Omicron SARS-CoV-2 Spike-1 Protein's Decreased Binding Affinity to α7nAChr: Implications for Autonomic Dysregulation of the Parasympathetic Nervous System and the Cholinergic Anti-Inflammatory Pathway—An In Silico Analysis

Omicron is the dominant strain of COVID-19 in the United States and worldwide. Although this variant is highly transmissible and may evade natural immunity, vaccines, and therapeutic antibodies, preclinical results in animal models and clinical data in humans suggest omicron causes a less severe form of infection. The molecular basis for the attenuation of virulence when compared to previous variants is currently not well understood. Using protein–ligand docking simulations to evaluate and compare the capacity of SARS-CoV-2 spike-1 proteins with the different COVID-19 variants to bind to the human α7nAChr (i.e., the core receptor under the control of the vagus nerve regulating the parasympathetic nervous system and the cholinergic anti-inflammatory pathway), we found that 10 out of the 14 mutated residues on the RBD of the B.1.1.529 (Omicron) spike, compared to between 0 and 2 in all previous variants, were present at the interaction interface of the α7nAChr. We also demonstrated, through protein–protein docking simulations, that these genetic alterations cause a dramatic decrease in the ability of the Omicron SARS-CoV-2 spike-1 protein to bind to the α7nAChr. These results suggest, for the first time, that the attenuated nature of Omicron infection in humans and animals compared to previous variants may be attributable to a particular set of genetic alterations, specifically affecting the binding site of the SARS-CoV-2 spike-1 protein to the α7nAChr. [ FROM AUTHOR]

In Silico Analysis of the Multi-Targeted Mode of Action of Ivermectin and Related Compounds

Some clinical studies have indicated activity of ivermectin, a macrocyclic lactone, against COVID-19, but a biological mechanism initially proposed for this anti-viral effect is not applicable at physiological concentrations. This in silico investigation explores potential modes of action of ivermectin and 14 related compounds, by which the infectivity and morbidity of the SARS-CoV-2 virus may be limited. Binding affinity computations were performed for these agents on several docking sites each for models of (1) the spike glycoprotein of the virus, (2) the CD147 receptor, which has been identified as a secondary attachment point for the virus, and (3) the alpha-7 nicotinic acetylcholine receptor (α7nAChr), an indicated point of viral penetration of neuronal tissue as well as an activation site for the cholinergic anti-inflammatory pathway controlled by the vagus nerve. Binding affinities were calculated for these multiple docking sites and binding modes of each compound. Our results indicate the high affinity of ivermectin, and even higher affinities for some of the other compounds evaluated, for all three of these molecular targets. These results suggest biological mechanisms by which ivermectin may limit the infectivity and morbidity of the SARS-CoV-2 virus and stimulate an α7nAChr-mediated anti-inflammatory pathway that could limit cytokine production by immune cells.