Development of a rapid and sensitive multiple reaction monitoring proteomic approach for quantification of transporters in human liver tissue

Developments in on-line, post separation sample manipulation in the last 22 years: Pharmaceutical and biomedical applications

On-line post separation sample manipulation is a powerful approach increasing the sensitivity and selectivity in chemical analysis. Post separation sample manipulation includes the treatment of the analytes after their separation through a suitable separation technique, mainly liquid chromatography and capillary electrophoresis. Typically, post separation approaches include either the addition of a reagent/solvent to derivatize the analyte/enhance the sensitivity, pH change, or the conversion of the analyte through a photochemical/electrochemical system (reagent-free systems). This review focuses on the developed methods using post-column manipulation of sample with pharmaceuticals and biomedical applications, covering the period from 2000 to midle-2023. Chemistries combined with fluorescence, UV-vis and mass spectrometric detection are discussed employing both liquid chromatography and electrophoretic techniques for separation. Noteworthy instrumental modifications are also discussed.

Data-independent acquisition (DIA): An emerging proteomics technology for analysis of drug-metabolizing enzymes and transporters

Data-independent acquisition (DIA) proteomics is a recently-developed global mass spectrometry (MS)-based proteomics strategy. In a DIA method, precursor ions are isolated into pre-defined isolation windows and fragmented; all fragmented ions in each window are then analyzed by a high-resolution mass spectrometer. DIA proteomics analysis is characterized by a broad protein coverage, high reproducibility, and accuracy, and its combination with advances in other techniques such as sample preparation and computational data analysis could lead to further improvements in assay performances. DIA technology has been increasingly utilized in various proteomics studies, including quantifying drug-metabolizing enzymes and transporters. Quantitative proteomics study of drug-metabolizing enzymes and transporters could lead to a better understanding of pharmacokinetics and pharmacodynamics and facilitate drug development. This review summarizes the application of DIA technology in proteomic analysis of drug-metabolizing enzymes and transporters.

A simple unlabeled human chorionic gonadotropin biosensor based on a peptide aptamer

As an essential biochemical indicator in the fields of pregnancy and oncology, human chorionic gonadotropin (HCG) can be evaluated using colloidal gold immunochromatographic paper and quantified using a biochemical analyzer based on the principle of the antibody sandwich method. In view of the inaccuracy of the former and the complication of the latter, this study constructed an accurate, sensitive and simple unlabeled biosensor based on peptide aptamer CGGGPPLRINRHILTR for HCG detection. Molecular Operating Environment (MOE) was used to simulate the aptamer and protein docking, and western blot (WB) was used to verify the binding effect and ratio. The peptide aptamer was characterized and was then reduced with tris-(2-carboxyethyl)-phosphine hydrochloride (TCEP). After electrochemical deposition of chloroauric acid on the screen-printed electrode (SPE), the aptamer was self-assembled on the electrode surface under optimal conditions. The active site of the electrode surface was blocked with 6-mercapto-1-hexanol (MCH) and BSA. The electrochemical impedance spectrum (EIS) was used to quantify HCG in the matrix. Showing a good linear relationship in the range of 5-1500 mIU mL^-1, with a detection limit of 1 mIU mL^-1, the biosensor remained stable at room temperature for 14 days. Because of its small size, stability, sensitivity and accuracy, this biosensor has great potential to become a portable diagnostic device for HCG.

First comprehensive analysis of lysine succinylation in paper mulberry (Broussonetia papyrifera)

BACKGROUND

Lysine succinylation is a naturally occurring post-translational modification (PTM) that is ubiquitous in organisms. Lysine succinylation plays important roles in regulating protein structure and function as well as cellular metabolism. Global lysine succinylation at the proteomic level has been identified in a variety of species; however, limited information on lysine succinylation in plant species, especially paper mulberry, is available. Paper mulberry is not only an important plant in traditional Chinese medicine, but it is also a tree species with significant economic value. Paper mulberry is found in the temperate and tropical zones of China. The present study analyzed the effects of lysine succinylation on the growth, development, and physiology of paper mulberry.

RESULTS

A total of 2097 lysine succinylation sites were identified in 935 proteins associated with the citric acid cycle (TCA cycle), glyoxylic acid and dicarboxylic acid metabolism, ribosomes and oxidative phosphorylation; these pathways play a role in carbon fixation in photosynthetic organisms and may be regulated by lysine succinylation. The modified proteins were distributed in multiple subcellular compartments and were involved in a wide variety of biological processes, such as photosynthesis and the Calvin-Benson cycle.

CONCLUSION

Lysine-succinylated proteins may play key regulatory roles in metabolism, primarily in photosynthesis and oxidative phosphorylation, as well as in many other cellular processes. In addition to the large number of succinylated proteins associated with photosynthesis and oxidative phosphorylation, some proteins associated with the TCA cycle are succinylated. Our study can serve as a reference for further proteomics studies of the downstream effects of succinylation on the physiology and biochemistry of paper mulberry.

Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)-Based Proteomics of Drug-Metabolizing Enzymes and Transporters

Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a powerful tool for identifying and quantifying proteins in biological samples, outperforming conventional antibody-based methods in many aspects. LC-MS/MS-based proteomics studies have revealed the protein abundances of many drug-metabolizing enzymes and transporters (DMETs) in tissues relevant to drug metabolism and disposition. Previous studies have consistently demonstrated marked interindividual variability in DMET protein expression, suggesting that varied DMET function is an important contributing factor for interindividual variability in pharmacokinetics (PK) and pharmacodynamics (PD) of medications. Moreover, differential DMET expression profiles were observed across different species and in vitro models. Therefore, caution must be exercised when extrapolating animal and in vitro DMET proteomics findings to humans. In recent years, DMET proteomics has been increasingly utilized for the development of physiologically based pharmacokinetic models, and DMET proteins have also been proposed as biomarkers for prediction of the PK and PD of the corresponding substrate drugs. In sum, despite the existence of many challenges in the analytical technology and data analysis methods of LC-MS/MS-based proteomics, DMET proteomics holds great potential to advance our understanding of PK behavior at the individual level and to optimize treatment regimens via the DMET protein biomarker-guided precision pharmacotherapy.

Practical Synthesis of [18F]Pitavastatin and Evaluation of Hepatobiliary Transport Activity in Rats by Positron Emission Tomography

We developed a practical synthetic method for fluorine-18 (¹⁸F)-labeled pitavastatin ([¹⁸F]PTV) as a positron emission tomography (PET) tracer to assess hepatobiliary transporter activity and conducted a PET scan as a preclinical study for proof-of-concept in rats. This method is a one-pot synthesis involving aromatic ¹⁸F-fluorination of an arylboronic acid ester followed by deprotection under acidic conditions, which can be reproduced in general clinical sites equipped with a standard radiolabeling system due to the simplified procedure. PET imaging confirmed that intravenously administered [¹⁸F]PTV was rapidly accumulated in the liver and gradually transferred into the intestinal lumen through the bile duct. Radiometabolite analysis showed that [¹⁸F]PTV was metabolically stable, and 80% of the injected dose was detected as the unchanged form in both blood and bile. We applied integration plot analysis to assess tissue uptake clearance (CL_{uptake, liver} and CL_{uptake, kidney}) and canalicular efflux clearance (CL_int, bile), and examined the effects of inhibitors on membrane transport. Treatment with rifampicin, an organic anion transporting polypeptide inhibitor, significantly reduced CL_{uptake, liver} and CL_{uptake, kidney} to 44% and 64% of control, respectively. In contrast, Ko143, a breast cancer resistance protein inhibitor, did not affect CL_{uptake, liver} but significantly reduced CL_int, bile to 39% of control without change in [¹⁸F]PTV blood concentration. In addition, we found decreased CL_{uptake, liver} and increased CL_int, bile in Eisai hyperbilirubinemic rats in response to altered expression levels of transporters. We expect that [¹⁸F]PTV can be translated into clinical application, as our synthetic method does not need special apparatus in the radiolabeling system and PET scan with [¹⁸F]PTV can quantitatively evaluate transporter activity in vivo.

Optimization of sample preparation for transporter protein quantification in tissues by LC-MS/MS

BACKGROUND

Reproducible quantification of drug transporter protein expression in tissues is important for predicting transporter mediated drug disposition. Many mass-spectrometry based transporter protein quantification methods result in high variability of the estimated transporter quantities. Therefore, we aimed to evaluate and optimize mass spectrometry-based quantification method for drug transporter proteins in tissues.

MATERIALS AND METHODS

Plasma membrane (PM) proteins from mouse tissues were isolated by applying three extraction protocols: commercial plasma membrane extraction kit, tissue homogenization by Potter-Elvehjem homogenizer in combination with sucrose-cushion ultracentrifugation, and PM enrichment with Tween 40. Moreover, five different protein digestion protocols were applied on the same PM fraction. PM isolation and digestion protocols were evaluated by measuring the amount of transporter proteins by liquid chromatography-tandem mass spectrometry in selected reaction monitoring mode.

RESULTS

Mouse liver homogenization by Potter-Elvehjem homogenizer in combination with sucrose-cushion ultracentrifugation and PM enrichment with Tween 40 resulted in two times higher transporter protein quantity (Breast cancer resistance protein (Bcrp) 18.0 fmol/μg protein) in comparison with the PM samples isolated by extraction kit (Bcrp 9.8 fmol/μg protein). The evaluation of protein digestion protocols revealed that the most optimal protocol for PM protein digestion is with Lys-C and trypsin, in combination with trypsin enhancer and heat denaturation. Overall, quantities of Bcrp and Na+/K + ATPase proteins evaluated in mouse liver and kidney cortex by using our optimized PM isolation method, as well as, established digestion protocol were two to three times higher than previously reported and coefficient of variation (CV) for technical replicates was below 10%.

CONCLUSION

We have established an improved transporter protein quantification methodology by optimizing PM isolation and protein digestion procedures. The optimized procedure resulted in a higher transporter protein yield and improved precision.

Applications of proteomics in pharmaceutical research and development

The significance of proteomics in the pharmaceutical industry has increased since overcoming initial difficulties. This review discusses recent proteomics publications from pharmaceutical companies to identify new trends in proteomics applications to research and development. Applications of proteomics such as chemical proteomics, protein expression profiling, targeted protein quantitation, analysis of protein-protein interactions and post-translational modification are widely used by various sections of the industry. Technological advancements in proteomics will further accelerate pharmaceutical research and development.