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Updated: Mar 14, 2026
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
Published on: May 20, 2020
Affinity enhancement of nanobody binding to EGFR: in silico site-directed mutagenesis and molecular dynamics
Alireza Farasat1, Fatemeh Rahbarizadeh1, Ghader Hosseinzadeh2
1a Department of Medical Biotechnology, Faculty of Medical Sciences , Tarbiat Modares University , Tehran , Iran.
Abstract:
Epidermal growth factor receptor (EGFR), a transmembrane glycoprotein, is overexpressed in many cancers such as head-neck, breast, prostate, and skin cancers for this reason it is a good target in cancer therapy and diagnosis. In nanobody-based cancer diagnosis and treatment, nanobodies with high affinity toward receptor (e.g. EGFR) results in effective treatment or diagnosis of cancer. In this regard, the main aim of this study is to develop a method based on molecular dynamic (MD) simulations for designing of 7D12 based nanobody with high affinity compared with wild-type nanobody. By surveying electrostatic and desolvation interactions between different residues of 7D12 and EGFR, the critical residues of 7D12 that play the main role in the binding of 7D12 to EGFR were elucidated and based on these residues, five logical variants were designed. Following the 50 ns MD simulations, pull and umbrella sampling simulation were performed for 7D12 and all its variants in complex with EGFR. Binding free energy of 7D12 (and all its variants) with EGFR was obtained by weighted histogram analysis method. According to binding free energy results, GLY101 to GLU mutation showed the highest binding affinity but this variant is unstable after 50 ns MD simulations. ALA100 to GLU mutation shows suitable binding enhancement with acceptable structural stability. Suitable position and orientation of GLU in residue 100 of 7D12 against related amino acids of EGFR formed some extra hydrogen and electrostatic interactions which resulted in binding enhancement.
Insights
Researchers designed a high-affinity nanobody targeting the epidermal growth factor receptor (EGFR) for cancer therapy. Molecular dynamics simulations identified a key mutation (ALA100 to GLU) enhancing binding affinity and stability.
Area of Science:
- Biochemistry
- Molecular Biology
- Computational Chemistry
Background:
- Epidermal growth factor receptor (EGFR) is a transmembrane glycoprotein overexpressed in various cancers, making it a crucial target for cancer therapy and diagnosis.
- Nanobody-based approaches offer promising strategies for cancer treatment and diagnosis, with high-affinity nanobodies towards EGFR enhancing therapeutic efficacy.
Purpose of the Study:
- To develop a computational method using molecular dynamics (MD) simulations for designing a high-affinity nanobody (7D12) targeting EGFR.
- To identify critical residues in the 7D12 nanobody responsible for EGFR binding and engineer variants with enhanced affinity and stability.
Main Methods:
- Molecular dynamics (MD) simulations were employed to analyze electrostatic and desolvation interactions between 7D12 nanobody and EGFR.
- Five variants of the 7D12 nanobody were designed based on identified critical residues.
- Binding free energy calculations using pull and umbrella sampling simulations, followed by weighted histogram analysis method (WHAM), were performed on the nanobody-EGFR complexes.
Main Results:
- Analysis revealed critical residues in 7D12 essential for EGFR binding.
- A GLY101 to GLU mutation exhibited the highest binding affinity but lacked stability.
- An ALA100 to GLU mutation demonstrated significant binding enhancement with acceptable structural stability due to favorable hydrogen and electrostatic interactions.
Conclusions:
- The study successfully designed a 7D12 nanobody variant with improved binding affinity and stability for EGFR.
- The ALA100 to GLU mutation represents a promising candidate for developing advanced nanobody-based cancer diagnostics and therapeutics targeting EGFR.
