Investigation of Affinity at Binding Site Between Human Epidermal Growth Factor Receptor 2 (HER2) and Herceptin
Authors: Kondrashova Maria , Miller Bill 
Published: November 2023

Background

Human epidermal growth factor receptor 2 (HER2)‐positive breast cancer results from uncontrolled synthesis of HER2 protein due to amplification of the HER2 gene and has a poor prognosis for patients. Herceptin (trastuzumab) is a receptor‐blocking monoclonal antibody that prevents downstream signaling and marks cancer cells for destruction by the immune system. Many patients often develop resistance to Herceptin caused by mutations on HER2 as cancer progresses, which allows the tumor cells to continue replicating. The current study investigated the binding free energies between the HER2 receptor and Herceptin at the three known binding sites to determine if the amino acid sequence can be mutated to create a stronger interaction between the HER2 receptor and the antibody. This research could potentially increase the efficacy of Herceptin and improve survival rates of patients with HER2‐positive breast cancer.

Methods

The investigated protein‐antibody complex was obtained from the Protein Data Bank (PDB code: 1N8Z). Using the HER2 protein, the Herceptin molecule, and the HER2/Herceptin complex, three computational simulations were performed. These simulations were completed using the AMBER 14 Molecular Dynamics software package. After the simulations were performed, the binding sites of HER2 and Herceptin were analyzed at the atomic level. The Molecular‐Mechanics Generalized Born Surface Area (MM‐GBSA) method was utilized to determine the overall binding affinity between HER2 and Herceptin, as well as the per‐residue free energy decomposition values.

Results

The binding affinity of Herceptin to the HER2 receptor was calculated as −68.55 kcal/mol, suggesting a strongly favorable interaction between the two molecules. Additionally, amino acids located at the interface between the HER2 protein and Herceptin were closely evaluated to determine if any could be replaced to create a stronger affinity between HER2 proteins and Herceptin. Results from the current study suggest that of the three binding sites/loops, the residues in the third loop (residues 1027–1037) have significantly less favorable energies than the first two binding loops (first loop: residues 991–995 and second loop: residues 1004–1007). The proposed residues Ser50 (+0.116 kcal/mol) and Asn30 (−0.999 kcal/mol) on Herceptin will be mutated to amino acids that will favor stronger binding and stabilize the third binding loop. Along with the proposed mutations the computational simulations will be extended to further evaluate the behavior of Herceptin when bound to the HER2 receptor.

Conclusions

The binding free energies generated for every residue in the HER2/Herceptin complex allowed close examination of each residue's contribution to binding. The least favorable residue in the complex was Lys1027, the starting residue of the third binding loop. The third loop will be further evaluated to determine if any other residues can be mutated to strengthen the total binding affinity of the HER2/Herceptin complex. Future research will work towards replacing old residues within the third loop and possibly creating another binding loop to further stabilize the HER2/Herceptin complex.

Support or Funding Information

We would like to acknowledge funding received from the Office of Student Research at Truman State University. Additionally, we would like to acknowledge the space and resources provided by Truman State University and the Truman State University Chemistry Department.