Structure–Activity Relationship Study of Protoberberine Alkaloids Reveals Molecular Planarity as a Key Determinant of Membrane Interaction and Protection from Misfolded Protein Oligomers

Abstract

Interaction of berberine (Brb) with cell membranes is crucial for its bioavailability, blood–brain barrier permeation, and neuroprotection against misfolded protein oligomers in neurodegenerative diseases. Although Brb follows Lipinski’s rule of five, the structural drivers of its membrane permeation remain unclear. We combined biophysical analyses on biomimetic liposomes with cell culture assays to evaluate eight natural protoberberine alkaloids (PBAs), assessing membrane interactions and protective effects. While traditional physicochemical descriptors varied minimally across the series, molecular planarity, quantified by non-hydrogen out-of-plane atoms, emerged as the key structural feature determining membrane binding affinity, kinetics, stiffening, and protein-oligomer displacement. These membrane effects correlated with the ability of the compounds to mitigate oligomer-induced calcium influx in cell cultures, an early cytotoxicity marker. ANS fluorescence and circular dichroism spectroscopy showed no direct oligomer–PBA interaction, ruling out this mechanism. These findings establish a rational framework for optimizing the Brb benzylisoquinoline scaffold, indicating that increasing molecular planarity enhances membrane affinity and neuroprotection.