Molecular Dynamics and Experimental Validation of Natural Products from Chuanxiong Rhizoma as VEGFR2 Inhibitors for nAMD Therapy

Age-related macular degeneration (AMD) is a leading cause
of blindness
among the elderly worldwide. Neovascular AMD (nAMD) is a significant
subtype of AMD, responsible for the blindness of over 90% of patients
with AMD. The hallmark of nAMD is choroidal angiogenesis dysregulation,
a condition that can result in severe inflammation, leakage, and bleeding,
ultimately leading to a precipitous decline in visual acuity. Inhibition
of the vascular endothelial growth factor (VEGF) pathway has been
proven to be an effective therapeutic strategy for this disease. Intraocular
injection of anti-VEGF macromolecule drugs is a clinical therapy for
this disease, but it has shortcomings, such as severe side effects,
high cost, long treatment cycle, and complex administration methods.
Consequently, the identification of novel small-molecule drugs and
the development of innovative delivery mechanisms are of paramount
importance for the treatment of this condition. Chuanxiong Rhizoma
(CX), a type of traditional Chinese medicine (TCM), has been employed
in the treatment of vascular-related diseases. Contemporary pharmacological
research has demonstrated that CX contains a substantial quantity
of natural compounds that exhibit anti-VEGF activity. In this study,
we employed molecular simulation docking and molecular dynamics (MD)
to examine the anti-VEGFR2 effects of 10 natural compounds derived
from CX. Sorafenib was selected as the reference ligand, which is
a marketed VEGFR2 inhibitor for cancer treatment. As a DFG-out inhibitor,
sorafenib stabilizes the inactive conformation of the kinase by binding
to an allosteric site near the ATP-binding pocket. In our research,
natural products exhibiting a strong binding affinity were identified
using computer-simulated docking technology and detailed binding sites
were predicted. The findings of the research indicate that apigenin
exhibits the strongest affinity for the VEGFR2 receptor with the formation
of three hydrogen bonds. The molecular docking results indicate that
the CYS919 and ASP1046 amino acid residues of VEGFR2 are the primary
groups that form hydrogen bonds with the ligands. Furthermore, the
AutoQSAR module of Schrödinger Suite predicted apigenin to
have the highest predicted pIC50 value among the ten candidate
compounds, suggesting its potential for significant VEGFR2 inhibitory
activity. A subsequent MD simulation revealed that the binding of
apigenin to the protein was more stable, and the conformation was
stronger. According to the ADMET prediction results, apigenin is characterized
by low toxicity. To ascertain the capacity of apigenin to impede the
proliferation of choroidal angiogenesis, the choroid sprouting assay
was utilized as a methodological framework. An in vitro experiment
demonstrated that apigenin can significantly inhibit the growth of
choroidal vessels in a dose-dependent manner. The present study was
conducted with the objective of assessing the potential of natural
products in the treatment of nAMD. In addition, the study offered
valuable insights for the development of new natural agents.