Theoretical causes of the Brazilian P.1 and P.2 lineages of the SARS-CoV-2 virus through molecular dynamics

The novel {beta}-coronavirus has caused sad losses worldwide and the emergence of new variants has been causing great concern. Thus throughout this research the lineage B.1.1.28 of clade P.2 (K417N, N501Y, E484K) that emerged in Brazil was studied but also in a less depth the P.1 lineage, where through simulations of molecular dynamics in the NAMD 3 algorithm in the 8ns interval it was possible to understand the thermodynamic impacts in the interaction of the ACE2-RBD complex and the neutralizing antibody RBD-IgG. From the molecular dynamics, we noticed that the RMSF averages in the P.2 strain were more expressive in comparison to the ACE2-RBD wild-type and consequently some regions have undergone more expressive conformational changes although, in general, a greater stabilization of the complex was perceived. In addition, was an increase in the average number of Hydrogen bonds generating a lower RMSD and greater system compaction measured by Radius of Gyration (Rg). The change in native contacts was also important where the decrease from 0.992 {+/-} 0.002 to 0.988 {+/-} 0.002 reflects structural changes, which could reflect in greater transmissibility and difficulty in recognizing neutralizing antibodies. Through the MM-PBSA decomposition, we found that Van der Waals interactions predominated and were more favorable when the structure has mutations of the P.2 lineage. Therefore we believe that the greater stabilization of the ACE2-RBD complex may be a plausible explanation of why some mutations are converging in different lineages such as E484K and N501Y.