Conformational editing and intracellular delivery of intrinsically disordered protein domain

Targeting the interaction between severe acute respiratory syndromecoronavirus 2 (SARS-CoV-2) receptor-binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2) is believed to be an effective strategy for drug design to inhibit the infection of SARS-CoV-2.Herein, several ultrashort peptidase inhibitors against the RBD-ACE2 interaction were obtained by a computer-aided approach based on the RBD-binding residues on the protease domain (PD) of ACE2.The designed peptides were tested on a model coronavirus GX_P2V, which has 92.2 and 86% amino acid identity to the SARS-CoV-2 spike protein and RBD, respectively.Molecular dynamics simulations and binding free energy analysis predicted a potential binding pocket on the RBD of the spike protein, and this was confirmed by the specifically designed peptides SI5alpha and SI5alpha-b.They have only seven residues, showing potent antiviral activity and low cytotoxicity.Enzyme-linked immunosorbent assay result also confirmed their inhibitory ability against the RBD-ACE2 interaction.The ultrashort peptides are promising precursor molecules for the drug development of SARS-CoV-2, and the novel binding pocket on the RBD may be helpful for the design of RBD inhibitors or antibodies against SARS-CoV-2.