Computer-Aided Design of Peptides for Suppressing Liquid-Liquid Phase Separation

Abstract

Liquid-liquid phase separation (LLPS) is a fundamental process in cellular biology, critical for the formation of membraneless organelles. Dysregulation of LLPS is linked to various diseases, highlighting the need for targeted therapeutics. Traditional computer-aided drug design has struggled to address LLPS due to the involvement of intrinsically disordered regions (IDRs). In this study, we identified a peptide derived from the low-complexity (LC) region of FUS, with serine-to-glutamic acid mutations (S2E), which significantly suppresses LC phase separation. GPU-based molecular dynamics simulations reveal that the interaction between S2E and LC is essential for their suppressive effect. Inspired by this finding, we proposed a strategy that employs multivalent interactions to design peptides capable of inhibiting phase separation. As a proof of concept, we engineered peptides that combine the LARKS domain from FUS-LC with an E-rich sequence from HSP90, yielding two potent peptides. These peptides effectively inhibit phase separation, as validated by both computer simulation and experimental data. Our findings provide a new avenue for the primary design of peptides aimed at controlling phase separation and protein aggregation, with potential applications in therapeutic development for LLPS-related diseases.