Targeting the SARS-CoV-2-spike protein: from antibodies to miniproteins and peptides

Abstract

Coronavirus disease-19, caused by the novel β-coronavirus SARS-CoV-2, has created a global pandemic unseen in a century. Rapid worldwide efforts have enabled the characterization of the virus and its pathogenic mechanism. An early key finding is that SARS-CoV-2 uses spike proteins, the virus' most exposed structures, to bind to human ACE2 receptors and initiate cell invasion. Competitive targeting of the spike protein is a promising strategy to neutralize virus infectivity. This review article summarizes the discovery, binding modes and eventual applications of several classes of (bio)molecules targeting the spike protein: antibodies, nanobodies, soluble ACE2 variants, miniproteins, peptides and small molecules.

Fig. 1. SARS-CoV-2 initiates cell entry upon spike protein binding to human ACE2 receptors: targeting the spike protein is a powerful strategy to neutralize virus infection. A) Schematic representation of a SARS-CoV-2 particle and several (bio) molecules binding to the spike protein. B) Simplified SARS-CoV-2 cell invasion mechanism scheme: the virus engages with human cells via SARS-CoV-2-spike protein binding to human ACE2 followed by proteolytic cleavage of the spike protein (by TMPRSS2) and fusion. C) Lateral representation of the trimeric SARS-CoV-2-spike protein. Human ACE2 (blue) is bound by one RBD (red) in ‘up’ conformation, the other two RBDs (red) are in ‘down’ conformation. The image was obtained by aligning PDB structures 6m0j and 6vsb with Pymol. D) Top view of the SARS-CoV-2-spike trimer (6vsb).

Fig. 2. Antibodies and nanobodies can bind to the SARS-CoV-2-spike protein and neutralize virus infection. A) Top view of the spike trimer (surface shown in raspberry) with an antibody (from COVID-19 patient serum) Fab fragment (blue cartoons) bound to the RBD (red surface). All three RBDs are in ‘down’ conformation. PDB 6xey. B) Antibody Fab fragments (light blue cartoons) binding to the SARS-CoV-2-spike NTD (raspberry surface); PDB 7c21. C) SARS-CoV-2-spike protein with all three RBDs in ‘up’ conformation. One antibody Fab fragment (green cartoons) binds to two RBDs (red surface). PDB 7jw0 D) nanobodies H11-H4 (pink cartoon) and VHH-72 (gold cartoon) bound to SARS-CoV-2-spike RBD (red surface). Image obtained by combining PDB structures 6zh9 and 6waq.

Fig. 3. ACE2 derived and de novo designed miniproteins and peptides binding to the SARS-CoV-2-spike protein. A) Crystal structure 6m0j of ACE2 (blue) bound to SARS-CoV-2-spike-RBD (red). The ACE2 N-terminal helix-1 contains most of the residues interacting with the RBD and has been used as starting point for several design strategies for SARS-CoV-2 inhibitors. B) Cryo-EM structure (7jzm) of a computationally designed miniprotein (yellow cartoon) neutralizing SARS-CoV-2 in picomolar concentrations. C) Structural model (5zuv) of the fusion inhibitor EK1 (green cartoon) bound to the heptad repeat domain of the SARS-CoV-2 (grey surface).

Fig. 4. Short peptides with nanomolar affinity for the SARS-CoV-2-spike-RBD were identified by affinity selection – mass spectrometry. A) AS – MS scheme and sequences of peptide hits binding to SARS-CoV-2-spike-RBD. B) Structure of peptide hit 1 with important residue features evidence in yellow.

Sebastian Pomplun