Exploration of tropocollagen unwinding by cathepsin K dimer with chondroitin 4-sulphate through microsecond timescale...

Cathepsin K (CatK), a promising therapeutic target for bone-related diseases, uniquely unfolds triple-helical collagen and digests tropocollagen into soluble peptides in the presence of chondroitin 4-sulphate (C4-S). However, the molecular mechanism of CatK-mediated collagenolysis remains poorly understood, hindering the rational design of selective inhibitors. In this study, we performed microsecond-scale molecular dynamics simulations of a fully solvated ternary complex comprising the CatK dimer, tropocollagen segment, and C4-S, to indicate the structural and dynamical basis of tropocollagen unwinding. The process was initiated by the progressive disruption of six key inter-chain hydrogen bonds within the tropocollagen. C4-S adopted a cosine-like conformation that bridged CatK and tropocollagen, thereby stabilising the ternary complex. Unwinding occurred at the active site cleft, with Cys²⁵ and Trp¹⁸⁴ serving as critical residues that may contribute hydrogen bond disruption and substrate stabilisation. Our findings provided mechanistic insights into CatK-dependent collagen degradation and rational development of next-generation CatK inhibitors.