s)
- Dmitri R. Davydov
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA;
- Correspondence:
| | - Bikash Dangi
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA;
| | - Guihua Yue
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (G.Y.); (D.S.A.); (B.P.)
| | - Deepak S. Ahire
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (G.Y.); (D.S.A.); (B.P.)
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99202, USA; (G.Y.); (D.S.A.); (B.P.)
| | - Victor G. Zgoda
- Orekhovich Institute of Biomedical Chemistry, Pogodinskaya 10, 119121 Moscow, Russia;
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He J, Zhang L, Liu L. The hydrogen-bond configuration modulates the energy transfer efficiency in helical protein nanotubes. NANOSCALE 2021; 13:991-999. [PMID: 33367447 DOI: 10.1039/d0nr06031c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Energy transport in proteins is critical to a variety of physical, chemical, and biological processes in living organisms. While strenuous efforts have been made to study vibrational energy transport in proteins, thermal transport processes across the most fundamental building blocks of proteins, i.e. helices, are not well understood. This work studies energy transport in a group of "isomer" helices. The π-helix is shown to have the highest thermal conductivity, 110% higher than that of the α-helix and 207% higher than that of the 310-helix. The H-bond connectivity is found to govern thermal transport mechanisms including the phonon spectral energy density, dispersion, mode-specific transport, group velocity, and relaxation time. The energy transport is strongly correlated with the H-bond strength which is also modulated by the H-bond connectivity. These fundamental insights provide a novel perspective for understanding energy transfer in proteins and guiding a rational molecule-level design of novel materials with configurable H-bonds.
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Affiliation(s)
- Jinlong He
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA. and Department of Mechanical and Aerospace Engineering, Utah State University, Logan, Utah 84322, USA
| | - Lin Zhang
- Department of Engineering Mechanics, School of Civil Engineering, Shandong University, Jinan, 250061, P.R. China and Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ling Liu
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA.
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Li X, Lu Y, Ou X, Zeng S, Wang Y, Qi X, Zhu L, Liu Z. Changes and sex- and age-related differences in the expression of drug metabolizing enzymes in a KRAS-mutant mouse model of lung cancer. PeerJ 2020; 8:e10182. [PMID: 33240601 PMCID: PMC7680056 DOI: 10.7717/peerj.10182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/23/2020] [Indexed: 01/16/2023] Open
Abstract
Background This study aimed to systematically profile the alterations and sex- and age-related differences in the drug metabolizing enzymes (DMEs) in a KRAS-mutant mouse model of lung cancer (KRAS mice). Methodology In this study, the LC-MS/MS approach and a probe substrate method were used to detect the alterations in 21 isoforms of DMEs, as well as the enzymatic activities of five isoforms, respectively. Western blotting was applied to study the protein expression of four related receptors. Results The proteins contents of CYP2C29 and CYP3A11, were significantly downregulated in the livers of male KRAS mice at 26 weeks (3.7- and 4.4-fold, respectively, p < 0.05). SULT1A1 and SULT1D1 were upregulated by 1.8- to 7.0- fold at 20 (p = 0.015 and 0.017, respectively) and 26 weeks (p = 0.055 and 0.031, respectively). There were positive correlations between protein expression and enzyme activity for CYP2E1, UGT1A9, SULT1A1 and SULT1D1 (r2 ≥ 0.5, p < 0.001). Western blotting analysis revealed the downregulation of AHR, FXR and PPARα protein expression in male KRAS mice at 26 weeks. For sex-related differences, CYP2E1 was male-predominant and UGT1A2 was female-predominant in the kidney. UGT1A1 and UGT1A5 expression was female-predominant, whereas UGT2B1 exhibited male-predominant expression in liver tissue. For the tissue distribution of DMEs, 21 subtypes of DMEs were all expressed in liver tissue. In the intestine, the expression levels of CYP2C29, CYP27A1, UGT1A2, 1A5, 1A6a, 1A9, 2B1, 2B5 and 2B36 were under the limitation of quantification. The subtypes of CYP7A1, 1B1, 2E1 and UGT1A1, 2A3, 2B34 were detected in kidney tissue. Conclusions This study, for the first time, unveils the variations and sex- and age-related differences in DMEs in C57 BL/6 (WT) mice and KRAS mice.
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Affiliation(s)
- Xiaoyan Li
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yiyan Lu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaojun Ou
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Sijing Zeng
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoxiao Qi
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lijun Zhu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
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Wang J, Lv Z, Lei Z, Chen Z, Lv B, Yang H, Wang Z, Song Q. Expression and functional analysis of cytochrome P450 genes in the wolf spider Pardosa pseudoannulata under cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 172:19-25. [PMID: 30669070 DOI: 10.1016/j.ecoenv.2019.01.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/13/2018] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
Cytochrome P450 enzymes (CYPs), encoded by Halloween genes, mediate the biosynthesis of molting hormone, ecdysteroids, in arthropods. In this report, the effect of heavy metal cadmium (Cd) stress on the expression of cytochrome P450 genes in the wolf spider Pardosa pseudoannulata was analyzed. The results showed the expression levels of genes encoding for Cd transporters including ABC transporters, zinc transporters, calcium channel proteins and calcium binding proteins were inhibited or induced by Cd stress. In addition, the increase in metallothionein (MT) content and glutathione peroxidase (GPX) activity and decrease in total acetylcholine esterase (AChE) activity were also detected. Apparently, these detoxification methods did not completely protect the spider from the cytotoxicity of Cd stress. Increased mortality of P. pseudoannulata was observed when they were under Cd tress. In total 569 CYP genes belonging to 62 CYP subfamilies were obtained from P. pseudoannulata RNA-seq databases. BlaxtX analysis showed that 150, 161, 11, and 40 CYP genes were similar to the genes dib, phm, sad and shd, respectively, which are thought to catalyze the biosynthesis of ecdysteroids. Gene expression analysis suggested that 25 dib encoding genes, 27 phm encoding genes, 2 sad encoding genes, and 6 shd encoding genes were differentially expressed in TS2 vs. S2 comparison (Cd-treated 2nd instar spider vs. 2nd instar spider), respectively. There were 70 dib, 70 phm and 19 shd encoding genes either upregulated or downregulated, while 3 sad encoding genes were upregulated in TS5 vs. S5 (Cd-treated 5nd instar spider vs. 5nd instar spider). Genes related to heme binding and essential for activating the CYPs were also differentially expressed. Expression levels of cuticle related genes were significant differentially expressed, implying the changes in activities of chitin synthases and chitinase. Therefore we assume that unsuccessful molting process may occur on P. pseudoannulata due to influenced ecdysteroids levels, thus increasing mortality of spider.
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Affiliation(s)
- Juan Wang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China; College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Zhiyue Lv
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 China
| | - Ziyan Lei
- College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Zhaoyang Chen
- College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Bo Lv
- College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Huilin Yang
- College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha, Hunan 410128, China
| | - Zhi Wang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
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On identifying collective displacements in apo-proteins that reveal eventual binding pathways. PLoS Comput Biol 2019; 15:e1006665. [PMID: 30645590 PMCID: PMC6333327 DOI: 10.1371/journal.pcbi.1006665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023] Open
Abstract
Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces—those which are “affine” i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo- protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450. Designing drugs which target specific proteins involved in diseases consumes a lot of time and effort in the pharmaceutical industry. In recent times, in silico design of drugs using all-atom molecular modelling has started to provide crucial inputs. Even so, discovery of binding pathways of small molecules both at the primary binding site, as well as sites for allosteric control, is time consuming and often fortuitous. We provide here a framework within which critical conformational changes likely to occur during binding are quantified from statistical analysis of configurations of proteins in their apo, or inactive form, greatly simplifying identification of target residues. We illustrate this idea by analysing ligand binding pathways for three proteins T4- Lysozyme, P450 and Src kinase, which are active respectively in the immune system, metabolism and cancer.
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8
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Fang Y, Gao J, Wang T, Tian X, Gao N, Zhou J, Zhang HF, Wen Q, Jin H, Xing YR, Qiao HL. Intraindividual Variation and Correlation of Cytochrome P450 Activities in Human Liver Microsomes. Mol Pharm 2018; 15:5312-5318. [PMID: 30346185 DOI: 10.1021/acs.molpharmaceut.8b00787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We systematically studied and explored intraindividual variation and correlation in the activities of cytochrome P450 (CYP) using 105 normal liver samples. The intraindividual percentage coefficients of variation of relative Km, Vmax, and CLint were 45.9% (18.3-140%), 44.0% (16.8-127%), and 52.0% (24.2-134%). Overall values of relative Km, Vmax, and CLint for 10 CYPs were sorted. The order, from highest to lowest, was CYP2D6, 3A4/5, 2C19, 2C9, 2B6, 1A2, 2A6, 2C8, and 2E1 for Km; CYP3A4/5, 2C19, 2D6, 2C8, 2E1, 2B6, 1A2, 2A6, and 2C9 for Vmax; and CYP2D6, 2B6, 3A4/5, 2C19, 2C9, 1A2, 2E1, 2C8, and 2A6 for CLint. CYP2A6*4, 2B6 785A>G, and 2D6 100C>T contributed to intraindividual variation of CYP activities. The correlations and similarities among 10 CYP activities were analyzed, and it was found that the highest correlation and similarity for Vmax, Km, and CLint occurred between CYP2C9 and 2C8, CYP2C9 and 1A2, and CYP2C9 and 2C8, respectively. In conclusion, CYP activities exhibit considerable intraindividual variation, with some notable correlations, which might be helpful to comprehensively understand the internal connection among CYP activities and to guide the rational use of drugs.
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Affiliation(s)
- Yan Fang
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Jie Gao
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Tong Wang
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Xin Tian
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Na Gao
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Jun Zhou
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Hai-Feng Zhang
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Qiang Wen
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Han Jin
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Yu-Rong Xing
- The First Affiliated Hospital of Zhengzhou University , Zhengzhou , 450052 Henan , China
| | - Hai-Ling Qiao
- Institute of Clinical Pharmacology , Zhengzhou University , Zhengzhou , 450052 Henan , China
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Toward a systems approach to the human cytochrome P450 ensemble: interactions between CYP2D6 and CYP2E1 and their functional consequences. Biochem J 2017; 474:3523-3542. [PMID: 28904078 DOI: 10.1042/bcj20170543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/30/2017] [Accepted: 09/11/2017] [Indexed: 12/31/2022]
Abstract
Functional cross-talk among human drug-metabolizing cytochrome P450 through their association is a topic of emerging importance. Here, we studied the interactions of human CYP2D6, a major metabolizer of psychoactive drugs, with one of the most prevalent human P450 enzymes, ethanol-inducible CYP2E1. Detection of P450-P450 interactions was accomplished through luminescence resonance energy transfer between labeled proteins incorporated into human liver microsomes and the microsomes of insect cells containing NADPH-cytochrome P450 reductase. The potential of CYP2D6 to form oligomers in the microsomal membrane is among the highest observed with human cytochrome P450 studied up to date. We also observed the formation of heteromeric complexes of CYP2D6 with CYP2E1 and CYP3A4, and found a significant modulation of these interactions by 3,4-methylenedioxymethylamphetamine, a widespread drug of abuse metabolized by CYP2D6. Our results demonstrate an ample alteration of the catalytic properties of CYP2D6 and CYP2E1 caused by their association. In particular, we demonstrated that preincubation of microsomes containing co-incorporated CYP2D6 and CYP2E1 with CYP2D6-specific substrates resulted in considerable time-dependent activation of CYP2D6, which presumably occurs via a slow substrate-induced reorganization of CYP2E1-CYP2D6 hetero-oligomers. Furthermore, we demonstrated that the formation of heteromeric complexes between CYP2E1 and CYP2D6 affects the stoichiometry of futile cycling and substrate oxidation by CYP2D6 by means of decreasing the electron leakage through the peroxide-generating pathways. Our results further emphasize the role of P450-P450 interactions in regulatory cross-talk in human drug-metabolizing ensemble and suggest a role of interactions of CYP2E1 with CYP2D6 in pharmacologically important instances of alcohol-drug interactions.
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Maharao NV, Joshi AA, Gerk PM. Inhibition of glucuronidation and oxidative metabolism of buprenorphine using GRAS compounds or dietary constituents/supplements:in vitroproof of concept. Biopharm Drug Dispos 2017; 38:139-154. [DOI: 10.1002/bdd.2050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/11/2016] [Accepted: 11/30/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Neha V. Maharao
- Department of Pharmaceutics; VCU School of Pharmacy; Richmond VA 23298-0533 USA
| | - Anand A. Joshi
- Department of Pharmaceutics; VCU School of Pharmacy; Richmond VA 23298-0533 USA
| | - Phillip M. Gerk
- Department of Pharmaceutics; VCU School of Pharmacy; Richmond VA 23298-0533 USA
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Improving the activity of surface displayed cytochrome P450 enzymes by optimizing the outer membrane linker. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:104-116. [DOI: 10.1016/j.bbamem.2016.10.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/17/2016] [Accepted: 10/31/2016] [Indexed: 01/31/2023]
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12
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Diaz-Franulic I, Poblete H, Miño-Galaz G, González C, Latorre R. Allosterism and Structure in Thermally Activated Transient Receptor Potential Channels. Annu Rev Biophys 2016; 45:371-98. [DOI: 10.1146/annurev-biophys-062215-011034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ignacio Diaz-Franulic
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
- Fraunhofer Chile Research, Las Condes 7550296, Santiago, Chile
| | - Horacio Poblete
- Institute of Computational Comparative Medicine, Nanotechnology Innovation Center of Kansas State, Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506-5802
| | - Germán Miño-Galaz
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago 8370146, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
| | - Carlos González
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
| | - Ramón Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile; ,
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Bostick CD, Hickey KM, Wollenberg LA, Flora DR, Tracy TS, Gannett PM. Immobilized Cytochrome P450 for Monitoring of P450-P450 Interactions and Metabolism. ACTA ACUST UNITED AC 2016; 44:741-9. [PMID: 26961240 DOI: 10.1124/dmd.115.067637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/09/2016] [Indexed: 11/22/2022]
Abstract
Cytochrome P450 (P450) protein-protein interactions have been shown to alter their catalytic activity. Furthermore, these interactions are isoform specific and can elicit activation, inhibition, or no effect on enzymatic activity. Studies show that these effects are also dependent on the protein partner cytochrome P450 reductase (CPR) and the order of protein addition to purified reconstituted enzyme systems. In this study, we use controlled immobilization of P450s to a gold surface to gain a better understanding of P450-P450 interactions between three key drug-metabolizing isoforms (CYP2C9, CYP3A4, and CYP2D6). Molecular modeling was used to assess the favorability of homomeric/heteromeric P450 complex formation. P450 complex formation in vitro was analyzed in real time utilizing surface plasmon resonance. Finally, the effects of P450 complex formation were investigated utilizing our immobilized platform and reconstituted enzyme systems. Molecular modeling shows favorable binding of CYP2C9-CPR, CYP2C9-CYP2D6, CYP2C9-CYP2C9, and CYP2C9-CYP3A4, in rank order.KDvalues obtained via surface plasmon resonance show strong binding, in the nanomolar range, for the above pairs, with CYP2C9-CYP2D6 yielding the lowestKD, followed by CYP2C9-CYP2C9, CYP2C9-CPR, and CYP2C9-CYP3A4. Metabolic incubations show that immobilized CYP2C9 metabolism was activated by homomeric complex formation. CYP2C9 metabolism was not affected by the presence of CYP3A4 with saturating CPR concentrations. CYP2C9 metabolism was activated by CYP2D6 at saturating CPR concentrations in solution but was inhibited when CYP2C9 was immobilized. The order of addition of proteins (CYP2C9, CYP2D6, CYP3A4, and CPR) influenced the magnitude of inhibition for CYP3A4 and CYP2D6. These results indicate isoform-specific P450 interactions and effects on P450-mediated metabolism.
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Affiliation(s)
- Chris D Bostick
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Katherine M Hickey
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Lance A Wollenberg
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Darcy R Flora
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Timothy S Tracy
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Peter M Gannett
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
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14
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Long Y, Han S, Zhang X, Zhang X, Chen T, Gao Y, Tian H. The combination of a novel 2 bp deletion mutation and p.D63H in CYP11B1 cause congenital adrenal hyperplasia due to steroid 11β-hydroxylase deficiency. Endocr J 2016; 63:301-10. [PMID: 26806323 DOI: 10.1507/endocrj.ej15-0433] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Deficiency of steroid 11β-hydroxylase activity occurs in 5-8% of patients with congenital adrenal hyperplasia (CAH). The aim of the current study was to identify mutations in the CYP11B1 gene of a patient with CAH due to deficiency of steroid 11β-hydroxylase activity, and to study the functional and structural consequences of these mutations. A molecular genetic analysis of the CYP11B1 gene in this patient and her parents identified a known missense mutation g.5194G>C (p.D63H) and a novel 2 bp deletion mutation (g.9525_9526delCT, corresponding to p.L380V…R420X) in the patient. In vitro expression studies in COS7 cells revealed a decreased 11β-hydroxylase activity in the p.D63H mutant to 2.0±0.8% and in the p.L380V…R420X mutant to 0.2±2.2% for the conversion of 11-deoxycortisol to cortisol. Three dimensional homology models for the normal and mutant proteins were built by using the recently published x-ray structure of the human CYP11B2 as a template. Presumably, the g.9525_9526delCT mutation in CYP11B1 resulted in a truncated protein with a misfolded C-terminal domain that could not efficiently bind heme iron, substrate, and adrenodoxin and had lost its biochemical function. In summary, CAH due to steroid 11β-hydroxylase deficiency can be attributed to both the novel deletion mutation (g.9525_9526delCT, corresponding to p.L380V…R420X) and known missense mutation (g.5194G>C corresponding to p.D63H) in CYP11B1.
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Affiliation(s)
- Yang Long
- Laboratory of Endocrinology and Metabolism, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P R China
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15
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Mustafa G, Nandekar PP, Yu X, Wade RC. On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer. J Chem Phys 2015; 143:243139. [DOI: 10.1063/1.4936909] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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16
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Yan T, Lu L, Xie C, Chen J, Peng X, Zhu L, Wang Y, Li Q, Shi J, Zhou F, Hu M, Liu Z. Severely Impaired and Dysregulated Cytochrome P450 Expression and Activities in Hepatocellular Carcinoma: Implications for Personalized Treatment in Patients. Mol Cancer Ther 2015; 14:2874-86. [PMID: 26516155 PMCID: PMC4674380 DOI: 10.1158/1535-7163.mct-15-0274] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 09/17/2015] [Indexed: 12/22/2022]
Abstract
This study aims to systematically determine the activities and expressions of cytochrome P450s (CYP) in hepatocellular carcinoma (HCC) patients to support their optimal use in personalized treatment of HCC. Activities of seven major drug-metabolizing CYP enzymes (CYP1A2, 2A6, 2C8, 2C9, 2D6, 2E1, and 3A4) were determined in tumors and pericarcinomatous tissues harvested from 26 patients with hepatitis B virus-positive HCC using probe substrates. Protein and mRNA levels of these CYPs were also measured using isotope label-free LC/MS-MS method and real-time PCR, respectively. Maximal metabolic velocity (Vmax) of CYP probe substrates was decreased by 2.5- to 30-fold in tumor microsomes, accompanied by a corresponding decrease in their protein and mRNA expression levels. However, Km values and turnover numbers of substrates in tumor microsomes were not changed. High correlations between activities and CYP protein levels were also observed, but the correlation between activities and mRNA levels was often poor. There was a major decrease in the degree of correlation in CYP expression in tumor tissues, suggesting that CYP expression levels are greatly disrupted by the tumorigenic process. Our unprecedented systemic study of the effects of HCC on CYPs demonstrated that activities of CYPs were seriously impaired and their expression patterns were severely altered by HCC. We proposed that determination of the CYP protein expression profile by LC/MS-MS in each patient is a promising approach that can be clinically used for individualized treatment of HCC.
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Affiliation(s)
- Tongmeng Yan
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Linlin Lu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Cong Xie
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jiamei Chen
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaojuan Peng
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Lijun Zhu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ying Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Qiang Li
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Shi
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Fuyuan Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ming Hu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas.
| | - Zhongqiu Liu
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China. International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
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17
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Miño-Galaz GA, Gutierrez G. Hydrogen bonds and asymmetrical heat diffusion in α-helices. A computational analysis. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Modulation of Metabolic Detoxification Pathways Using Foods and Food-Derived Components: A Scientific Review with Clinical Application. J Nutr Metab 2015; 2015:760689. [PMID: 26167297 PMCID: PMC4488002 DOI: 10.1155/2015/760689] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/20/2015] [Indexed: 12/16/2022] Open
Abstract
Research into human biotransformation and elimination systems continues to evolve. Various clinical and in vivo studies have been undertaken to evaluate the effects of foods and food-derived components on the activity of detoxification pathways, including phase I cytochrome P450 enzymes, phase II conjugation enzymes, Nrf2 signaling, and metallothionein. This review summarizes the research in this area to date, highlighting the potential for foods and nutrients to support and/or modulate detoxification functions. Clinical applications to alter detoxification pathway activity and improve patient outcomes are considered, drawing on the growing understanding of the relationship between detoxification functions and different disease states, genetic polymorphisms, and drug-nutrient interactions. Some caution is recommended, however, due to the limitations of current research as well as indications that many nutrients exert biphasic, dose-dependent effects and that genetic polymorphisms may alter outcomes. A whole-foods approach may, therefore, be prudent.
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19
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Miño-Galaz GA. Allosteric communication pathways and thermal rectification in PDZ-2 protein: a computational study. J Phys Chem B 2015; 119:6179-89. [PMID: 25933631 DOI: 10.1021/acs.jpcb.5b02228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Allosteric communication in proteins is a fundamental and yet unresolved problem of structural biochemistry. Previous findings, from computational biology ( Ota, N.; Agard, D. A. J. Mol. Biol. 2005 , 351 , 345 - 354 ), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 protein, and confirmed that this protein has two cognate allosteric pathways and that heat flows preferentially through these. Also, a new property was also observed for protein structures: heat diffuses asymmetrically through the structures. The underling structure of this asymmetrical heat flow was a normal length hydrogen bond (∼2.85 Å) that acted as a thermal rectifier. In contrast, thermal rectification was compromised in short hydrogen bonds (∼2.60 Å), giving rise to symmetrical thermal diffusion. Asymmetrical heat diffusion was due, on a higher scale, to the local, structural organization of residues that, in turn, was also mediated by hydrogen bonds. This asymmetrical/symmetrical energy flow may be relevant for allosteric signal communication directionality in proteins and for the control of heat flow in materials science.
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Affiliation(s)
- Germán A Miño-Galaz
- †Group of Nanomaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile.,‡Centro Interdisciplinario de Neurociencias de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile.,§Universidad Andres Bello Center for Bioinformatics and Integrative Biology (CBIB), Facultad en Ciencias Biologicas, Santiago, Chile
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20
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Yan T, Gao S, Peng X, Shi J, Xie C, Li Q, Lu L, Wang Y, Zhou F, Liu Z, Hu M. Significantly decreased and more variable expression of major CYPs and UGTs in liver microsomes prepared from HBV-positive human hepatocellular carcinoma and matched pericarcinomatous tissues determined using an isotope label-free UPLC-MS/MS method. Pharm Res 2015; 32:1141-57. [PMID: 25288013 PMCID: PMC7728448 DOI: 10.1007/s11095-014-1525-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/12/2014] [Indexed: 12/22/2022]
Abstract
PURPOSE To determine the liver expression of cytochrome P450 (CYPs) and uridine 5'-diphosphate-glucuronosyltransferases (UGTs), the major phase I and II metabolism enzymes responsible for clearance and detoxification of drugs, xenobiotic and endogenous substances. METHODS A validated isotope label-free method was established for absolute and simultaneous quantification of 9 CYPs (1A2, 2A6, 2B6, 2C8, 2C9, 2C19, 2D, 2E1 and 3A4) and 5 UGTs (1A1, 1A4, 1A6, 1A9 and 2B7) in human liver microsomes using LC-MS/MS. RESULTS The LC-MS/MS method displayed excellent dynamic range (at least 250-fold) and high sensitivity for each of the signature peptides with acceptable recovery, accuracy and precision. The protein expression profile of CYP and UGT isoforms were then determined in match microsomes samples prepared from patients with HBV-positive human hepatocellular carcinoma (HCC). In the tumor microsomes, the average absolute amounts of 8 major CYP isoforms (except CYP2C19) and 3 UGT isoforms (UGT1A1, UGT1A4 and UGT2B7) were decreased significantly (p < 0.05), whereas UGT1A6 and UGT1A9 levels were unchanged (p > 0.05). In addition, among isoforms with altered expression, 6 of 8 CYP isoforms and all three UGT isoforms were much more variable in tumor microsomes. Lastly, the importance of CYP3A4 was greatly diminished whereas the importance of UGT1A6 was enhanced in tumor microsomes. CONCLUSION The use of an isotope label-free absolute quantification method for the simultaneous determination of 9 CYPs and 5 UGTs in human liver microsomes reveals that expression levels of CYPs and UGTs in human liver are severely impact by HCC, which could impact drug metabolism, disposition and pharmacotherapy.
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Affiliation(s)
- Tongmeng Yan
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China, 510515
| | - Song Gao
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77030, USA
| | - Xiaojuan Peng
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China, 510515
| | - Jian Shi
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China, 510515
| | - Cong Xie
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China, 510515
| | - Qiang Li
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China, 510515
| | - Linlin Lu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
| | - Ying Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
| | - Fuyuan Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China, 510515
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, 510006
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China, 510515
| | - Ming Hu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77030, USA
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21
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Davydov DR, Davydova NY, Sineva EV, Halpert JR. Interactions among cytochromes P450 in microsomal membranes: oligomerization of cytochromes P450 3A4, 3A5, and 2E1 and its functional consequences. J Biol Chem 2015; 290:3850-64. [PMID: 25533469 PMCID: PMC4319048 DOI: 10.1074/jbc.m114.615443] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/02/2014] [Indexed: 12/31/2022] Open
Abstract
The body of evidence of physiologically relevant P450-P450 interactions in microsomal membranes continues to grow. Here we probe oligomerization of human CYP3A4, CYP3A5, and CYP2E1 in microsomal membranes. Using a technique based on luminescence resonance energy transfer, we demonstrate that all three proteins are subject to a concentration-dependent equilibrium between the monomeric and oligomeric states. We also observed the formation of mixed oligomers in CYP3A4/CYP3A5, CYP3A4/CYP2E1, and CYP3A5/CYP2E1 pairs and demonstrated that the association of either CYP3A4 or CYP3A5 with CYP2E1 causes activation of the latter enzyme. Earlier we hypothesized that the intersubunit interface in CYP3A4 oligomers is similar to that observed in the crystallographic dimers of some microsomal drug-metabolizing cytochromes P450 (Davydov, D. R., Davydova, N. Y., Sineva, E. V., Kufareva, I., and Halpert, J. R. (2013) Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone. Biochem. J. 453, 219-230). Here we report the results of intermolecular cross-linking of CYP3A4 oligomers with thiol-reactive bifunctional reagents as well as the luminescence resonance energy transfer measurements of interprobe distances in the oligomers of labeled CYP3A4 single-cysteine mutants. The results provide compelling support for the physiological relevance of the dimer-specific peripheral ligand-binding site observed in certain CYP3A4 structures. According to our interpretation, these results reveal an important general mechanism that regulates the activity and substrate specificity of the cytochrome P450 ensemble through interactions between multiple P450 species. As a result of P450-P450 cross-talk, the catalytic properties of the cytochrome P450 ensemble cannot be predicted by simple summation of the properties of the individual P450 species.
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Affiliation(s)
- Dmitri R Davydov
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and the V. N. Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Str., Moscow 119832, Russia
| | - Nadezhda Y Davydova
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and
| | - Elena V Sineva
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and
| | - James R Halpert
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and
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22
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Relationship between honeybee nutrition and their microbial communities. Antonie Van Leeuwenhoek 2015; 107:921-33. [DOI: 10.1007/s10482-015-0384-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/12/2015] [Indexed: 10/24/2022]
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23
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Kalescky R, Liu J, Tao P. Identifying key residues for protein allostery through rigid residue scan. J Phys Chem A 2014; 119:1689-700. [PMID: 25437403 DOI: 10.1021/jp5083455] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Allostery is a ubiquitous process for protein regulatory activity in which a binding event can change a protein's function carried out at a distal site. Despite intensive theoretical and experimental investigation of protein allostery in the past five decades, effective methods have yet to be developed that can systematically identify key residues involved in allosteric mechanisms. In this study, we propose the rigid residue scan as a systematic approach to identify important allosteric residues. The third PDZ domain (PDZ3) in the postsynaptic density 95 protein (PSD-95) is used as a model system, and each amino acid residue is treated as a single rigid body during independent molecular dynamics simulations. Various indices based on cross-correlation matrices are used, which allow for two groups of residues with different functions to be identified. The first group is proposed as "switches" that are needed to "turn on" the binding effect of protein allostery. The second group is proposed as "wire residues" that are needed to propagate energy or information from the binding site to distal locations within the same protein. Among the nine residues suggested as important for PDZ3 intramolecular communication in this study, eight have been reported as critical for allostery in PDZ3. Therefore, the rigid residue scan approach is demonstrated to be an effective method for systemically identifying key residues in protein intramolecular communication and allosteric mechanisms.
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Affiliation(s)
- Robert Kalescky
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), and Center for Scientific Computation, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275, United States
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24
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Miño G, Barriga R, Gutierrez G. Hydrogen Bonds and Heat Diffusion in α-Helices: A Computational Study. J Phys Chem B 2014; 118:10025-34. [DOI: 10.1021/jp503420e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- German Miño
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
- Centro
Interdisciplinario de Neurociencias de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile
- Facultad
de Ciencias Biologicas, Centro de Bioinformatica y Biologia Integrativa, Universidad Andres Bello, Av.Republica 239, Santiago, Chile
| | - Raul Barriga
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Gonzalo Gutierrez
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
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25
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Gong L, Chen X, Liu C, Jin F, Hu Q. Gene expression profile of Bombyx mori hemocyte under the stress of destruxin A. PLoS One 2014; 9:e96170. [PMID: 24801594 PMCID: PMC4011735 DOI: 10.1371/journal.pone.0096170] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/04/2014] [Indexed: 01/10/2023] Open
Abstract
Destruxin A (DA) is a cyclo-peptidic mycotoxin from the entomopathogenic fungus Metarhizium anisopliae. To uncover potential genes associated with its molecular mechanisms, a digital gene expression (DGE) profiling analysis was used to compare differentially expressed genes in the hemocytes of silkworm larvae treated with DA. Ten DGE libraries were constructed, sequenced, and assembled, and the unigenes with least 2.0-fold difference were further analyzed. The numbers of up-regulated genes were 10, 20, 18, 74 and 8, as well as the numbers of down-regulated genes were 0, 1, 8, 13 and 3 at 1, 4, 8, 12 and 24 h post treatment, respectively. Totally, the expression of 132 genes were significantly changed, among them, 1, 3 and 12 genes were continually up-regulated at 4, 3 and 2 different time points, respectively, while 1 gene was either up or down-regulated continually at 2 different time points. Furthermore, 68 genes were assigned to one or multiple gene ontology (GO) terms and 89 genes were assigned to specific Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology. In-depth analysis identified that these genes putatively involved in insecticide resistance, cell apoptosis, and innate immune defense. Finally, twenty differentially expressed genes were randomly chosen and validated by quantitative real-time PCR (qRT-PCR). Our studies provide insights into the toxic effect of this microbial insecticide on silkworm's hemocytes, and are helpful to better understanding of the molecular mechanisms of DA as a biological insecticide.
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Affiliation(s)
- Liang Gong
- College of Natural Resource and Environment, South China Agricultural University, Guangzhou, China
| | - Xiurun Chen
- College of Natural Resource and Environment, South China Agricultural University, Guangzhou, China
| | - Chenglan Liu
- College of Natural Resource and Environment, South China Agricultural University, Guangzhou, China
| | - Fengliang Jin
- College of Natural Resource and Environment, South China Agricultural University, Guangzhou, China
| | - Qiongbo Hu
- College of Natural Resource and Environment, South China Agricultural University, Guangzhou, China
- * E-mail:
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