Discovery of specific inhibitors of Porphyromonas gingivalis gingipains from food-derived flavonoids by high-throughput virtual screening and molecular simulations

Abstract

This study represents a significant advancement in the search for natural compounds that can inhibit the activity of Gingipain K (KGP), a key virulence factor secreted by Porphyromonas gingivalis. At present, there are few studies on the inhibition of gingipains by natural products, and there is an urgent need to find more candidate compounds. By employing molecular docking technology, the researchers screened a large number of natural compounds to assess their binding ability to KGP proteins. As a result, 14 flavonoid compounds were identified as potential inhibitors of KGP. The findings from molecular docking analysis revealed a close relationship between the inhibitory effect of candidate compounds and their molecular structures. Further investigation on their inhibitory abilities against KGP proteins was in accordance with the molecular docking results. Among them, trilobatin showed the highest inhibitory rate on the proteolytic ability of KGP (54.86%), while hesperetin 7-O-glucoside showed the highest inhibitory rate on the hemolytic ability of KGP (46.47%). The MIC of phloretin is 12.5 μg/mL, followed by trilobatin, phlorizin, and hesperetin dihydrochalcone (50 μg/mL), and then naringenin 7-O-glucoside and naringenin (100 μg/mL). In further validation, replacing hemoglobin with heme in culture medium increases the MIC of some flavonoids to 2–4 times, indicating the loss of the open-ring structure on the C-ring will lead to a decrease in inhibitory ability. This is the first report of the role of these flavonoids in this field, which will help discover food ingredients to develop products that can help solve the problem of P. gingivalis.