The reversible process where a homogenous fluid de-mixes into two distinctively separate liquid phases is referred to as LLPS (liquid-liquid phase separation). The resulting liquid is made up of one dilute phase and one condensed phase. An increasing number of studies have shown that the liquid-liquid phase separation is an important principle that underlies intracellular organization in biological systems, forming liquid condensates without a membrane envelope, otherwise known as MLOs (membraneless organelles). Such organelles include the P bodies, nucleolus, and stress granules. Moreover, the regulation of many other biological processes such as signal transduction, chromatin rearrangement, and RNA metabolism has been linked to the liquid-liquid phase separation [1].
A growing number of studies in recent years have focused on the mechanism of phase separation of a variety of biomolecules. Such studies have demonstrated that some proteins, such as the RNA helicase DEAD-Box 4 (DDX4), P granule protein LAF-1, transactive response DNA-binding protein (TDP-43), and the RNA-binding FUS protein, can undergo liquid-liquid phase separation both in vitro and in vivo. The resultant liquid condensates from the liquid-liquid phase separation process generally are deemed as a product of multivalent weak interactions between the numerous interacting motifs in IDRs (intrinsically disordered regions) or multiple folded domains. The LCRs (low complexity regions), which are generally covered by the intrinsically disordered regions, are suggested to play very important roles in driving liquid-liquid phase separation through Pi-Pi, hydrophobic, cation-Pi, and electrostatic interactions. These regions exhibit an overrepresentation of specific amino acid residues compared to the proteome proportion, such as the proline-arginine (PR)/glycine-arginine (GR) repeats, arginine-glycine-glycine (RGG) motifs, and prion-like domains [2].
The spike protein of the SARS-CoV-2 is an envelope glycoprotein that contributes mostly during the attachment process of the virus, its fusion, and host cell entry. It is also an important target for the development of vaccines, neutralizing antibodies, and inhibitors of viral entry. Its synthesis begins as a precursor protein which is cleaved into an amino-terminal S1 subunit composed of 700 amino acid residues and a carboxyl-terminal S2 subunit which is made up of 600 amino acid residues. Both residues respectively mediate the attachment and membrane fusion of the viral protein [3]. Our study is targeted at the design of a novel drug-like compound that can interfere with the molecular grammar that governs the liquid-liquid phase separation of the SARS-CoV-2 spike receptor-binding domain.