Estudios bioinformáticos sobre la proteína Spike del SARS CoV-2 para el desarrollo de posibles inhibidores

Abstract

With the worldwide alarm of COVID-19 multiple laboratories were dedicated to the search for a vaccine, for these studies it is imperative to work in a laboratory, however, there are ways in which you can contribute to the development of treatments against this disease, one way that is addressed in this project is an in silico analysis, which by molecular docking. Molecular docking was performed with the SARS-CoV-2 Spike protein as a receptor and 13,602 compounds from the CASPeR, ChemBridge and Pathogen Box libraries as ligands. The docking yielded binding affinity (BA) data, results that helped to choose the ligands whose BA was between -6.8 and -5.8 kcal/mol, however, since it was too large a number it was reduced to the 11 best ligands, these were analyzed graphically, so that the distance, number and type of non-covalent interactions were collected. In addition to the BA, the dissociation constant (Kd) was also calculated, which verified that the chosen ligands were able to form interactions that can be taken into account for the development of inhibitors, however, the Kd found are not comparable with the Kd of 14.7 nM that exists between the hACE2 receptor and spike of SARS-CoV-2. Graphical analysis of the 11 ligands revealed that they were able to form highly valuable interactions such as hydrogen bridges, aromatic, hydrophobic and halogen interactions. Interactions with the potential to block the interactions between hACE2 and Spike of SARS-CoV-2, leaving grounds for further studies.