Decoding Synaptic Diversity: Molecular Architectures, Phase Transitions, and Shared Postsynaptic Failure in Alzheimer’s and Parkinson’s Disease

Synaptic failure is the most accurate pathological correlate of cognitive and motor decline in neurodegenerative diseases. However, the molecular logic governing selective synaptic vulnerability in Alzheimer’s (AD) and Parkinson’s (PD) remains a fundamental enigma. This review dissects the hierarchical organization of the synaptome, arguing that synaptic decay is not a generic process of attrition but a specific collapse of subsynaptic domains (SSDs) and trans-synaptic nanocolumns, considered here within the framework of the tetrapartite synapse, which comprises the presynaptic and postsynaptic compartments together with glia and the perisynaptic extracellular matrix. We use the term pathological convergence in a restricted sense, to denote that, although the primary aggregates differ, the two diseases converge on the same postsynaptic scaffolding hubs and on a comparable loss of condensate fluidity. We propose a biophysical model where the Post-Synaptic Density (PSD) matrix, governed by liquid–liquid phase separation (LLPS), may undergo a pathological liquid-to-solid transition—characterized by condensate maturation and the formation of insoluble protein aggregates—driven by proteotoxic species. Specifically, we analyze how Aβ-mediated zinc sequestration disrupts the Shank-SAM scaffold hierarchy in AD, while α-synuclein aggregates arrest presynaptic vesicle dynamics and mitochondrial homeostasis in PD. Furthermore, we explore the emerging frontier of “Precision Synaptopharmacology,” highlighting how targeted modulation of protein–protein interaction (PPIs), synthetic synaptic organizers (e.g., CPTX), and phase-stabilizing chaperones can restore nanocolumn alignment and synaptic fluidity. We also set out the principal limitations of these strategies, including blood–brain barrier delivery, off-target effects, the immaturity of condensate-directed pharmacology and the incomplete translation of rodent findings to human disease, and we consider the vascular and peripheral contributions that modify the synaptic environment. By integrating recent advances in super-resolution microscopy, systems biology, and activity-based neurorehabilitation, we provide a comprehensive framework for shifting neuroprotective strategies toward the precision engineering and functional recovery of synaptic nano-architecture.