Immunoinformatics and MD-simulation data suggest that Omicron spike epitopes are more interacting to IgG via better MHC class-II recognition than Delta variant.

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Background Recently, in Nov 2021, in South Africa, the SARS CoV-2 variant Omicron was found to be highly infectious and transmissible but with the least fatality. It occupies the nasopharynx-oropharynx and easily spreads. The epidemiological data/reports suggest that several vaccines failed to neutralize Omicron. It has a large number of spike mutations and the RNA/protein vaccines were developed from its predecessors that may justify its escape in most neutralization reactions. It’s lower immuno-suppression/cytokine-storming/inflammatory-response effects need explorations. Objectives In the current study, we attempted to delineate the comparative interaction of different variants’ spikes with IgG and a few HLA-typing of MHC-II. Methods All SARS-CoV-2 spike-proteins/human-IgG/MHC-II were obtained from the NCBI/ PDB/GISAID database. Initial 3D-structures of the unavailable proteins were constructed by Homology-Modeling (Swissmodel-Expasy) and optimized (PROCHECK). Molecular-docking of spike-IgG/spike-MHC-II was performed (HADDOCK2.4/HawkDock) with active-residue screening (CPORT). Antigenicity of epitopes was determined (Vaxigen v2.0-server) and epitope-model prepared (PEP-FOLD3-server). The binding-affinity/biological-interfaces/visualize were performed (PRODIGY-PyMOL2). We also examined Molecular-Dynamic-Simulation ( myPresto verson-5) of MHC-II with different epitopes and antibody IgG with different variants. The MD-simulation was run with 9000-cycles after 300k-heating/1-atm pressure adjustment for the system-equilibration. Finally, 1000ps production was run. Results Surface-area with interactomes, H-bonding and polar/non-polar bonding were the highest in Omicron spike-IgG interaction. Unlike other variants, both the L and H chains of the IgG interact with the N-terminal and C-terminal RBD of the S1-portion and partially bind to S2. In other cases, binding was observed in either NTD or CTD with a lesser number of bonding-interactomes, especially in Delta spike-Ab interaction. In the case of MHC class-II, the highest binding affinity/surface was noticed by omicron and least by the Delta variant. Better binding to the IgG and MHC molecules explains its lesser ability to immune invasion.