Computational and biochemical design of a nanopore cleavable by a cancer-secreted enzyme

Many proteinaceous macromolecules selectively transport substrates across lipid bilayers and effectively serve as gated nanopores. Here, we engineered cleavage-site motifs for human matrix metalloprotease 7 (MMP-7) into the extracellular and pore-constricting loops of OprD, a bacterial substrate-specific transmembrane channel. Concurrent removal of two extracellular loops allowed MMP-7 to access and hydrolyze a cleavage-site motif engineered within the pore's major constricting loop, in both membrane-incorporated and detergent-solubilized OprDs. Import of antibiotics by the engineered OprDs into living bacteria pointed to their proper folding and integration in biological membranes. Purified engineered OprDs were also found to be properly folded in detergent. Hence, this study demonstrates the design of nanopores with a constriction cleavable by tumor-secreted enzymes (like MMP-7) for their potential incorporation in lipid-based nanoparticles to accelerate drug release at the tumor site.