Structure-Based Development of SARS-CoV-2 Spike Interactors

• Published in: International journal of molecular sciences Vol. 23; no. 10; p. 5601
• Main Authors: Squeglia, Flavia, Romano, Maria, Esposito, Luciana, Barra, Giovanni, Campiglia, Pietro, Sala, Marina, Scala, Maria Carmina, Ruggiero, Alessia, Berisio, Rita
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 17.05.2022; MDPI
• Subjects: ACE2; Affinity; Angiotensin; Angiotensin-converting enzyme 2; Antibodies; Binding; Computer applications; Coronaviridae; Coronaviruses; COVID-19; Domains; Dynamic stability; E coli; Etiology; Hydrogen bonds; infectious disease; Medical research; Melt temperature; Molecular dynamics; Mutation; Peptidyl-dipeptidase A; Plugs; protein structure; Proteins; Regulatory approval; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Simulation; Spike glycoprotein; Spike protein; Thermal stability; Vaccines; viral entry; COVID-19; protein structure; viral entry; SARS-CoV-2; infectious disease; spike protein
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms23105601

Coronaviruses, including SARS-CoV-2 (the etiological agent of the current COVID-19 pandemic), rely on the surface spike glycoprotein to access the host cells, mainly through the interaction of their receptor-binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with the binding of the SARS-CoV-2 spike protein to ACE2 have great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 spike protein and the host ACE2 receptor, we engineered a set of soluble and stable spike interactors, here denoted as S-plugs. Starting from the prototype S-plug, we adopted a computational approach by combining stability prediction, associated to single-point mutations, with molecular dynamics to enhance both S-plug thermostability and binding affinity to the spike protein. The best developed molecule, S-plug3, possesses a highly stable α-helical con-formation (with melting temperature Tm of 54 °C) and can interact with the spike RBD and S1 domains with similar low nanomolar affinities. Importantly, S-plug3 exposes the spike RBD to almost the same interface as the human ACE2 receptor, aimed at the recognition of all ACE2-accessing coronaviruses. Consistently, S-plug3 preserves a low nanomolar dissociation constant with the delta B.1.617.2 variant of SARS-CoV-2 spike protein (K = 29.2 ± 0.6 nM). Taken together, we provide valid starting data for the development of therapeutical and diagnostic tools against coronaviruses accessing through ACE2.