Computational predictions of cysteine cathepsin‐mediated fibrinogen proteolysis

Abstract

Fibrin clot formation is a proteolytic cascade of events with thrombin and plasmin identified as the main proteases cleaving fibrinogen precursor, and the fibrin polymer, respectively. Other proteases may be involved directly in fibrin(ogen) cleavage, clot formation, and resolution, or in the degradation of fibrin-based scaffolds emerging as useful tools for tissue engineered constructs. Here, cysteine cathepsins are investigated for their putative ability to hydrolyze fibrinogen, since they are potent proteases, first identified in lysosomal protein degradation and known to participate in extracellular proteolysis. To further explore this, we used two independent computational technqiues, molecular docking and bioinformatics sequence analysis (PACMANS), to predict potential binding interactions and sites of hydrolysis between cathepsins K, L, and S and fibrinogen. By comparing the results from these two objective, computational methods, it was determined that cathepsins K, L, and S do bind and cleave fibrinogen α, β, and γ chains at similar and unique sites. These differences were visualized experimentally by the unique cleaved fibrinogen banding patterns after incubation with each of the cathepsins, separately. In conclusion, human cysteine cathepsins K, L, and S are a new class of proteases that should be considered during fibrin(ogen) degradation studies both for disease processes where coagulation is a concern, and also in the implementation and design of bioengineered systems.

Human cathepsins K, L, and S: Related proteases, but unique fibrinolytic activity

“…Cathepsin partial or complete fibrinolysis may prevent full solid clots from forming or staying in a protective way during thrombin-mediated clot formation. However, our recent study also shows that cathepsins potentially can be involved in fibrin formation as they can hydrolyze fibrinogen as well [19]. This putative conflict will need to be resolved to understand the participation of this additional class of proteases in hemostasis.…”

“…Our lab has used molecular docking and bioinformatics sequence specificity analysis (PACMANS), to predict potential binding and cleavage sites of cathepsins K, L and S on fibrin [19]. It was determined that catK, L, and S are capable of binding to the α, β, and γ chains on fibrinogen at overlapping and different sites.…”

Cysteine Cathepsins and Their Extracellular Roles: Shaping the Microenvironment

“…In the case of pre-adipocyte cells, cleavage of fibronectin by cathepsin S was suggested as a possible mechanism for their differentiation [173]. Recent in silico and in vitro studies reported that cathepsins K, L, and S could cleave fibrinogen and fibrin, resulting in fragments that differ from the ones produced by plasmin, which opened the door to further investigate their roles in vascular homeostasis, especially in coagulation-associated diseases [174,175]. Moreover, cathepsin K was recently demonstrated to have an essential role in skeletal muscle remodeling, dysfunction, and fibrosis following injury [176].…”

Long-Term Cryopreservation and Revival of Tissue-Engineered Skeletal Muscle

“…Our previous characterization of engineered skeletal muscle tissues demonstrated the activity of proteolytic enzymes (such as myotube-secreted catL) that can degrade the fibrin-based ECM and thus lead to diminished mechanical integrity and functionality over time. 24 Along with recently described modeling, 46 we underscore catL as an alternative fibrin(ogen)lytic protease. In this study, we show preliminary evidence that secreted cathepsin had fibrinogenolytic activity (Fig.…”