Improved identification of host cell proteins in a protein biopharmaceutical by LC-MS/MS using the ProteoMiner™ Enrichment Kit.

Host cell proteins (HCPs) in biotherapeutics can be identified by the use of enzymatic digestion and LC-MS/MS analysis. However, the major challenge is that HCPs are often present at very low levels in relation to the protein drug (low ppm-levels). In this study, the ProteoMiner™ Enrichment Kit (Bio-Rad) was evaluated as a strategy to enable identification of HCPs by LC-MS/MS by enrichment of low-abundant HCPs and a simultaneous depletion of the high-abundant product protein. A recombinant protein produced in Chinese hamster ovary (CHO) cells was spiked with six standard proteins at varying concentrations (10-1000 ppm). The sample was split into two aliquots; one that was prepared with the ProteoMiner™ Enrichment Kit and one control, where the enrichment procedure was omitted. The ProteoMiner™ Enrichment Kit was combined with the ProteoMiner Sequential Elution Large-Capacity Kit (Bio-Rad), eluting the proteins into four fractions. The samples were then digested with trypsin and analyzed with LC-MS/MS. In addition, multiple reaction monitoring (MRM) was applied to obtain an estimate of the protein abundance of HCPs and spiked proteins. The results demonstrated that with the untargeted LC-MS/MS method, 30 HCPs and four of the six spiked standard proteins were identified in the four fractions. The spiked standard proteins were identified down to 30 ppm in the ProteoMiner treated samples, while no HCPs and only the most abundant standard protein (≈1000 ppm) were identified in the non-enriched control sample. MRM assays were developed for 14 out of the 30 identified HCPs. All targeted HCPs and five of the six standard proteins were detected in all fractions as well as in the control sample by MRM. There was an acceptable agreement between estimated concentrations of spiked standard proteins and expected values. An 80-700 fold enrichment of individual HCPs was observed in the fractions. In conclusion, the results clearly demonstrated that the ProteoMiner technology can be used for enriching HCPs in biotherapeutics, enabling their identification by LC-MS/MS.

Robust LC-MS/MS methods for analysis of heparan sulfate levels in CSF and brain for application in studies of MPS IIIA.

Aim: Accumulation of heparan sulfate (HS) is associated with the neurodegenerative disorder Mucopolysaccharidosis type IIIA (MPS IIIA). Here, we compare HS levels in brain and cerebrospinal fluid (CSF) of MPS IIIA mice after treatment with a chemically modified sulfamidase (CM-rhSulfamidase). Materials & methods: Two LC-MS/MS methods were adapted from literature methodology, one to measure HS metabolites (HSmet), the other to measure digests of HS after heparinase treatment (HSdig). Results: The HSmet and HSdig methods showed similar relative reduction of HS in brain after CM-rhSulfamidase administration to MPS IIIA mice and the reduction was reflected also in CSF. Conclusion: The results of the two methods correlated and therefore the HSdig method can be used in clinical studies to determine HS levels in CSF from patients with MPS IIIA.

A novel assay of cellular stearoyl-CoA desaturase activity of primary rat hepatocytes by HPLC.

The stearoyl-CoA desaturase (SCD) activity is involved in regulation of metabolism, energy storage, and membrane fluidity. However, only few cellular assays have been developed. We describe a simple and robust method to quantitate SCD activity and its inhibition in primary rat hepatocytes. Hepatocytes assimilate stearic acid, with or without modification by SCD, into its lipid pool. To measure the extent of this conversion primary rat hepatocytes were cultivated 4h or overnight with [1-(14)C]18:0 and extracellular fatty acids were washed out. Total cell lipids were then hydrolyzed and extracted. Recoveries of 18:0 were secured with a modified Folch method by addition of 0.1% Triton X-114 to the samples. The extracted fatty acids were dissolved in 85% ethanol and separated by reverse phase HPLC, which took 10 min including column recovery time. [1-(14)C]18:0 and [1-(14)C]18:1(n9) were detected and quantified by on-line flow scintillation analysis. Incubation of the cells with SCD inhibitors resulted in decreased ratios of 18:1/18:0 in dose-dependent manners. The improvements enabled us to establish a novel robust assay based solely on HPLC analysis of cellular SCD activity, which was developed in 12-well format.

Development of a two-dimensional liquid chromatography system for isolation of drug metabolites.

The separation, isolation and identification of drug metabolites from complex endogenous matrices like urine, plasma and tissue extracts are challenging tasks. Metabolites are usually first identified by mass spectrometry and tentative structures proposed from product ion spectra. In many cases mass spectrometry cannot be used to determine positional isomers and metabolites have to be fractionated in microgram amounts for analysis by NMR. To overcome the difficulties associated with separation and isolation of drug metabolites from biological matrices, a new two-dimensional liquid chromatography system has been developed. The retention times of 45 acidic, basic and neutral compounds were determined on liquid chromatographic columns with different stationary phases in order to identify two columns with highly different selectivity to be used for two-dimensional liquid chromatography. Drug metabolites of three model compounds were first generated in vitro with liver microsomes and then compared with potential metabolites formed by oxidation with hydrogen peroxide catalyzed by meso-tetra (4-sulphonatophenyl) porphine (porphine). The results showed that the porphine system could be used as a complementary system for the generation of phase I microsomal metabolites with high yield of some metabolites in a less complex matrix. The two-dimensional liquid chromatography system was used to separate and isolate microsomal and porphine generated drug metabolites in off-line and on-line mode. Finally, to verify the utility of the developed system, urine samples were spiked with metabolite standards of model compounds for separation in the two-dimensional system. Excellent separations were obtained with an amide column in the first dimension and a pentafluorophenylpropyl (PFPP) column in the second dimension. The metabolites were successfully separated from each other as well as from the complex biological matrix. The results demonstrate the applicability of the system for fractionation of drug metabolites but it could also be used in many other analytical purposes, especially for basic compounds. Trace levels of metabolites were successfully separated in the on-line mode which failed in the off-line mode.

Metabolism of 2-substituted quinolines with antileishmanial activity studied in vitro with liver microsomes, hepatocytes and recombinantly expressed enzymes analyzed by LC/MS.

Liver microsome and hepatocyte-mediated biotransformation of three oral antileishmanial 2-substituted quinolines were investigated. One quinoline contains an n-propyl group (1) and the other a propenyl chain functionalized at the gamma position either by a nitrile (2) or an alcohol (3). The different isoforms of rat cytochrome P450 responsible for biotransformation of 1 were also investigated. Compounds 2 and 3 mainly reacted with glutathione, preventing further metabolism. Compound 3 however, the reaction being reversible, could be released from glutathione and take alternative reaction pathways. Microsomal incubations of 1 mainly led to hydroxylation of the side chain, involving many cytochromes, predominantly CYP2B1, CYP2A6 and CYP1A1 (at more than 80%). In contrary, minor metabolites hydroxylated on the quinoline ring involved a few cytochromes. The hydroxylated products of 1 were conjugated with glucuronic acid in rat hepatocyte incubations.

Introduction to early in vitro identification of metabolites of new chemical entities in drug discovery and development.

The introduction of combinatorial chemistry and robotics for high throughput screening has changed the way drugs are discovered today compared with 10-15 years ago when fewer compounds were tested in animal or organ models. The introduction of new analytical techniques, especially liquid chromatography/mass spectrometry (LC/MS) has made it possible to characterize the chemical properties, permeability, metabolic stability and metabolic fate of a large number of screening hits for further development in a funnel-like manner. The purpose of this contribution is to discuss principles and recent strategies for metabolite identification and to give an introduction to biotransformation studies. Metabolites are experimentally generated with the use of animal and human recombinant expressed enzymes, and different liver and other tissue fractions like microsomes and slices. For separation and identification of structurally diverse metabolites, LC/MS and tandem mass spectrometry (LC/MS/MS) techniques are commonly used. The LC/MS and LC/MS/MS techniques are rapid, sensitive, easy to automate and robust, and therefore, they are the methods of choice for these studies. The outcome of the metabolite identification studies is detection of metabolites that could be pharmacologically active and contribute to the efficacy of a new chemical entity (NCE), and elimination of compounds that form reactive intermediates and/or toxic metabolites that could cause adverse effects of NCE. If such information is available at an early stage during the drug discovery process, the chemical structure of the compound may be modified to reduce the risk of idiosyncratic and/or adverse drug reactions during clinical development.

Characterization of the cytochrome P450 enzymes and enzyme kinetic parameters for metabolism of BVT.2938 using different in vitro systems.

An important step in the drug development process is identification of enzymes responsible for metabolism of drug candidates and determination of enzyme kinetic parameters. These data are used to increase understanding of the pharmacokinetics and possible metabolic-based drug interactions of drug candidates. The aim of the present study was to characterize the cytochrome P450 enzymes and enzyme kinetic parameters for metabolism of BVT.2938 [1-(3-{2-[(2-ethoxy-3-pyridinyl)oxy]ethoxy}-2-pyrazinyl)-2(R)-methylpiperazine], a potent and selective 5HT2c-receptor agonist. The enzyme kinetic parameters were determined for formation of three main metabolites of BVT.2938 using human liver microsomes and expressed cytochrome P450 (CYP) isoforms. The major metabolite was formed by hydroxylation of the pyridine ring (CL(int)=27 microl/mgmin), and was catalysed by both CYP2D6*1 and CYP1A1, with K(m) values corresponding to 1.4 and 2.7 microM, respectively. The results from enzyme kinetic studies were confirmed by incubation of BVT.2938 in the presence of the chemical inhibitor of CYP2D6*1, quinidine. Quinidine inhibited the formation of the major metabolite by approximately 90%. Additionally, studies with recombinant expressed CYP isoforms from rat indicated that formation of the major metabolite of BVT.2938 was catalysed by CYP2D2. This result was further confirmed by experiments with liver slices from different rat strains, where the formation of the metabolite correlated with phenotype of CYP2D2 isoform (Sprague-Dawley male, extensive; Dark Agouti male, intermediate; Dark Agouti female, poor metabolizer). The present study showed that the major metabolite of BVT.2938 is formed by hydroxylation of the pyridine ring and catalysed by CYP2D6*1. CYP1A1 is also involved in this reaction and its role in extra-hepatic metabolism of BVT.2938 might be significant.

Metabolic fingerprinting of rat urine by LC/MS Part 2. Data pretreatment methods for handling of complex data.

Metabolic fingerprinting of biofluids like urine is a useful technique for detecting differences between individuals. With this approach, it might be possible to classify samples according to their biological relevance. In Part 1 of this work a method for the comprehensive screening of metabolites was described, using two different liquid chromatography (LC) column set-ups and detection by electrospray ionization mass spectrometry (ESI-MS). Data pretreatment of the resulting data described in is needed to reduce the complexity of the data and to obtain useful metabolic fingerprints. Three different approaches, i.e., reduced dimensionality (RD), MarkerLynx, and MS Resolver, were compared for the extraction of information. The pretreated data were then subjected to multivariate data analysis by partial least squares discriminant analysis (PLS-DA) for classification. By combining two different chromatographic procedures and data analysis, the detection of metabolites was enhanced as well as the finding of metabolic fingerprints that govern classification. Additional potential biomarkers or xenobiotic metabolites were detected in the fraction containing highly polar compounds that are normally discarded when using reversed-phase liquid chromatography.

Metabolic fingerprinting of rat urine by LC/MS Part 1. Analysis by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry.

Complex biological samples, such as urine, contain a very large number of endogenous metabolites reflecting the metabolic state of an organism. Metabolite patterns can provide a comprehensive signature of the physiological state of an organism as well as insights into specific biochemical processes. Although the metabolites excreted in urine are commonly highly polar, the samples are generally analyzed using reversed-phase liquid chromatography mass spectrometry (RP-LC/MS). In Part 1 of this work, a method for detecting highly polar metabolites by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry (HILIC/ESI-MS) is described as a complement to RP-LC/ESI-MS. In addition, in an accompanying paper (Part 2), different multivariate approaches to extracting information from the resulting complex data are described to enable metabolic fingerprints to be obtained. The coverage of the method for the screening of as many metabolites as possible is highly improved by analyzing the urine samples using both a C(18) column and a ZIC-HILIC column. The latter was found to be a good alternative when analyzing highly polar compounds, e.g., hydroxyproline and creatinine, to columns typically used for reversed-phase liquid chromatography.

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

Most proteins in blood plasma bind ligands. Human serum albumin (HSA) is the main transport protein with a very high capacity for binding of endogenous and exogenous compounds in plasma. Many pharmacokinetic properties of a drug depend on the level of binding to plasma proteins. This work reports studies of noncovalent interactions by means of nanoelectrospray ionization mass spectrometry (nanoESI-MS) for determination of the specific binding of selected drug candidates to HSA. Warfarin, iopanoic acid and digitoxin were chosen as site-specific probes that bind to the main sites of HSA. Two drug candidates and two known binders to HSA were analyzed using a competitive approach. The drugs were incubated with the target protein followed by addition of site-specific probes, one at a time. The drug candidates showed predominant affinity to site I (warfarin site). Naproxen and glyburide showed affinity to both sites I and II. The advantages of nanoESI-MS for these studies are the sensitivity, the absence of labeled molecules and the short method development time.

Determination of corticosteroids in tissue samples by liquid chromatography-tandem mass spectrometry.

A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for determination of corticosterone and 11-dehydrocorticosterone (11-DHC) levels in KKA(y) mouse liver and adipose tissue, and hydrocortisone and cortisone levels in human adipose tissue has been developed. The corticosteroids were extracted from liver tissue with methanol/water and ethyl acetate for adipose tissue samples. Corticosterone and 11-DHC were separated with a methanol gradient and hydrocortisone and cortisone with an acetonitrile gradient containing trifluoroacetic acid on a reversed-phase column within 15 min. The corticosteroids were detected after electrospray ionization in positive mode with multiple reaction monitoring (MRM). The limits of quantification (LOQ) were estimated to be 15 nmol/kg liver and 1.6 nmol/kg adipose tissue for corticosterone and 5.4 nmol/kg liver and 0.92 nmol/kg adipose tissue for 11-DHC. The LOQ was estimated to be 0.2 nmol/kg adipose tissue for hydrocortisone and 0.4 nmol/kg adipose tissue for cortisone. The limits of detection (LOD) at 3 times S/N were estimated to be 0.07 nmol/kg adipose tissue for hydrocortisone 0.1 nmol/kg adipose tissue for cortisone. The variation of endogenous levels in KKA(y) mouse from different animals (CV%) was high with mean liver tissue levels of 117+/-25 (S.D.)nmol/kg for corticosterone and 62+/-19 (S.D.)nmol/kg for 11-DHC (n=5) and adipose tissue levels of 39+/-20 (S.D.)nmol/kg for corticosterone and 2.4+/-0.9 (S.D.)nmol/kg for 11-DHC (n=9). Endogenous levels in human biopsy samples from adipose tissue were 12+/-7.0 (S.D.)nmol/kg for hydrocortisone and 3.0+/-1.6 (S.D.)nmol/kg for cortisone (n=16). The new LC-MS/MS methods showed sufficient sensitivity and selectivity for determination of endogenous levels of corticosteroids in both KKA(y) mouse liver and adipose tissue samples and human adipose tissue samples. The selectivity of the methods was verified by analysis of two different productions from each analyte.

Influence of droplet size, capillary-cone distance and selected instrumental parameters for the analysis of noncovalent protein-ligand complexes by nano-electrospray ionization mass spectrometry.

It has been suggested in the literature that nano-electrospray ionization (nano-ESI) mass spectrometry better reflects the equilibrium between complex and free protein in solution than pneumatically assisted electrospray ionization (ESI) in noncovalent interaction studies. However, no systematic studies of the effects of ionization conditions have been performed to support this statement. In the present work, different instrumental and sample-derived parameters affecting the stability of noncovalent complexes during analysis by nano-ESI were investigated. In general, increased values of parameters such as drying gas flow-rate, ion-source temperature, capillary tip voltage and buffer concentration lead to a dissociation of ribonuclease A (RNAse)-cytidine 2'-monophosphate (CMP) and cytidine 5'-triphosphate (CTP) complexes. The size of the electrosprayed droplets was shown to be an important issue. Increasing the capillary to cone distance yielded an increased complex to free protein ratio when a hydrophilic ligand was present and the reverse effect was obtained with a hydrophobic ligand. Important in this regard is the degree of sampling of ions originating from late-generation residue droplets, that is, ions present in the droplet bulk. Sampling of these ions increases with longer capillary-cone distance (flight time). Furthermore, when the sample flow-rate was increased by increasing the capillary internal tip i.d. from 4 to 30 microm, a decreased complex to free protein ratio for the RNAse-CTP system was observed. This behavior was consistent with the change in surface to volume ratio for flow-rates between 2 and 100 nl min(-1). Finally, polarity switching between positive and negative ion modes gave a higher complex to free protein ratio when the ligand and the protein had the same polarity.

Determination of dissociation constants for protein-ligand complexes by electrospray ionization mass spectrometry.

A fully automated biophysical assay based on electrospray ionization mass spectrometry (ESI-MS) for the determination of the dissociation constants (KD) between soluble proteins and low molecular mass ligands is presented. The method can be applied to systems where the relative MS response of the protein and the protein-ligand complexes do not reflect relative concentrations. Thus, the employed approach enables the use of both electrostatically and nonpolar bound complexes. The dynamic range is wider than for most biological assays, which facilitates the process of establishing a structure-activity relationship. This fully automated ESI-MS assay is now routinely used for ligand screening. The entire procedure is described in detail using hGHbp, a 25-kDa extracellular soluble domain of the human growth hormone receptor, as a model protein.

Multivariate approaches for efficient detection of potential metabolites from liquid chromatography/mass spectrometry data.

This work describes a novel method for rapid screening of unknown metabolites in urine samples that narrows down the list of potential metabolites. Prior to analysis by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS), urine samples were prepared using solid-phase extraction (SPE). Automatic curve resolution was used for deconvolution of the LC/MS data, followed by peak alignment. Preprocessed data were then used for metabolite pattern recognition using principal component analysis (PCA), parallel factor analysis (PARAFAC), and multilinear partial least squares (N-PLS). This approach enabled the rapid detection of metabolites of citalopram in urine by maximizing the information extracted. The metabolites thus identified were compared with earlier studies on the metabolism of citalopram. In addition, new, unreported metabolites were found and characterized by LC/MS/MS and accurate mass measurements. A combination of data from positive and negative ionization enhanced the identification of metabolites.

Identification of BVT.2938 metabolites by LC/MS and LC/MS/MS after in vitro incubations with liver microsomes and hepatocytes.

The metabolism of the 5HT2c agonist BVT.2938, 1-(3-[2-[(2-ethoxy-3-pyridinyl)oxy]ethoxy]-2-pyrazinyl)-2(R)-methylpiperazine, was studied in vitro by incubation with rat, monkey and human liver microsomes as well as cryopreserved hepatocytes, followed by liquid chromatography/mass spectrometry (LC/MS) and LC/MS/MS analysis on a quadrupole-time of flight mass spectrometer for structural elucidation. Deuterium exchange on column was used to differentiate between hydroxylation and N-oxidation. Liver microsomes were incubated in two different buffer systems with optimum conditions for cytochrome P450 activity or UDP-glucuronosyltransferase activity. The major phase I metabolites of BVT.2938 originated from O-deethylation of the pyridine ring, O-dealkylation of the ethylene bridge, pyrazine ring hydroxylation, hydroxylation of pyridine ring and piperazine ring N-hydroxylation. When a hydrogen carbonate buffer system was supplemented with UDPGA, the piperazine carbamoyl-glucuronide from the parent compound was identified together with several glucuronides of the phase I metabolites. The metabolite pattern in hepatocytes was similar to microsomes except that the sulphate at the N-position of the piperazine ring of BVT.2938 was identified, while the carbamoyl-glucuronide was missing. Excellent correlation was obtained between radioactivity detection and the chemiluminescent nitrogen detector when the nitrogen content of the analytes was taken into account.

Screening of biomarkers in rat urine using LC/electrospray ionization-MS and two-way data analysis.

Biofluids, like urine, form very complex matrixes containing a large number of potential biomarkers, that is, changes of endogenous metabolites in response to xenobiotic exposure. This paper describes a fast and sensitive method of screening biomarkers in rat urine. Biomarkers for phospholipidosis, induced by an antidepressant drug, were studied. Urine samples from rats exposed to citalopram were analyzed using solid-phase extraction (SPE) and liquid chromatography mass spectrometry (LC/MS) analysis detecting negative ions. A fast iterative method, called Gentle, was used for the automatic curve resolution, and metabolic fingerprints were obtained. After peak alignment principal component analysis (PCA) was performed for pattern recognition, PCA loadings were studied as a means of discovering potential biomarkers. In this study a number of potential biomarkers of phospholipidosis in rats are discussed. They are reported by their retention time and base peak, as their identification is not within the scope of the study. In addition to the fact that it was possible to differentiate control samples from dosed samples, the data were very easy to interpret, and signals from xenobiotic-related substances were easily removed without affecting the endogenous compounds. The proposed method is a complement or an alternative to NMR for metabolomic applications.

Automated nano-electrospray mass spectrometry for protein-ligand screening by noncovalent interaction applied to human H-FABP and A-FABP.

A method for ligand screening by automated nano-electrospray ionization mass spectrometry (nano-ESI/MS) is described. The core of the system consisted of a chip-based platform for automated sample delivery from a 96-well plate and subsequent analysis based on noncovalent interactions. Human fatty acid binding protein, H-FABP (heart) and A-FABP (adipose), with small potential ligands was analyzed. The technique has been compared with a previously reported method based on nuclear magnetic resonance (NMR), and excellent correlation with the found hits was obtained. In the current MS screening method, the cycle time per sample was 1.1 min, which is approximately 50 times faster than NMR for single compounds and approximately 5 times faster for compound mixtures. High reproducibility was achieved, and the protein consumption was in the range of 88 to 100 picomoles per sample. Futhermore, a novel protocol for preparation of A-FABP without the natural ligand is presented. The described screening approach is suitable for ligand screening very early in the drug discovery process before conventional high-throughput screens (HTS) are developed and/or used as a secondary screening for ligands identified by HTS.

On-line microdialysis for enhanced resolution and sensitivity during electrospray mass spectrometry of non-covalent complexes and competitive binding studies.

Many proteins and macromolecules easily form metal adduct ions which impairs their analysis by mass spectrometry. The present study describes how the formation of undesired adducts can be minimized by on-line microdialysis for non-covalent binding studies of macromolecules with low molecular mass ligands with electrospray ionization mass spectrometry (ESI-MS). The technique was indispensable for protein-ligand studies due to reduction of unwanted adduct ions, and thus gave excellent resolution and a sensitivity improvement of at least 5 times. The core of the analytical system was a modified microdialysis device, which was operated in countercurrent mode. A novel technique based on microdialysis for competitive binding studies is also presented. The non-covalent complex between a protein and a ligand was formed in the sample vial prior to analysis. The complex was injected into an on-line microdialysis system where a competitive ligand was administered in the dialysis buffer outside of the fiber. The second ligand competitively displaced the first ligand through transport via the wall of the dialysis fiber, and the intact complexes were detected by ESI-MS.