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Shamovsky I, Ripa L, Narjes F, Bonn B, Schiesser S, Terstiege I, Tyrchan C. Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations. J Med Chem 2021; 64:8545-8563. [PMID: 34110134 DOI: 10.1021/acs.jmedchem.1c00514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aromatic and heteroaromatic amines (ArNH2) are activated by cytochrome P450 monooxygenases, primarily CYP1A2, into reactive N-arylhydroxylamines that can lead to covalent adducts with DNA nucleobases. Hereby, we give hands-on mechanism-based guidelines to design mutagenicity-free ArNH2. The mechanism of N-hydroxylation of ArNH2 by CYP1A2 is investigated by density functional theory (DFT) calculations. Two putative pathways are considered, the radicaloid route that goes via the classical ferryl-oxo oxidant and an alternative anionic pathway through Fenton-like oxidation by ferriheme-bound H2O2. Results suggest that bioactivation of ArNH2 follows the anionic pathway. We demonstrate that H-bonding and/or geometric fit of ArNH2 to CYP1A2 as well as feasibility of both proton abstraction by the ferriheme-peroxo base and heterolytic cleavage of arylhydroxylamines render molecules mutagenic. Mutagenicity of ArNH2 can be removed by structural alterations that disrupt geometric and/or electrostatic fit to CYP1A2, decrease the acidity of the NH2 group, destabilize arylnitrenium ions, or disrupt their pre-covalent transition states with guanine.
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Abstract
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As
a field, computational toxicology is concerned with using in silico models to predict and understand the origins of
toxicity. It is fast, relatively inexpensive, and avoids the ethical
conundrum of using animals in scientific experimentation. In this
perspective, we discuss the importance of computational models in
toxicology, with a specific focus on the different model types that
can be used in predictive toxicological approaches toward mutagenicity
(SARs and QSARs). We then focus on how quantum chemical methods, such
as density functional theory (DFT), have previously been used in the
prediction of mutagenicity. It is then discussed how DFT allows for
the development of new chemical descriptors that focus on capturing
the steric and energetic effects that influence toxicological reactions.
We hope to demonstrate the role that DFT plays in understanding the
fundamental, intrinsic chemistry of toxicological reactions in predictive
toxicology.
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Affiliation(s)
- Piers A Townsend
- Centre for Sustainable Chemical Technologies, Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Matthew N Grayson
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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Allen TEH, Grayson MN, Goodman JM, Gutsell S, Russell PJ. Using Transition State Modeling To Predict Mutagenicity for Michael Acceptors. J Chem Inf Model 2018; 58:1266-1271. [PMID: 29847119 DOI: 10.1021/acs.jcim.8b00130] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The Ames mutagenicity assay is a long established in vitro test to measure the mutagenicity potential of a new chemical used in regulatory testing globally. One of the key computational approaches to modeling of the Ames assay relies on the formation of chemical categories based on the different electrophilic compounds that are able to react directly with DNA and form a covalent bond. Such approaches sometimes predict false positives, as not all Michael acceptors are found to be Ames-positive. The formation of such covalent bonds can be explored computationally using density functional theory transition state modeling. We have applied this approach to mutagenicity, allowing us to calculate the activation energy required for α,β-unsaturated carbonyls to react with a model system for the guanine nucleobase of DNA. These calculations have allowed us to identify that chemical compounds with activation energies greater than or equal to 25.7 kcal/mol are not able to bind directly to DNA. This allows us to reduce the false positive rate for computationally predicted mutagenicity assays. This methodology can be used to investigate other covalent-bond-forming reactions that can lead to toxicological outcomes and learn more about experimental results.
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Affiliation(s)
- Timothy E H Allen
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Matthew N Grayson
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Jonathan M Goodman
- Centre for Molecular Informatics, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Steve Gutsell
- Unilever Safety and Environmental Assurance Centre , Colworth Science Park , Sharnbrook , Bedfordshire MK44 1LQ , United Kingdom
| | - Paul J Russell
- Unilever Safety and Environmental Assurance Centre , Colworth Science Park , Sharnbrook , Bedfordshire MK44 1LQ , United Kingdom
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Bezençon O, Heidmann B, Siegrist R, Stamm S, Richard S, Pozzi D, Corminboeuf O, Roch C, Kessler M, Ertel EA, Reymond I, Pfeifer T, de Kanter R, Toeroek-Schafroth M, Moccia LG, Mawet J, Moon R, Rey M, Capeleto B, Fournier E. Discovery of a Potent, Selective T-type Calcium Channel Blocker as a Drug Candidate for the Treatment of Generalized Epilepsies. J Med Chem 2017; 60:9769-9789. [PMID: 29116786 DOI: 10.1021/acs.jmedchem.7b01236] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report here the discovery and pharmacological characterization of N-(1-benzyl-1H-pyrazol-3-yl)-2-phenylacetamide derivatives as potent, selective, brain-penetrating T-type calcium channel blockers. Optimization focused mainly on solubility, brain penetration, and the search for an aminopyrazole metabolite that would be negative in an Ames test. This resulted in the preparation and complete characterization of compound 66b (ACT-709478), which has been selected as a clinical candidate.
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Affiliation(s)
- Olivier Bezençon
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Bibia Heidmann
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Romain Siegrist
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Simon Stamm
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Sylvia Richard
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Davide Pozzi
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Olivier Corminboeuf
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Catherine Roch
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Melanie Kessler
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Eric A Ertel
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Isabelle Reymond
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Thomas Pfeifer
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Ruben de Kanter
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Michael Toeroek-Schafroth
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Luca G Moccia
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Jacques Mawet
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Richard Moon
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Markus Rey
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Bruno Capeleto
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Elvire Fournier
- Chemistry, Biology and Pharmacology & Pre-clinical Development, Drug Discovery, Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
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