1
|
Wang M, Wang S, Cui J, Lian D, Li Y, Du Y, Li L. Interactions studies of CYP2D6 with quercetin and hyperoside by spectral analysis and molecular dynamics simulations. LUMINESCENCE 2024; 39:e4605. [PMID: 37795938 DOI: 10.1002/bio.4605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/12/2023] [Accepted: 10/01/2023] [Indexed: 10/06/2023]
Abstract
Some ingredients from herbal medicine can significantly affect the activity of CYP2D6, thus leading to serious interactions between herbs and drugs. Quercetin and hyperoside are active ingredients widely found in vegetables, fruits, and herbal medicines. Quercetin and hyperoside have many biological activities. In this work, the characteristic bindings of CYP2D6 with quercetin/hyperoside are revealed by multi-spectroscopy analysis, molecular docking, and molecular dynamics simulations. The fluorescence of CYP2D6 is statically quenched by quercetin and hyperoside. The binding constant (Ka ) values of CYP2D6-quercetin/hyperoside range from 104 L mol-1 , which indicates that these two flavonoids bind moderately to CYP2D6. Meanwhile, quercetin has a stronger quenching ability to CYP2D6 than that of hyperoside. The secondary structure of CYP2D6 is obviously changed by binding with quercetin/hyperoside. The docking results reveal that the quercetin/hyperoside enters the active site of CYP2D6 near heme and binds to CYP2D6 by hydrogen bonds and van der Waals forces. The molecular dynamics simulation results indicate that the binding of quercetin/hyperoside can stabilize the two complexes, enhance the flexibility of CYP2D6 backbone atoms, and make a more unfolded and looser structure of CYP2D6.
Collapse
Affiliation(s)
- Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Suqing Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Jingjing Cui
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Di Lian
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yuan Li
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yutong Du
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun, China
| |
Collapse
|
2
|
Tao Y, Fan Y, Wang M, Wang S, Cui JJ, Lian D, Lu S, Li L. Comparative study of the interaction mechanism of astilbin, isoastilbin, and neoastilbin with CYP3A4. LUMINESCENCE 2023; 38:1654-1667. [PMID: 37421260 DOI: 10.1002/bio.4553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
The interactions of human CYP3A4 with three selected isomer flavonoids, such as astilbin, isoastilbin and neoastilbin, were clarified using spectral analysis, molecular docking, and molecular dynamics simulation. During binding with the three flavonoids, the intrinsic fluorescence of CYP3A4 was statically quenched in static mode with nonradiative energy conversion. The fluorescence and ultraviolet/visible (UV/vis) data revealed that the three flavonoids had a moderate and stronger binding affinity with CYP3A4 due to the order of the Ka1 and Ka2 values ranging from 104 to 105 L·mol-1 . In addition, astilbin had the highest affinity with CYP3A4, then isoastilbin and neoastilbin, at the three experimental temperatures. Multispectral analysis confirmed that binding of the three flavonoids resulted in clear changes in the secondary structure of CYP3A4. It was found from fluorescence, UV/vis and molecular docking analyses that these three flavonoids strongly bound to CYP3A4 by means of hydrogen bonds and van der Waals forces. The key amino acids around the binding site were also elucidated. Furthermore, the stabilities of the three CYP3A4 complexes were evaluated using molecular dynamics simulation.
Collapse
Affiliation(s)
- Yanzhou Tao
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yangyang Fan
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Suqing Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Jing Jing Cui
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Di Lian
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Shuning Lu
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun, China
| |
Collapse
|
3
|
Lukáčová Bujňáková Z, Dutková E, Jakubíková J, Cholujová D, Varhač R, Borysenko L, Melnyk I. Investigation of the Interaction between Mechanosynthesized ZnS Nanoparticles and Albumin Using Fluorescence Spectroscopy. Pharmaceuticals (Basel) 2023; 16:1219. [PMID: 37765027 PMCID: PMC10536685 DOI: 10.3390/ph16091219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
In this paper, ZnS nanoparticles were bioconjugated with bovine serum albumin and prepared in a form of nanosuspension using a wet circulation grinding. The stable nanosuspension with monomodal particle size distribution (d50 = 137 nm) and negative zeta potential (-18.3 mV) was obtained. The sorption kinetics and isotherm were determined. Interactions between ZnS and albumin were studied using the fluorescence techniques. The quenching mechanism, describing both static and dynamic interactions, was investigated. Various parameters were calculated, including the quenching rate constant, binding constant, stoichiometry of the binding process, and accessibility of fluorophore to the quencher. It has been found that tryptophan, in comparison to tyrosine, can be closer to the binding site established by analyzing the synchronous fluorescence spectra. The cellular mechanism in multiple myeloma cells treated with nanosuspension was evaluated by fluorescence assays for quantification of apoptosis, assessment of mitochondrial membrane potential and evaluation of cell cycle changes. The preliminary results confirm that the nontoxic nature of ZnS nanoparticles is potentially applicable in drug delivery systems. Additionally, slight changes in the secondary structure of albumin, accompanied by a decrease in α-helix content, were investigated using the FTIR method after analyzing the deconvoluted Amide I band spectra of ZnS nanoparticles conjugated with albumin. Thermogravimetric analysis and long-term stability studies were also performed to obtain a complete picture about the studied system.
Collapse
Affiliation(s)
- Zdenka Lukáčová Bujňáková
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia; (E.D.); (I.M.)
| | - Erika Dutková
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia; (E.D.); (I.M.)
| | - Jana Jakubíková
- Cancer Research Institute of Biomedical Research Center, Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (J.J.)
| | - Danka Cholujová
- Cancer Research Institute of Biomedical Research Center, Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (J.J.)
| | - Rastislav Varhač
- Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154 Košice, Slovakia;
| | - Larysa Borysenko
- Chuiko Institute of Surface Chemistry, National Academy of Science of Ukraine, Generala Naumova 17, 03164 Kyiv, Ukraine;
| | - Inna Melnyk
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia; (E.D.); (I.M.)
| |
Collapse
|
4
|
Lukáčová Bujňáková Z, Melnyk I, Dutková E, Varhač R, Jakubíková J, Cholujová D, Tóthová E, Storozhuk L, Briančin J. Nano-bio Interface between As 4S 4 Nanoparticles and Albumin Influenced by Wet Stirred Media Milling. Int J Pharm 2023; 640:123046. [PMID: 37178791 DOI: 10.1016/j.ijpharm.2023.123046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
Arsenic sulfide (As4S4) nanoparticles have been intensively researched as a promising drug in a cancer treatment. For the first time, the interaction between As4S4 and bovine serum albumin has been studied in this paper. Initially, the sorption kinetics of albumin on the surface of nanoparticles was investigated. Subsequently, its structural changes influenced by interaction with the As4S4 nanoparticles during wet stirred media milling were studied in deep. Both the dynamic and static quenching were detected after analyzing the fluorescence quenching spectra. From the synchronous fluorescence spectra it was investigated, that the fluorescence intensity for tyrosine residues decreased by about 55%, and for tryptophan it was about 80%. It indicates the fluorescence from tryptophan is more intense and gets more efficiently quenched than those from tyrosine residues in presence of As4S4, implying that the tryptophan can be closer to the binding site. From the circular dichroisms and FTIR spectra it was observed that conformation of the protein remains almost unchanged. The content of appropriate secondary structures was determined by deconvolution of the absorption peak attributed to the amide I band in FTIR spectra. The preliminary anti-tumor cytotoxic effect of prepared albumin-As4S4 system was also tested on multiple myeloma cell lines.
Collapse
Affiliation(s)
| | - Inna Melnyk
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia
| | - Erika Dutková
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia
| | - Rastislav Varhač
- Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 04154 Košice, Slovakia
| | - Jana Jakubíková
- Cancer Research Institute BMC, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
| | - Danka Cholujová
- Cancer Research Institute BMC, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovakia
| | - Erika Tóthová
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia
| | - Liudmyla Storozhuk
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia; Healthcare Biomagnetic and Nanomaterials Laboratory, University College London, 21 Albemarle Street, London W1S 4BS, United Kingdom
| | - Jaroslav Briančin
- Institute of Geotechnics, Slovak Academy of Sciences, Watsonova 45, 04001 Košice, Slovakia
| |
Collapse
|
5
|
Pascarella G, Antonelli L, Narzi D, Battista T, Fiorillo A, Colotti G, Guidoni L, Morea V, Ilari A. Investigation of the Entry Pathway and Molecular Nature of σ1 Receptor Ligands. Int J Mol Sci 2023; 24:ijms24076367. [PMID: 37047338 PMCID: PMC10094450 DOI: 10.3390/ijms24076367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
The σ1 receptor (σ1-R) is an enigmatic endoplasmic reticulum resident transmembrane protein implicated in a variety of central nervous system disorders and whose agonists have neuroprotective activity. In spite of σ1-R’s physio-pathological and pharmacological importance, two of the most important features required to fully understand σ1-R function, namely the receptor endogenous ligand(s) and the molecular mechanism of ligand access to the binding site, have not yet been unequivocally determined. In this work, we performed molecular dynamics (MD) simulations to help clarify the potential route of access of ligand(s) to the σ1-R binding site, on which discordant results had been reported in the literature. Further, we combined computational and experimental procedures (i.e., virtual screening (VS), electron density map fitting and fluorescence titration experiments) to provide indications about the nature of σ1-R endogenous ligand(s). Our MD simulations on human σ1-R suggested that ligands access the binding site through a cavity that opens on the protein surface in contact with the membrane, in agreement with previous experimental studies on σ1-R from Xenopus laevis. Additionally, steroids were found to be among the preferred σ1-R ligands predicted by VS, and 16,17-didehydroprogesterone was shown by fluorescence titration to bind human σ1-R, with significantly higher affinity than the prototypic σ1-R ligand pridopidine in the same essay. These results support the hypothesis that steroids are among the most important physiological σ1-R ligands.
Collapse
Affiliation(s)
- Gianmarco Pascarella
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy (A.I.)
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy
| | - Lorenzo Antonelli
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy (A.I.)
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy
| | - Daniele Narzi
- Department of Physical and Chemical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
- Correspondence: (D.N.); (V.M.)
| | - Theo Battista
- Protein Production Facility, Structural Biology Laboratory, Elettra Sincrotrone Trieste, 34149 Basovizza, Italy
| | - Annarita Fiorillo
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy (A.I.)
| | - Leonardo Guidoni
- Department of Physical and Chemical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Veronica Morea
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy (A.I.)
- Correspondence: (D.N.); (V.M.)
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy (A.I.)
| |
Collapse
|
6
|
Dutta S, Bose D, Ghosh S, Chakrabarti A. Spectrin: an alternate target for cytoskeletal drugs. J Biomol Struct Dyn 2022:1-12. [PMID: 35994328 DOI: 10.1080/07391102.2022.2109063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Cytoskeletal drugs having enormous therapeutic potential act on the cytoskeletal components like actin, tubulin either by promoting polymerization or destabilizing the same. Here we present the interaction of the popular cytoskeletal drugs such as taxol, latrunculin and cytochalasin with spectrin, a huge protein with multi domains that forms the cytoskeletal network. Particularly, the actin binding domain of spectrin regulates the dynamics of the actin cytoskeleton. We followed the binding of these drugs to its actin binding domain and intact spectrin as well. These drugs bind with moderate affinity (Kb ∼ 104 M-1) and the interaction with actin binding domain is entropy driven and hydrophobic in nature as determined by Van't Hoff plot. The docking studies and molecular dynamics simulations further corroborate the experimental findings. Particularly the higher binding constants in the case of latrunculin and cytochalasin to the actin binding domain of spectrin suggest the binding sites are presumably located in its actin binding domain.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sansa Dutta
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Dipayan Bose
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Semanti Ghosh
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
| |
Collapse
|
7
|
Ma D, Zhang L, Yin Y, Gao Y, Wang Q. Spectroscopic studies of the interaction between phosphorus heterocycles and cytochrome P450. J Pharm Anal 2022; 11:757-763. [PMID: 35028181 PMCID: PMC8740452 DOI: 10.1016/j.jpha.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022] Open
Abstract
P450 fatty acid decarboxylase OleT from Staphylococcus aureus (OleTSA) is a novel cytochrome P450 enzyme that catalyzes the oxidative decarboxylation of fatty acids to yield primarily terminal alkenes and CO2 or minor α- and β-hydroxylated fatty acids as side-products. In this work, the interactions between a series of cycloalkyl phosphorus heterocycles (CPHs) and OleTSA were investigated in detail by fluorescence titration experiment, ultraviolet-visible (UV-vis) and 31P NMR spectroscopies. Fluorescence titration experiment results clearly showed that a dynamic quenching occurred when CPH-6, a representative CPHs, interacted with OleTSA with a binding constant value of 15.2 × 104 M-1 at 293 K. The thermodynamic parameters (ΔH, ΔS and ΔG) showed that the hydrogen bond and van der Waals force played major roles in the interaction between OleTSA and CPHs. The UV-vis and 31P NMR studies indicated the penetration of CPH-6 into the interior environment of OleTSA, which greatly affects the enzymatic activity of OleTSA. Therefore, our study revealed an effective way to use phosphorus heterocyclic compounds to modulate the activity of cytochrome P450 enzymes.
Collapse
Affiliation(s)
- Dumei Ma
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China.,Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Yingwu Yin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China
| | - Yuxing Gao
- Department of Chemistry and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, Fujian, China
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| |
Collapse
|
8
|
Fan Y, Tao Y, Liu G, Wang M, Wang S, Li L. Interaction study of engeletin toward cytochrome P450 3A4 and 2D6 by multi-spectroscopy and molecular docking. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120311. [PMID: 34481255 DOI: 10.1016/j.saa.2021.120311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The inhibitory effects of engeletin on the activities of human cytochrome P450 3A4 and 2D6 (CYP3A4 and CYP2D6) were investigated by enzyme kinetics, multi-spectroscopy and molecular docking. Engeletin was found to strongly inhibit CYP3A4 and CYP2D6, with the IC50 of 1.32 μM and 2.87 μM, respectively. The inhibition modes of engeletin against CYP3A4 and CYP2D6 were a competitive type and a mixed type, respectively. The fluorescence of the two CYPs was quenched statically by engeletin, which was bound to CYP3A4 stronger than to CYP2D6 at the same temperature. Circular dichroism spectroscopy, three-dimensional fluorescence, ultraviolet-visible spectroscopy and synchronous fluorescence confirmed that the conformation and micro-environment of the two CYPs protein were changed after binding with engeletin. Molecular docking, ultraviolet-visible spectroscopy and the fluorescence data revealed that engeletin had strong binding affinity to the two CYPs through hydrogen and van der Waals forces. The findings here suggested that engeletin may cause the herb-drug interactions for its inhibition of CYP3A4 and CYP2D6 activities.
Collapse
Affiliation(s)
- Yangyang Fan
- The College of Chemistry, Changchun Normal University, Changchun 130032,China
| | - Yanzhou Tao
- The College of Chemistry, Changchun Normal University, Changchun 130032,China
| | - Guiming Liu
- The College of Chemistry, Changchun Normal University, Changchun 130032,China
| | - Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun 130032,China
| | - Suqing Wang
- The College of Chemistry, Changchun Normal University, Changchun 130032,China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun 130032,China.
| |
Collapse
|
9
|
Ducharme J, Polic V, Thibodeaux CJ, Auclair K. Combining Small-Molecule Bioconjugation and Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) to Expose Allostery: the Case of Human Cytochrome P450 3A4. ACS Chem Biol 2021; 16:882-890. [PMID: 33913317 DOI: 10.1021/acschembio.1c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report a novel approach to study allostery which combines the use of carefully selected bioconjugates and hydrogen-deuterium exchange mass spectrometry (HDX-MS). This strategy avoids issues related to weak substrate binding and ligand relocalization. The utility of our method is demonstrated using human cytochrome P450 3A4 (CYP3A4), the most important drug-metabolizing enzyme. Allosteric activation and inhibition of CYP3A4 by pharmaceuticals is an important mechanism of drug interactions. We performed HDX-MS analysis on several CYP3A4-effector bioconjugates, some of which mimic the allosteric effect of positive effectors, while others show activity enhancement even though the label does not occupy the allosteric pocket (agonistic) or do not show activation while still blocking the allosteric site (antagonistic). This allowed us to better define the position of the allosteric site, the protein structural dynamics associated with allosteric activation, and the presence of coexisting conformers.
Collapse
Affiliation(s)
- Julie Ducharme
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Vanja Polic
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Christopher J. Thibodeaux
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 0B8
| |
Collapse
|
10
|
Tao Y, Fan Y, Liu G, Zhang Y, Wang M, Wang X, Li L. Interaction study of astilbin, isoastilbin and neoastilbin toward CYP2D6 by multi-spectroscopy and molecular docking. LUMINESCENCE 2021; 36:1412-1421. [PMID: 33949102 DOI: 10.1002/bio.4065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/23/2022]
Abstract
Astilbin, isoastilbin and neoastilbin are the three flavonoid isomers prevalent in Rhizoma Smilax glabra. The interactions between human cytochrome P450 2D6 (CYP2D6) and the three isomers were investigated by multiple spectroscopic coupled with molecular docking. As a result, the fluorescence intensity of CYP2D6 was quenched statically by the three isomers. Meanwhile, astilbin had the strongest binding ability to CYP2D6, followed by isoastilbin and neoastilbin under the identical temperature. Synchronous fluorescence, three-dimensional fluorescence, ultraviolet-visible spectroscopy, circular dichroism and Fourier-transform infrared spectra confirmed that the conformation and micro-environment of CYP2D6 protein were changed after binding with the three isomers. As suggested from molecular docking, the three isomers had strong binding affinity to CYP2D6 via the bonding of hydrogen and van der Waals forces, and the results were in agreement with the fluorescence results. The findings here suggested that astilbin, isoastilbin and neoastilbin may cause the herb-drug interactions for their inhibition of CYP2D6 activity.
Collapse
Affiliation(s)
- Yanzhou Tao
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yangyang Fan
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Guiming Liu
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yuhang Zhang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Xiaolin Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun, China
| |
Collapse
|
11
|
Dangi B, Davydova NY, Maldonado MA, Abbasi A, Vavilov NE, Zgoda VG, Davydov DR. Effects of alcohol-induced increase in CYP2E1 content in human liver microsomes on the activity and cooperativity of CYP3A4. Arch Biochem Biophys 2021; 698:108677. [PMID: 33197431 PMCID: PMC7856178 DOI: 10.1016/j.abb.2020.108677] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/15/2020] [Accepted: 11/08/2020] [Indexed: 12/23/2022]
Abstract
We investigate the effect of the alcohol-induced increase in the content of CYP2E1 in human liver microsomes (HLM) on the function of CYP3A4. Membrane incorporation of the purified CYP2E1 into HLM considerably increases the rate of metabolism of 7-benzyloxyquinoline (BQ) and attenuates the homotropic cooperativity observed with this CYP3A4-specific substrate. It also eliminates the activating effect of α-naphthoflavone (ANF) seen in some HLM samples. To probe the physiological relevance of these effects, we compared three pooled preparations of HLM from normal donors (HLM-N) with a pooled preparation from ten heavy alcohol consumers (HLM-A). The composition of the P450 pool in all samples was characterized by the mass-spectrometric determination of 11 cytochrome P450 species. The fractional content of CYP2E1 in HLM-A was from 2.0 to 3.4 times higher than in HLM-N. In contrast, the content of CYP3A4 in HLM-A was the lowest among all samples. Despite that, HLM-A exhibited a much higher metabolism rate and a lower homotropic cooperativity with BQ, similar to CYP2E1-enriched HLM-N. To substantiate the involvement of interactions between CYP2E1 and CYP3A4 in these effects, we probed hetero-association of these proteins in CYP3A4-containing Supersomes™ with a technique employing CYP2E1 labeled with BODIPY-618 maleimide. These experiments evinced the interactions between the two enzymes and revealed an inhibitory effect of ANF on their association. Our results demonstrate that the functional properties of CYP3A4 are fundamentally dependent on the composition of the cytochrome P450 ensemble and suggest a possible impact of chronic alcohol exposure on the pharmacokinetics of drugs metabolized by CYP3A4.
Collapse
Affiliation(s)
- Bikash Dangi
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Nadezhda Y Davydova
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Marc A Maldonado
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Armina Abbasi
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry, Moscow, 119121, Russia; Skolkovo Institute of Science and Technology, 143025, Skolkovo, Moscow Region, Russia
| | - Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA.
| |
Collapse
|
12
|
Yadav J, Paragas E, Korzekwa K, Nagar S. Time-dependent enzyme inactivation: Numerical analyses of in vitro data and prediction of drug-drug interactions. Pharmacol Ther 2020; 206:107449. [PMID: 31836452 PMCID: PMC6995442 DOI: 10.1016/j.pharmthera.2019.107449] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 (CYP) enzyme kinetics often do not conform to Michaelis-Menten assumptions, and time-dependent inactivation (TDI) of CYPs displays complexities such as multiple substrate binding, partial inactivation, quasi-irreversible inactivation, and sequential metabolism. Additionally, in vitro experimental issues such as lipid partitioning, enzyme concentrations, and inactivator depletion can further complicate the parameterization of in vitro TDI. The traditional replot method used to analyze in vitro TDI datasets is unable to handle complexities in CYP kinetics, and numerical approaches using ordinary differential equations of the kinetic schemes offer several advantages. Improvement in the parameterization of CYP in vitro kinetics has the potential to improve prediction of clinical drug-drug interactions (DDIs). This manuscript discusses various complexities in TDI kinetics of CYPs, and numerical approaches to model these complexities. The extrapolation of CYP in vitro TDI parameters to predict in vivo DDIs with static and dynamic modeling is discussed, along with a discussion on current gaps in knowledge and future directions to improve the prediction of DDI with in vitro data for CYP catalyzed drug metabolism.
Collapse
Affiliation(s)
- Jaydeep Yadav
- Amgen Inc., 360 Binney Street, Cambridge, MA 02142, United States; Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Erickson Paragas
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA 19140, United States.
| |
Collapse
|
13
|
Ducharme J, Polic V, Auclair K. A Covalently Attached Progesterone Molecule Outcompetes the Binding of Free Progesterone at an Allosteric Site of Cytochrome P450 3A4. Bioconjug Chem 2019; 30:1629-1635. [DOI: 10.1021/acs.bioconjchem.9b00248] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Julie Ducharme
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 0B8
| | - Vanja Polic
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec, Canada H3A 0B8
| |
Collapse
|
14
|
Rath SN, Jena L, Patri M. Understanding ligands driven mechanism of wild and mutant aryl hydrocarbon receptor in presence of phytochemicals combating Parkinson’s disease: an in silico and in vivo study. J Biomol Struct Dyn 2019; 38:807-826. [DOI: 10.1080/07391102.2019.1590240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Surya Narayan Rath
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
- Neurobiology Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Lingaraja Jena
- Bioinformatics Centre, Mahatma Gandhi Institute of Medical Sciences, Wardha, Maharashtra, India
| | - Manorama Patri
- Neurobiology Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| |
Collapse
|
15
|
Polic V, Sevrioukova IF, Auclair K. Steroid bioconjugation to a CYP3A4 allosteric site and its effect on substrate binding and coupling efficiency. Arch Biochem Biophys 2018; 653:90-96. [PMID: 29958895 DOI: 10.1016/j.abb.2018.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/11/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022]
Abstract
Human cytochrome P450 3A4 (CYP3A4) is an important drug metabolizing enzyme involved in a number of drug-drug and food-drug interactions. As such, much effort has been devoted into investigating its mechanism of interaction with ligands. CYP3A4 has one of the highest levels of substrate promiscuity for an enzyme, and can even bind multiple ligands simultaneously. The location and orientation of these ligands depend on the chemical structure and stoichiometry, and are generally poorly understood. In the case of the steroid testosterone, up to three copies of the molecule can associate with the enzyme at once, likely two in the active site and one at a postulated allosteric site. Recently, we demonstrated that steroid bioconjugation at the allosteric site results in an increase in activity of CYP3A4 toward testosterone and 7-benzyloxy-4-trifluoromethylcoumarin oxidation. Here, using the established bioconjugation methodology, we show how steroid bioconjugation at the allosteric site affects the heme spin state, the binding affinity (KS) of CYP3A4 for testosterone, as well as the enzyme coupling efficiency.
Collapse
Affiliation(s)
- Vanja Polic
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, United States
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.
| |
Collapse
|