Exploring the "intensity fading" phenomenon in the study of noncovalent interactions by MALDI-TOF mass spectrometry

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.

Comprehensive investigation of in-vivo ingredients and action mechanism of iridoid extract from Gardeniae Fructus by liquid chromatography combined with mass spectrometry, microdialysis sampling and network pharmacology

Gardeniae Fructus is a widely used Traditional Chinese Medicines in treating various diseases. However, the absorbed components and metabolites of its main bioactive iridoid ingredients from iridoid extract of the fruits of Gardeniae Fructus in rat plasma need further study. In this study, a systematic method based on ultra-performance liquid chromatography-quadrupole-time-of-flight/mass spectrometry (UPLC-Q-TOF/MS) technique was developed to speculate the absorbed components and metabolites of iridoid extract in rat plasma after oral administration. A total of 19 compounds, including 9 prototype components and 10 metabolites were identified in plasma. 5 metabolites containing 4 new metabolites (M1, M2, M7, M10) were tentatively determined in rat plasma. Besides, Microdialysis-intensity-fading mass spectrometry (MD-IF-MS) method was originally employed to reveal the binding affinities with α-glucosidase for in-vivo prototype components and their metabolites. Finally, the absorbed constituents and the corresponding target proteins were used to generate compound-target network to find the related diseases and action pathways by a network pharmacology method. The results provide useful information for further study of pharmacology and in vivo mechanism of action of iridoid extract from the fruits of Gardeniae Fructus.

Systematic study on metabolism and activity evaluation of Radix Scutellaria extract in rat plasma using UHPLC with quadrupole time-of-flight mass spectrometry and microdialysis intensity-fading mass spectrometry

Radix Scutellaria is a widely used traditional Chinese medicine in the treatment of various diseases. However, the activities of the absorbed components and metabolites of its main flavones in rat plasma need further investigation. In this study, a systematic method based on ultra-high performance liquid chromatography with quadruple time-of-flight mass spectrometry was developed to speculate the absorbed components and metabolites of the main flavonoids in Radix Scutellaria extract in rat plasma sample after oral administration of the extract. Twelve compounds, including four prototype components and eight metabolites, were confirmed in drug-containing plasma. In these metabolites, five were originally detected in rat plasma. The possible metabolic pathways of these polyhydroxy flavones in vivo were described and clarified. Microdialysis with intensity-fading mass spectrometry was originally employed to investigate the binding affinities of the absorbed components and metabolites with α-glucosidase. The order of their binding affinities was P4 > P3 > P2 > P1≥M5 > M3 > M1. The research result is helpful to deepen the understanding of the absorbed components and metabolic pathways of main flavones from Radix Scutellaria, and provide a new approach to screen potential inhibitors from in vivo components originated from Chinese herb.

New comprehensive studies of a gold(III) Dithiocarbamate complex with proven anticancer properties: Aqueous dissolution with cyclodextrins, pharmacokinetics and upstream inhibition of the ubiquitin-proteasome pathway

The gold(III)-dithiocarbamate complex AuL12 (dibromo [ethyl-N-(dithiocarboxy-kS,kS')-N-methylglycinate] gold(III)), is endowed with promising in vitro/in vivo antitumor activity and toxicological profile. Here, we report our recent strategies to improve its water solubility and stability under physiological conditions along with our efforts for unravelling its tangled mechanism of action. We used three types of α-cyclodextrins (CDs), namely β-CD, Me-β-CD and HP-β-CD to prepare aqueous solutions of AuL12. The ability of these natural oligosaccharide carriers to enhance water solubility of hydrophobic compounds, allowed drug stability of AuL12 to be investigated. Moreover, pharmacokinetic experiments were first carried out for a gold(III) coordination compound, after i.v. injection of the nanoformulation AuL12/HP-β-CD to female mice. The gold content in the blood samples was detected at scheduled times by AAS (atomic absorption spectrometry) analysis, highlighting a fast biodistribution with a t_β1/2 of few minutes and a slow escretion (t_α1/2 of 14.3 h). The in vitro cytotoxic activity of AuL12 was compared with the AuL12/HP-β-CD mixture against a panel of three human tumor cell lines (i.e., HeLa, KB and MCF7). Concerning the mechanism of action, we previously reported the proteasome-inhibitory activity of some our gold(III)-based compounds. In this work, we moved from the proteasome target to upstream of the important ubiquitin-proteasome pathway, testing the effects of AuL12 on the polyubiquitination reactions involving the Ub-activating (E1) and -conjugating (E2) enzymes.

Indirect study of non-covalent protein complexes by MALDI mass spectrometry: Origins, advantages, and applications of the "intensity-fading" approach

This review article describes the origins, advantages, and application of an indirect approach with which to study protein and other macromolecular complexes and identify the nature and site of interaction interfaces by means of conventional matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). First reported in 1999, it involves the detection of ion depletion or the absence of ions associated with a binding partner or domain in the MALDI mass spectrum of a mixture of interacting components compared to that for an untreated control. Later referred to as intensity-fading in some applications, the method offers numerous advantages over the direct detection of protein and other macromolecule complexes by MALDI-MS and even electrospray ionization (ESI) MS. The origins of this indirect method, its development for use with gel-separated components, validation using companion biochemical assays, and application to a range of protein-antibody and protein-drug complexes are reviewed together with software specifically developed to aid with data interpretation. The sensitivity of the approach for revealing how subtle differences in the structure of the binding partners can be detected by MALDI-MS is also demonstrated. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:559-573, 2016.

A Model Sea Urchin Spicule Matrix Protein Self-Associates To Form Mineral-Modifying Protein Hydrogels

In the purple sea urchin Strongylocentrotus purpuratus, the formation and mineralization of fracture-resistant skeletal elements such as the embryonic spicule require the combinatorial participation of numerous spicule matrix proteins such as the SpSM30A-F isoforms. However, because of limited abundance, it has been difficult to pursue extensive biochemical studies of the SpSM30 proteins and deduce their role in spicule formation and mineralization. To circumvent these problems, we expressed a model recombinant spicule matrix protein, rSpSM30B/C, which possesses the key sequence attributes of isoforms "B" and "C". Our findings indicate that rSpSM30B/C is expressed in insect cells as a single polypeptide containing variations in glycosylation that create microheterogeneity in rSpSM30B/C molecular masses. These post-translational modifications incorporate O- and N-glycans and anionic mono- and bisialylated and mono- and bisulfated monosaccharides on the protein molecules and enhance its aggregation propensity. Bioinformatics and biophysical experiments confirm that rSpSM30B/C is an intrinsically disordered, aggregation-prone protein that forms porous protein hydrogels that control the in vitro mineralization process in three ways: (1) increase the time interval for prenucleation cluster formation and transiently stabilize an ACC polymorph, (2) promote and organize single-crystal calcite nanoparticles, and (3) promote faceted growth and create surface texturing of calcite crystals. These features are also common to mollusk shell nacre proteins, and we conclude that rSpSM30B/C is a spiculogenesis protein that exhibits traits found in other calcium carbonate mineral modification proteins.

Enzyme-coupled nanoparticles-assisted laser desorption ionization mass spectrometry for searching for low-mass inhibitors of enzymes in complex mixtures

In this report, enzyme-coupled magnetic nanoparticles (EMPs) were shown to be an effective affinity-based tool for finding specific interactions between enzymatic targets and the low-mass molecules in complex mixtures using classic MALDI-TOF apparatus. EMPs used in this work act as nonorganic matrix enabling ionization of small molecules without any interference in the low-mass range (enzyme-coupled nanoparticles-assisted laser desorption ionization MS, ENALDI MS) and simultaneously carry the superficial specific binding sites to capture inhibitors present in a studied mixture. We evaluated ENALDI approach in two complementary variations: 'ion fading' (IF-ENALDI), based on superficial adsorption of inhibitors and 'ion hunting' (IH-ENALDI), based on selective pre-concentration of inhibitors. IF-ENALDI was applied for two sets of enzyme-inhibitor pairs: tyrosinase-glabridin and trypsin-leupeptin and for the real plant sample: Sparrmannia discolor leaf and stem methanol extract. The efficacy of IH-ENALDI was shown for the pair of trypsin-leupeptin. Both ENALDI approaches pose an alternative for bioassay-guided fractionation, the common method for finding inhibitors in the complex mixtures.

Screening calmodulin-binding ligands using intensity-fading matrix-assisted laser desorption/ionization mass spectrometry

RATIONALE

Calmodulin (CaM) plays an important role in the regulation of metabolism, cytoskeleton and cell proliferation. CaM antagonists are a class of drugs that can bind to CaM and modulate the interactions between CaM and their target biological processes. Screening new calmodulin antagonists and developing novel methods for detecting calmodulin ligands are important for developing novel anti-cancer drugs that bind specifically to CaM.

METHODS

An intensity-fading matrix-assisted laser desorption/ionization mass spectrometry (IF-MALDI-MS) method for screening calmodulin ligands was established, with the non-binding drug propranolol as the internal control. The experimental sample was prepared by mixing the positive ligand trifluoperazine (or chlorpromazine), propranolol and Ca(2+)-CaM. The control sample was treated in the same way without the addition of CaM. The experimental and control samples were both analyzed by MALDI-MS. Based on the relative intensity fading (IF) of the ligand to propranolol, the MS conditions were optimized and then used to study the binding of eight alkaloids and calmodulin. Competitive experiments were performed in a similar way by adding two drugs to compare their binding affinities with calmodulin.

RESULTS

The matrix 2,6-dihydroxyacetophenone (DHAP) was suitable for detecting calmodulin ligands. Compared with propranolol, the relative intensities of six free drugs (berbamine, tetrandrine, papaverine, reserpine, brucine and tetrahydropalmatine) clearly faded after the addition of calmodulin, indicating that they can bind with CaM. The other two alkaloids (strychnine and piperine) had no or weak interaction with the target protein. Based on the data from the competitive binding experiments, the binding affinities of five drugs to calmodulin were obtained in the order: tetrandrine > trifluoperazine > berbamine > chlorpromazine > imipramine.

CONCLUSIONS

The IF-MALDI-MS method was successfully applied to screen novel calmodulin agents at both qualitative and semiquantitative levels. The new ligands may be novel leads for CaM antagonists.

MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.

Analysis of noncovalent chitinase-chito-oligosaccharide complexes by infrared-matrix assisted laser desorption ionization and nanoelectrospray ionization mass spectrometry

Transferring noncovalently bound complexes from the condensed phase into the gas phase represents a challenging task due to weak intermolecular bonds that have to be maintained during the phase transition. Currently, electrospray ionization (ESI) is the standard mass spectrometric (MS) technique to analyze noncovalent complexes. Although infrared matrix-assisted laser desorption ionization (IR-MALDI)-MS also provides particular soft desorption/ionization conditions, this method has so far hardly been applied for the analysis of noncovalent complexes. In this study, we employed IR-MALDI orthogonal time-of-flight (o-TOF)-MS in combination with the liquid matrix glycerol to characterize the specific complex formation of chito-oligosaccharide (CHOS) ligands with two variants of Chitinase A (ChiA) from Serratia marcescens, the inactive E315Q mutant and the active W167A mutant, respectively. The IR-MALDI-o-TOF-MS results were compared to those obtained using nano-ESI-quadrupole (q)-TOF-MS and ultraviolet (UV)-MALDI-o-TOF-MS. Using IR-MALDI-o-TOF-MS, specific noncovalent complexes between ChiA and CHOS were detected with distributions between enzymes with bound oligosaccharides vs free enzymes that were essentially identical to those obtained by nano-ESI-q-TOF-MS. Chitinase-CHOS complexes were not detected when UV-MALDI was employed for desorption/ionization. The results show that IR-MALDI-MS can be a valuable tool for fast and simple screening of noncovalent enzyme-ligand interactions.

Binding of alpha 1-acid glycoprotein with aconitum alkaloids: an investigation using an intensity fading matrix-assisted laser desorption/ionization Fourier transform mass spectrometry method

Intensity fading matrix-assisted laser desorption/ionization (IF-MALDI) mass spectrometry has become an alternative screening approach for the affinity-binding analysis of proteins and peptides with ligands. In this study, an attempt has been made to study the interaction of alpha 1-acid glycoprotein (AGP) with aconitum alkaloids by IF-MALDI Fourier transform ion cyclotron resonance mass spectrometry (IF-MALDI-FT-MS). Compared with the nonbinding internal standard, clear reduction in the ion abundances of the target alkaloids was observed with the addition of AGP. Relative binding affinities of different alkaloids towards the protein could also be estimated using IF-MALDI-FT-MS. The binding affinity was also investigated by using ultrafiltration liquid chromatography with photodiode array detection coupled to electrospray ionization mass spectrometry (ultrafiltration LC-DAD/ESI-MS), and results were consistent with that of IF-MALDI-FT-MS.

Studies on the non-covalent interactions between cyclodextrins and aryl alkanol piperazine derivatives by mass spectrometry and fluorescence spectroscopy

The non-covalent complexes of alpha- and beta-cyclodextrins (alpha-, beta-CDs) with two aryl alkanol piperazine derivatives (Pipe I and Pipe II) have been studied by electrospray ionization mass spectrometry (ESI-MS) and fluorescence spectroscopy. The ESI-MS experimental results demonstrated that Pipe I can conjugate to beta-CD and form 1:1 or 1:2 stoichiometric non-covalent complexes, and Pipe II can only form 1:1 complexes with alpha- or beta-CD. Fluorescence spectra indicated that the fluorescence intensities of Pipe I and Pipe II can be enhanced by increasing the content of beta-CD. The mass spectrometric titration experiments showed that the dissociation constants K(d1) were 5.77 and 9.52 x 10(-4) mol L(-1) for the complexes of alpha-CD with Pipe I and Pipe II, respectively, revealing that the binding of alpha-CD-Pipe I was stronger than alpha-CD-Pipe II. The K(d1) and K(d2) values were 9.81 x 10(-4) mol L(-1) and 1.11 x 10(-7) (mol L(-1))(2) for 1:1 and 1:2 complexes of Pipe I with beta-CD, respectively. The K(d) values obtained from fluorescence spectroscopy were in agreement with those from ESI-MS titration.

Investigation of calmodulin-Peptide interactions using matrix-assisted laser desorption/ionization mass spectrometry

In this report, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was used to study the binding interactions between calmodulin and two target peptides (melittin and substance P). Various matrix conditions were tested and the less acidic matrix DHAP and THAP were found to favor the survival of the intact calcium-calmodulin as well as the calmodulin-peptide complexes. However, the application of direct MALDI-MS to detect the intact complexes turned out to be very difficult due to the dissociation of the complexes and the formation of nonspecific aggregates. In contrast, the specific binding of the target peptides to calmodulin could be easily deduced using intensity-fading (IF) MALDI-MS. Compared with the nonbinding control, clear reduction in the ion abundances of the target peptides was observed with the addition of calmodulin. Relative binding affinities of different peptides towards the protein could also be estimated using IF-MALDI-MS. This study may extend the application of IF-MALDI-MS in the analysis of noncovalent complexes and offer a perspective into the utility of MALDI-MS as an alternative approach to study the peptides binding to calmodulin.

A novel, simple and sensitive ligand affinity capture method for detecting molecular interactions by MALDI mass spectrometry

A simple and sensitive ligand affinity capture method (LAC) was developed to detect biotinylated biomolecules bound to a biotin-avidin base by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI ToF MS). Glass slides covered with a metal film for MALDI MS applications were treated with amino-silane and derivatized with biotin followed by binding of avidin. Washing buffers with high ionic strength increased the specificity of the subsequent binding of biotinylated biomolecules to the avidin layer. A combined thin layer-dried droplet method using alpha-cyano-4-hydroxycinnamic acid (CHCA) in acetone or ethyl acetate resulted in the most intense ions of biotinylated polymyxin B, whereas the matrix conditions did not influence the detection of angiotensin II. Addition of biotinylated biomolecules in the low femtomole to low picomole range resulted in sufficient ion intensity for detection by the LAC method. The LAC concept was extended by binding of biotinylated lipopolysaccharide to the biotin-avidin base followed by preferential capture and specific detection of the binding antagonist polymyxin B.

Investigation of non-covalent complexes of glutathione with common amino acids by electrospray ionization mass spectrometry

AIM

To study the non-covalent interaction between glutathione and common amino acids.

METHODS

A stoichiometry of glutathione and common amino acids were mixed to reach the equilibrium, and then the mixed solution was investigated by electrospray ionization mass spectrometry (ESI-MS). The binding of the complexes was further examined by collision-induced dissociation (CID) in a tandem mass spectrometer as well as UV spectroscopy. To avoid distinct ionization efficiency discrepancy and signal suppression in the ESI-MS measurements, the interaction between glutathione (GSH) and glutamate (Glu) was quantitatively evaluated. The total concentrations and series of m/z of peak intensities for glutathione and amino acids could be achieved, respectively. Due to the existence of some oligomeric species arising from glutathione or amino acids, an improved calculation formula was proposed to calculate the dissociation constants of glutathione binding to amino acids.

RESULTS

The ESI mass spectra revealed that glutathione could interact easily with Met, Phe, Tyr, Ser, or Ile to form non-covalent complexes. The binding of the complexes was further confirmed by CID experiments in a tandem mass spectrometer as well as UV spectroscopy. Moreover, an improved calculation formula was successfully applied to determine the dissociation constants of glutathione binding to Glu, His, or Gln. Finally, a possible formation mechanism for the complexes of glutathione with amino acids was proposed.

CONCLUSION

The reduced polypeptide gamma-glutathione can interact with each of 8 common amino acids, including Glu, His, and Gln to form non-covalent complexes with different affinity.

Study of Papain–Cystatin Interaction by Intensity Fading MALDI-TOF-MS

Intensity fading (IF) matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS ) has become an alternative screening approach for the affinity-binding analysis of proteins and peptides with molecular ligands. In this investigation an attempt has been made to study the protein ligand interaction by intensity fading (IF) MALDI-MS using papain and cystatin as model system for protein-ligand interactions. The intensity fading of cystatin was monitored using various concentration of cystatin ranging from (1 to 8.6 microM) in presence of target protein, papain. The results indeed indicate that the intensity of cystatin decreases upon addition of papain. Furthermore, for the first time we have used IF-MALDI-MS for determining the number of binding sites for cystatin on papain by Scatchard analysis.

Detection of non-covalent protein interactions by 'intensity fading' MALDI-TOF mass spectrometry: applications to proteases and protease inhibitors

Among the main objectives of biomedical and proteomic research is to identify non-covalent interactions involving proteins. Here we provide a detailed protocol to apply matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry for such a purpose using proteases and protease inhibitors in complex biological samples. Our methodology is based on monitoring the reduction in intensity of inhibitors' mass spectrometric signals when their protease target is added to the MALDI sample. The versatility of the protocol permits the target to be added in a soluble form (direct protocol) or immobilized form (indirect protocol). The 'intensity fading' phenomenon is greatly favored when the binding assay is carried out in the sub-micromolar range and the interacting partners occur in mixtures of non-binding compounds. This protocol can be completed in 10 h, taking 20 or 30 min per sample to perform the mass spectrometric data acquisition, depending on whether a soluble or an immobilized target is used.