Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations


Aromatic amines are chemical structures that often are embeded in drug molecules. However, they are also structural fragments that are considered a risk for mutagenicity and therefore these structures can have a pronounced impact on a drug discovery program. Indeed in the field of drug-discovery, mutagenicity can halt development of a particular chemotype and possibly the work on an entire drug target. Potential genotoxicity is a serious issue that needs to be avoided in most therapeutic applications.

According to quantitative structure−mutagenicity relationships, many factors influence the mutagenic potency of aromatic amines. Previous research work showed that attempts to remove the mutagenicity can result in a significant reduction of the pharmacological activity. Finding opportunities to eliminate mutagenicity while keeping the efficacy is of high importance in drug research. To that end, scientists from the Department of Medicinal Chemistry at BioPharmaceuticals R&D, AstraZeneca: Dr. Igor Shamovsky, Dr. Lena Ripa, Dr. Frank Narjes, Britta Bonn, Dr. Stefan Schiesser, Dr. Ina Terstiege, and Dr. Christian Tyrchan developed strategies to predict and eliminate mutagenicity of aromatic amine structural fragment to enable use of these when optimizing drug candidates. The enzyme CYP1A2 bioactivates aromatic amines to mutagenic N-hydroxylamines, and the mechanism for this activation was investigated using a quantum mechanical modeling method called density functional theory (DFT). Two mechanistic pathways of N-hydroxylation were studied, the radicaloid route and the alternative anionic pathway. The radicaloid route involves the classical ferryl-oxo oxidant, and the anionic pathway comprises the Fenton-like oxidation by ferriheme-bound H2O2. The presented results showed that several strategies can be used to remove the mutagenicity of aromatic amines. The original research article is now published in the Journal of medicinal chemistry.

The research team found that the most favored pathway for bioactivation of aromatic amines by CYP1A2 is the anionic pathway rather than the radicaloid route. Several factors contribute to the mutagenicity of aromatic amines including hydrogen-bonding pattern and geometric fit of aromatic amines to the CYP1A2 active site, the viability of proton removal by a ferriheme-peroxo base in CYP1A2 and how prone the formed arylhydroxylamines are to heterolytic cleavage. The authors found that the mutagenic potential can be removed by structural alterations of the aromatic amine. These structural alterations consist of disruption of the hydrogen-bonding and the geometric fit of aromatic amines to the CYP1A2 active site, destabilization of arylnitrenium ions, reducing the acidity of the amine group, and disruption of the formation of covalent bonds between guanine in DNA and arylnitrenium ions.

The authors used the dispersion-correcting density functional B3LYP-D3 which is an accepted quantum mechanical method to study catalytic reactions within enzymes. In order to understand the mechanisms of mutagenicity, they focused on the bioactivation of primary aromatic amines by human CYP1A2. They found that the classical radicaloid pathway is inconsistent with the observed structure-mutagenicity relationships of aromatic amines and show higher activation barriers of the rate-limiting steps. This inconsistency is caused by the disruption of hydrogen-bonding and π−π interactions in the transition state structures within the CYP1A2 active cite. In contrast, the anionic pathway is enabled by lower activation barriers of the rate-limiting steps and optimum hydrogen-bonding and π−π interactions throughout the pathway. In addition, the anionic pathway provides the explanation for the anionic stabilization as one of the primary factors that increse mutagenic potency of aromatic amines and is consitent with the observed structure-mutagenicity relationships.

The authors proposed four approaches to convert a mutagenic aromatic amine into non-mutagenic variants. These include destabilization of pre-reaction binding of aromatic amines to CYP1A2, impeding the initial proton removal via electron-rich five-membered aromatic amine scaffolds, stabilization of the formed N-hydroxylamine under acidic environment, and reducing the reactivity of arylnitrenium ions toward DNA guanines. In a nutshell, AstraZenca scientists successfully provided medicinal chemists with novel approaches to avoid mutagenicity of aromatic amines with a variety of small structural alterations that either prevent their N-hydroxylation by CYP1A2 or by decresing the reactivity of the formed N-hydroxylamine with DNA guanines to improve the chances of successful drug optimization.


Shamovsky, I., Ripa, L., Narjes, F., Bonn, B., Schiesser, S., Terstiege, I., & Tyrchan, C. (2021). Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations. Journal of medicinal chemistry, 64(12), 8545–8563.

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