Modeling and Molecular Dynamic Simulation of F(ab′)₂ Fragment of Nimotuzumab for Lung Cancer Diagnostics

Abstract

Lung cancer is one of the leading causes of cancer-related deaths in the world among both men and women. Several studies in the literature report that overexpression and mutation of the epidermal growth factor receptor (EGFR) are implicated in the pathogenesis of some lung cancers. Nimotuzumab is a humanized monoclonal antibody (mAb) that inhibits EGF binding because it binds to the extracellular domain of the EGFR. Nimotuzumab requires bivalent binding for stable attachment to cellular surface, which leads to nimotuzumab selectively binding to cells that express mAbs of moderate to high EGFR levels, and this could explain its low toxicity. This property has an advantage for development of nimotuzumab as a therapeutic and diagnostic agent. Monoclonal antibodies are large in size (150 kDa), thus penetrating slowly and residing in the blood for extended periods of time (from days to weeks); their use in imaging studies can result in low signal-to-background ratios and poor image quality. A reduction in the size of the immunoglobulin molecule has also been proposed as a means for increasing tumor penetration by mAbs. Nevertheless, it is known that the penetration of mAb into tumor cell is slow, due to its high molecular weight. Therefore, mAb is not very attractive to be used for imaging diagnostic purpose because of its kinetics and potential to elicit antibody response. The objective of this research was to study the homology modeling of a simpler functional molecule based on nimotuzumab, which consists of 2 antigen-binding fragments (Fab), namely, F(ab′)2, using MODELER. The crystal structure of Fab of nimotuzumab from protein data bank was used as a template to construct the model of F(ab′)2. Molecular dynamic simulation was performed to evaluate the stability of F(ab′)2 and conformational changes of F(ab′)2 in simulation. The result showed the dynamic behavior of antigen-binding site region of F(ab′)2 throughout simulation. This result is expected to be useful in the further development of F(ab′)2 fragment nimotuzumab as a lung cancer diagnostic.

Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics

“…The crystal structure of nimotuzumab (Protein Data Bank (PDB) entry 3GKW) also shows that its N-terminal is disordered, as the five N-terminal residues (Q1 to Q5) were not resolved due to smears in the electron density map. Other studies involving MD simulations of nimotuzumab did not report this effect, probably because of shorter simulation times, which did not allow for a more extensive observation of the disordered N-terminal. − …”

Nimotuzumab Increases the Recovery Rate of Severe and Critical COVID-19 Patients: Evaluation in the Real-World Scenario

“…Apart from other EGFR antibodies or small tyrosine kinase inhibitors, nimotuzumab exhibit an intermediate affinity against its target (10 −9 M) (28). Previously, several authors have demonstrated that nimotuzumab requires bivalent binding for stable attachment to the cellular surface, leading to selectively targeting cells with high EGFR expression (29,30). The biodistribution study in patients with epithelial tumors found that the percent of the injected dose of nimotuzumab per gram of tissue decreased 24 h post-treatment for normal organs, while the uptake in the tumor remained relatively constant (31).…”