Modeling of Squalene Epoxidase Mutations Suggest Subtle Structural Modifications Confer Resistance to Terbinafine

Fungal resistance in infections represents an escalating global health concern, particularly among elderly and immunocompromised populations. Terbinafine, a front-line fungicide targeting squalene epoxidase (SQLE) faces increasing resistance from strains featuring mutated SQLEs. Almost no structural information exists for wild-type (terbinafine sensitive) or mutant (terbinafine resistant) fungal SQLEs. While a human SQLE structure with a terbinafine analog is available, it features a significantly different sequence. Alphafold2 was used to generate models of wild-type and mutant SQLEs. These models were aligned with the human SQLE crystal structure using sequence and structural alignments to determine potential causes of terbinafine resistance. Structural analyses reveal that terbinafine resistance arises from point mutations that alter the space within the binding pocket causing either gaps that terbinafine can not fill or creating steric conflicts. Both cases result in improper interactions between terbinafine and the binding pocket that reduce binding affinity. The human SQLE also exhibits reduced affinity for terbinafine and can also be explained by similar principles. We find that even conserved residues exhibit different orientations which further influence resistance. Understanding these structural changes provides a foundation for developing new antifungal agents capable of targeting resistant SQLE variants.