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Sandhu H, Garg P. Machine Learning Enables Accurate Prediction of Quinone Formation during Drug Metabolism. Chem Res Toxicol 2023; 36:1876-1890. [PMID: 37885227 DOI: 10.1021/acs.chemrestox.3c00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Metabolism helps in the elimination of drugs from the human body by making them more hydrophilic. Sometimes, drugs can be bioactivated to highly reactive metabolites or intermediates during metabolism. These reactive metabolites are often responsible for the toxicities associated with the drugs. Identification of reactive metabolites of drug candidates can be very helpful in the initial stages of drug discovery. Quinones are soft electrophiles that are generated as reactive intermediates during metabolism. Quinones make up more than 40% of the reactive metabolites. In this work, a reliable data set of 510 molecules was used to develop machine learning and deep learning-based predictive models to predict the formation of quinone-type metabolites. For representing molecules, two-dimensional (2D) descriptors, PubChem fingerprints, electro-topological state (E-state) fingerprints, and metabolic reactivity-based descriptors were used. Developed models were compared to the existing Xenosite web server using the untouched test set of 102 molecules. The best model achieved an accuracy of 86.27%, while the Xenosite server could achieve an accuracy of only 52.94% on the test set. Descriptor analysis revealed that the presence of greater numbers of polar moieties in a molecule can prevent the formation of quinone-type metabolites. In addition, the presence of a nitrogen atom in an aromatic ring and the presence of metabolophores V51, V52, and V53 (SMARTCyp descriptors) decrease the probability of quinone formation. Finally, a tool based on the best machine learning models was developed, which is accessible at http://14.139.57.41/quinonepred/.
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Affiliation(s)
- Hardeep Sandhu
- Department of pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar 160062, Punjab, India
| | - Prabha Garg
- Department of pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar 160062, Punjab, India
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2
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Dixit VA, Kulkarni A. Applications of Bond Energy‐Based Thermodynamic Analysis to the Feasibility of Unfunctionalized C−C Cross‐Coupling Reactions. ChemistrySelect 2022. [DOI: 10.1002/slct.202203111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Medicinal Chemistry National Institute of Pharmaceutical Education and Research Guwahati NIPER Guwahati) Department of Pharmaceuticals Ministry of Chemicals & Fertilizers, Govt. of India, Sila Katamur (Halu-gurisuk) Changsari Kamrup 781101 Guwahati Assam India
| | - Aniket Kulkarni
- Department of Pharmacy Birla Institute of Technology and Sciences Pilani (BITS Pilani) Vidya Vihar Campus, 41 Pilani 333031 Rajasthan India
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3
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Kapoor S, Dubey G, Khatun S, Bharatam PV. Remdesivir: Mechanism of Metabolic Conversion from Prodrug to Drug. Curr Drug Metab 2021; 23:73-81. [PMID: 34963432 DOI: 10.2174/1389200223666211228160314] [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: 09/29/2021] [Revised: 10/25/2021] [Accepted: 12/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Remdesivir (GS-5734) has emerged as a promising drug during the challenging times of COVID-19 pandemic. Being a prodrug, it undergoes several metabolic reactions before converting to its active triphosphate metabolite. It is important to establish the atomic level details and explore the energy profile of the prodrug to drug conversion process. METHODS In this work, Density Functional Theory (DFT) calculations were performed to explore the entire metabolic path. Further, the potential energy surface (PES) diagram for the conversion of prodrug remdesivir to its active metabolite was established. The role of catalytic triad of Hint1 phosphoramidase enzyme in P-N bond hydrolysis was also studied on a model system using combined molecular docking and quantum mechanics approach. RESULTS The overall energy of reaction is 11.47 kcal/mol exergonic and the reaction proceeds through many steps requiring high activation energies. In the absence of a catalyst, the P-N bond breaking step requires 41.78 kcal/mol, which is reduced to 14.26 kcal/mol in a catalytic environment. CONCLUSION The metabolic pathways of model system of remdesivir (MSR) were completely explored completely and potential energy surface diagrams at two levels of theory, B3LYP/6-311++G(d, p) and B3LYP/6-31+G(d), were established and compared. The results highlight the importance of an additional water molecule in the metabolic reaction. The P-N bond cleavage step of the metabolic process requires the presence of an enzymatic environment.
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Affiliation(s)
- Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
| | - Gurudutt Dubey
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
| | - Samima Khatun
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar (Mohali), 160062 Punjab, India
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4
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Computer-Aided Estimation of Biological Activity Profiles of Drug-Like Compounds Taking into Account Their Metabolism in Human Body. Int J Mol Sci 2020; 21:ijms21207492. [PMID: 33050610 PMCID: PMC7593915 DOI: 10.3390/ijms21207492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/06/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022] Open
Abstract
Most pharmaceutical substances interact with several or even many molecular targets in the organism, determining the complex profiles of their biological activity. Moreover, due to biotransformation in the human body, they form one or several metabolites with different biological activity profiles. Therefore, the development and rational use of novel drugs requires the analysis of their biological activity profiles, taking into account metabolism in the human body. In silico methods are currently widely used for estimating new drug-like compounds' interactions with pharmacological targets and predicting their metabolic transformations. In this study, we consider the estimation of the biological activity profiles of organic compounds, taking into account the action of both the parent molecule and its metabolites in the human body. We used an external dataset that consists of 864 parent compounds with known metabolites. It is shown that the complex assessment of active pharmaceutical ingredients' interactions with the human organism increases the quality of computer-aided estimates. The toxic and adverse effects showed the most significant difference: reaching 0.16 for recall and 0.14 for precision.
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Jaladanki CK, Gahlawat A, Rathod G, Sandhu H, Jahan K, Bharatam PV. Mechanistic studies on the drug metabolism and toxicity originating from cytochromes P450. Drug Metab Rev 2020; 52:366-394. [DOI: 10.1080/03602532.2020.1765792] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chaitanya K. Jaladanki
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Anuj Gahlawat
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Gajanan Rathod
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Hardeep Sandhu
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Kousar Jahan
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry and Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, India
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6
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Comparison of three human liver cell lines for in vitro drug-induced liver injury assessment: Huh7, HepaRG, and stem cell-derived hepatocytes. Mol Cell Toxicol 2019. [DOI: 10.1007/s13273-019-0031-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Dixit VA. A simple model to solve a complex drug toxicity problem. Toxicol Res (Camb) 2018; 8:157-171. [PMID: 30997019 DOI: 10.1039/c8tx00261d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/28/2018] [Indexed: 02/06/2023] Open
Abstract
Linear drug toxicity models like therapeutic index (TI), physicochemical rules (rule of five, 3/75), ligand efficiency indices (LEI), ideal pharmacokinetic (PK) and pharmacodynamic (PD) profiles are widely used in drug discovery and development. In spite of this, predicting drug toxicity at various stages remains challenging and the overall productivity (<20%) and ultimate benefit to the patients remain low. A simple drug toxicity model, "Drug Toxicity Index" (DTI), is developed here using 711 oral drugs. DTI redefines drug toxicity as scaled biphasic and exponential functions of PD, PK and physicochemical parameters. PD, PK and physicochemical toxicity contributions were estimated from the on and off target IC50, maximum unbound plasma drug concentration (free C max), and log D values, respectively. These contributions are then scaled by molar dose and oral bioavailability and the logarithm of the sum of scaled contributions is DTI. Drugs with DTI above the WHO ATC drug category specific average values consistently have toxic profiles, while drugs with DTI below this average are relatively safe. DTI performs better than standard rules for lead optimization, LEI and exposure based TIs in identifying safe and toxic drugs. DTI classifies 392 drugs reported in the US-FDA's Liver Toxicity Knowledge Base (LTKB) with an AUC for ROC curves of 0.91-0.64 for different WHO ATC categories. DTI has been used to predict network meta-analysis results on relative toxicity within/across eight different therapeutic areas. It is useful in understanding PD, PK and physicochemical toxicity contributions and identifying potentially toxic drugs and the toxicity of recently approved drugs. Decision trees are proposed for applying the DTI concept in preclinical drug discovery and clinical trial settings. DTI can potentially reduce failure in drug discovery and might be useful in therapeutic drug monitoring and in xenobiotic and environmental toxicity studies.
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Affiliation(s)
- Vaibhav A Dixit
- Department of Pharmacy , Birla Institute of Technology and Sciences Pilani (BITS Pilani) , Vidya Vihar Campus , Street number 41 , Pilani , 333031 , Rajasthan , India . ; ; Tel: +91 1596 255652 ; Tel: +91-7709129400
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8
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Bruckner DM, Connerney JJ, Dordick JS. Advancing in vitro
- in vivo
toxicity correlations via high-throughput three-dimensional primary hepatocyte culture. AIChE J 2018. [DOI: 10.1002/aic.16442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dylan M. Bruckner
- Dept. of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy NY, 12180
| | | | - Jonathan S. Dordick
- Dept. of Chemical and Biological Engineering, Center for Biotechnology & Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy NY, 12180
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9
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Birringer M, Siems K, Maxones A, Frank J, Lorkowski S. Natural 6-hydroxy-chromanols and -chromenols: structural diversity, biosynthetic pathways and health implications. RSC Adv 2018; 8:4803-4841. [PMID: 35539527 PMCID: PMC9078042 DOI: 10.1039/c7ra11819h] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/18/2018] [Indexed: 01/26/2023] Open
Abstract
We present the first comprehensive and systematic review on the structurally diverse toco-chromanols and -chromenols found in photosynthetic organisms, including marine organisms, and as metabolic intermediates in animals. The focus of this work is on the structural diversity of chromanols and chromenols that result from various side chain modifications. We describe more than 230 structures that derive from a 6-hydroxy-chromanol- and 6-hydroxy-chromenol core, respectively, and comprise di-, sesqui-, mono- and hemiterpenes. We assort the compounds into a structure-activity relationship with special emphasis on anti-inflammatory and anti-carcinogenic activities of the congeners. This review covers the literature published from 1970 to 2017.
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Affiliation(s)
- Marc Birringer
- Department of Nutritional, Food and Consumer Sciences, Fulda University of Applied Sciences Leipziger Straße 123 36037 Fulda Germany
| | - Karsten Siems
- AnalytiCon Discovery GmbH Hermannswerder Haus 17 14473 Potsdam Germany
| | - Alexander Maxones
- Department of Nutritional, Food and Consumer Sciences, Fulda University of Applied Sciences Leipziger Straße 123 36037 Fulda Germany
| | - Jan Frank
- Institute of Biological Chemistry and Nutrition, University of Hohenheim Garbenstr. 28 70599 Stuttgart Germany
| | - Stefan Lorkowski
- Institute of Nutrition, Friedrich Schiller University Jena Dornburger Str. 25 07743 Jena Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD), Halle-Jena-Leipzig Germany
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10
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Dixit VA, Lal LA, Agrawal SR. Recent advances in the prediction of non‐
CYP450
‐mediated drug metabolism. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
| | - L. Arun Lal
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
| | - Simran R. Agrawal
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
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11
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Dixit VA, Goundry WRF, Tomasi S. CC/B–N substitution in five membered heterocycles. A computational analysis. NEW J CHEM 2017. [DOI: 10.1039/c7nj00950j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel five-membered azaboroles are aromatic, stable under neutral conditions, isomer stabilization energy is explained using σ-bond and aromatic stabilization energies.
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Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry
- School of Pharmacy & Technology Management (SPTM)
- Shri Vile Parle Kelavani Mandal's (SVKM's)
- Narsee Monjee Institute of Management Studies (NMIMS)
- Mukesh Patel Technology Park
| | | | - Simone Tomasi
- Global Medicines Development
- Process Research and Development
- Macclesfield
- UK
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12
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Dixit VA, Deshpande S. Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s. ChemistrySelect 2016. [DOI: 10.1002/slct.201601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
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13
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Chianese G, Yu HB, Yang F, Sirignano C, Luciano P, Han BN, Khan S, Lin HW, Taglialatela-Scafati O. PPAR Modulating Polyketides from a Chinese Plakortis simplex and Clues on the Origin of Their Chemodiversity. J Org Chem 2016; 81:5135-43. [DOI: 10.1021/acs.joc.6b00695] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Giuseppina Chianese
- Department
of Pharmacy, University of Naples Federico II, Via D. Montesano
49, 80131 Naples, Italy
| | - Hao-Bing Yu
- Research
Center for Marine Drugs, Department of Pharmacy, State Key Laboratory
of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People’s Republic of China
| | - Fan Yang
- Research
Center for Marine Drugs, Department of Pharmacy, State Key Laboratory
of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People’s Republic of China
| | - Carmina Sirignano
- Department
of Pharmacy, University of Naples Federico II, Via D. Montesano
49, 80131 Naples, Italy
| | - Paolo Luciano
- Department
of Pharmacy, University of Naples Federico II, Via D. Montesano
49, 80131 Naples, Italy
| | - Bing-Nan Han
- Research
Center for Marine Drugs, Department of Pharmacy, State Key Laboratory
of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People’s Republic of China
| | - Shabana Khan
- National
Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Hou-Wen Lin
- Research
Center for Marine Drugs, Department of Pharmacy, State Key Laboratory
of Oncogenes and Related Genes, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, People’s Republic of China
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14
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Dixit VA, Rathi PC, Bhagat S, Gohlke H, Petersen RK, Kristiansen K, Chakraborti AK, Bharatam PV. Design and synthesis of novel Y-shaped barbituric acid derivatives as PPARγ activators. Eur J Med Chem 2016; 108:423-435. [DOI: 10.1016/j.ejmech.2015.11.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
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15
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Montagut-Romans A, Boulven M, Lemaire M, Popowycz F. 3-Methylene-2,4-chromandione in situ trapping: introducing molecular diversity on 4-hydroxycoumarin. RSC Adv 2016. [DOI: 10.1039/c5ra22440c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
3-Methylene-2,4-chromandione trapped in a solid-state stable Mannich adduct, is released in solution.
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Affiliation(s)
- Adrien Montagut-Romans
- Equipe Chimie Organique et Bioorganique
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires
- Institut National des Sciences Appliquées (INSA Lyon)
- F-69621 Villeurbanne Cedex
- France
| | - Manon Boulven
- Equipe Chimie Organique et Bioorganique
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires
- Institut National des Sciences Appliquées (INSA Lyon)
- F-69621 Villeurbanne Cedex
- France
| | - Marc Lemaire
- Equipe Chimie Organique et Bioorganique
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires
- Institut National des Sciences Appliquées (INSA Lyon)
- F-69621 Villeurbanne Cedex
- France
| | - Florence Popowycz
- Equipe Chimie Organique et Bioorganique
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires
- Institut National des Sciences Appliquées (INSA Lyon)
- F-69621 Villeurbanne Cedex
- France
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16
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Jaladanki CK, Taxak N, Varikoti RA, Bharatam PV. Toxicity Originating from Thiophene Containing Drugs: Exploring the Mechanism using Quantum Chemical Methods. Chem Res Toxicol 2015; 28:2364-76. [PMID: 26574776 DOI: 10.1021/acs.chemrestox.5b00364] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drug metabolism of thiophene containing substrates by cytochrome P450s (CYP450) leads to toxic side effects, for example, nephrotoxicity (suprofen, ticlopidine), hepatotoxicity (tienilic acid), thrombotic thrombocytopenic purpura (clopidogrel), and aplastic anemia (ticlopidine). The origin of toxicity in these cases has been attributed to two different CYP450 mediated metabolic reactions: S-oxidation and epoxidation. In this work, the molecular level details of the bioinorganic chemistry associated with the generation of these competitive reactions are reported. Density functional theory was utilized (i) to explore the molecular mechanism for S-oxidation and epoxidation using the radical cationic center Cpd I [(iron(IV)-oxo-heme porphine system with SH(-) as the axial ligand, to mimic CYP450s] as the model oxidant, (ii) to establish the 3D structures of the reactants, transition states, and products on both the metabolic pathways, and (iii) to examine the potential energy (PE) profile for both the pathways to determine the energetically preferred toxic metabolite formation. The energy barrier required for S-oxidation was observed to be 14.75 kcal/mol as compared to that of the epoxidation reaction (13.23 kcal/mol) on the doublet PE surface of Cpd I. The formation of the epoxide metabolite was found to be highly exothermic (-23.24 kcal/mol), as compared to S-oxidation (-8.08 kcal/mol). Hence, on a relative scale the epoxidation process was observed to be thermodynamically and kinetically more favorable. The energy profiles associated with the reactions of the S-oxide and epoxide toxic metabolites were also explored. This study helps in understanding the CYP450-catalyzed toxic reactions of drugs containing the thiophene ring at the atomic level.
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Affiliation(s)
- Chaitanya K Jaladanki
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Nikhil Taxak
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Rohith A Varikoti
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Prasad V Bharatam
- Department of Medicinal Chemistry and ‡Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER) , Sector-67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
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17
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Fashe MM, Juvonen RO, Petsalo A, Vepsäläinen J, Pasanen M, Rahnasto-Rilla M. In Silico Prediction of the Site of Oxidation by Cytochrome P450 3A4 That Leads to the Formation of the Toxic Metabolites of Pyrrolizidine Alkaloids. Chem Res Toxicol 2015; 28:702-10. [DOI: 10.1021/tx500478q] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Muluneh M. Fashe
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Risto O. Juvonen
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Aleksanteri Petsalo
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Jouko Vepsäläinen
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Markku Pasanen
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Minna Rahnasto-Rilla
- School of Pharmacy, Faculty
of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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18
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DFT study on the oxygen transfer mechanism in nitroethenediamine based H2-receptor antagonists using the bis-dithiolene complex as the model catalyst for N-oxide reductase enzyme. J Inorg Biochem 2014; 142:84-91. [PMID: 25450022 DOI: 10.1016/j.jinorgbio.2014.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/24/2022]
Abstract
Nitroethenediamine is an important functional unit, which is present in H2-receptor antagonists. These drugs show low bioavailability due to the bacterial degradation caused by the N-oxide reductase type of enzymes present in the human colon. Quantum chemical studies have been carried out to elucidate the mechanism of metabolic degradation of nitroethenediamine in the active site of N-oxide reductase. Three different pathways have been explored for the N-oxide bond cleavage by the model system, Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)2](-), (where mdt=1,2-dimethyl-ethene-1,2-dithiolate) using B3LYP/6-311+G(d,p) and M06/6-311+G(d,p) Density Functional Theory methods. The oxygen atom transfer from the nitrogen atom of nitroethenediamine to the Mo(IV) complex, involves simultaneous weakening of the N-oxide bond and the formation of Mo-O bond through a least motion path. During this transfer, Mo center is converted from a square pyramidal geometry to a distorted octahedral geometry, to facilitate the process of oxygen atom transfer. The energy barrier for the oxygen atom transfer from the imine tautomer has been estimated to be 25.9kcal/mol however, the overall reaction has been found to be endothermic. On the other hand, oxygen transfer reaction from the nitronic acid tautomer requires 30.5kcal/mol energy leading to a highly exothermic metabolite (M-1) directly hence, this path can be considered thermodynamically favorable for this metabolite. The alternative path involving the oxygen atom transfer from the enamine tautomer requires comparatively a higher energy barrier (32.6kcal/mol) and leads to a slightly endothermic metabolite. This study established the structural and energetic details associated with the Mo(IV) bis-dithiolene complex that catalyzes the degradation of nitroethenediamine based drug molecules.
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Arfeen M, Patel DS, Abbat S, Taxak N, Bharatam PV. Importance of cytochromes in cyclization reactions: Quantum chemical study on a model reaction of proguanil to cycloguanil. J Comput Chem 2014; 35:2047-55. [DOI: 10.1002/jcc.23719] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Minhajul Arfeen
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Dhilon S. Patel
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Sheenu Abbat
- Department of Pharmacoinformatics; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Nikhil Taxak
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research (NIPER); S. A. S. Nagar (Mohali) 160 062 Punjab India
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20
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Bordessa A, Colin-Cassin C, Grillier-Vuissoz I, Kuntz S, Mazerbourg S, Husson G, Vo M, Flament S, Martin H, Chapleur Y, Boisbrun M. Optimization of troglitazone derivatives as potent anti-proliferative agents: towards more active and less toxic compounds. Eur J Med Chem 2014; 83:129-40. [PMID: 24953030 DOI: 10.1016/j.ejmech.2014.06.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/16/2014] [Accepted: 06/09/2014] [Indexed: 11/25/2022]
Abstract
Δ2-Troglitazone derivatives were shown to exhibit anti-proliferative activity in a PPARγ-independent manner. We prepared various compounds in order to increase their potency and decrease their toxicity towards non-malignant primary cultured hepatocytes. Many compounds induced viabilities less than 20% at 10 μM on various cancer cell lines. Furthermore, five of them showed hepatocyte viability of 80% or more at 200 μM. In addition, compounds 17 and 18 exhibited promising maximum tolerated doses on a murine model, enabling future investigations.
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Affiliation(s)
- Andrea Bordessa
- Université de Lorraine, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France; CNRS, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France
| | - Christelle Colin-Cassin
- Université de Lorraine, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France; CNRS, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France
| | - Isabelle Grillier-Vuissoz
- Université de Lorraine, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France; CNRS, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France
| | - Sandra Kuntz
- Université de Lorraine, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France; CNRS, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France
| | - Sabine Mazerbourg
- Université de Lorraine, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France; CNRS, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France
| | - Gauthier Husson
- Université de Lorraine, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France; CNRS, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France
| | - Myriam Vo
- Université de Lorraine, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France; CNRS, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France
| | - Stéphane Flament
- Université de Lorraine, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France; CNRS, CRAN, UMR 7039, BP 70239, F-54506 Vandœuvre-lès-Nancy Cedex, France
| | - Hélène Martin
- Université de Franche-Comté, Laboratoire de Toxicologie Cellulaire, EA 4267, 25030 Besançon Cedex, France
| | - Yves Chapleur
- Université de Lorraine, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France; CNRS, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France
| | - Michel Boisbrun
- Université de Lorraine, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France; CNRS, SRSMC, UMR 7565, BP 70239, F-54506 Vandœuvre-lès-Nancy, France.
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21
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Xie C, Zhong D, Chen X. A fragmentation-based method for the differentiation of glutathione conjugates by high-resolution mass spectrometry with electrospray ionization. Anal Chim Acta 2013; 788:89-98. [DOI: 10.1016/j.aca.2013.06.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/11/2013] [Accepted: 06/14/2013] [Indexed: 12/16/2022]
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Gunness P, Mueller D, Shevchenko V, Heinzle E, Ingelman-Sundberg M, Noor F. 3D organotypic cultures of human HepaRG cells: a tool for in vitro toxicity studies. Toxicol Sci 2013; 133:67-78. [PMID: 23377618 DOI: 10.1093/toxsci/kft021] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Drug-induced human hepatotoxicity is difficult to predict using the current in vitro systems. In this study, long-term 3D organotypic cultures of the human hepatoma HepaRG cell line were prepared using a high-throughput hanging drop method. The organotypic cultures were maintained for 3 weeks and assessed for (1) liver specific functions, including phase I enzyme and transporter activities, (2) expression of liver-specific proteins, and (3) responses to three drugs (acetaminophen, troglitazone, and rosiglitazone). Our results show that the organotypic cultures maintain high liver-specific functionality during 3 weeks of culture. The immunohistochemistry analyses illustrate that the organotypic cultures express liver-specific markers such as albumin, CYP3A4, CYP2E1, and MRP-2 throughout the cultivation period. Accordingly, the production rates of albumin and glucose, as well as CYP2E1 activity, were significantly higher in the 3D versus the 2D cultures. Toxicity studies show that the organotypic cultures are more sensitive to acetaminophen- and rosiglitazone-induced toxicity but less sensitive to troglitazone-induced toxicity than the 2D cultures. Furthermore, the EC50 value (2.7mM) for acetaminophen on the 3D cultures was similar to in vivo toxicity. In summary, the results from our study suggest that the 3D organotypic HepaRG culture is a promising in vitro tool for more accurate assessment of acute and also possibly for chronic drug-induced hepatotoxicity.
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Affiliation(s)
- Patrina Gunness
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
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23
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Mechanistic insights into the bioactivation of phenacetin to reactive metabolites: A DFT study. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Saha S, Chan DSZ, Lee CY, Wong W, New LS, Chui WK, Yap CW, Chan ECY, Ho HK. Pyrrolidinediones reduce the toxicity of thiazolidinediones and modify their anti-diabetic and anti-cancer properties. Eur J Pharmacol 2012; 697:13-23. [DOI: 10.1016/j.ejphar.2012.09.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 09/04/2012] [Accepted: 09/17/2012] [Indexed: 11/28/2022]
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Taxak N, Dixit VA, Bharatam PV. Density functional study on the cytochrome-mediated S-oxidation: identification of crucial reactive intermediate on the metabolic path of thiazolidinediones. J Phys Chem A 2012; 116:10441-50. [PMID: 23025570 DOI: 10.1021/jp308023g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
S-Oxidation is an important cytochrome P450 (CYP450)-catalyzed reaction, and the structural and energetic details of this process can only be studied by using quantum chemical methods. Thiazolidinedione (TZD) ring metabolism involving initial S-oxidation leads to the generation of reactive metabolites (RMs) and subsequent toxicity forcing the withdrawal of the glitazone class of drugs, thus, the study of the biochemical pathway of TZD ring metabolism is a subject of interest. The S-oxidation of the TZD ring and the formation of the isocyanate intermediate (ISC) was implicated as a possible pathway; however, there are several questions still unanswered in this biochemical pathway. The current study focuses on the CYP450-mediated S-oxidation, fate of the sulfoxide product (TZDSO), ring cleavage to ISC, and formation of nucleophilic adducts. The process of S-oxidation was explored by using Cpd I (iron(IV)-oxo porphyrin, to mimic CYP450) at TZVP/6-311+G(d) basis set. The barriers were calculated after incorporating dispersion and solvent corrections. The metabolic conversion from TZDSO to ISC (studied at B3LYP/6-311++G(2df,3pd)//B3LYP/6-31+G(d)) required a novel protonated intermediate, TZDSOH(+). The effect of higher basis sets (6-311+G(d,p), aug-cc-pvqz) on this conversion was studied. TZDSOH(+) was observed to be more reactive and thermodynamically accessible than ISC, indicating that TZDSOH(+) is the actual reactive intermediate leading to toxicity of the TZD class of compounds.
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Affiliation(s)
- Nikhil Taxak
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar (Mohali), 160 062 Punjab, India
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Salamone S, Colin C, Grillier-Vuissoz I, Kuntz S, Mazerbourg S, Flament S, Martin H, Richert L, Chapleur Y, Boisbrun M. Synthesis of new troglitazone derivatives: anti-proliferative activity in breast cancer cell lines and preliminary toxicological study. Eur J Med Chem 2012; 51:206-15. [PMID: 22409968 DOI: 10.1016/j.ejmech.2012.02.044] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 02/08/2023]
Abstract
Breast cancer is the most prevalent cancer in women. The development of resistances to therapeutic agents and the absence of targeted therapy for triple negative breast cancer motivate the search for alternative treatments. With this aim in mind, we synthesised new derivatives of troglitazone, a compound which was formerly used as an anti-diabetic agent and which exhibits anti-proliferative activity on various cancer cell lines. Among the compounds prepared, some displayed micromolar activity against hormone-dependent and hormone-independent breast cancer cells. Furthermore, the influence of the compounds on the viability of primary cultures of human hepatocytes was evaluated. This enabled us to obtain for the first time interesting structure-toxicity relationships in this family of compounds, resulting in 6b and 8b, which show good anti-proliferative activities and poor toxicity towards hepatocytes, compared to troglitazone.
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Affiliation(s)
- Stéphane Salamone
- Groupe SUCRES, UMR 7565, Nancy-Université-CNRS, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France
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