Proteases are enzymes that degrade proteins and play a major role in cellular homeostasis. One such class, cysteine cathepsins, contain the most powerful mammalian collagenase and elastase. When studied in combination, there are protease-on-protease interactions, “cathepsin cannibalism” interactions, that ultimately reduce the pool of active protease in a system. Part of my thesis work has focused on using computational techniques to tease apart these cathepsin cannibalism interactions as well as design and test mutant cathepsins to resist these interactions. Furthermore, my research also evaluated what role proteases play in locomoting biological machine stability. Our findings have shown that cysteine cathepsins are secreted by these machines and can degrade the fibrin matrix and destabilizing the machine. The culmination of this work is in developing a computational model to predict the lifespan of these biological machines and design interventions using inhibitors and mutant cathepsins to control the lifespan of these machines.

Deciphering the Cathepsin Proteolytic Network

Cysteine cathepsins are a family of lysosomal proteases involved in extracellular matrix remodeling. This family contains the most potent mammalian collagenase and elastase and are often found upregulated in tissue destructive diseases such as cancer, osteoporosis, atherosclerosis, rheumatoid arthritis, and tendinopathy. Since cathepsins are so potent and involved in many different pathologies, they have been a key target for pharmaceutical companies. However, although well-design, specific cathepsin inhibitors have been developed and proven effective at stopping disease progression, all have failed phase II and III clinical trials due to off-target side effects. We hypothesize that an incomplete understanding of how individual cathepsin species interact with each other could be causing problems appropriately dosing inhibitors for treatment. Previously our lab has shown that cathepsin S will preferentially degrade cathepsin K, in the presence of substrate, a phenomenon termed “cathepsin cannibalism”. My research has focused on using computational modeling to tease apart these cathepsin cannibalism interactions between cathepsin K, L, S, and V and verifying these interactions by designing and making cannibalism-resistant cathepsin mutants.

Biological Machine Protease Activity

Locomoting biological machines are innovative cell-based soft robotic devices that have the capability to dynamically sense and respond to environmental stimuli. However with current designs after a couple weeks, the C2C12 cells have reduced contractility due to some unknown causes. My research has focused on characterizing the protease activity in these biological machines for cathepsin and matrix metalloproteinase (MMP) activities using gelatin zymography and Western blots, which we hypothesized as the cause for machine failure. I characterized the protease activity in these biological machines with and without electrically stimulated contraction and under different design parameters. Once characterized, the biological machine lifespan potential was modeling, so we can design strategies to control the lifespan of the machine.