Molecular modeling of antibodies for the treatment of TNFα‐related immunological diseases

Abstract

Therapeutic monoclonal antibodies (mAbs) have high efficacy in treating TNF α‐related immunological diseases. Other than neutralizing TNF α, these IgG1 antibodies exert Fc receptor‐mediated effector functions such as the complement‐dependent cytotoxicity (CDC) and antibody‐dependent cell cytotoxicity (ADCC). The crystallizable fragment (Fc) of these IgG1 contains a single glycosylation site at Asn 297/300 that is essential for the CDC and ADCC. Glycosylated antibodies lacking core fucosylation showed an improved ADCC. However, no structural data are available concerning the ligand‐binding interaction of these mAbs used in TNF α‐related diseases and the role of the fucosylation. We therefore used comparative modeling for generating complete 3D mAb models that include the antigen‐binding fragment (Fab) portions of infliximab, complexed with TNF α (4G3Y.pdb), the Fc region of the human IGHG1 fucosylated (3SGJ) and afucosylated (3SGK) complexed with the Fc receptor subtype Fcγ RIIIA, and the Fc region of a murine immunoglobulin (1IGT). After few thousand steps of energy minimization on the resulting 3D mAb models, minimized final models were used to quantify interactions occurring between Fcγ RIIIA and the fucosylated/afucosylated Fc fragments. While fucosylation does not affect Fab‐TNF α interactions, we found that in the absence of fucosylation the Fc–mAb domain and Fcγ RIIIA are closer and new strong interactions are established between G129 of the receptor and S301 of the Chimera 2 Fc mAb; new polar interactions are also established between the Chimera 2 Fc residues Y299, N300, and S301 and the Fcγ RIIIA residues K128, G129, R130, and R155. These data help to explain the reduced ADCC observed in the fucosylated mAbs suggesting the specific AA residues involved in binding interactions.

Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies

“…In conclusion, the presented analysis highlights the importance to use fold recognition tools along the approach to a drug design problem according to a rational protocol (similar to what previously reported (29,30,49)), like the ones presented. (77)), for preventing trimer formation and stabilization, or a small molecule/peptide with high affinity for the trimer, aiming to prevent conformational changes leading to the fusion of the viral envelope with host cell plasma membranes.…”

“…The sequences of the retrieved 48 crystallized structures (with reference to those crystallized structures indicated with "Certain" or "High" confidence level in pGenThreader output) were aligned by using ClustalW (31) implemented in the Jalview package (32). The 3D coordinates from the 48 crystallized structures were superimposed for comparative purposes by using PyMOL (33) according to our validated protocols (29,34).…”

“…The proposed complete IgG chimeric antibodies were obtained by superimposing the above cited m396 and the resulting engineered FAB portions, in complex with SARS-CoV-1/2 RBD, to the 3D atomic model of a crystallized IgG, available on the PDB (1igt.pdb, (48)) by using SPDBV and PyMOL, according to our validated protocols (29,30,49), that allow to model missing residues, solving clashes and breaks in the backbone.…”

“…After superimposition operations, allowing backbone connections, we renumbered all the atoms and the residues present in the resulting final pdb file, by using an in-house developed Perl script. The obtained final models were examined in VMD, PyMOL, and SPDBV according to our protocols (30,49). All the generated 3D all atom models were energetically minimized by using the Yasara Minimization server (35).…”

FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function

“…Several oxidative pathways depend on the ability of cells to oxidize NADH (reduced form of nicotinamide adenine dinucleotide cofactor), FADH 2 (reduced form of flavin adenine Cofactor-binding regions were highlighted for comparative purposes by selecting residues within 4 Å from the cofactor crystallized in the sampled structures. When necessary, cofactors were also inserted in some crystal structures by comparative analyses and superimposition by using PyMOL according to what previously reported [27,30,[34][35][36][37][38][39].…”