Autophagy-Lysosomal Clearance Capacity Determines Therapeutic Window—Substrate…

Molecular Mechanism and Rationale

This therapeutic hypothesis targets the autophagy-lysosomal degradation pathway’s kinetic limitations in clearing pathological protein aggregates, specifically focusing on the LC3-II/p62-mediated selective autophagy mechanism. At the molecular level, misfolded protein aggregates are recognized by p62/SQSTM1 adaptor proteins through their ubiquitin-binding domain (UBA), which simultaneously interact with LC3-II anchored in autophagosomal membranes via the LC3-interacting region (LIR). This cargo recognition system exhibits saturable kinetics where the rate-limiting step involves autophagosome-lysosome fusion mediated by SNARE proteins (STX17, SNAP29, VAMP8) and the RAB7 GTPase.

The kinetic model predicts that aggregate clearance follows capacity-limited kinetics, where the lysosomal degradation machinery exhibits maximum processing velocity (Vmax) determined by lysosomal protease activity (cathepsins B, D, L), lysosomal pH maintenance via V-ATPase, and autophagosome biogenesis rate controlled by ULK1/ATG13 complex activity. The critical threshold emerges when aggregate influx exceeds lysosomal processing capacity, leading to autophagosome accumulation and lysosomal stress. Beyond this threshold, substrate competition occurs between different aggregate species for limited p62 adaptors and LC3-II binding sites, creating a bottleneck effect.

TFEB (Transcription Factor EB) serves as the master regulator of lysosomal biogenesis, translocating from cytoplasm to nucleus under starvation or lysosomal stress conditions. However, TFEB activation requires time to increase lysosomal capacity, creating a temporal mismatch between acute aggregate burden and adaptive clearance capacity. This mechanism explains why early intervention is critical—therapeutic enhancement of autophagy flux through mTOR inhibition or TFEB activation is most effective when baseline aggregate levels remain within the system’s processing range, before competitive inhibition and lysosomal dysfunction compromise clearance efficiency.