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Zhao X, Ren J, Wang Z, Chen X. Analyzing noncovalent interactions between notoginseng saponins and lysozyme by deposition scanning intensity fading MALDI-TOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5058. [PMID: 38842112 DOI: 10.1002/jms.5058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/06/2024] [Accepted: 05/12/2024] [Indexed: 06/07/2024]
Abstract
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.
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Affiliation(s)
- Xintong Zhao
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Juan Ren
- Department of Pharmaceutical Science, Zunyi Medical University at Zhuhai Campus, Zhuhai, China
| | - Ze Wang
- Department of Pharmaceutical Science, Zunyi Medical University at Zhuhai Campus, Zhuhai, China
| | - Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
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Du Y, Zhao F, Xing J, Liu Z, Cui M. Stabilization of Labile Lysozyme-Ligand Interactions in Native Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:366-373. [PMID: 36735536 DOI: 10.1021/jasms.2c00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Flavonoids are polyphenolic secondary metabolites with extensive biological activities and pharmacological effects. Exploring the interactions of flavonoids with proteins may be helpful for understanding their biological processes. Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool to characterize the noncovalent protein-ligand (PL) complexes. However, some protein-flavonoid complexes are labile during electrospray ionization. Here, the labile lysozyme-flavonoid (rutin, icariin, and naringin) complexes were determined by direct ESI-MS without derivation. It has been found that low amounts of N-methylpyrrolidinone and dimethylformamide can protect labile lysozyme-flavonoid complexes away from dissociation during electrospray ionization process. The intact lysozyme-flavonoid complexes were specifically observed in mass spectra, and the measured binding affinities by ESI-MS were matched with the fluorescence data. The effects of additives on the analysis of lysozyme-flavonoid complexes were investigated by ESI-MS, combined with the molecular docking and fluorescence. This strategy was helpful to investigate the labile PL interactions by direct ESI-MS.
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Affiliation(s)
- Yang Du
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin130022, China
- University of Science and Technology of China, Hefei, Anhui230029, China
| | - Fengjiao Zhao
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin130022, China
- University of Science and Technology of China, Hefei, Anhui230029, China
| | - Junpeng Xing
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin130022, China
| | - Zhiqiang Liu
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin130022, China
| | - Meng Cui
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin130022, China
- University of Science and Technology of China, Hefei, Anhui230029, China
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Du Y, Du Y, Cui M, Liu Z. Characterization of the Noncovalent Interactions between Lysozyme and Panaxadiol Glycosides by Intensity-Fading – Matrix-Assisted Laser Desorption Ionization – Mass Spectrometry (IF-MALDI-MS). ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1867995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Yonggang Du
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Yang Du
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Meng Cui
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Zhiqiang Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- University of Science and Technology of China, Hefei, Anhui, China
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Du Y, Zhao F, Xing J, Cui M, Liu Z. Investigation of interactions between cytochrome c and ginsenosides by native mass spectrometry and molecular docking simulations. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8853. [PMID: 32511843 DOI: 10.1002/rcm.8853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/22/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Ginsenosides are considered to be the main functional components in ginseng and possess various important pharmacological activities. The study of the interactions between ginsenosides and proteins is indispensable for understanding the pharmacological activities of ginsenosides. In this work, the interactions of ginsenosides with cytochrome c (cyt c) were investigated by native mass spectrometry and molecular docking simulations. METHODS The interactions of four ginsenosides (Rb1 , Rb3 , Rf, Rg1 ) and cyt c in NH4 OAc solution were investigated by electrospray ionization linear ion trap mass spectrometry (ESI-LTQ-MS). Molecular docking simulations of cyt c complexes were carried out by AutoDock. RESULTS The native mass spectrometry results showed that the four ginsenosides were directly bound to cyt c, with stoichiometric ratios of 1:1 and 2:1 in NH4 OAc. The order of relative binding abilities of ginsenosides to cyt c obtained by ESI-MS was Rb1 > Rb3 > Rf > Rg1 , which was consistent with the docking results. Moreover, molecular docking simulations also indicated potential binding sites of cyt c and ginsenosides. Hydrogen-bond interaction played a very important role in cyt c binding with ginsenosides. CONCLUSIONS It has been demonstrated that native MS is a useful tool to investigate the interactions of ginsenosides with cyt c. Molecular docking is a good complement to ESI analysis, and can provide information on potential binding sites of cyt c-ginsenoside complexess. This strategy will be helpful to further understand the interactions of proteins and small molecules.
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Affiliation(s)
- Yang Du
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Fengjiao Zhao
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Junpeng Xing
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Meng Cui
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
- University of Science and Technology of China, Hefei, Anhui, 230029, China
| | - Zhiqiang Liu
- National Center for Mass Spectrometry in Changchun, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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Chen S, Gong X, Tan H, Liu Y, He L, Ouyang J. Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches. Talanta 2020; 211:120762. [PMID: 32070628 DOI: 10.1016/j.talanta.2020.120762] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 12/29/2022]
Abstract
Elucidating the recognition mechanisms of the noncovalent interactions between pharmaceutical molecules and proteins is important for understanding drug delivery in vivo, and for the further rapid screening of clinical drug candidates and biomarkers. In this work, a strategy based on cold spray ionization mass spectrometry (CSI-MS), combined with fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR), and molecular docking methods, was developed and applied to the study of the noncovalent interactions between phenolic acid and lysozyme (Lys). Based on the real characterization of noncovalent complex, the detailed binding parameters, as well as the protein conformational changes and specific binding sites could be obtained. CSI-MS and tandem mass spectrometry (MS/MS) technique were used to investigate the phenolic acid-Lys complexes and the structure-affinity relationship, and to assess their structural composition and gas phase stability. The binding affinity was obtained by direct and indirect MS methods. The fluorescence spectra showed that the intrinsic fluorescence quenching of Lys in solution was a static quenching mechanism caused by complex formation, which supported the MS results. The CD and FTIR spectra revealed that phenolic acid changed the secondary structure of Lys and increased the α-helix content, indicating an increase in the tryptophan (W) hydrophobicity near the protein binding site resulting in a conformational alteration of the protein. In addition, molecular docking studies were performed to investigate the binding sites and binding modes of phenolic acid on Lys. This strategy can more comprehensively and truly characterize the noncovalent interactions and can guide further research on the interactions of phenolic acid with other proteins.
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Affiliation(s)
- Su Chen
- National Institutes for Food and Drug Control, Beijing, 102629, China; College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Xin Gong
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Yang Liu
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Lan He
- National Institutes for Food and Drug Control, Beijing, 102629, China.
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.
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Ali MS, Al-Lohedan HA. Spectroscopic and Molecular Docking Investigation on the Noncovalent Interaction of Lysozyme with Saffron Constituent "Safranal". ACS OMEGA 2020; 5:9131-9141. [PMID: 32363265 PMCID: PMC7191604 DOI: 10.1021/acsomega.9b04291] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/26/2020] [Indexed: 05/05/2023]
Abstract
Owing to the various beneficial properties of the popular spice saffron, the interaction of safranal, a secondary metabolite of the former, with hen egg white lysozyme was investigated. The formation of a complex was evidenced by UV-visible spectroscopy. Fluorescence quenching experiments were also performed to understand the binding mechanism and to evaluate the forces involved in binding. The strong absorption of safranal in the range of excitation and emission wavelengths of lysozyme fluorescence required the correction of the inner filter effect for fluorescence spectra to obtain the apparent extent of binding. There was a considerable difference between the observed spectra and corrected spectra, and a similar observation was found in the case of synchronous fluorescence spectra. From the analysis of quenching data, it was found that the mechanism involved in quenching was static with 1:1 binding between them. The interaction was found to be driven, mainly, by hydrophobic forces and hydrogen bonding. Safranal had negligible impact on the secondary structure of lysozyme. The interaction was also studied by molecular docking, and the results were in good agreement with the results obtained experimentally. The binding site of safranal was in the big hydrophobic cavity of lysozyme. The amino acids involved in the interaction were Asp52, Ile58, Gln57, Asn59, Trp62, Trp63, Trp108, Ile98, Asp101, and Ala107.
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Zhou Y, Chen S, Qiao J, Cui Y, Yuan C, He L, Ouyang J. Study of the noncovalent interactions of ginsenosides and amyloid-β-peptide by CSI-MS and molecular docking. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4463. [PMID: 31671229 DOI: 10.1002/jms.4463] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/07/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Noncovalent interactions between drugs and proteins play significant roles for drug metabolisms and drug discoveries. Mass spectrometry has been a commonly used method for studying noncovalent interactions. However, the harsh ionization process in electrospray ionization mass spectrometry (ESI-MS) is not conducive to the preservation of noncovalent and unstable biomolecular complexes compared with the cold spray ionization mass spectrometry (CSI-MS). A cold spray ionization providing a stable solvation-ionization at low temperature is milder than ESI, which was more suitable for studying noncovalent drug-protein complexes with exact stoichiometries. In this paper, we apply CSI-MS to explore the interactions of ginsenosides toward amyloid-β-peptide (Aβ) and clarify the therapeutic effect of ginsenosides on Alzheimer's disease (AD) at the molecular level for the first time. The interactions of ginsenosides with Aβ were performed by CSI-MS and ESI-MS, respectively. The ginsenosides Rg1 bounded to Aβ at the stoichiometries of 1:1 to 5:1 could be characterized by CSI-MS, while dehydration products are more readily available by ESI-MS. The binding force depends on the number of glycosyls and the type of ginsenosides. The relative binding affinities were sorted in order as follows: Rg1 ≈ Re > Rd ≈ Rg2 > Rh2, protopanaxatriol by competition experiments, which were supported by molecular docking experiment. CSI-MS is expected to be a more appropriate approach to determine the weak but specific interactions of proteins with other natural products especially polyhydroxy compounds.
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Affiliation(s)
- Yanan Zhou
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Su Chen
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Jinping Qiao
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Yanyun Cui
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
- School of Science, Beijing Technology and Business University, Beijing, 100048, China
| | - Chang Yuan
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Lan He
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
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Tang J, Fu Q, Cui M, Liu Z, Liu S. Investigation on the labile interactions of proteins and ligands using electrospray ionization mass spectrometry combined with a mathematical method. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:578-582. [PMID: 28239966 DOI: 10.1002/jms.3785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/21/2016] [Accepted: 05/02/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Jun Tang
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Qiang Fu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Meng Cui
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
| | - Zhiqiang Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
| | - Shuying Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, 130022, China
- Changchun University of Chinese Medicine, Changchun, 130117, China
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