Binding site analysis, 3D-QSAR studies, and molecular design of flavonoids derivatives as potent neuraminidase inhibitors

3D-QSAR studies on the structure-bitterness analysis of citrus flavonoids

Despite their important bioactivities, the unpleasant bitter taste of citrus derived flavonoids limits their applications in the food industry, and the structure-bitterness relationship of flavonoids is still far from clear. In this study, 26 flavonoids were characterized by their bitterness threshold and their common skeleton using sensory evaluation and molecular superposition, respectively. The quantitative conformational relationship of the structure-bitterness of flavonoids was explored using 3D-QSAR based on comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA). The results showed that increases of a hydrogen bond donor at A-5 or B-3', a bulky group at A-8, or an electron-withdrawing group at B-4' would enhance the bitterness of flavonoids. The bitterness of some flavonoids was predicted and evaluated, and the results were similar to the bitter intensity of the counterparts from the 3D-QSAR and contour plots, confirming the validation of 3D-QSAR. This study explains the theory of the structure-bitterness relationship of flavonoids, by showing potential information for understanding the bitterness in citrus flavonoids and developing a debittering process.

3D-QSAR and docking studies of flavonoids as potent Escherichia coli inhibitors

Flavonoids are potential antibacterial agents. However, key substituents and mechanism for their antibacterial activity have not been fully investigated. The quantitative structure-activity relationship (QSAR) and molecular docking of flavonoids relating to potent anti-Escherichia coli agents were investigated. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were developed by using the pIC50 values of flavonoids. The cross-validated coefficient (q(2)) values for CoMFA (0.743) and for CoMSIA (0.708) were achieved, illustrating high predictive capabilities. Selected descriptors for the CoMFA model were ClogP (logarithm of the octanol/water partition coefficient), steric and electrostatic fields, while, ClogP, electrostatic and hydrogen bond donor fields were used for the CoMSIA model. Molecular docking results confirmed that half of the tested flavonoids inhibited DNA gyrase B (GyrB) by interacting with adenosine-triphosphate (ATP) pocket in a same orientation. Polymethoxyl flavones, flavonoid glycosides, isoflavonoids changed their orientation, resulting in a decrease of inhibitory activity. Moreover, docking results showed that 3-hydroxyl, 5-hydroxyl, 7-hydroxyl and 4-carbonyl groups were found to be crucial active substituents of flavonoids by interacting with key residues of GyrB, which were in agreement with the QSAR study results. These results provide valuable information for structure requirements of flavonoids as antibacterial agents.

Inhibitory potency of flavonoid derivatives on influenza virus neuraminidase

The constant risk of emerging new influenza virus strains that are resistant to established inhibitors like oseltamivir leaves influenza neuraminidase (NA) a prominent target for drug design. The inhibitory activity of several flavonoid derivatives was experimentally tested in comparison to oseltamivir for the NA expressed by the seasonal influenza virus strains A/California/7/09 (A(H1N1)pdm09), A/Perth/16/09 (A(H3N2)), and B/Brisbane/60/08. IC50 values of polyphenols confirmed moderate inhibition in the μM range. Structurally, the amount and site of glycosylation of tested flavonoids have no significant influence on their inhibitory potency. In a pharmacophore-based docking approach the structure-activity relationship was evaluated. Molecular dynamics simulations revealed highly flexible parts of the enzyme and the contribution of salt bridges to the structural stability of NA. The findings of this study elucidate the impact of flavonoids on viral neuraminidase activity and the analysis of their modes of action provide valuable information about the mechanism of NA inhibition.

Substituent effects on the binding of natural product anthocyanidin inhibitors to influenza neuraminidase with mass spectrometry

The binding of three closely related anthocyanins within the 430-cavity of influenza neuraminidase is studied using a combination of mass spectrometry and molecular docking. Despite their similar structures, which differ only in the number and position of the hydroxyl substituents on the phenyl group attached to the chromenylium ring, subtle differences in their binding characteristics are revealed by mass spectrometry and molecular docking that are in accord with their inhibitory properties by neuraminidase inhibition assays. The cyanidin and delphinidin, with the greatest number of hydroxyl groups, bind more strongly and are better inhibitors than pelargonidin that contains a lone hydroxyl group at the 4' position. The study demonstrates, for the first time, the sensitivity of the mass spectrometry based approach for investigating the molecular basis and relative affinity of antiviral inhibitors, with subtly different structures, to their target protein. It has broader application for the screening of other protein interactions more generally with reasonable high-throughput.