Aspartic proteases and proteolytic systems controlled by these enzymes play a critical role in several human pathologies such as cancer, neurodegenerative and immune diseases. Cathepsin-like proteases are also essential for viability or virulence of important human pathogens, parasites, and pests. Therefore, strong efforts have gone into the design and testing of compounds that could become new drugs1. Unlike the serine protease family, naturally occurring inhibitors of aspartic proteases are relatively rare, and only three of them have been structurally characterized so far in complex with a target protease2-4.
Here we present new crystal structures of cathepsin D in complex with three proteinaceous inhibitors: potato inhibitors pAPI-1 and pAPI-2 from the plant Kunitz family, and equistatin domain 2 (Eqd2) from sea anemone belonging to the thyropin (thyroglobulin type-1-like) family. The inhibitors show distinct designs of structural binding motifs that are based on disulfide-stabilized loops forming a network of interactions in the extended non-primed part of the enzyme active site. Our results serve as a basis for the development of biomimetic inhibitors of medicinally relevant aspartic proteases.
This work was supported by the project ChemBioDrug CZ.02.1.01/0.0/0.0/16_019/0000729 from the European Regional Development Fund (OP RDE) and institutional project RVO 61388963.