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

Int J Mol Sci. 2022 May 17;23(10):5601. 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 (KD = 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.

Keywords: COVID-19; SARS-CoV-2; infectious disease; protein structure; spike protein; viral entry.

MeSH terms

  • Angiotensin-Converting Enzyme 2* / genetics
  • COVID-19*
  • Humans
  • Membrane Glycoproteins / metabolism
  • Pandemics
  • Peptidyl-Dipeptidase A / metabolism
  • SARS-CoV-2
  • Spike Glycoprotein, Coronavirus
  • Viral Envelope Proteins / chemistry


  • Membrane Glycoproteins
  • Spike Glycoprotein, Coronavirus
  • Viral Envelope Proteins
  • spike protein, SARS-CoV-2
  • Peptidyl-Dipeptidase A
  • Angiotensin-Converting Enzyme 2

Supplementary concepts

  • SARS-CoV-2 variants

Grant support

Research was supported by the project “DELETE_COVID” (DEveLopmEnT of a rapid biosEnsor against COVID19). FISR2020IP_00014. 2021-2022 and “RECOVER-COVID19” (RicErCa e sviluppO VERsus COVID19 in Campania), POR FESR CAMPANIA 2014-2020- Asse III Obiettivo Specifico 1.3 – 2020-2021. Authors also acknowledge CINECA Supercomputing (framework ISCRA@CINECA—project code HP10CSBSQC) for computational support.