HER2
August 2024
The human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor family of tyrosine kinase receptors and plays a crucial role in cell growth. Dysregulation of HER2 is linked to various types of cancer, especially breast cancer.
The HER2 extracellular domain can form heterodimers with other receptors of the family, leading to increased cell proliferation. This dimerization is a key target for cancer therapies, which use monoclonal antibodies and antibody-drug conjugates to block it.
Trastuzumab, approved by the FDA in the late 1990s, was the first HER2 antibody approved for breast cancer treatment. Since then, additional therapies have been developed, including pertuzumab, another HER2-directed antibody. The combination of these two antibodies has synergistic effects and is currently used as an effective immunotherapy for breast cancer.
Recently, a new high-resolution cryo-EM Sanofi study of the HER2 ternary complex with trastuzumab and pertuzumab (HTP) provided detailed insights into simultaneous antibody binding, offering new information specifically on the binding of trastuzumab.
The overall structure of the HTP complex shows that the antibody-binding fragment (Fab) from pertuzumab binds HER2 at domains I, II, and III, which pack together, while trastuzumab Fab binds the IV domain, which has an elongated shape (Image 1). Although a previous 3D structure of the HTP complex was available from the PDB, its low resolution (4.36 Å) limited the detailed visualization of the HER2-trastuzumab interface. The newly solved 3D structure exploited advanced cryo-EM methods and significantly improved the resolution to 3.17 Å.
Image 1. HTP overall complex (PDB: 8PWH). HER2 is colored by domains (blue: I; grey: II; orange: III; cyan: IV), the pertuzumab Fab is colored in green and dark red, and the trastuzumab Fab in purple and orange. The domains of HER2 are highlighted using the 3decision® Annotation Browser.
How does the 3decision Annotation Browser feature work? Check out this short video description.
In the HER2-pertuzumab Fab interface, the local resolution reached 2.5 Å almost throughout this region, offering detailed insights into the interactions. The interface closely resembles that of the crystal structure of the HER2-pertuzumab complex alone (Image 2). This indicates that the simultaneous binding of trastuzumab does not affect the conformation of HER2-pertuzumab interface.
Image 2. Comparison of the cryo-EM HTP complex (PDB: 8PWH; HER2 in brown, pertuzumab variable light chain VL in red, pertuzumab variable heavy chain in green VH) with the HER2-pertuzumab crystal structure (PDB: 1S78; white). The antibody-antigen interactions on the cryo-EM solved structure are shown (calculated with the 3decision® protein-protein interactions tool). Residue side chains are represented as lines. The picture is produced with the 3decision® software.
The map quality of the region comprising the HER2 IV domain and the trastuzumab Fab is lower than the pertuzumab-binding region (local resolution of 3.3 Å) likely due to the high flexibility of this domain.
However, the electron density map at the HER2-trastuzumab interface was sufficiently defined to analyze the antibody-antigen interactions. Previous structural studies identified three regions of contacts (HER2 residues 570–573, 557–561, 593–603) at this interface, all of which were confirmed in the new HTP cryo-EM structure.
Notably, the new structure also revealed an additional interaction point involving a long loop on the HER2 IV domain (HER2 residues 581–590) that was not observed in previous structures (Image 3). Molecular dynamics studies suggest that despite the flexibility of domain IV, this fourth epitope remains consistently associated with trastuzumab in all conformations.
Image 3. HER2-trastuzumab interface analysis. A) The new cryo-EM HTP complex focused on the HER/terstuzumab interface (PDB: 8PWH). HER2 IV domain in cyan, trastuzumab variable heavy chain in purple with CDR3 highlighted in green. The electron density map is shown as a white mesh with a contour level set to 11. The yellow arrow points to the map, highlighting the interaction between the residue R98 of trastuzumab and the IV domain loop residue D585. The antibody-antigen interactions are shown with the 3decision® protein-protein interactions tool.
B) A previous cryo-EM HTP complex structure focused on the HER/terstuzumab interface (PDB: 6OGE). HER2 IV domain in cyan, trastuzumab variable heavy chain in brown with CDR3 highlighted in green. The electron density map is a white mesh with a contour level set to 11. No electron density map is observed between the R98 and the IV loop residues (highlighted in white).
This new high-resolution HTP structure provides a more comprehensive and detailed understanding of this important ternary complex, revealing a previously overlooked epitope and offering new insights into the molecular interactions that could inform future therapeutic strategies.
Reference
Ruedas R, Vuillemot R, Tubiana T, Winter JM, Pieri L, Arteni AA, Samson C, Jonic S, Mathieu M, Bressanelli S. Structure and conformational variability of the HER2-trastuzumab-pertuzumab complex. J Struct Biol. 2024 Jun;216(2):108095. doi: 10.1016/j.jsb.2024.108095. Epub 2024 May 7. PMID: 38723875.