Estudo da estabilidade estrutural do scFv do anticorpo obinutuzumab e da sua interação com um peptídeo cíclico de CD20 via dinâmica molecular

Abstract

Obinutuzumab is a type II anti-CD20 antibody, which has been shown to be promising in the treatment of chronic lymphocytic leukemia and Non-Hodgkin lymphomas. Obinutuzumab was co-crystallized with a cyclic peptide (ligand) of CD20 in 2010 and an electron density was detected at the interface of interaction, which was interpreted as a chloride ion (PDB code: 3pp4). This work aimed to elucidate the effects of the chloride ion in the antibody-antigen interaction, through Molecular Dynamics (MD) simulations, using a scFv as antibody model. Three systems were simulated using MD: scFv (SCFV); scFv and ligand (SCFV-L); scFv, ligand and chloride ion (SCFV-L-CL). The SCFV system was simulated for 200 ns, whereas the systems containing the ligand were simulated for 300 ns. Structural analysis were conducted through RMSD calculations of the protein structures. After, the intermolecular interaction potential (IIP) was calculated using the gmx energy tool of the GROMACS package and softwares developed by the group. The RMSD analysis has shown distinct structural modifications in the presence or absence of the ion. From the IIP analysis, it was possible to observe that, in the absence of the chloride ion, there is interaction between the C-Terminal of the ligand and the scFv and this behaviour is not observed in the presence of the ion. The IIP of each residue revealed which CDR residues were attractive or repulsive towards the ligand, with the CDR H2 being the most affected by the ion presence. The hydrogen bond (HB) analysis enabled the observation of which and how many connections were established between the scFv and the ligand, in the presence or absence of the ion. Furthermore, a higher number of hydrogen bonds between the scFv and the ligand was observed in the presence of the ion (5.70) than in its absence (3.44). Regardless the presence of the ion, most hydrogen bonds occurred between the ligand backbone and the side chains of the scFv residues. In conclusion, the ion presence emphasized the interaction between the CDR H2 and the epitope and caused a higher number of hydrogen bonds between the scFv and the ligand, highlighting the possibility of the ion having a major role in the affinity and specificity of the Obinutuzumab-Ligand interaction.