Electrospray ionization mass spectrometry as a tool for determination of drug binding sites to human serum albumin by noncovalent interaction

Effect of the presence of berberine/curcumin on the binding of limonin to human serum albumin and antitumor activity in vitro

The competition among drugs for binding to plasma proteins is regarded as a pharmacokinetic drug interaction. Competition between antitumor agents and other drugs for plasma protein binding can alter the free concentration of the drug, potentially impacting its efficacy and increasing the risk of toxic side effects. Through a range of spectroscopic techniques, this study examined the interaction between limonin and human serum albumin (HSA) in the context of berberine (Ber) and curcumin (Cur) under physiological conditions to clarify the binding mechanisms of binary and ternary systems at the molecular level. As demonstrated by fluorescence quenching experiments, Static quenching was identified as the mechanism of interaction between HSA and limonin. The results of site competition experiments indicated that the binding site between limonin and HSA was site I, a result further supported by molecular docking simulations. Through the use of thermodynamic data calculations, it was determined that limonin forms a stable complex with HSA by establishing hydrogen bonds and van der Waals forces. Circular dichroism (CD) spectroscopy, three-dimensional (3D) fluorescence spectroscopy, and synchronous fluorescence spectroscopy (SFS) employed to validate the notion that limonin perturbed the microenvironment of amino acids and induced conformational changes in HSA. What's more, the presence of Ber or Cur was found to have further modified the alterations observed in the interaction between the original HSA-limonin binary system. In vitro cellular experiments showed that interaction with HSA reduced the antitumor activity of limonin. In contrast, adding Ber or Cur increased the inhibition rate of tumor cells. The coexistence of both Ber and Cur significantly diminished limonin's binding affinity to HSA. The current investigation enhances comprehension regarding the binding characteristics and interaction mechanisms involving limonin, Ber, Cur, and HSA. It explores the potential of HSA as a versatile drug carrier and furnishes theoretical underpinnings for co-administrative strategies.

Measuring the NQO2: Melatonin Complex by Native Nano-Electrospray Ionization Mass Spectrometry

Melatonin exerts its effects through a series of target proteins/receptors and enzymes. Its antioxidant capacity might be due to its capacity to inhibit a quinone reductase (NQO2) at high concentration (50 μM). Demonstrating the existence of a complex between a compound and a protein is often not easy. It requires either that the compound is an inhibitor-and the complex translates by an inhibition of the catalytic activity-or the compound is radiolabeled-and the complex translates in standard binding approaches, such as in receptology. Outside these two cases, the detection of the protein:small molecule complexes by mass spectrometry has recently been made possible, thanks to the development of so-called native mass spectrometry. Using this approach, one can measure masses corresponding to an intact noncovalent complex between a compound and its target, usually after titration or competition experiments. In the present chapter, we detail the characterization of NQO2:melatonin interaction using native mass spectrometry.

Analysis on the interaction and binding properties of daphnoretin and human serum albumin in the presence of cisplatin: multi-spectroscopic methods and docking simulation

The interaction between anticancer drugs and HSA may have a significant impact on the pharmacology and efficacy of drugs. Drugs change the binding properties of HSA by regulating the quenching mechanism, binding mode and binding affinity. In this study, the interactions of cisplatin (cDDP), HSA, and daphnoretin were elucidated by multi-spectroscopic analyses and docking simulation. Fluorescence quenching showed that cDDP could not change the static quenching mechanism of HSA-daphnoretin, but could enhance their binding affinity. Site competition experiments revealed that daphnoretin and cDDP both bound to site I, which was consistent with the results of molecular docking. Thermodynamic date indicated that cDDP and daphnoretin formed a more stable complex with HSA via hydrophobic, van der Waals interaction and hydrogen bond. Three-dimensional fluorescence and circular dichroism spectra showed that cDDP changed the conformation and micro-environment of HSA induced by daphnoretin. This work could provide valuable information for the binding properties and interaction among cDDP, daphnoretin and HSA, and put forward the possibility of using HSA as a multidrug carrier.

MS methods to study macromolecule-ligand interaction: Applications in drug discovery

The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.

Proteoform-Specific Protein Binding of Small Molecules in Complex Matrices

Characterizing the specific binding between protein targets and small molecules is critically important for drug discovery. Conventional assays require isolation and purification of small molecules from complex matrices through multistep chromatographic fractionation, which may alter their original bioactivity. Most proteins undergo posttranslational modification, and only certain proteoforms have the right conformation with accessible domains and available residues for small molecule binding. We developed a top-down mass spectrometry (MS) centric workflow for rapid evaluation of the bioactivity of crude botanical extracts after a one-step reaction. Our assay distinguished covalent from noncovalent binding and mapped the residue for covalent binding between bioactive constituents and specific proteoforms of the target protein. We augmented our approach with a nanoflow liquid chromatography-selected reaction monitoring (SRM)-MS assay for simultaneous identification and label-free multiplex quantitation of small molecules in the crude botanical extracts. Our assay was validated for various proteoforms of human serum albumin, which plays a key role in pharmacokinetics of small molecules in vivo. We demonstrated the utility of our proteoform-specific assay for evaluating thymoquinone in crude botanical extracts, studying its pharmacokinetics in human blood, and interpreting its toxicity to human breast cancer cells in tissue culture.

Impact of germline and somatic missense variations on drug binding sites

Advancements in next-generation sequencing (NGS) technologies are generating a vast amount of data. This exacerbates the current challenge of translating NGS data into actionable clinical interpretations. We have comprehensively combined germline and somatic nonsynonymous single-nucleotide variations (nsSNVs) that affect drug binding sites in order to investigate their prevalence. The integrated data thus generated in conjunction with exome or whole-genome sequencing can be used to identify patients who may not respond to a specific drug because of alterations in drug binding efficacy due to nsSNVs in the target protein's gene. To identify the nsSNVs that may affect drug binding, protein–drug complex structures were retrieved from Protein Data Bank (PDB) followed by identification of amino acids in the protein–drug binding sites using an occluded surface method. Then, the germline and somatic mutations were mapped to these amino acids to identify which of these alter protein–drug binding sites. Using this method we identified 12 993 amino acid–drug binding sites across 253 unique proteins bound to 235 unique drugs. The integration of amino acid–drug binding sites data with both germline and somatic nsSNVs data sets revealed 3133 nsSNVs affecting amino acid–drug binding sites. In addition, a comprehensive drug target discovery was conducted based on protein structure similarity and conservation of amino acid–drug binding sites. Using this method, 81 paralogs were identified that could serve as alternative drug targets. In addition, non-human mammalian proteins bound to drugs were used to identify 142 homologs in humans that can potentially bind to drugs. In the current protein–drug pairs that contain somatic mutations within their binding site, we identified 85 proteins with significant differential gene expression changes associated with specific cancer types. Information on protein–drug binding predicted drug target proteins and prevalence of both somatic and germline nsSNVs that disrupt these binding sites can provide valuable knowledge for personalized medicine treatment. A web portal is available where nsSNVs from individual patient can be checked by scanning against DrugVar to determine whether any of the SNVs affect the binding of any drug in the database.

Mass spectrometric strategies to improve the identification of Pt(II)-modification sites on peptides and proteins

To further explore the binding chemistry of cisplatin (cis-Pt(NH3)2Cl2) to peptides and also establish mass spectrometry (MS) strategies to quickly assign the platinum-binding sites, a series of peptides with potential cisplatin binding sites (Met(S), His(N), Cys(S), disulfide, carboxyl groups of Asp and Glu, and amine groups of Arg and Lys, were reacted with cisplatin, then analyzed by electron capture dissociation (ECD) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). Radical-mediated side-chain losses from the charge-reduced Pt-binding species (such as CH3S(•) or CH3SH from Met, SH(•) from Cys, CO2 from Glu or Asp, and NH2(•) from amine groups) were found to be characteristic indicators for rapid and unambiguous localization of the Pt-binding sites to certain amino acid residues. The method was then successfully applied to interpret the top-down ECD spectrum of an inter-chain Pt-crosslinked insulin dimer, insulin + Pt(NH3)2 + insulin (>10 kDa). In addition, ion mobility MS shows that Pt binds to multiple sites in Substance P, generating multiple conformers, which can be partially localized by collisionally activated dissociation (CAD). Platinum(II) (Pt(II)) was found to coordinate to amine groups of Arg and Lys, but not to disulfide bonds under the conditions used. The coordination of Pt to Arg or Lys appears to arise from the migration of Pt(II) from Met(S) as shown by monitoring the reaction products at different pH values by ECD. No direct binding of cisplatin to amine groups was observed at pH 3 ~ 10 unless Met residues were present in the sequence, but noncovalent interactions between cisplatin hydrolysis and amination [Pt(NH3)4](2+) products and these peptides were found regardless of pH.

Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte

The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research.

Strong associations of short-chain perfluoroalkyl acids with serum albumin and investigation of binding mechanisms

Interactions of perfluoroalkyl acids (PFAAs) with tissue and serum proteins likely contribute to their tissue distribution and bioaccumulation patterns. Protein-water distribution coefficients (K(PW) ) based on ligand associations with bovine serum albumin (BSA) as a model protein were recently proposed as biologically relevant parameters to describe the environmental behavior of PFAAs, yet empirical data on such protein binding behavior are limited. In the present study, associations of perfluoroalkyl carboxylates (PFCAs) with two to 12 carbons (C₂-C₁₂) and perfluoroalkyl sulfonates with four to eight carbons (C₄, C₆, and C₈) with BSA are evaluated at low PFAA:albumin mole ratios and various solution conditions using equilibrium dialysis, nanoelectrospray ionization mass spectrometry, and fluorescence spectroscopy. Log K(PW) values for C₄ to C₁₂ PFAAs range from 3.3 to 4.3. Affinity for BSA increases with PFAA hydrophobicity but decreases from the C₈ to C₁₂ PFCAs, likely due to steric hindrances associated with longer and more rigid perfluoroalkyl chains. The C₄-sulfonate exhibits increased affinity relative to the equivalent chain-length PFCA. Fluorescence titrations support evidence that an observed dependence of PFAA-BSA binding on pH is attributable to conformational changes in the protein. Association constants determined for perfluorobutanesulfonate and perfluoropentanoate with BSA are on the order of those for long-chain PFAAs (K(a) ∼10⁶/M), suggesting that physiological implications of strong binding to albumin may be important for short-chain PFAAs.

One-pot synthesis of a new antifungal polymerisable monomer and its characterisation by coordination-ion spray mass spectrometry

We have investigated the synthesis of a new antifungal agent with a polymerisable moiety for the prevention of denture stomatisis. Nystatin (antifungal polyene) is modified in one step by reaction with isocyanatoethylmethacrylate to afford a new polymerisable antifungal agent in good yield (90%). In order to prove the monografting of the acrylate derivative and to localise the new group in the skeleton of the molecule, a rapid and efficient analytical method involving electrospray ionisation mass spectrometry (ESI-MS) was developed for the study. In view of the structures of such antifungal agents, their complexation with metal cations was investigated by Coordination-Ion Spray Mass Spectrometry (CIS-MS). This mass spectrometry study covers two aspects: improving the MS signal to overcome the low ionisation efficiency in ESI-MS and exploring the complexation behaviour of the induced structure to optimise the antifungal properties.

Some critical aspects in the determination of binding constants by electrospray ionisation mass spectrometry at the example of arsenic bindings to sulphur-containing biomolecules

The influences of reactant concentrations, solvent type, acid strength, pH conditions and ionic strength on the determination of apparent gas-phase equilibrium constants K using electrospray ionisation mass spectrometry (ESI-MS) were elucidated. As example serves the interaction of the tripeptide glutathione (GSH) with phenylarsine oxide (PAO). It was shown that rising initial concentrations of both reactants were not adequately compensated by increasing signal intensities of the reaction products in the mass spectra. The equilibrium constant for the formation of the phenylarsenic-substituted peptide species decreased from 1.42 x 10(5) +/- 1.81 x 10(4) l micromol(-1) to 1.54 x 10(4) +/- 1.5 x 10(3) l micromol(-1) with rising initial GSH concentrations from 1 to 10 microM at fixed PAO molarity of 50 microM. K values resulting from a series with a fixed GSH molarity of 5 microM and a PAO molarity varied from 10 to 100 microM remained in a narrower range between 4.59 x 10(4) +/- 2.15 x 10(4) l micromol(-1) and 1.07 x 10(4) +/- 4.0 x 10(3) l micromol(-1). In contrast, consumption numbers calculated from the ion intensity ratios of reaction products to the unreacted peptide were not influenced by the initial reactant concentrations. In a water-acetonitrile-acetic acid mixture (48:50:2, v:v), the consumption of 5 micro M GSH increased from 8.3 +/- 1.4% to 39.6 +/- 1.6% with increased molar excess of PAO from 2 to 20, respectively. The GSH consumption was considerably enhanced in a changed solvent system consisting of 25% acetonitrile and 75% 10 mM ammonium formate, pH 5.0 (v:v) up to 80% of the original peptide amount at an only threefold molar arsenic excess.

Investigation of the interactions between ginsenosides and amino acids by mass spectrometry and theoretical chemistry

In order to evaluate the essence of the interactions of ginsenosides and proteins which are composed by alpha-amino acids, electrospray ionization mass spectrometry was employed to study the noncovalent interactions between ginsenosides (Rb(2), Rb(3), Re, Rg(1) and Rh(1)) and 18 kinds of alpha-amino acids (Asp, Glu, Asn, Phe, Gln, Thr, Ser, Met, Trp, Val, Gly, Ile, Ala, Leu, Pro, His, Lys and Arg). The 1:1 and 2:1 noncovalent complexes of ginsenosides and amino acids were observed in the mass spectra. The dissociation constants for the noncovalent complexes were directly calculated based on peak intensities of ginsenosides and the noncovalent complexes in the mass spectra. Based on the dissociation constants, it can be concluded that the acidic and the basic amino acids, Asp, Glu, Lys and Arg, bound to ginsenosides more strongly than other amino acids. The experimental results were verified by theoretical calculations of parameters of noncovalent interaction between ginsenoside Re and Arg which served as a representative example. Two kinds of binding forms, "head-tail" ("H-T") and "head-head" ("H-H"), were proposed to explain the interaction between ginsenosides and amino acids. And the interaction in "H-T" form was stronger than that in "H-H" form.

Electrospray ionization mass spectrometric observation of ligand exchange of zinc pyrithione with amino acids

Zinc pyrithione (ZnPT) is widely used as an antidandruff or antifouling reagent. However, this compound is considered toxic, such as the teratogenic effect, to aquatic lives, and it is important to clarify the mechanism of its toxicity. In this study, the interactions between ZnPT and amino acids were observed using electrospray ionization mass spectrometry (ESI-MS) in order to obtain information on the activity of ZnPT within the living body. The ZnPT complex ([ZnPT-ligand+Amino acid]+), in which the ligand of ZnPT was exchanged by the amino acid, was detected in ZnPT solutions mixed with one of 20 amino acids by ESI-MS. Histidine and cysteine, in particular, showed a high reactivity with ZnPT, while serine and glycine showed a low reactivity. The complexes of ZnPT and a peptide were also observed by the ESI-MS measurement of the solution containing ZnPT with the peptide. These results would be useful to understand the mechanism of ZnPT toxicities to living creatures.

Effect of tanshinone IIA on the noncovalent interaction between warfarin and human serum albumin studied by electrospray ionization mass spectrometry

Enhanced anticoagulation and/or even bleeding are often observed when patients on long-term warfarin (WAR) therapy consumed Danshen, a well-known medicinal herb in traditional Chinese medicine (TCM). This study demonstrates that altered WAR metabolism, arising from its interaction with the active components in Danshen, played a significant role in this curative effect. Mass spectrometric techniques including ESI-ITMS (electrospray ionization ion-trap mass spectrometry) and ESI-TOF (time-of-flight)-MS have been developed for the study of such drug-herb interactions. The experimental approach involved a detailed analysis and comparison of WAR metabolites in vivo from blood or urine of rats that had been orally administrated with WAR, either singly or together with the representative bioactive component of Danshen-lipid soluble TIIA (Tanshinon IIA), and a study of the interaction of human serum albumin (HSA), WAR, and water-soluble sodium tanshinone IIA sulfonate (STS) in vitro. Results demonstrate that TIIA accelerates the metabolic rate of WAR, whereas STS displaces WAR from the WAR-HSA complex, resulting in an increase of free WAR concentration in blood. It is suggested that the elevated level and enhanced metabolism of WAR is responsible for the over-anticoagulation effect observed.

Direct screening of natural product extracts using mass spectrometry

The authors describe first a proof-of-concept experiment to show direct affinity screening using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) is a rapid and informative approach for natural product extract screening. The study used 10 alkaloid-enriched plant extracts and 8 desalted marine extracts spiked with specific inhibitors of bovine carbonic anhydrase II (bCAII; EC4.2.1.1) as a model set. The spiked extracts were incubated with bCAII and then analyzed by ESI-FTICR-MS. The noncovalent complexes were detected, and the specific inhibitors were reidentified in the spiked natural product extracts. There was no interference from the desalted/alkaloid-enriched extracts to the formation of the noncovalent complexes. The method allowed quick identification of the molecular mass of the bound ligand. The authors then applied the screening to identify active compounds in natural product extracts. They employed direct infusion and online size exclusion chromatography (SEC) ESI-FTICR-MS to detect intact target-ligand complex. Eighty-five methanolic plant extracts were screened against bCAII by direct infusion ESI-FTICR-MS and by online SEC-ESI-FTICR-MS. One noncovalent complex was identified from the same plant extract by both methods. The molecular weight of the bound ligand from this extract was determined. Mass-directed purification gave 6-(1S-hydroxy-3-methylbutyl)-7-methoxy-2H-chromen-2-one (1) as the active compound. Subsequently, the binding to bCAII was confirmed by ESI-FTICR-MS. The binding specificity was determined by competition experiments between 1 and furosemide, a specific ligand of bCAII.

Sequential injection affinity chromatography utilizing an albumin immobilized monolithic column to study drug–protein interactions

In this study, sequential injection affinity chromatography was used for drug-protein interactions studies. The analytical system used consisted of a sequential injection analysis (SIA) manifold directly connected with convective interaction media (CIM) monolithic epoxy disks modified by ligand-immobilization of protein. A non-steroidal, anti-inflammatory drug, naproxen (NAP) and bovine serum albumin (BSA) were selected as model drug and protein, respectively. The SIA system was used for sampling, introduction and propulsion of drug towards to the monolithic column. Association equilibrium constants, binding capacity at various temperatures and thermodynamic parameters (free energy DeltaG, enthalpy DeltaH) of the binding reaction of naproxen are calculated by using frontal analysis mathematics. The variation of incubation time and its effect in on-line binding mode was also studied. The results indicated that naproxen had an association equilibrium constant of 2.90 x 10(6)M(-1) at pH 7.4 and 39 degrees C for a single binding site. The associated change in enthalpy (DeltaH) was -27.36 kcal mol(-1) and the change in entropy (DeltaS) was -73 cal mol(-1)K(-1) for a single type of binding sites. The location of the binding region was examined by competitive binding experiments using a biphosphonate drug, alendronate (ALD), as a competitor agent. It was found that the two drugs occupy the same class of binding sites on BSA. All measurements were performed with fluorescence (lambda(ext)=230 nm, lambda(em)=350 nm) and spectrophotometric detection (lambda=280 nm).

A deconvolution method for the separation of specific versus nonspecific interactions in noncovalent protein-ligand complexes analyzed by ESI-FT-ICR mass spectrometry

A method to separate specific and nonspecific noncovalent interactions observed in ESI mass spectra between a protein and its ligands is presented. Assuming noncooperative binding, the specific ligand binding is modeled as a statistical distribution on identical binding sites. For the nonspecific fraction we assume a statistical distribution on a large number of "nonspecific" interacting sites. The model was successfully applied to the noncovalent interaction between the protein creatine kinase (CK) and its ligands adenosine diphosphate (ADP) and adenosine triphosphate (ATP) that both exhibit nonspecific binding in the mass spectrum. The two sequential dissociation constants obtained by applying our method are K(1,diss) = 11.8 +/- 1.5 microM and K(2,diss) = 48 +/- 6 microM for ADP. For ATP, the constants are K(1,diss) = 27 +/- 7 microM and K(2,diss) = 114 +/- 27 microM. All constants are in good correlation with reported literature values. The model should be valuable for systems with a large dissociation constant that require high ligand concentrations and thus have increased potential of forming nonspecific adducts.

Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes

For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand-macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.

Characterization of the binding epitope of ciprofloxacin bound to human serum albumin

Aqueous solutions of ciprofloxacin in phosphate buffer were measured by NMR under physiological conditions. The chemical shifts differ substantially compared to earlier investigations at low pH or in DMSO. Protein binding experiments using saturation transfer were optimized to measure proton resonances of ciprofloxacin that are in close proximity to human serum albumin. The relative intensities were mapped on the molecule to define the binding epitope. According to this methodology the cyclopropane ring and the chinolon ring constitute the binding epitope. Competition experiments with increasing amounts of salicylic acid did not change the saturation transfer to the ciprofloxacin protons indicating at least two different binding sites.