A screening pipeline for human proteins interacting with dyes and toxins applied to the melanin virulence determinant 1,8-dihydroxynaphthalene of Aspergillus fumigatus

Human-pathogenic molds produce various natural products (xenobiotics) that interact with human host proteins. Here, a sequence- and structure-based virtual screening pipeline for protein-xenobiotic interactions was established. Verification tests run on Methylene Blue and Fumagillin identified the known top interaction targets in both cases. The pipeline was then applied to 1,8-dihydroxynaphthalene (DHN)-melanin, an Aspergillus fumigatus spore pigment and virulence determinant. Our sequence-structure aggregated scoring for DHN-melanin-interacting proteins included protein localization, evolution, and function. Experimental data validated our identified candidates and support ranking accuracy. Conserved targets were further assessed: for their possible participation in the macrophage response to A. fumigatus (using gene ontology terms). Lower-scoring targets, such as glucosidase alpha (GAA; experimental data in this paper) and sentrin-specific protease 8 (SENP8), were shown not to bind DHN-melanin by molecular dynamics (MD) simulations as well as experiments, supporting their lower pipeline scores. The best DHN-melanin interacting candidates were validated by docking and molecular dynamics simulations, resulting in the identification of the most likely DHN-melanin-interacting proteins in human immune and epithelial cells. The pipeline identified the following previously validated DHN-melanin interaction targets with top score: C-type lectin receptor MelLec (CLEC1A) and surfactant protein-D (SP-D). In addition, two novel targets share the same top score, the aromatic hydrocarbon receptor (AHR) and methionine aminopeptidase 2 (METAP2), the latter of which was experimentally validated. • A sequence-structure-based virtual screening pipeline for xenobiotic interactions. • Test runs on methylene blue and fumagillin found the known top targets. • Confirmed DHN-melanin targets are MelLec and surfactant protein-D. • Two novel targets are aromatic hydrocarbon receptor and methionine aminopeptidase 2. • Experiments validate DHN-melanin inhibition of methionine aminopeptidase 2.