Encoded Resistance: Structural Disruption and Signaling Crosstalk Undermine Sorafenib Binding in Mutant VEGFR2-Driven HCC

Tufael^1*, Most Farhana Akter², Md. Robiul Islam², Md Abu Bakar Siddique³, Nashitha Hassan¹, Abdullah Al Numan⁴, Asika Ayrin Naher⁴, Md Mahedi Hasan Shabuj⁴, Amena Khatun Manica⁵, Bulbul Shaikat⁶, Tahsin Bin Rabbani⁶

VEGFR2 mutations weaken sorafenib binding and start backup pathways, explaining resistance and supporting combined, multi-target treatments for liver cancer.

Abstract

Background: Hepatocellular carcinoma (HCC) is one of the most aggressive liver cancers, where anti-angiogenic therapies targeting VEGFR2-such as Sorafenib-are widely used. However, the emergence of drug resistance significantly limits long-term treatment success. Despite its clinical relevance, the molecular mechanisms behind this resistance remain inadequately understood. Structural alterations in VEGFR2 and activation of compensatory signaling pathways are suspected contributors.

Aim: This study aimed to evaluate how specific mutations in VEGFR2 affect Sorafenib binding affinity and to elucidate the molecular interactions and signaling disruptions that may underlie drug resistance in HCC.

Methods: The 3D structure of VEGFR2 (PDB ID: 3WZE) and the Sorafenib ligand (CID: 216239) were retrieved and prepared using BIOVIA Discovery Studio. Site-specific mutations (ASP1046→ALA, CYS919→ALA, GLU917→GLN) were introduced into the protein. Molecular docking was conducted using AutoDock Vina in PyRx, followed by interaction analysis using Discovery Studio Visualizer. Additionally, protein-protein interaction (PPI) analysis was performed using the STRING database, and KEGG pathway mapping was employed to explore signaling mechanisms associated with resistance.

Results: Docking results revealed reduced binding affinity between Sorafenib and the mutant VEGFR2 protein, accompanied by disruption of key hydrogen bonding and hydrophobic interactions. PPI and KEGG analyses identified upregulation of angiogenesis-related and alternative signaling pathways, suggesting possible bypass mechanisms that sustain tumor cell survival despite targeted therapy.

Conclusion: Mutations in VEGFR2 may compromise Sorafenib efficacy by altering its binding site and activating alternative molecular pathways. Understanding these resistance mechanisms may support the development of multi-targeted therapeutic strategies for more effective HCC treatment.

Keywords: Hepatocellular carcinoma (HCC), VEGFR2, Sorafenib, Molecular docking, Protein mutation.

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