Metabolite identification in preclinical and clinical phase of drug development

An Integrated Hepatocyte Stability Assay for Simultaneous Metabolic Stability Assessment and Metabolite Profiling

The determination of metabolic stability is critical for drug discovery programs, allowing for the optimization of chemical entities and compound prioritization. As such, it is common to perform high-volume in vitro metabolic stability experiments early in the lead optimization process to understand metabolic liabilities. Additional metabolite identification experiments are subsequently performed for a more comprehensive understanding of the metabolic clearance routes to aid medicinal chemists in the structural design of compounds. Collectively, these experiments require extensive sample preparation and a substantial amount of time and resources. To overcome the challenges, a high-throughput integrated assay for simultaneous hepatocyte metabolic stability assessment and metabolite profiling was developed. This assay platform consists of four parts: 1) an automated liquid-handling system for sample preparation and incubation, 2) a liquid chromatography and high-resolution mass spectrometry-based system to simultaneously monitor the parent compound depletion and metabolite formation, 3) an automated data analysis and report system for hepatic clearance assessment; and 4) streamlined autobatch processing for software-based metabolite profiling. The assay platform was evaluated using eight control compounds with various metabolic rates and biotransformation routes in hepatocytes across three species. Multiple sample preparation and data analysis steps were evaluated and validated for accuracy, repeatability, and metabolite coverage. The combined utility of an automated liquid-handling instrument, a high-resolution mass spectrometer, and multiple streamlined data processing software improves the process of these highly demanding screening assays and allows for simultaneous determination of metabolic stability and metabolite profiles for more efficient lead optimization during early drug discovery. SIGNIFICANCE STATEMENT: Metabolic stability assessment and metabolite profiling are pivotal in drug discovery to fully comprehend metabolic liabilities for chemical entity optimization and lead selection. Process of these assays can be repetitive and resource demanding. Here, we developed an integrated hepatocyte stability assay that combines automation, high-resolution mass spectrometers, and batch-processing software to improve and combine the workflow of these assays. The integrated approach allows simultaneous metabolic stability assessment and metabolite profiling, significantly accelerating screening and lead optimization in a resource-effective manner.

Metabolism investigation of the peptide-drug conjugate LN005 in rats using UHPLCHRMS

LN005, as a peptide-drug conjugate (PDC), is a conjugate of the homing peptide VAP and doxorubicin (DOX). The exceptional targeting ability of the homing peptide VAP is directed toward glucose-regulated protein (GRP78), a highly expressed protein primarily found in the endoplasmic reticulum of various solid tumors. However, there are limited reports regarding the metabolism of peptide-drug conjugates (PDCs), and the in vivo metabolism of LN005 has yet to be investigated. After intravenous injection of 18 mg/kg LN005 in SD rats, biological samples including plasma, urine, fecal, and bile samples, were collected and analyzed by ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). A total of 11 possible metabolites of LN005 were identified. Unchanged LN005 was found to be the main component in rat blood and urine, accounting for 46.46% and 63.79% of the total peak areas, respectively. M1057 was the most abundant metabolite in feces, accounting for 57.65% of the total peak area. Only one metabolite, M398, was identified in rat bile. The metabolism of LN005 is closely related to DOX, and the primary metabolic pathways involved oxidative deamination or hydrolysis, reductive glycosidic cleavage, hydrolytic glycosidic cleavage, and dehydrogenation.

Two Multidimensional Chromatography/High-Resolution Mass Spectrometry Approaches Enabling the In-Depth Metabolite Characterization Simultaneously from Three Glycyrrhiza Species: Method Development, Comparison, and Integration

Two offline multidimensional chromatography/high-resolution mass spectrometry systems (method 1: fractionation and online two-dimensional liquid chromatography, 2D-LC; method 2: fractionation and offline 2D-LC) were established to characterize the metabolites simultaneously from three Glycyrrhiza species. Ion exchange chromatography in the first-dimensional (1D) separation was well fractionated between the acidic (mainly triterpenoids) and weakly acidic components (flavonoids). These obtained subsamples got sophisticated separation by the second (2D) and third dimension (3D) of chromatography either by online reversed-phase chromatography × reversed-phase chromatography (RPC × RPC) or offline hydrophilic interaction chromatography × RPC (HILIC × RPC). Orthogonality for the 2D/3D separations reached 0.73 for method 1 and 0.81 for method 2, respectively. We could characterize 1097 compounds from three Glycyrrhiza species based on an in-house library and 33 reference standards, involving 618 by method 1 and 668 by method 2, respectively. They exhibited a differentiated performance and complementarity in identifying the multiple subclasses of Glycyrrhiza components.

Structural Elucidation of Agrochemical Metabolic Transformation Products Based on Infrared Ion Spectroscopy to Improve In Silico Toxicity Assessment

Toxicological assessments of newly developed agrochemical agents consider chemical modifications and their metabolic and biotransformation products. To carry out an in silico hazard assessment, understanding the type of chemical modification and its location on the original compound can greatly enhance the reliability of the evaluation. Here, we present and apply a method based on liquid chromatography-mass spectrometry (LC-MS) enhanced with infrared ion spectroscopy (IRIS) to better delineate the molecular structures of transformation products before in silico toxicology evaluation. IRIS facilitates the recording of IR spectra directly in the mass spectrometer for features selected by retention time and mass-to-charge ratio. By utilizing quantum-chemically predicted IR spectra for candidate molecular structures, one can either derive the actual structure or significantly reduce the number of (isomeric) candidate structures. This approach can assist in making informed decisions. We apply this method to a plant growth stimulant, digeraniol sinapoyl malate (DGSM), that is currently under development. Incubation of the compound in Caco-2 and HepaRG cell lines in multiwell plates and analysis by LC-MS reveals oxidation, glucuronidation, and sulfonation metabolic products, whose structures were elucidated by IRIS and used as input for an in silico toxicology assessment. The toxicity of isomeric metabolites predicted by in silico tools was also assessed, which revealed that assigning the right metabolite structure is an important step in the overall toxicity assessment of the agrochemical. We believe this identification approach can be advantageous when specific isomers are significantly more hazardous than others and can help better understand metabolic pathways.

Production of an O-desmethylated product, a major human metabolite, of rabeprazole sulfide by bacterial P450 enzymes

Rabeprazole is a common type of proton pump inhibitor (PPI) used to treat various peptic disorders. Unlike most PPI drugs, rabeprazole is spontaneously reduced to rabeprazole sulfide (thioether) when it is given to patients. As a result, rabeprazole sulfide is considered one of the active metabolites of rabeprazole. Rabeprazole sulfide is mainly metabolized to desmethyl rabeprazole sulfide by CYP2C19 and CYP2D6 in people. However, the pharmacological efficacy and safety of desmethyl rabeprazole sulfide have not yet been investigated. Its usage is challenging due to the high cost associated with the drug. In this study, we found CYP102A1 mutants that can produce desmethyl rabeprazole sulfide as a major metabolite of rabeprazole sulfide. The chemical characteristics of the major product were confirmed using high-performance liquid chromatography, LC-mass spectrometry, and nuclear magnetic resonance spectroscopy. CYP102A1 mutants R47L/F87V/L188Q, R47L/F87V/L188Q/A335V/Q359R, and R47L/F87V/L188Q/I254V/D351E showed kcat values of 39, 93, and 88 min-1, respectively, for O-desmethylation of rabeprazole sulfide. Furthermore, the highest concentration of desmethyl rabeprazole sulfide product from 2 mM rabeprazole sulfide at optimal conditions was obtained in bacterial whole-cell biotransformation with the R47L/F87V/L188Q mutant, reaching 0.63 mM at 4-h incubation. In conclusion, we present a platform that facilitates the efficient and sustainable production of the desmethylated product from rabeprazole sulfide for use in the biopharmaceutical industry.

Rapid extraction of osimertinib and its active metabolite in urine by miniaturized centrifugal spin-column extraction using ionic liquid hybrid hierarchical porous adsorbent

Osimertinib (OSIM) is widely used as a mainstream drug for the treatment of non-small cell lung cancer (NSCLC). However, the lack of a rapid extraction and detection method for OSIM and its metabolite, AZ-5104, has limited clinical drug metabolism and drug resistance research because the drug is unstable. In this study, a new ionic liquid hybrid hierarchical porous material (IL-HHPM) was synthesized with hierarchical porous structures, including micropores (1.6-2.0 nm), mesopores (2.0-50.0 nm), macropores (50.0-148.7 nm), and multiple functional groups via a one-step hydrothermal method using silanized ionic liquids (IL) as functionalized hybrid monomer. The IL-HHPM has the advantages of a high specific surface area (437.4 ± 4.6 m2 g-1), sizable pore volume (0.74 cm3 g-1), and fast mass transfer, additionally, the IL-HHPM adsorbed OSIM and AZ-5104 via π-π interactions and hydrogen bonding. OSIM and AZ-5104 were rapidly extracted and measured in human urine using rapid and miniaturized centrifugal spin-column extraction (MCSCE), which was based on the IL-HHPM. The optimized factors for the extraction recoveries of OSIM and AZ-5104 were adsorbent dosage (8.0 mg), sample volume (0.5 mL), and operation time (9.0 min), and markedly reduced the adsorbent dosage and operation time. The IL-HHPM-MCSCE-HPLC method displayed good linearity (0.02-5.00 μg mL-1, r ≥ 0.9997), satisfying accuracy (spiked recoveries of 87.7%-100.0%), and good precision (RSDs ≤ 7.0%). The developed method is rapid, sensitive, and reproducible for the simultaneous determination of trace level of OSIM and AZ-5104 in human urine.

Comprehensive Metabolite Identification of Genipin in Rats Using Ultra-High-Performance Liquid Chromatography Coupled with High Resolution Mass Spectrometry

Genipin, an aglycone of geniposide, is a rich iridoid component in the fruit of Gardenia jasminoides Ellis and has numerous biological activities. However, its metabolic profiles in vivo and vitro remain unclear. In this study, an effective analytical strategy based on ultra-high-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) in positive and negative ion modes was developed to analyze and identify genipin metabolites in rat urine, blood, feces, and fecal fermentation in combination with many methods including post-collection data mining methods, high-resolution extracted ion chromatography (HREIC), and multiple mass defect filtering (MMDF). Simultaneously, the metabolites of genipin in vivo were verified by fecal fermentation of SD rats at different times. Finally, based on information such as reference substances, chromatographic retention behavior, and accurate mass determination, a total of 50 metabolites (including prototypes) were identified in vivo. Among them, 7, 31 and 28 metabolites in vivo were identified in blood, urine, and feces, respectively. Our results showed that genipin could generate different metabolites that underwent multiple metabolic reactions in vivo including methylation, hydroxylation, dehydroxylation, hydrogenation, sulfonation, glucuronidation, demethylation, and their superimposed reactions. Forty-six metabolites were verified in vitro. Meanwhile, 2 and 19 metabolites identified in blood and urine were also verified in fecal fermentation at different times. These results demonstrated that metabolites were produced in feces and reabsorbed into the body. In conclusion, the newly discovered metabolites of genipin can provide a new perspective for understanding its pharmacological effects and build the foundation for thee toxicity and safety evaluations of genipin.

A multidimensional chromatography/high-resolution mass spectrometry approach for the in-depth metabolites characterization of two Astragalus species

To address the chemical complexity is indispensable in a number of research fields. Herb metabolome is typically composed by more than one class of structure analogs produced via different biosynthetic pathways. Multidimensional chromatography (MDC), due to the greatly enhanced separation space, offers the potential solution to comprehensive characterization of herbal metabolites. Here, we presented a strategy, by integrating MDC and quadrupole time-of-flight mass spectrometry (QTOF-MS), to accomplish the in-depth herbal metabolites characterization. Using the metabolome of two Astragalus species (A. membranaceus var. mongholicus,AMM; A. membranaceus, AM) as the case, an off-line three-dimensional liquid chromatography (3D-LC) system was established: hydrophilic interaction chromatography using an XAmide column as the first dimension (¹D) for fractionating the total extract, on-line reversed-phase × reversed-phase liquid chromatography separately configuring a CSH Fluoro-Phenyl column and a Cosmocore C18 column as the second dimension (²D) and the third dimension (³D) of chromatography to enable the explicit separation of three well fractionated samples. Moreover, the negative-mode collision-induced dissociation by QTOF-MS under the optimized condition could provide diversified fragments that were useful for the structural elucidation of AMM and AM. An in-house library (composed by 247 known compounds) and comparison with 43 reference standards were utilized to assist more reliable characterization. We could characterize 513 compounds from two Astragalus species (344 from AMM and 323 from AM), including 236 flavonoids, 150 triterpenoids, 18 organic acids, and 109 others. Conclusively, the established MDC approach gained excellent performance favoring the analogs-oriented in-depth characterization of herbal metabolites, but received uncompromising analytical efficiency.

Covalent Binding Mechanism of Furmonertinib and Osimertinib With Human Serum Albumin

As third-generation tyrosine kinase inhibitors, furmonertinib and osimertinib exhibit better efficacy than first- and second-generation tyrosine kinase inhibitors in patients with advanced non-small cell lung cancer. However, radioactive pharmacokinetics studies showed that parent-related components remain in human plasma for at least 21 days after oral administration. Similar pharmacokinetic profiles were found in pyrotinib and neratinib, which have been identified to covalently bind with human serum albumin at Lys-190, leading to low extraction recovery in protein precipitation. However, the binding mechanism of furmonertinib and osimertinib in human plasma has not been confirmed. Comprehensive techniques were used to investigate the mechanism of this binding, including ultra high-performance liquid chromatography coupled with high-resolution mass spectrometry and online/offline radioactivity profiling. SDS-PAGE and further autoradiography were also used to detect drug-protein adducts. We found that most furmonertinib exists in the human plasma following ex vivo incubation in the form of protein-drug adducts. Only lysine-furmonertinb adducts were found in pronase digests. A standard reference of lysine-furmonertinib was synthesized and confirmed by NMR. Through peptide mapping analysis, we confirmed that furmonertinib almost exclusively binds with human serum albumin (HSA) in plasma following ex vivo incubation, via Michael addition at Lys-195 and Lys-199, instead of Lys-190. Two peptides found to bond with furmonertinib were ASSAKQR and LKCASLQK. Osimertinib was also found to bond with Lys-195 and Lys-199 of HSA via peptide mapping analysis. SIGNIFICANCE STATEMENT: Here we report that furmonertinib and osimertinib can covalently bind with human serum albumin at the site of Lys-195 and Lys-199 instead of Lys-190, potentially leading to the long duration of drug-protein adducts in the human body.

Roles of Human Liver Cytochrome P450 Enzymes in Tenatoprazole Metabolism

Tenatoprazole, a newly developed proton pump inhibitor candidate, was developed as an acid inhibitor for gastric acid hypersecretion disorders such as gastric ulcer and reflux esophagitis. It is known that tenatoprazole is metabolized to three major metabolites of 5'-hydroxy tenatoprazole, tenatoprazole sulfide, and tenatoprazole sulfone in human liver, primarily catalyzed by CYPs 2C19 and 3A4. While CYP2C19 prefers the hydroxylation of tenatoprazole at C-5' position, CYP3A4 is mainly involved in sulfoxidation reaction to make tenatoprazole sulfone. Tenatoprazole sulfide is a major human metabolite of tenatoprazole and is formed spontaneously and non-enzymatically from tenatoprazole. However, its metabolic fate in the human liver is not fully known. Furthermore, no systematic metabolic study has been performed to study tenatoprazole or tenatoprazole sulfide. Here, we studied the functions of human cytochromes P450 in the metabolic pathway of tenatoprazole and tenatoprazole sulfide by using recombinant human P450s and human liver microsomes. Both CYP 2C19 and CYP3A4 showed distinct regioselective and stereospecific monooxygenation activities toward tenatoprazole and tenatoprazole sulfide. Furthermore, a new major metabolite of tenatoprazole sulfide was found, 1'-N-oxy-5'-hydroxytenatoprzole sulfide, which has never been reported. In conclusion, the metabolic fates of tenatoprazole and tenatoprazole sulfide should be considered in the clinical use of tenatoprazole.

Stereoselective toxicity, bioaccumulation, and metabolic pathways of triazole fungicide cyproconazole in zebrafish

Cyproconazole (CPZ) is a broad-spectrum fungicide that is widely used around the world. CPZ can persist in water which raised concerns about its potential adverse effects on aquatic life. In this study, the stereoselective toxicity, bioaccumulation, elimination, and kinetic biotransformation in zebrafish were investigated. The LC₅₀ of 96 h acute toxicity was 15.88, 19.68, 26.99, and 17.10 mg/L for SR-, SS-, RS-, and RR-CPZ, respectively. The uptake and elimination experiment showed the bioconcentration factor in order of SR- > RR- > SS- > RS-CPZ at the exposure concentration of 0.1 and 1 mg/L. In the depuration stage, CPZ isomers were rapidly eliminated by 99% within 24 h. Moreover, the oxidative stress responses (POD, SOD, and CAT) were stereoselectively induced by CPZ stereoisomers, the activity of POD was significantly increased in all CPZ treatment groups compared to the control while the activity of CAT exhibited a concentration-dependent decrease in the CPZ treatment group. Multiple metabolic pathways of CPZ in zebrafish were proposed for the first time and 7 phase I metabolites and 25 phase II conjugates were found. This study determined the potential toxicity of CPZ to zebrafish and provided a strategy for the risk evaluation of CPZ stereoisomers in aquatic ecosystems.

Metabolite Identification of a Novel Anti-Leishmanial Agent OJT007 in Rat Liver Microsomes Using LC-MS/MS

The purpose of this study was to identify potential metabolic pathways and metabolites of OJT007, a methionine aminopeptidase 1 (MetAP1) inhibitor. OJT007 is a novel drug with potent antiproliferative effects against Leishmania Major. We conducted in vitro Phase I oxidation and Phase II glucuronidation assays on OJT007 using rat liver microsomes. Four unknown metabolites were initially identified using a UPLC-UV system from microsomal incubated samples. LC-MS/MS analysis was then used to identify the structural characteristics of these metabolites via precursor ion scan, neutral loss scan, and product ion scan. A glucuronide metabolite was further confirmed by β-glucuronidase hydrolysis. The kinetic parameters of OJT007 glucuronidation demonstrated that OJT007 undergoes rapid metabolism. These results demonstrate the liver's microsomal ability to mediate three mono-oxidated metabolites and one mono-glucuronide metabolite. This suggests hepatic glucuronidation metabolism of OJT007 may be the cause of its poor oral bioavailability.