Bioinformatic analysis of xenobiotic reactive metabolite target proteins and their interacting partners

Sorting 171 known reactive metabolite target proteins revealed a number of GO categories and KEGG pathways to be significantly enriched in targets, but in most cases the classes were too large, and the "percent coverage" too small, to allow meaningful conclusions about mechanisms of toxicity. However, a similar analysis of the directlyinteracting partners of 28 common targets of multiple reactive metabolites revealed highly significant enrichments in terms likely to be highly relevant to cytotoxicity (e.g., MAP kinase pathways, apoptosis, response to unfolded protein). Machine learning was used to rank the contribution of 211 computed protein features to determining protein susceptibility to adduction. Protein lysine (but not cysteine) content and protein instability index (i.e., rate of turnover in vivo) were among the features most important to determining susceptibility.As yet there is no good explanation for why some low-abundance proteins become heavily adducted while some abundant proteins become only lightly adducted in vivo. Analyzing the directly interacting partners of target proteins appears to yield greater insight into mechanisms of toxicity than analyzing target proteins per se. The insights provided can readily be formulated as hypotheses to test in future experimental studies.More than half a century has passed since the discovery that reactive electrophilic metabolites derived from xenobiotic agents covalently modify endogenous cellular proteins [1,2]. Since then such covalent binding by reactive metabolites has been strongly correlated with, and is widely believed to be responsible for, the acute organ-damaging effects of a wide range of xenobiotic agents including drugs and natural products [3-5]. Tissue injury is a complex phenomenon. Most tissues are comprised of more than one cell type, and macroscopic tissue injury often involves various secreted chemical mediators such as cytokines, tumor necrosis factor, nitric oxide and pro-inflammatory cel