Study on the interactions between ginsenosides and lysozyme under acidic condition by ESI-MS and molecular docking

Analyzing noncovalent interactions between notoginseng saponins and lysozyme by deposition scanning intensity fading MALDI-TOF mass spectrometry

Analysis of noncovalent interactions between natural products and proteins is important for rapid screening of active ingredients and understanding their pharmacological activities. In this work, the intensity fading MALDI-TOF mass spectrometry (IF-MALDI-MS) method with improved reproducibility was implemented to investigate the binding interactions between saponins from Panax notoginseng and lysozyme. The benchmark IF-MALDI-MS experiment was established using N,N',N″-triacetylchitotriose-lysozyme as a model system. The reproducibility of ion intensities in IF-MALDI-MS was improved by scanning the whole sample deposition with a focused laser beam. The relative standard deviation (RSD) of deposition scanning IF-MALDI-MS is 5.7%. Similar decay trends of the relative intensities of notoginseng saponins against increasing amounts of lysozyme were observed for all six notoginseng saponins. The half-maximal fading concentration (FC50) was calculated to quantitatively characterize the binding affinity of each ligand based on the decay curve. According to the FC50 values obtained, the binding affinities of the six notoginseng saponins were evaluated in the following order: notoginsenoside S > notoginsenoside Fc > ginsenoside Rb1 > ginsenoside Rd > notoginsenoside Ft1 > ginsenoside Rg1. The binding order was in accordance with molecular docking studies, which showed hydrogen bonding might play a key role in stabilizing the binding interaction. Our results demonstrated that deposition scanning IF-MALDI-MS can provide valuable information on the noncovalent interactions between ligands and proteins.

Deciphering the complexes of zinc ions and hen egg white lysozyme: Instrumental analysis, molecular docking, and antimicrobial assessment

In the research presented in this manuscript, an intricate study has been carried out on the interaction of zinc ions with the hen egg white lysozyme (HEWL) protein. Utilizing a spectroscopic technique, the alterations that arise due to the binding of Zn2+ to the HEWL were scrutinized, underscoring the paramount significance of deprotonated carboxyl and thiol groups in the process of binding. The binding phenomena were substantiated using capillary electrophoresis integrated with inductively coupled plasma mass spectrometry (CE-ICP-MS). Further spectrometric assessments (MALDI-TOF MS and FT-ICR-MS) shed light on the direct interaction of zinc ions with the functional groups of the protein. Importantly, high-resolution FT-ICR-MS techniques elucidated the capability of a single protein molecule to bind to multiple zinc ions. The empirically derived spectroscopic data received additional confirmation via a molecular docking study of the Zn2+ binding process, which highlighted a substantial affinity between the predicted 3D model of zinc-lysozyme complexes. Predominantly, the interaction between the bound entities was observed at the cysteine residues. Lastly, the conducted antimicrobial tests revealed that the zinc-lysozyme complexes manifest an inhibitory effect against bacterial (E. coli and S. aureus) and yeast (C. albicans) strains.

Molecular docking analysis of two bioactive molecules KLUF10 and KLUF13 isolated from the marine bacteria Micrococcus sp. OUS9 with TNF alpha

Tumor necrosis factor-alpha (TNF-α) is known to be linked with tumor. Therefore, it is of interest to document the Molecular docking analysis of two bioactive molecules KLUF10 and KLUF13 isolated from the marine bacteria Micrococcus sp. OUS9 with TNF alpha. We report the molecular interactions of KLUF10 and KLUF13 with TNF alpha.

Lysozyme Improves the Inhibitory Effects of Panax notoginseng Saponins on Phenotype Transformation of Vascular Smooth Muscle Cells by Binding to Ginsenoside Re

Panax notoginseng saponins (PNS) have been used to treat cardiovascular diseases for hundreds of years in China. Lysozyme can bind to exogenous compounds and promote their activity. Nevertheless, knowledge of whether there is a synergistic role between lysozyme and PNS is far from sufficient. In this study, we show that the mixture of PNS and lysozyme synergistically inhibited platelet derived growth factor BB (PDGF-BB)-induced vascular smooth muscle cell (VSMC) viability, and in the five main components of PNS, GS-Re, but not GS-Rb1, NG-R1, GS-Rg1, or GS-Rd, reduced VSMC viability by combined application with lysozyme. Next, the supramolecular complexes formed by GS-Re and lysozyme were detected by mass spectrometry, and the binding ability increased with the concentration ratio of GS-Re to lysozyme from 4:1 to 12:1. In the supramolecular complexes, the relative contents of α-helix of lysozyme were increased, which was beneficial for stabilizing the structure of lysozyme. The 12:1 mixture of GS-Re and lysozyme (12.8 μmol/L GS-Re+1.067 μmol/L lysozyme) repressed PDGF-BB-induced VSMC viability, proliferation, and migration, which were associated with the upregulated differentiated markers and downregulated dedifferentiated markers. Finally, in CaCl₂-induced rodent abdominal aortic aneurysm (AAA) models, we found that the 12:1 mixture of GS-Re and lysozyme slowed down AAA progression and reversed phenotype transformation of VSMCs. Thus, Gs-Re combined with a small amount of lysozyme may provide a novel therapeutic strategy for vascular remodeling-associated cardiovascular diseases.

In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (Panax vietnamesis)

Tumor necrosis factor-alpha (TNF-α) is a cytokine that plays an important role in inflammatory process and tumor development. Recent studies demonstrate that triterpene saponins from Vietnamese ginseng are efficient inhibitors of TNF-α. But the interactions between TNF-α and the saponins are still unclear. In this study, molecular docking and molecular dynamics simulations of TNF-α with three different triterpene saponins (majonoside R2, vina-ginsenoside R1 and vina-ginsenoside R2) were performed to evaluate their binding ability. Our results showed that the triterpene saponins have a good binding affinity with protein TNF-α. The saponins were docked to the pore at the top of the "bell" or "cone" shaped TNF-α trimer and the complexes were structurally stable during 100 ns molecular dynamics simulation. The predicted binding sites would help to subsequently investigate the inhibitory mechanism of triterpene saponins.

Study of the non-covalent interactions of ginsenosides and lysozyme using electrospray ionization mass spectrometry

RATIONALE

Ginsenosides are an important class of natural products extracted from ginseng that possess various important biological activities. Studies of interactions of ginsenosides with proteins are essential for comprehensive understanding of the biological activities of ginsenosides. In this study, the interactions of ginsenosides with lysozyme were investigated by electrospray ionization mass spectrometry (ESI-MS).

METHODS

Both protopanaxadiol-type and protopanaxatriol-type ginsenosides were chosen to explore the interactions of ginsenosides towards lysozyme near the physiological conditions by direct ESI-MS, respectively. Comparative experiments were conducted to confirm the interactions were specific. In addition, the dissociation constants of ginsenoside-lysozyme complexes were determined by a ESI-MS titration strategy.

RESULTS

The results showed ginsenosides bound to lysozyme at the stoichiometries of 1:1 and 2:1. The association constants of ginsenosides to lysozyme were in the order of Re>Rd>Rf>Rg2 >Rg3 . According to their structures, the binding affinities associated with the type of aglycone and the type and the number of sugar moieties linked on the aglycone.

CONCLUSIONS

It has been demonstrated that ESI-MS is a powerful tool to probe the non-covalent interactions between lysozyme and ginsenosides. These results provide insights into the interaction of ginsenosides with lysozyme at the molecular level. The developed strategy could be applied to determine the interactions of proteins with other natural products.