Application of Support Vector Machine Classification Model to Identification of Vascular Endothelial Growth Factor Receptor Inhibitors

Abstract

Background: Nowadays, with the increasing prevalence of cancer mortality, finding the best cancer inhibitors is vital. Angiogenesis, which refers to the formation of new blood vessels from existing ones, undergoes abnormal changes in the physiological process of solid tumors. Vascular endothelial growth factor receptor (VEGFR) plays a crucial role in angiogenesis. Hence, one of the suggestions in cancer treatment has been inhibiting VEGFR signaling to prevent angiogenesis. The computational approach as an in vitro alternative method is crucial to reduce time and cost. This study aimed to use classification algorithm to separate potent inhibitors from inactive ones. Materials and Methods: In order to apply the machine learning model, biological compounds were extracted from the BindingDB database. Due to the large number of molecular features, the classification model was susceptible to overfitting. To address this issue, a correlation-based feature selection algorithm was proposed as a means of feature reduction. Subsequently, for the classification step, a support vector machine model that utilizes both linear and non-linear kernels was employed. Results: The implementation of the support vector machine model with the radial basis function kernel, along with the correlation-based feature selection method, resulted in a higher accuracy (81.8%, P value = 0.008) compared to other feature selection methods used in this study. Finally, two structures were introduced with the highest binding affinity to inhibit the second VEGFR. Conclusion: According to the results, the correlation-based feature selection method is more accurate than other methods.

Keywords

• algorithms
• computing methodologies
• quantitative structure–activity relationship
• vascular endothelial growth factor receptor 2