mAb806 binding to epidermal growth factor receptor: a computational study

Abstract

The epidermal growth factor receptor (EGFR) is an important target in the treatment of cancer. A very potent antibody, mAb806, has been developed against overexpressed EGFR and was found to be particularly active in brain tumours. Structural studies reveal that it binds an epitope on the extracellular region of the EGFR. However, this epitope is cryptic / buried in crystal structures of the active (untethered) and inactive (tethered) EGFR and it is unclear as to how the antibody interacts with this region. To explore this interaction we combined molecular docking, steered molecular dynamics and equilibrium molecular dynamics simulations. Our computational models reveal that the antibody induces local unfolding around the epitope to form the antibody -EGFR complex. In addition, regions in the vicinity of the epitope also modulate the interaction, which are in accord with several other known antibody-antigen interactions, and offers new possibilities for the design of antibodies with increased potency and specificity for this receptor.

Role of N‐glycosylation in EGFR ectodomain ligand binding

“…Several antibodies have been used to target EGFR‐ed. These include mAbC225 (Cetuximab/Erbitux) which blocks ligand binding to EGFR‐ed, Matuzumab (EMD72000) which inhibits EGFR by blocking dimerization, and mAb806 which targets a cryptic pocket in the proximity of the dimerization arm . To get an insight into the role of glycosylation on EGFR–antibody interactions, the available crystal structures of EGFR‐ed bound to antibodies were analyzed in the context of simulations presented here.…”

“…To get an insight into the role of glycosylation on EGFR–antibody interactions, the available crystal structures of EGFR‐ed bound to antibodies were analyzed in the context of simulations presented here. While there is only one crystal structure of mAb806 bound to the epitope peptide, a previously generated model of this antibody bound to the EGFR‐ed was used here . These antibodies were divided into two groups; antibodies which target subdomain III of EGFR‐ed (C225, IMC‐11F8, EMD72000, GC1118, MEHD7954A) and the antibody which targets subdomain II of EGFR‐ed (mAb806).…”

“…Long MD simulations will be needed to examine this in greater detail but they are very expensive and hence not part of this study. The antibody mAb806 targets a cryptic pocket in subdomain II and is known to inhibit wild‐type EGFR in cancerous cells; it is hypothesized that this cryptic pocket may become exposed in an intermediate state . The crystal structure of mAb806 has been computationally docked to the untethered and tethered EGFR‐ed and analyzed with MD simulations, suggesting more favorable binding to the untethered state .…”

“…The antibody mAb806 targets a cryptic pocket in subdomain II and is known to inhibit wild‐type EGFR in cancerous cells; it is hypothesized that this cryptic pocket may become exposed in an intermediate state . The crystal structure of mAb806 has been computationally docked to the untethered and tethered EGFR‐ed and analyzed with MD simulations, suggesting more favorable binding to the untethered state . Interestingly, the interplay of glycans on mAb806 binding to EGFR‐ed seems to be different from other mentioned antibodies (Supporting Information, Fig.…”

“…S.37). However, this arises because there are induced conformational changes in the receptor upon antibody binding and is beyond the scope of the current simulations. Asn337 is a site that is known to be usually glycosylated; the attached sugars protrude from the EGFR‐ed surface (Fig.…”