Computational Modeling of Functionalized Graphene Quantum Dots Binding to Tau Fibrils in Alzheimers Disease

Abstract

The aggregation of Tau protein into straight filaments (SFs) and paired helical filaments (PHFs) is central to Alzheimers disease (AD) pathology and a key target for therapeutic inhibition. Graphene quantum dots (GQDs) are biocompatible nanomaterials that have shown promise in inhibiting amyloidogenic protein aggregation across related neurological pathologies. The effect of GQD functionalization on interactions with Tau aggregates (TAs) is poorly understood, though recent evidence suggests that anionic GQDs are effective TA inhibitors. In this study, we survey how GQD functionalization influences binding to SFs and PHFs to guide future development of therapeutic GQDs. We identify binding sites in SFs and PHFs, dock our GQD library to these sites, and perform molecular dynamics simulations on promising complexes, totaling 28 {micro}s of sampling. We discover that anionic GQDs preferentially bind to the positively charged SF large protofilament interface, whereas in PHFs, anionic GQDs have a modest binding preference for the C-shaped curve region. Binding of GQDs at the C-shaped curve in both TAs induces distinct protofilament conformational dynamics resembling a pinching motion to capture the GQD. Together, these binding modes may represent early intermediates of the TA disaggregation mechanism. We find that functional groups capable of possessing a negative charge (e.g., COO-, O-, and S-) produce impressive binding affinities. We propose that enriching these functionalizations during GQD synthesis and preparation, particularly sulfur as it is less studied, may yield more potent TA inhibitors and generalize to other amyloid pathologies with positively charged fibril cores. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/741532v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@d5d794org.highwire.dtl.DTLVardef@13c59e1org.highwire.dtl.DTLVardef@130c369org.highwire.dtl.DTLVardef@6d3385_HPS_FORMAT_FIGEXP M_FIG C_FIG