Increased carcinogenic potency methyl/benzyl compared to benzyl/benzyl is also a trend in the methyl/cyclohexyl and cyclohexyl/cyclohexyl pair.
I understand the design of CPCA takes into account the intrinsic lability of the (pseudo)benzylic C-H and thus its susceptibility to alpha-hydroxylation and not the further generation, stability and reactivity of a (pseudo)benzylic carbocation.
For the symmetric example N,N-dibenzylnitrosamine unavoidably both topics get to the surface due to its symmetric nature:
- Benzyl on side âAâ: Benzyl influence on the lability of the C-H linked to formation of alpha-hydroxy N,N-dibenzylnitrosamine and benzaldehyde metabolite formation (though also the bulkiness of phenyls has to be considered as this influences enzyme interaction â approaches as worst case in CPCA).
- Benzyl on side âBâ: Benzyl influence of the further metabolization of the benzyl diazohydroxide (toxification or detoxification?).
What is clear though is that the worst case is the methyl-benzyl combination (and not the benzyl-benzyl): benzyl effect boosts (speed-wise) getting access to the methyl carbocation compared to methyl-methyl
â Get the benzyl on side âAâ effect (activation), expulsion of benzaldehyde and generate a methyl diazohydroxide, subsequently leading to an alkylating species.
But what is clear is also the problem: mechanistic understanding on the benzyl/benzyl and its DNA benzylation and other metabolisation risks was in the early days always linked to the data of more potent analogues. Nonetheless, in later years further studies shed a little bit more light. Citing all the literature searching for mechanisms and metabolites would lead me too far, but an in vivo study with transgenic rodents is worth citing (and not in the EFSA report it seems): Jiao, J., Douglas, G. R., Gingerich, J. D., & Soper, L. M. (1997). Analysis of tissue-specific lacZ mutations induced by N-nitrosodibenzylamine in transgenic mice. Carcinogenesis (New York) , 18 (11), 2239â2245. Analysis of tissue-specific lacZ mutations induced by N-nitrosodibenzylamine in transgenic mice. | Carcinogenesis | Oxford Academic.
From a pragmatic perspective and supported by mechanistic data and mutagenicity studies, readacross with NDMA possibly could be justified as conservative, while having the advantage NDMA data suitability for surrogate use purposes is established and not requiring full characterization of DNA adducts and the link between mutagenicity and carcinogenicity. Ranking against NDMA (e.g. in the sense of dr. Raphael Nudelman presentation during 20 May 2024, FDA Fiscal Year (FY) 2024 Generic Drug Science and Research Initiatives Public Workshop) is possibly not appropriate/in scope of these efforts, considering that the in vivo carcinogenicity/in vivo mutagenicity correlation establishment project seems mostly focused on rodent carcinogens, whereas nitrosodibenzylamine was found to not induce tumors.
I believe the alpha-(pseudo)benzylic feature is one which requires interpretation/regards for the local similarity and is often leading to a conservative AI. Overall there are quite some compounds in the limit lists which get this CPCA score punishment probably unnecessarily. Also the reference compound data used for design of the feature often is linked with fairly high TD50 or if not more complicated mechanisms hidden behind the feature, cf. Determining Recommended Acceptable Intake Limits for N-Nitrosamine Impurities in Pharmaceuticals: Development and Application of the Carcinogenic Potency Categorization Approach (CPCA) - ScienceDirect. The activating features surely were designed from a precautionary and semi-theoretic perspective, to minimize AI overestimation risks.
For detailed comments by NITWG including discussion of nitrosodibenzylamine see also section 3.3.1. Aryl Group Bonded to α-Carbon (i.e., Benzylic and Pseudo-Benzylic) of https://www.sciencedirect.com/science/article/pii/S0273230024000813