In silico comparison of apigenin and related compounds with diverse pharmacological activities using AutoDock 4.2.6

Abstract

In recent years, molecular docking has been used to predict the binding affinity and interaction between flavonoids (ligands) and specific protein targets (receptors). However, existing studies have focused on a limited number of flavonoids with a small number of targeted proteins. In this study, on the other hand, we used the AutoDock 4.2.6 molecular docking software to compare the binding energy values and interactions of apigenin and 15 flavonoids with 24 different proteins known to be associated with oxidative stress, inflammation, carcinogenesis, and bacterial infections. This comparison will be important for the development of flavonoid-based drugs, allowing for the optimization of flavonoid drugs to better interact with their target proteins alone or in combination with conventional drugs. We used three-dimensional crystal structures of the receptors to identify the amino acids in the active site for docking purposes. Our goal was to identify potential inhibitors of these proteins and understand the structural configurations of flavonoids that affect their binding energy (binding affinity or inhibitory effects). We found that apigenin was a highly effective inhibitor for all tested proteins, with the highest binding energy of -8.21 kcal/mol with p38 mitogen-activated protein kinases and the lowest binding energy of -5.34 kcal/mol with cyclin-dependent kinase 4. In fact, apigenin and most of the tested flavonoids were better inhibitors for xanthine oxidase or DNA methyltransferase than known inhibitors. Our results also suggest that apigenin and selected flavonoids could be used to inhibit the oncogenic activity of KRAS mutations at codon 12 (i.e., G12C, G12D, and G12V) frequently found in solid tumors since they possess high binding energies with these mutated proteins. This finding offers an advantage over targeted therapy drugs that focus on specific KRAS mutations. Furthermore, most flavonoids have good safety profiles, so our resulting data are crucial for developing flavonoid-based drugs and present new insights into developing effective treatments that can attenuate the resistance and side effects of chemotherapy.