Carbohydrates in the interaction of SARS Cov2 B.1.617.2 (Delta) with ACE2

Abstract

Abstract: 

Allergic patients, particularly those suffering from asthma, have focused attention due to the frequency with which they present respiratory symptoms that could make them highly vulnerable to Covid 19. It is also discussed whether their predisposition to trigger an IgE-mediated response could be protective against the entrance of the virus or it would only increase morbidity. Currently, variant B.1.617.2 (Delta strain)
affects our population, whose greater transmissibility might be due to mutations that reduce its affinity for ACE2, also giving it the ability to evade binding with neutralizing immunoglobulins (Ig). The affinity of  S protein has been studied considering only the primary, secondary and tertiary structures of ligand and receptor. On this occasion, we present an in silico exploration of the influence of some oligosaccharides common in biological structures on the affinity of S protein of the B.1.617.2 (Delta) variant compared to the original (GenBank MN908947, Wt).

The simulations of binding interactions between S protein´s receptor-binding domain (RBD) and ACE2 (RBD binding domain) were done with EADock, Autodock Vina, Chimera, widely accepted open source software. The structures of the proteins and oligosaccharides obtained by X-ray diffraction and electron microscopy were downloaded from RCSB-PDB and edited to reduce the volume of data according to the available hardware and software.

The affinities obtained (binding deltaG) were: for RBD-ACE2 -4.6: 0.0 kcal / mol and for oligosaccharide binding, galactose -6.1: -5.2; glucosyl galactosyl glucosaminyl galactosaminyl sialic -5.9: -4.8 ,; glucosyl galactosyl glucosaminyl galactosaminyl disialic -7.53: -5.5 kcal / mol  Wt : Delta variant respectively.

The results are preliminary but are consistent with recent literature that is based on structural studies, not on receptor-ligand binding analyses. The results indicate that RBD Wt has affinity for deglycosylated ACE2 while the Delta variant does not. The Delta variant would present a lower affinity for carbohydrates. In summary, the affinity (protein-protein) and avidity (RBD-carbohydrates) would be lower in the Delta variant, favoring its permanence in extracellular fluids and attenuating the aggressiveness of the onset of infection.