Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity

Highlights

• The G clade 23403A>G mutation on the spike glycoprotein (S protein) encodes a virulent strain of SARS-CoV-2.

• The D614G substitution causes the loss of a hydrogen bond between the loop (chain A) and the α-helix (chain B), resulting in a more flexible loop region.

• A more dynamic structure made the S protein RRAR binding site more accessible for furin cleavage.

• The severe acute respiratory syndome coronavirus 2 (SARS-CoV-2) strain being more accessible for cleavage enhances viral entry to the host cell.

Abstract

Objective

The coronavirus disease 2019 (COVID-19) pandemic has caused an exponential rise in death rates and hospitalizations. The aim of this study was to characterize the D614G substitution in the severe acute respiratory syndome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S protein), which may affect viral infectivity.

Methods

The effect of D614G substitution on the structure and thermodynamic stability of the S protein was analyzed with use of DynaMut and SCooP. HDOCK and PRODIGY were used to model furin protease binding to the S protein RRAR cleavage site and calculate binding affinities. Molecular dynamics simulations were used to predict the S protein apo structure, the S protein–furin complex structure, and the free binding energy of the complex.

Results

The D614G substitution in the G clade of SARS-CoV-2 strains introduced structural mobility and decreased the thermal stability of the S protein (ΔΔG = −0.086 kcal mol⁻¹). The substitution resulted in stronger binding affinity (K_d = 1.6 × 10⁻⁸) for furin, which may enhance S protein cleavage. The results were corroborated by molecular dynamics simulations demonstrating higher binding energy of furin and the S protein D614G mutant (−61.9 kcal mol⁻¹ compared with −56.78 kcal mol⁻¹ for wild-type S protein).

Conclusions

The D614G substitution in the G clade induced flexibility of the S protein, resulting in increased furin binding, which may enhance S protein cleavage and infiltration of host cells. Therefore, the SARS-CoV-2 D614G substitution may result in a more virulent strain.