Covalent histone modification by an electrophilic derivative of the anti-HIV drug nevirapine

Abstract

Nevirapine (NVP), a non-nucleoside reverse transcriptase inhibitor widely used in combined antiretroviral therapy and to prevent mother-to-child transmission of the human immunodeficiency virus type 1, is associated with several adverse side effects. Using 12-mesyloxy-nevirapine, a model electrophile of the reactive metabolites derived from the NVP Phase I metabolite, 12-hydroxy-NVP, we demonstrate that the nucleophilic core and C-terminal residues of histones are targets for covalent adduct formation. We identified multiple NVP-modification sites at lysine (e.g., H2BK47, H4K32), histidine (e.g., H2BH110, H4H76), and serine (e.g., H2BS33) residues of the four histones using a mass spectrometry-based bottom-up proteomic analysis. In particular, H2BK47, H2BH110, H2AH83, and H4H76 were found to be potential hot spots for NVP incorporation. Notably, a remarkable selectivity to the imidazole ring of histidine was observed, with modification by NVP detected in three out of the 11 histidine residues of histones. This suggests that NVP-modified histidine residues of histones are prospective markers of the drug's bioactivation and/or toxicity. Importantly, NVP-derived modifications were identified at sites known to determine chromatin structure (e.g., H4H76) or that can undergo multiple types of post-translational modifications (e.g., H2BK47, H4H76). These results open new insights into the molecular mechanisms of drug-induced adverse reactions. ; This work was supported in part by the PRIME-XS project, grant agreement number 262067, funded by the European Union seventh Framework Programme. We also thank Fundação para a Ciência e a Tecnologia (FCT), Portugal, for financial support through projects UID/QUI/00100/2020 (to CQE), RECI/QEQ-MED/0330/2012 and PTDC/QUI-QAN/32242/2017, as well as contract CEECIND/02001/2017 (to A.M.M.A) and doctoral fellowships SFRH/BD/80690/2011 (to SGH), SFRH/BD/75426/2010 (to ILM), and SFRH/BD/102846/2014 (to CC). Joint funding from FCT and the COMPETE Program through grant SAICTPAC/0019/2015 and RNEM-LISBOA-01-0145-FEDER-022125 funding are also gratefully acknowledged. The CRG/UPF Proteomics Unit is part of the "Plataforma de Recursos Biomoleculares y Bioinformáticos (ProteoRed)" supported by grant PT13/0001 of the Instituto de Salud Carlos III (ISCIII)