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. 2022 May 30;13:864798. doi: 10.3389/fphar.2022.864798

FIGURE 1.

FIGURE 1

SPIKENET Structure and Binding Affinity to the ACE2 Binding Domain of the SARS-CoV-2 Spike Glycoprotein. (A) Structure of SPIKENET, a 15 amino acid synthetic peptide targeted to the ACE2 binding domain of the SARS-CoV-2 spike glycoprotein. (B) Computational protein docking approach shows highly specific SPIKENET binding affinity to the ACE2 binding domain of the SARS-CoV-2 spike glycoprotein (S1). (C) Spectroscopic analysis shows highly specific SPIKENET (SPK) binding affinity to the ACE2 binding domain of the SARS-CoV-2 spike glycoprotein (S1). (D) High affinity binding of SPIKENET to the CEACAM1 binding domain of the MHV-1 spike glycoprotein: Computer modeling studies. (E) highly specific SPIKENET binding affinity to S1-RBD of the recently identified Omicron SARS-CoV-2 variant. Ab, absorbance; Wl, wavelength. High affinity binding of SPIKENET to the CEACAM1 binding domain of the MHV-1 spike glycoprotein. High affinity binding of SPIKENET to the CEACAM1 binding domain of the MHV-1 spike glycoprotein: Computer modeling studies. Ab, absorbance; Wl, wavelength. High affinity binding of SPIKENET to the CEACAM1 binding domain of the MHV-1 spike glycoprotein: Confirmatory computer molecular dynamic studies. The RMSD of both complexes with their respective native proteins are shown in (F,G). Comparing the RMSD of both NTD and NTD + SPK (F) after 50 ns dynamic simulation, the structures showed complete equilibration in the system and the SPK peptide was well stabilized with high affinity at the CCM binding location of NTD. However, the RMSD analysis of CCM and CCM+ SPK structures after the 50 ns dynamic simulation exhibited more flexibility at the NTD binding site of CCM than native CCM (G), suggesting the SPK peptide detachment and displacement over the CCM.