Dynamical rearrangement of human epidermal growth factor receptor 2 upon antibody binding: effects on the dimerization

Abstract

23Human epidermal growth factor 2 (HER2) is a ligand-free tyrosine kinase receptor of the HER 24 family that is overexpressed in some of the most aggressive tumours. Treatment of HER2+ breast 25 cancers with the humanized monoclonal anti-HER2 antibody (Trastuzumab) revealed highly 26 effective, encouraging the development of various HER2-specific antibodies, kinase inhibitors 27 and dimerization inhibitors for cancer therapy. Although it is known that HER2 dimerization 28 involves a specific region of its extracellular domain, the so-called "dimerization arm", the 29 mechanism of dimerization inhibition remains uncertain. However, uncovering how antibody 30 interactions lead to inhibition of HER2 dimerization is of key importance in understanding its role 31 in tumour progression and therapy. Herein, we employed several computational modelling 32 techniques for a molecular-level understanding of the interactions between HER and specific anti- 33HER2 antibodies, namely an antigen-binding (Fab) fragment (F0178) and a single chain variable 34 fragment from Trastuzumab (scFv). Specifically, we investigated the effects of antibody-HER2 35interactions on the key residues of "dimerization arm" from molecular dynamics (MD) 36 simulations of unbound HER (in a total of 1 µs), as well as scFv:HER2 and F0178:HER2 37 complexes (for a total of 2.5 µs). A deep surface analysis of HER receptor revealed that the 38 binding of specific anti-HER2 antibodies induced conformational changes both in the interfacial 39 residues, which was expected, and in the ECDII, in particular at the "dimerization arm", which is 40 critical in establishing protein-protein interface (PPI) interactions. Our results support and 41 advance the knowledge on the already described trastuzumab effect on blocking HER2 42 dimerization through synergistic inhibition and/or steric hindrance. Furthermore, our approach 43 offers a new strategy for fine-tuning target activity through allosteric ligands. 45 Keywords 46Breast cancer; dimerization inhibition; human epidermal growth factor 2 (HER2); molecular

Predicting stable binding modes from simulated dimers of the D76N mutant of β2-microglobulin

“…In doing so, we discard spurious structural variability due to loops, and unstructured N- and C- terminal regions. The interfacial areas of the dimers were calculated using the SAS values of both monomers in the presence and absence of the partner [37] . This procedure was also applied to each residue individually, with the final area being normalized (converted into a percentage) by the maximum SAS area of each residue type observed in all simulations.…”

Interfacial dynamics and growth modes ofβ2-microglobulin dimers

“…The interfacial area of the dimers was calculated using the difference between the SASA values of both monomers in the presence and absence of the partner. 44,45 This procedure was also applied to each residue individually, with the final area being normalized (converted into a percentage) by the maximum SAS area of each residue type observed in all simulations. Residues with interfacial area higher than 10%, were considered to be located at the interface.…”