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Perugino F, Pedroni L, Galaverna G, Dall'Asta C, Dellafiora L. A mechanistic toxicology study to grasp the mechanics of zearalenone estrogenicity: Spotlighting aromatase and the effects of its genetic variability. Toxicology 2024; 501:153686. [PMID: 38036094 DOI: 10.1016/j.tox.2023.153686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/02/2023]
Abstract
Zearalenone (ZEN) is a mycoestrogen produced by Fusarium fungi contaminating cereals and in grain-based products threatening human and animal health due to its endocrine disrupting effects. Germane to the mechanisms of action, ZEN may activate the estrogen receptors and inhibit the estrogens-producing enzyme aromatase (CYP19A1). Both show single nucleotide variants (SNVs) among humans associated with a diverse susceptibility of being activated or inhibited. These variations might modify the endocrine disrupting action of ZEN, requiring dedicated studies to improve its toxicological understanding. This work focused on human aromatase investigating via 3D molecular modelling whether some of the SNVs reported so far (n = 434) may affect the inhibitory potential of ZEN. It has been also calculated the inhibition capability of α-zearalenol, the most prominent and estrogenically potent phase I metabolite of ZEN, toward those aromatase variants with an expected diverse sensitivity of being inhibited by ZEN. The study: i) described SNVs likely associated with a different susceptibility to ZEN and α-zearalenol inhibition - like T310S that is likely more susceptible to inhibition, or D309G and S478F that are possibly inactive variants; ii) proofed the possible existence of inter-individual susceptibility to ZEN; iii) prioritized aromatase variants for future investigations toward a better comprehension of ZEN xenoestrogenicity at an individual level.
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Affiliation(s)
- Florinda Perugino
- Department of Food and Drug, University of Parma, Parma, Italy; Department of Biology, University of Naples Federico II, Naples, Italy
| | - Lorenzo Pedroni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Parma, Italy.
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2
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Vybornykh DE, Ivanov SV, Gemdzhian EG, Esina LV, Gaponova TV. [Therapy of mental disorders in patients with hematological malignancies]. Zh Nevrol Psikhiatr Im S S Korsakova 2024; 124:127-136. [PMID: 38676687 DOI: 10.17116/jnevro2024124041127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
OBJECTIVE To assess the possibilities of therapy with minimal effective doses (MED) of psychotropic drugs for mental disorders (MD) that manifest during the treatment of hematological malignancies (HM). MATERIAL AND METHODS A prospective study was conducted at the National Medical Research Center for Hematology of the Russian Ministry of Health (Moscow), which included 204 (39.4%) men and 314 (60.6%) women (518 patients in total), aged 17 to 83 years (median 45 years), with various HM, in which the manifestation of MD occurred during the treatment of the underlying disease. To minimize the side-effects of psychotropic drugs and given the relatively mild level of MD, psychopharmacotherapy of patients was carried out mainly at MED. The severity of MD, manifested in patients, was assessed by the illness severity scale of the Clinical Global Impression (CGI) scale, and the effectiveness of the treatment was assessed by the improvement scale (CGI-I). RESULTS Mainly mild (188, 36%) and moderately pronounced (270, 52%) MD were noted in patients with HM during the treatment of the underlying disease. Severe psychopathological disorders (60, 12%) were observed much less often. Because of psychopharmacotherapy with MED, patients experienced a very significant (97, 19%) and significant improvement (354, 68%) of their mental state, less often the improvement was regarded as minimal (67, 13%). Therefore, almost all patients showed a stable relief of MD; in 87% (95% CI 84-90) of patients, this improvement was significant. CONCLUSION The tactics of treatment MD that manifest in patients with HM with MED of psychotropic drugs turned out to be therapeutically effective according to the results of the assessment on CGI scales.
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Affiliation(s)
- D E Vybornykh
- National Medical Research Center for Hematology, Moscow, Russia
| | - S V Ivanov
- Mental Health Research Center, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - E G Gemdzhian
- National Medical Research Center for Hematology, Moscow, Russia
| | - L V Esina
- National Medical Research Center for Hematology, Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - T V Gaponova
- National Medical Research Center for Hematology, Moscow, Russia
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3
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Pedroni L, Louisse J, Dorne JLCM, Dall'Asta C, Dellafiora L. A computational study on the biotransformation of alkenylbenzenes by a selection of CYPs: Reflections on their possible bioactivation. Toxicology 2023; 488:153471. [PMID: 36863505 DOI: 10.1016/j.tox.2023.153471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
Alkenylbenzenes are aromatic compounds found in several vegetable foods that can cause genotoxicity upon bioactivation by members of the cytochrome P450 (CYP) family, forming 1'-hydroxy metabolites. These intermediates act as proximate carcinogens and can be further converted into reactive 1'-sulfooxy metabolites, which are the ultimate carcinogens responsible for genotoxicity. Safrole, a member of this class, has been banned as a food or feed additive in many countries based on its genotoxicity and carcinogenicity. However, it can still enter the food and feed chain. There is limited information about the toxicity of other alkenylbenzenes that may be present in safrole-containing foods, such as myristicin, apiole, and dillapiole. In vitro studies showed safrole as mainly bioactivated by CYP2A6 to form its proximate carcinogen, while for myristicin this is mainly done by CYP1A1. However, it is not known whether CYP1A1 and CYP2A6 can activate apiole and dillapiole. The present study uses an in silico pipeline to investigate this knowledge gap and determine whether CYP1A1 and CYP2A6 may play a role in the bioactivation of these alkenylbenzenes. The study found that the bioactivation of apiole and dillapiole by CYP1A1 and CYP2A6 is limited, possibly indicating that these compounds may have limited toxicity, while describing a possible role of CYP1A1 in the bioactivation of safrole. The study expands the current understanding of safrole toxicity and bioactivation and helps understand the mechanisms of CYPs involved in the bioactivation of alkenylbenzenes. This information is essential for a more informed analysis of alkenylbenzenes toxicity and risk assessment.
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Affiliation(s)
- Lorenzo Pedroni
- Department of Food and Drug, University of Parma, Parma 43124, Italy
| | - Jochem Louisse
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE Wageningen, the Netherlands
| | | | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Parma 43124, Italy
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Parma 43124, Italy.
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4
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Pedroni L, Louisse J, Punt A, Dorne JLCM, Dall’Asta C, Dellafiora L. A Computational Inter-Species Study on Safrole Phase I Metabolism-Dependent Bioactivation: A Mechanistic Insight into the Study of Possible Differences among Species. Toxins (Basel) 2023; 15:toxins15020094. [PMID: 36828409 PMCID: PMC9962551 DOI: 10.3390/toxins15020094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Safrole, a 162.2 Da natural compound belonging to the alkenylbenzenes class, is classified as a possible carcinogen to humans by IARC (group IIB) and has proven to be genotoxic and carcinogenic to rodents. Despite its use as a food or feed additive, it is forbidden in many countries due to its documented toxicity; yet, it is still broadly present within food and feed and is particularly abundant in spices, herbs and essential oils. Specifically, safrole may exert its toxicity upon bioactivation to its proximate carcinogen 1'-hydroxy-safrole via specific members of the cytochrome P450 protein family with a certain inter/intra-species variability. To investigate this variability, an in-silico workflow based on molecular modelling, docking and molecular dynamics has been successfully applied. This work highlighted the mechanistic basis underpinning differences among humans, cats, chickens, goats, sheep, dogs, mice, pigs, rats and rabbits. The chosen metric to estimate the likeliness of formation of 1'-hydroxy-safrole by the species-specific cytochrome P450 under investigation allowed for the provision of a knowledge-based ground to rationally design and prioritise further experiments and deepen the current understanding of alkenylbenzenes bioactivation and CYPs mechanics. Both are crucial for a more informed framework of analysis for safrole toxicity.
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Affiliation(s)
- Lorenzo Pedroni
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Jochem Louisse
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Ans Punt
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Jean Lou C. M. Dorne
- Methodology and Scientific Support Unit (MESE), European Food Safety Authority, 43126 Parma, Italy
| | - Chiara Dall’Asta
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-0521-906079
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5
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Öeren M, Walton PJ, Suri J, Ponting DJ, Hunt PA, Segall MD. Predicting Regioselectivity of AO, CYP, FMO, and UGT Metabolism Using Quantum Mechanical Simulations and Machine Learning. J Med Chem 2022; 65:14066-14081. [PMID: 36239985 DOI: 10.1021/acs.jmedchem.2c01303] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unexpected metabolism in modification and conjugation phases can lead to the failure of many late-stage drug candidates or even withdrawal of approved drugs. Thus, it is critical to predict the sites of metabolism (SoM) for enzymes, which interact with drug-like molecules, in the early stages of the research. This study presents methods for predicting the isoform-specific metabolism for human AOs, FMOs, and UGTs and general CYP metabolism for preclinical species. The models use semi-empirical quantum mechanical simulations, validated using experimentally obtained data and DFT calculations, to estimate the reactivity of each SoM in the context of the whole molecule. Ligand-based models, trained and tested using high-quality regioselectivity data, combine the reactivity of the potential SoM with the orientation and steric effects of the binding pockets of the different enzyme isoforms. The resulting models achieve κ values of up to 0.94 and AUC of up to 0.92.
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Affiliation(s)
- Mario Öeren
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K
| | - Peter J Walton
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K.,School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - James Suri
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K.,School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, U.K
| | - David J Ponting
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds LS11 5PS, U.K
| | - Peter A Hunt
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K
| | - Matthew D Segall
- Optibrium Limited, Cambridge Innovation Park, Denny End Road, Cambridge CB25 9GL, U.K
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6
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Ridhwan MJM, Bakar SIA, Latip NA, Ghani NA, Ismail NH. A Comprehensive Analysis of Human CYP3A4 Crystal Structures as a Potential Tool for Molecular Docking-Based Site of Metabolism and Enzyme Inhibition Studies. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022; 21:259-285. [DOI: 10.1142/s2737416522300012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The notable ability of human liver cytochrome P450 3A4 (CYP3A4) to metabolize diverse xenobiotics encourages researchers to explore in-depth the mechanism of enzyme action. Numerous CYP3A4 protein crystal structures have been deposited in protein data bank (PDB) and are majorly used in molecular docking analysis. The quality of the molecular docking results depends on the three-dimensional CYP3A4 protein crystal structures from the PDB. Present review endeavors to provide a brief outline of some technical parameters of CYP3A4 PDB entries as valuable information for molecular docking research. PDB entries between 22 April 2004 and 2 June 2021 were compiled and the active sites were thoroughly observed. The present review identified 76 deposited PDB entries and described basic information that includes CYP3A4 from human genetic, Escherichia coli (E. coli) use for protein expression, crystal structure obtained from X-ray diffraction method, taxonomy ID 9606, Uniprot ID P08684, ligand–protein structure description, co-crystal ligand, protein site deposit and resolution ranges between 1.7[Formula: see text]Å and 2.95[Formula: see text]Å. The observation of protein–ligand interactions showed the various residues on the active site depending on the ligand. The residues Ala305, Ser119, Ala370, Phe304, Phe108, Phe213 and Phe215 have been found to frequently interact with ligands from CYP3A4 PDB. Literature surveys of 17 co-crystal ligands reveal multiple mechanisms that include competitive inhibition, noncompetitive inhibition, mixed-mode inhibition, mechanism-based inhibition, substrate with metabolite, inducer, or combination modes of action. This overview may help researchers choose a trustworthy CYP3A4 protein structure from the PDB database to apply the protein in molecular docking analysis for drug discovery.
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Affiliation(s)
- Mohamad Jemain Mohamad Ridhwan
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Syahrul Imran Abu Bakar
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Normala Abd Latip
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Nurunajah Ab Ghani
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
| | - Nor Hadiani Ismail
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam 40450, Selangor, Malaysia
- Atta-ur-Rahman Institute for Natural Products Discovery, Universiti Teknologi MARA (UiTM), Puncak Alam 42300, Selangor, Malaysia
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7
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Kim JS, Arango AS, Shah S, Arnold WR, Tajkhorshid E, Das A. Anthracycline derivatives inhibit cardiac CYP2J2. J Inorg Biochem 2022; 229:111722. [PMID: 35078036 PMCID: PMC8860876 DOI: 10.1016/j.jinorgbio.2022.111722] [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: 03/02/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/20/2022]
Abstract
Anthracycline chemotherapeutics are highly effective, but their clinical usefulness is hampered by adverse side effects such as cardiotoxicity. Cytochrome P450 2J2 (CYP2J2) is a cytochrome P450 epoxygenase in human cardiomyocytes that converts arachidonic acid (AA) to cardioprotective epoxyeicosatrienoic acid (EET) regioisomers. Herein, we performed biochemical studies to understand the interaction of anthracycline derivatives (daunorubicin, doxorubicin, epirubicin, idarubicin, 5-iminodaunorubicin, zorubicin, valrubicin, and aclarubicin) with CYP2J2. We utilized fluorescence polarization (FP) to assess whether anthracyclines bind to CYP2J2. We found that aclarubicin bound the strongest to CYP2J2 despite it having large bulky groups. We determined that ebastine competitively inhibits anthracycline binding, suggesting that ebastine and anthracyclines may share the same binding site. Molecular dynamics and ensemble docking revealed electrostatic interactions between the anthracyclines and CYP2J2, contributing to binding stability. In particular, the glycosamine groups in anthracyclines are stabilized by binding to glutamate and aspartate residues in CYP2J2 forming salt bridge interactions. Furthermore, we used iterative ensemble docking schemes to gauge anthracycline influence on EET regioisomer production and anthracycline inhibition on AA metabolism. This was followed by experimental validation of CYP2J2-mediated metabolism of anthracycline derivatives using liquid chromatography tandem mass spectrometry fragmentation analysis and inhibition of CYP2J2-mediated AA metabolism by these derivatives. Taken together, we use both experimental and theoretical methodologies to unveil the interactions of anthracycline derivatives with CYP2J2. These studies will help identify alternative mechanisms of how anthracycline cardiotoxicity may be mediated through the inhibition of cardiac P450, which will aid in the design of new anthracycline derivatives with lower toxicity.
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Affiliation(s)
- Justin S Kim
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Andres S Arango
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Swapnil Shah
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - William R Arnold
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Aditi Das
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America; Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America.
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8
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Dorne JLCM, Cirlini M, Louisse J, Pedroni L, Galaverna G, Dellafiora L. A Computational Understanding of Inter-Individual Variability in CYP2D6 Activity to Investigate the Impact of Missense Mutations on Ochratoxin A Metabolism. Toxins (Basel) 2022; 14:207. [PMID: 35324704 PMCID: PMC8950366 DOI: 10.3390/toxins14030207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Cytochrome P-450 (CYP) enzymes have a key role in the metabolism of xenobiotics of food origin, and their highly polymorphic nature concurs with the diverse inter-individual variability in the toxicokinetics (TK) and toxicodynamics (TD) of food chemicals. Ochratoxin A is a well-known mycotoxin which contaminates a large variety of food and is associated with food safety concerns. It is a minor substrate of CYP2D6, although the effects of CYP2D6 polymorphisms on its metabolism may be overlooked. Insights on this aspect would provide a useful mechanistic basis for a more science-based hazard assessment, particularly to integrate inter-individual differences in CYP2D6 metabolism. This work presents a molecular modelling approach for the analysis of mechanistic features with regard to the metabolic capacity of CYP2D6 variants to oxidise a number of substrates. The outcomes highlighted that a low-frequency CYP2D6 variant (CYP2D6*110) is likely to enhance ochratoxin A oxidation with possible consequences on TK and TD. It is therefore recommended to further analyse such TK and TD consequences. Generally speaking, we propose the identification of mechanistic features and parameters that could provide a semi-quantitative means to discriminate ligands based on the likelihood to undergo transformation by CYP2D6 variants. This would support the development of a fit-for-purpose pipeline which can be extended to a tool allowing for the bulk analysis of a large number of compounds. Such a tool would ultimately include inter-phenotypic differences of polymorphic xenobiotic-metabolising enzymes in the hazard assessment and risk characterisation of food chemicals.
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Affiliation(s)
- Jean Lou C. M. Dorne
- Scientific Committee and Emerging Risks Unit, European Food Safety Authority, Via Carlo Magno 1A, 43124 Parma, Italy;
| | - Martina Cirlini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
| | - Jochem Louisse
- Wageningen Food Safety Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands;
| | - Lorenzo Pedroni
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (L.P.); (G.G.)
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9
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Jawad B, Poudel L, Podgornik R, Ching WY. Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects. J Phys Chem B 2020; 124:7803-7818. [PMID: 32786213 DOI: 10.1021/acs.jpcb.0c05840] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Doxorubicin (DOX) is a cancer drug that binds to dsDNA through intercalation. A comprehensive microsecond timescale molecular dynamics study is performed for DOX with 16 tetradecamer dsDNA sequences in explicit aqueous solvent, in order to investigate the intercalation process at both binding stages (conformational change and insertion binding stages). The molecular mechanics generalized Born surface area (MM-GBSA) method is adapted to quantify and break down the binding free energy (BFE) into its thermodynamic components, for a variety of different solution conditions as well as different DNA sequences. Our results show that the van der Waals interaction provides the largest contribution to the BFE at each stage of binding. The sequence selectivity depends mainly on the base pairs located downstream from the DOX intercalation site, with a preference for (AT)2 or (TA)2 driven by the favorable electrostatic and/or van der Waals interactions. Invoking the quartet sequence model proved to be most successful to predict the sequence selectivity. Our findings also indicate that the aqueous bathing solution (i.e., water and ions) opposes the formation of the DOX-DNA complex at every binding stage, thus implying that the complexation process preferably occurs at low ionic strength and is crucially dependent on solvent effects.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City 64110, Missouri, United States.,Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Lokendra Poudel
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City 64110, Missouri, United States
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10
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Saranya V, Mary PV, Vijayakumar S, Shankar R. The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective. Biophys Chem 2020; 263:106394. [PMID: 32480019 DOI: 10.1016/j.bpc.2020.106394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ42 peptide due to its interaction of toxic gas (CO, CO2, SO2 and NO2). During the 400 ns simulation, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes have smaller Root Mean Square Deviation values when compared to the Aβ42 peptide, which shows that the interaction of toxic gases (CO, CO2, SO2, and NO2) would increase the Aβ42 peptide structural stability. The radius of gyration analysis also supports that Aβ42 interacted CO2 and SO2 complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ42 interacted CO2 and SO2 complexes have a greater compact structure in comparison to Aβ42 interacted CO and NO2 complexes. Furthermore, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India
| | - Pitchumani Violet Mary
- Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641 062, India
| | | | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India.
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11
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The Multifarious Link between Cytochrome P450s and Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3028387. [PMID: 31998435 PMCID: PMC6964729 DOI: 10.1155/2020/3028387] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/08/2019] [Accepted: 12/18/2019] [Indexed: 02/07/2023]
Abstract
Cancer is a leading cause of death worldwide. Cytochrome P450s (P450s) play an important role in the metabolism of endogenous as well as exogenous substances, especially drugs. Moreover, many P450s can serve as targets for disease therapy. Increasing reports of epidemiological, diagnostic, and clinical research indicate that P450s are enzymes that play a major part in the formation of cancer, prevention, and metastasis. The purposes of this review are to shed light on the current state of knowledge about the cancer molecular mechanism involving P450s and to summarize the link between the cancer effects and the participation of P450s.
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12
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Chaturvedi N, Mishra A, Rawat V. Synthesis and characterization of oxygen depleted tert-amine calix[4]arene ligands and study the effect on sigma non-opioid intracellular protein receptor. Struct Chem 2019. [DOI: 10.1007/s11224-019-01324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Kiani YS, Ranaghan KE, Jabeen I, Mulholland AJ. Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors. Int J Mol Sci 2019; 20:E4468. [PMID: 31510073 PMCID: PMC6769491 DOI: 10.3390/ijms20184468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/22/2019] [Accepted: 09/01/2019] [Indexed: 12/20/2022] Open
Abstract
The Cytochrome P450 family of heme-containing proteins plays a major role in catalyzing phase I metabolic reactions, and the CYP3A4 subtype is responsible for the metabolism of many currently marketed drugs. Additionally, CYP3A4 has an inherent affinity for a broad spectrum of structurally diverse chemical entities, often leading to drug-drug interactions mediated by the inhibition or induction of the metabolic enzyme. The current study explores the binding of selected highly efficient CYP3A4 inhibitors by docking and molecular dynamics (MD) simulation protocols and their binding free energy calculated using the WaterSwap method. The results indicate the importance of binding pocket residues including Phe57, Arg105, Arg106, Ser119, Arg212, Phe213, Thr309, Ser312, Ala370, Arg372, Glu374, Gly481 and Leu483 for interaction with CYP3A4 inhibitors. The residue-wise decomposition of the binding free energy from the WaterSwap method revealed the importance of binding site residues Arg106 and Arg372 in the stabilization of all the selected CYP3A4-inhibitor complexes. The WaterSwap binding energies were further complemented with the MM(GB/PB)SA results and it was observed that the binding energies calculated by both methods do not differ significantly. Overall, our results could guide towards the use of multiple computational approaches to achieve a better understanding of CYP3A4 inhibition, subsequently leading to the design of highly specific and efficient new chemical entities with suitable ADMETox properties and reduced side effects.
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Affiliation(s)
- Yusra Sajid Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
| | - Ishrat Jabeen
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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Jawad B, Poudel L, Podgornik R, Steinmetz NF, Ching WY. Molecular mechanism and binding free energy of doxorubicin intercalation in DNA. Phys Chem Chem Phys 2019; 21:3877-3893. [PMID: 30702122 DOI: 10.1039/c8cp06776g] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramolecular electrostatic interactions (ΔGele) and electrostatic polar solvation interactions (ΔGpolar-PB/GB) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the standard concentration dependent free energies of DOX (ΔGcon) and the ionic solution (ΔGion). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX-DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. We have calculated the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX-DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1 : 1 complex is -9.1 and -5.1 kcal mol-1 respectively. The same quantities from the modified MM-PBSA method are -12.74 and -8.35 kcal mol-1 respectively. The value of the total BFE ΔGt-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of -7.7 ± 0.3 kcal mol-1.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
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15
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Saranya V, Shankar R, Vijayakumar S. Structural exploration of viral matrix protein 40 interaction with the transition metal ions (Ag+ and Cu2+). J Biomol Struct Dyn 2018; 37:2875-2896. [DOI: 10.1080/07391102.2018.1498803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- V. Saranya
- Department of Physics, Bharathiar University, Coimbatore, India
| | - R. Shankar
- Department of Physics, Bharathiar University, Coimbatore, India
| | - S. Vijayakumar
- Department of Medical Physics, Bharathiar University, Coimbatore, India
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In vitro metabolism study of a novel P38 kinase inhibitor: in silico predictions, structure elucidation using MS/MS-I. Future Med Chem 2018; 10:201-220. [DOI: 10.4155/fmc-2017-0126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Metabolism study of PH-797804, a promising newly developed drug for treatment of chronic inflammation which inhibits P38 mitogen-activated protein kinase. Materials & methods: Susceptibility of PH-797804 to metabolism was first investigated using SMARTCyp and Xenosite web servers. Molecular docking of the drug into CYP3A4 crystal structures evaluated binding interactions with active site. The predicted results were confirmed by in vitro incubation with rat S9 fraction. Metabolites of PH-797804 were identified by MS/MS. Results: A hydroxy metabolite and a cysteine/glutathione conjugate were detected. Computational prediction of reactive site of PH-797804 was conducted. Conclusion: The probable cysteine/glutathione adduct is indicative of potential drug chemical reactivity with potential to damage DNA and may provide guidance to the design of analogs with minimum toxicity.
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17
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Kroeger T, Frieg B, Zhang T, Hansen FK, Marmann A, Proksch P, Nagel-Steger L, Groth G, Smits SHJ, Gohlke H. EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay. PLoS One 2017; 12:e0177024. [PMID: 28472107 PMCID: PMC5417642 DOI: 10.1371/journal.pone.0177024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/29/2017] [Indexed: 12/16/2022] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is widely used in the life sciences as chelating ligand of metal ions. However, formation of supramolecular EDTA aggregates at pH > 8 has been reported, which may lead to artifactual assay results. When applied as a buffer component at pH ≈ 10 in differential scanning fluorimetry (TSA) using SYPRO Orange as fluorescent dye, we observed a sharp change in fluorescence intensity about 20°C lower than expected for the investigated protein. We hypothesized that this change results from SYPRO Orange/EDTA interactions. TSA experiments in the presence of SYPRO Orange using solutions that contain EDTA-Na+ but no protein were performed. The TSA experiments provide evidence that suggests that at pH > 9, EDTA4- interacts with SYPRO Orange in a temperature-dependent manner, leading to a fluorescence signal yielding a "denaturation temperature" of ~68°C. Titrating Ca2+ to SYPRO Orange and EDTA solutions quenched fluorescence. Ethylene glycol tetraacetic acid (EGTA) behaved similarly to EDTA. Analytical ultracentrifugation corroborated the formation of EDTA aggregates. Molecular dynamics simulations of free diffusion of EDTA-Na+ and SYPRO Orange of in total 27 μs suggested the first structural model of EDTA aggregates in which U-shaped EDTA4- arrange in an inverse bilayer-like manner, exposing ethylene moieties to the solvent, with which SYPRO Orange interacts. We conclude that EDTA aggregates induce a SYPRO Orange-based fluorescence in TSA. These results make it relevant to ascertain that future TSA results are not influenced by interference between EDTA, or EDTA-related molecules, and the fluorescent dye.
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Affiliation(s)
- Tobias Kroeger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tao Zhang
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Finn K. Hansen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Marmann
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Proksch
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Georg Groth
- Institute for Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H. J. Smits
- Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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18
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Chaturvedi N, Yadav BS, Pandey PN, Tripathi V. The effect of β-glucan and its potential analog on the structure of Dectin-1 receptor. J Mol Graph Model 2017; 74:315-325. [PMID: 28475968 DOI: 10.1016/j.jmgm.2017.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
Dectin-1 is a recently discovered pattern-recognition receptor that plays an important role in antifungal innate immunity, which acts a specific receptor for β-glucan (BG). The present study, aimed at clarifying effect of BG and a new analog, maltotriose (MT) on Dectin-1 receptor. We implemented molecular docking of MT on Dectin-1 along with model-independent all-atom-molecular dynamics simulations. Simulations were carried out at three levels of complexity: (1) Apo-Dectin-1; (2) BG:Dectin-1; (3) MT:Dectin-1. All three system complexes were undergone stability check before showing a comparative analysis. A characteristic feature, noted for the MT:Dectin-1, is a shifting of loops (loop1 and loop2) orientation towards atoms of MT, a broad interaction suggested a robust and tight binding on comparison with BG:Dectin-1. Free energy estimation corroborated the observation, which furthermore, made a close agreement by revealing contribution of energy components of interacting residues. In addition, cluster analysis of complexes exhibit a smooth continuous transition to a new confirmation, represented by a series of clusters each having a longer lifetime. Principal component analysis revealed a broken pipe at binding site of BG:Dectin-1 during movement of atoms whereas in MT:Dectin-1 exhibited wide band and high amplitude motion of atoms in trajectory, was due to loop orientation toward MT. Observation was further shown by measuring distances and hydrogen binding calculation. Simulations of the BG:Dectin-1 and MT:Dectin-1 complex revealed first time the influence of BG and MT ligands. This study might extend the knowledge of the BG and MT interaction on Dectin-1 and proposed further potential bioassay of MT.
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Affiliation(s)
- Navaneet Chaturvedi
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Brijesh Singh Yadav
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | | | - Vijay Tripathi
- Institute of Soil, Water, Environmental Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
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Danielson ML, Hu B, Shen J, Desai PV. In Silico ADME Techniques Used in Early-Phase Drug Discovery. TRANSLATING MOLECULES INTO MEDICINES 2017. [DOI: 10.1007/978-3-319-50042-3_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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20
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Tyzack JD, Hunt PA, Segall MD. Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism Using Quantum Mechanical Simulations. J Chem Inf Model 2016; 56:2180-2193. [PMID: 27753488 DOI: 10.1021/acs.jcim.6b00233] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe methods for predicting cytochrome P450 (CYP) metabolism incorporating both pathway-specific reactivity and isoform-specific accessibility considerations. Semiempirical quantum mechanical (QM) simulations, parametrized using experimental data and ab initio calculations, estimate the reactivity of each potential site of metabolism (SOM) in the context of the whole molecule. Ligand-based models, trained using high-quality regioselectivity data, correct for orientation and steric effects of the different CYP isoform binding pockets. The resulting models identify a SOM in the top 2 predictions for between 82% and 91% of compounds in independent test sets across seven CYP isoforms. In addition to predicting the relative proportion of metabolite formation at each site, these methods estimate the activation energy at each site, from which additional information can be derived regarding their lability in absolute terms. We illustrate how this can guide the design of compounds to overcome issues with rapid CYP metabolism.
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Affiliation(s)
- Jonathan D Tyzack
- Optibrium Ltd. , 7221 Cambridge Research Park, Beach Drive, Cambridge CB25 9TL, U.K
| | - Peter A Hunt
- Optibrium Ltd. , 7221 Cambridge Research Park, Beach Drive, Cambridge CB25 9TL, U.K
| | - Matthew D Segall
- Optibrium Ltd. , 7221 Cambridge Research Park, Beach Drive, Cambridge CB25 9TL, U.K
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