A matrix-assisted laser desorption/ionization tandem mass spectrometry method for direct screening of small molecule mixtures against an aminoglycoside kinase

A novel strategy to screen inhibitors of multiple aminoglycoside-modifying enzymes with ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry

Resistance to aminoglycoside antibiotics occurs primarily as a result of aminoglycoside-modification enzymes (AMEs) that modify the antibiotics. In this work, a novel strategy to combat the effects of antibiotic resistance was developed by screening multiple AMEs inhibitors with ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF MS). The method screened inhibitors of three AMEs (AAC(6')-APH(2"), AAC(6') and APH(2")) simultaneously through measuring the acetyltransferase activity and phosphotransferase activity of AAC(6')-APH(2") enzyme in a single assay. Screening inhibitors of multiple targets could greatly improve the screening efficiency at early-stages of drug discovery. In this study, enzyme reaction conditions including cosubstrate, enzyme concentration and cosubstrate concentration were optimized. The inhibition constants (K_i) for two known inhibitors, paromomycin and quercetin, were determined to be 1.23 and 20.27 μM, respectively. The assay was further validated through the determination of a high Z' factor value of 0.73. The developed assay was applied to screen a chemical library against bifunctional AAC(6')-APH(2'') enzyme. Using this assay, two pyrimidinyl indole derivatives were found to be potent, and effective AAC(6')-APH(2'') inhibitors. The assay of exploring the selective inhibitory effect on two AAC(6')-APH(2'') active sites was further performed. Two pyrimidinyl indole derivatives were found to exhibit striking inhibitory activities on AAC(6').

Rapid detection and quantification of aminoglycoside phosphorylation products using direct-infusion high-resolution and ultra-high-performance liquid chromatography/mass spectrometry

RATIONALE

Worldwide efforts are underway to determine the extent of antimicrobial resistance (AMR). In 2015, the World Health Organization (WHO) founded the Global Antimicrobial Surveillance System (GLASS) focusing on surveillance and dissemination of data. In addition, the WHO advocates method development focused on rapid determination and close to real-time monitoring of antibiotic usage and its effectiveness. Rapid determination of aminoglycoside modification by O-phosphorylation, the most prevalent mechanism of clinical resistance, was performed using direct flow and liquid chromatography/mass spectrometry (LC/MS).

METHODS

A strain of Escherichia coli carrying a plasmid encoding an aminoglycoside modification enzyme (O-phosphotransferase) was incubated with kanamycin, an aminoglycoside. The antibiotic and its modified form were observed using direct flow and LC/MS. Direct flow high-resolution mass spectrometry (HRMS) using a Thermo Fisher Q-Exactive hybrid quadrupole-orbitrap mass spectrometer was employed for quantitative analysis and structural elucidation. Liquid chromatography coupled with the AB Sciex QTRAP 6500+ was also used for quantitative analysis.

RESULTS

Detection of phosphorylated kanamycin was achieved in less than 4 h of incubation. Calibration curves for modified kanamycin from 2.5-250 and 10-200 μg mL^-1  μg mL^-1 were obtained for LC/MS and direct injection high-resolution experiments, respectively. The high-resolution measurements were employed for conformation and structural elucidation of the novel precursor and product ion biomarkers with high mass accuracy (≤7 ppm). These results confirm previous in vitro O-phosphotransferase metabolite measurements.

CONCLUSIONS

A new analytical method capable of determination and quantification of the most common form of aminoglycoside resistance (via phosphorylation) was developed requiring short incubation times for a positive confirmation 100-fold lower than the minimum inhibitory concentration (MIC). High-resolution data simultaneously revealed quantitative abilities and provided numerous novel product ions confirming placement of the phosphate group on kanamycin.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014

This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.

Dual-target inhibitor screening against thrombin and factor Xa simultaneously by mass spectrometry

An accurate, rapid, and cost-effective methodology for enzyme assay is highly demanded to screen the effect of compounds on target at the molecular level. Thrombin (EC 3.4.21.5) and factor Xa (FXa, EC 3.4.21.6) have been identified as the critical targets for the development of potential drugs with anticoagulant activity. In this study, a rapid, sensitive and accurate assay based on UHPLC-MS/MS method has been developed for inhibitor screening against thrombin and factor Xa simultaneously. For thrombin and factor Xa, the Michaelis-Menten constants (K_m) were calculated to be 6.14 and 57.27 μM, respectively. The inhibition constants (K_i) for two known inhibitors, argatroban and rivaroxaban, were determined to be 16.23 and 0.41 nM, respectively. The assay was further validated through the determination of a high Z' factor value of 0.89. Finally, the developed assay was applied to screen a chemical library against two enzymes. Three hit compounds belonging to a class of sulfated polysaccharides were identified and their targets of inhibition action were further evaluated. The results indicated that the dual-target assay by UHPLC-MS/MS analysis could be used as a reliable method for screening anticoagulant agents.

A direct, ratiometric, and quantitative MALDI-MS assay for protein methyltransferases and acetyltransferases

Protein methylation and acetylation play important roles in biological processes, and misregulation of these modifications is involved in various diseases. Therefore, it is critical to understand the activities of the enzymes responsible for these modifications. Herein we describe a sensitive method for ratiometric quantification of methylated and acetylated peptides via MALDI-MS by direct spotting of enzymatic methylation and acetylation reaction mixtures without tedious purification procedures. The quantifiable detection limit for peptides with our method is approximately 10 fmol. This is achieved by increasing the signal-to-noise ratio through the addition of NH4H2PO4 to the matrix solution and reduction of the matrix α-cyanohydroxycinnamic acid concentration to 2 mg/ml. We have demonstrated the application of this method in enzyme kinetic analysis and inhibition studies. The unique feature of this method is the simultaneous quantification of multiple peptide species for investigation of processivity mechanisms. Its wide buffer compatibility makes it possible to be adapted to investigate the activity of any protein methyltransferase or acetyltransferase.

Simultaneous inhibition assay for human and microbial kinases via MALDI-MS/MS

Selective inhibition of one kinase over another is a critical issue in drug development. For antimicrobial development, it is particularly important to selectively inhibit bacterial kinases, which can phosphorylate antimicrobial compounds such as aminoglycosides, without affecting human kinases. Previous work from our group showed the development of a MALDI-MS/MS assay for the detection of small molecule modulators of the bacterial aminoglycoside kinase APH3'IIIa. Herein, we demonstrate the development of an enhanced kinase MALDI-MS/MS assay involving simultaneous assaying of two kinase reactions, one for APH3'IIIa, and the other for human protein kinase A (PKA), which leads to an output that provides direct information on selectivity and mechanism of action. Specificity of the respective enzyme substrates were verified, and the assay was validated through generation of Z'-factors of 0.55 for APH3'IIIa with kanamycin and 0.60 for PKA with kemptide. The assay was used to simultaneously screen a kinase-directed library of mixtures of ten compounds each against both enzymes, leading to the identification of selective inhibitors for each enzyme as well as one non-selective inhibitor following mixture deconvolution.