Characterization of reactive intermediates formation in dacomitinib metabolism and bioactivation pathways elucidation by LC-MS/MS: in vitro phase I metabolic investigation

Dacomitinib (DCB) is a second generation irreversible tyrosine kinase inhibitor (TKI) that is claimed to overcome the disadvantages of the resistance developed by the first line epidermal growth factor receptor (EGFR) TKIs. In the current study, metabolites of phase I for DCB were systematically explored. DCB reactive metabolites were also investigated in rat liver microsomes in presence of potassium cyanide or methoxylamine that were employed as capturing agents for iminium reactive intermediates and aldehyde, respectively, to form stable complexes which can be detected by LC-MS/MS. As a result, four in vitro phase I metabolites were observed with major pathway of piperidine ring hydroxylation. Additionally, two potentially reactive intermediates, one aldehyde and one iminium ions were characterized. Two different pathways of bioactivation were ultimately proposed.

Dacomitinib (DCB) is a second generation irreversible tyrosine kinase inhibitor (TKI) that is claimed to overcome the disadvantages of the resistance developed by the first line epidermal growth factor receptor (EGFR) TKIs.     

Sapitinib: reactive intermediates and bioactivation pathways characterized by LC-MS/MS

Sapitinib (AZD8931, SAP) is an epidermal growth factor receptor (EGFR) family (pan-erbB) tyrosine kinase inhibitor. In multiple tumor cell lines, SAP has been shown to be a much more potent inhibitor of EGF-driven cellular proliferation than gefitinib. In this in vitro metabolic study, we tested the generation of reactive intermediates from SAP using human liver microsomes and a capturing agent (potassium cyanide) to trap the iminium reactive intermediates. The same metabolic reaction was further repeated in the presence of methoxyamine to trap aldehyde intermediates. The identification of SAP metabolites revealed that the hydroxylation metabolic reaction represents the major in vitro metabolic pathway occurring at the piperidine moiety. We characterized six in vitro phase I metabolites in addition to three reactive intermediates (i.e., two iminiums and one aldehyde), therefore suggesting two probable SAP-bioactivation pathways. We hypothesized that the piperidine ring nitrogen (cyclic tertiary amine) activated the two adjacent α-carbons within the ring. The oxidative dealkylation of the N-acetamide group led to an unstable aldehyde that was trapped using methoxyamine, generating an oxime adduct that was detected using liquid chromatography-tandem mass spectrometry (LC-MS/MS). To the best of our knowledge, this is the first study presenting the structural characterization of SAP reactive intermediates.

Sapitinib is a competitive ATP inhibitor of EGFR and receptor tyrosine-protein kinase (erbB-2). Two cyano and one oxime adducts, and six in vitro metabolites of sapitinib were identified using LC-MS/MS. The bioactivation pathways were characterized.     

Phase I metabolic profiling and unexpected reactive metabolites in human liver microsome incubations of X-376 using LC-MS/MS: bioactivation pathway elucidation and in silico toxicity studies of its metabolites

X-376 is a novel new generation anaplastic lymphoma kinase (ALK) inhibitor that can cross the blood brain barrier, so it can be used in patients with both ALK-positive NSCLC with CNS metastases. In this study, X-376 was incubated with human liver microsomes, and in vitro phase-I metabolic reactions were performed to generate X-376 reactive intermediates, which cannot be detected directly as they are unstable. Utilizing LC-MS/MS, we characterized X-376 metabolites and checked for the reactive electrophile generation using nucleophilic trapping agents, namely, potassium cyanide and GSH, which form stable adducts for characterization by mass spectrometry. Four X-376 phase-I metabolites and three reactive intermediates (one quinone methide and two iminium ions) were characterized and the bioactivation pathways were proposed. X-376 bioactivation occurred through unexpected novel pathways. Although the pyridazine ring was found to be bioactivated, no bioactivation was detected in the expected N-methyl piperazine ring that is often found for similar structures. The dichloro-phenyl group was bioactivated by a novel mechanism that was verified by LC-MS/MS. We propose that the X-376 reported side effects may be due to the formation of reactive metabolites. The in silico toxicity assessment of X-376 metabolites was carried out using DEREK software and structural modification were proposed to reduce their side effects and to validate the bioactivation pathway theory using StarDrop DEREK module. Further drug discovery studies can be done according to this concept, thus allowing the development of new drugs with more safety profile that was confirmed by using StarDrop software. To our knowledge, this is the first study of in vitro metabolic profiling or structural characterization and toxicological properties of the generated metabolites for X-376.

Metabolites of X-376 were characterized by LC-MS/MS. Pyridazine ring and dichloro-phenyl groups were bioactivated by novel pathways.     

Reactive intermediates in copanlisib metabolism identified by LC-MS/MS: phase I metabolic profiling

Copanlisib (CNB; Aliqopa™) is a novel, intravenous phosphoinositide 3-kinase inhibitor used to treat various solid and hematological malignancies. CNB was recently approved by the U.S. FDA to treat adults that relapsed after two preceding systemic therapies. Using LC-MS/MS, we screened for the in vitro metabolites of CNB formed in human liver microsomes (HLMs) and probed for the generation of reactive electrophiles using methoxyamine and potassium cyanide as nucleophiles to capture reactive electrophiles by forming stable adducts that are suitable for identification by LC-MS/MS. Seven CNB phase I metabolites generated by oxidation, hydroxylation, oxidative dealkylation, reduction, and N-oxidation were identified. In addition, four reactive electrophiles, 2 aldehydes and 2 iminium ions, were identified, and a prediction of the corresponding bioactivation mechanism is presented. The formation of reactive metabolites may be associated with the side effects reported for CNB. To our knowledge, this is the first report on the detailed structural characterization of reactive intermediates generated in CNB metabolism.

Copanlisib (CNB; Aliqopa™) is a novel, intravenous phosphoinositide 3-kinase inhibitor used to treat various solid and hematological malignancies.     

Correction: In silico and in vitro metabolism of ribociclib: a mass spectrometric approach to bioactivation pathway elucidation and metabolite profiling

Correction for ‘In silico and in vitro metabolism of ribociclib: a mass spectrometric approach to bioactivation pathway elucidation and metabolite profiling’ by Thamer A. Alsubi et al., RSC Adv., 2020, 10, 22668–22683, DOI: 10.1039/D0RA01624A.

The authors regret that the email address for the corresponding author was shown incorrectly in the original article. The corrected email address is as shown above.The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.     

In silico and in vitro metabolism of ribociclib: a mass spectrometric approach to bioactivation pathway elucidation and metabolite profiling

Ribociclib (RBC, Kisqali®) is a highly selective CDK4/6 inhibitor that has been approved for breast cancer therapy. Initially, prediction of susceptible sites of metabolism and reactivity pathways were performed by the StarDrop WhichP450™ module and the Xenosite web predictor tool, respectively. Later, in vitro metabolites and adducts of RBC were characterized from rat liver microsomes using LC-MS/MS. Subsequently, in silico data was used as a guide for the in vitro work. Finally, in silico toxicity assessment of RBC metabolites was carried out using DEREK software and structural modification was proposed to reduce their side effects and to validate the bioactivation pathway theory using the StarDrop DEREK module. In vitro phase I metabolic profiling of RBC was performed utilizing rat liver microsomes (RLMs). Generation of reactive metabolites was investigated using potassium cyanide (KCN) as a trapping nucleophile for the transient and reactive iminium intermediates to form a stable cyano adduct that can be identified and characterized using mass spectrometry. Nine phase I metabolites and one cyano adduct of RBC were characterized. The proposed metabolic pathways involved in generation of these metabolites are hydroxylation, oxidation and reduction. The reactive intermediate generation mechanism of RBC may provide an explanation of its adverse reactions. Aryl piperazine is considered a structural alert for toxicity as proposed by the DEREK report. We propose that the generation of only one reactive metabolite of RBC in a very small concentration is due to the decreased reactivity of the piperazine ring compared to previous reports of similar drugs. Docking analysis was performed for RBC and its proposed derivatives at the active site of the human CDK6 enzyme. Methyl-RBC exhibited the best ADMET and docking analysis and fewer side effects compared to RBC and fluoro-RBC. Further drug discovery studies can be conducted taking into account this concept allowing the development of new drugs with enhanced safety profiles that were confirmed by using StarDrop software. To the best of our knowledge, this is the first literature report of RBCin vitro metabolic profiling and structural characterization and toxicological properties of the generated metabolites.

Nine phase I metabolites and one product of KCN trapping of RBC were characterized. Aryl piperazine is considered a structural alert for toxicity as proposed by the DEREK report. Methyl-RBC exhibited less toxicity and more binding affinity to CDK6.     

Identification and characterization of in silico,in vivo,in vitro,and reactive metabolites of infigratinib using LC-ITMS: bioactivation pathway elucidation and in silico toxicity studies of its metabolites

Infigratinib (INF) is a novel, small molecule that is orally administered to inhibit human fibroblast growth factor receptors (FGFRs), which are a family of receptor tyrosine kinases that may be upregulated in different tumor cell types. On 6 January 2020, the FDA granted fast track designation to INF for first-line treatment of cholangiocarcinoma. Prediction of susceptible sites of metabolism and reactivity pathways (cyanide and GSH) for INF was performed by the Xenosite web predictor tool. Then, we report the characterization and identification of in vitro, in vivo, and reactive intermediates of INF using liquid chromatography ion trap mass spectrometry (LC-ITMS). Finally, an in silico toxicity assessment of INF metabolites was carried out using the StarDrop DEREK module showing structural alerts. Rat liver microsomes (RLMs) and isolated perfused rat liver hepatocytes were incubated with INF in vitro and the generated metabolites were collected by protein precipitation. In vivo metabolism was evaluated by time-course urine sampling from Sprague-Dawley rats administered a single INF oral dose. A similar volume of acetonitrile was added to each collected urine sample and both organic and aqueous layers were analyzed by LC-ITMS to detect in vivo INF metabolites. N-Ethyl piperazine rings and benzene at part A of the INF structure are metabolized to form iminium and 1,4-benzoquinone, respectively, which are very reactive toward nucleophilic macromolecules. Incubation of INF with RLMs in the presence of 1.0 mM KCN and 1.0 mM glutathione was used to evaluate reactive metabolites potentially responsible for toxicities associated with INF. There were seven in vitro phase I metabolites, three in vitro phase II metabolites, three cyano adducts, and three GSH conjugate metabolites of INF detected by LC-ITMS. In vivo INF metabolites identified included four in vivo phase I and three in vivo phase II metabolites. In vitro and in vivo phase I metabolic pathways included N-dealkylation, N-demethylation, O-demethylation, hydroxylation, and dechlorination, while the in vivo phase II metabolic reaction was a direct conjugation of INF with glucuronic acid and sulphate.

An in silico web designer tool was utilized to guide laboratory work for infigratinib metabolism. Sixteen metabolites of infigratinib and seven reactive intermediates (three iminium ions and four 1,4 benzoquinones) were characterized using LC-ITMS.     

Global metabolomic profiling of trastuzumab resistant gastric cancer cells reveals major metabolic pathways and metabolic signatures based on UHPLC-Q exactive-MS/MS

Resistance mechanism exploration has become an urgent need owing to the widespread trastuzumab resistance in gastric cancer. In this study, UHPLC-Q exactive MS/MS was carried out to characterize the metabolic profiles of human gastric cancer cell lines NCI N87, MKN45 (trastuzumab-sensitive) and NCI N87/R, MKN45/R (trastuzumab-resistant), respectively. Metabolic signatures and different metabolites were identified using multivariate in combination with univariate analysis. Integrated pathway enrichment analysis was executed using MetaboAnalyst and KEGG metabolic libraries to analyze the altered metabolic pathways in trastuzumab resistant cells. A total of 79 and 75 different metabolites were positively identified by utilizing authentic standards in NCI N87/R and MKN45/R cells, respectively. Furthermore, enrichment analysis demonstrated that seven metabolic pathways in NCI N87/R cells and five in MKN45/R cells were significantly changed. These pathways are involved in amino acid, nucleotide, carbohydrate, cofactor and vitamin metabolism, of which alanine, aspartate and glutamate metabolism displayed the highest pathway impact and lower P value both in NCI N87/R and MKN45/R cells. Moreover, we constructed a metabolomics–proteomics network between substantially altered metabolites and target genes which revealed citrate being regulated by citrate synthase and ACLY, while proline regulation was due to EPRS, PYCRL and PYCR1/2, respectively. Overall, our findings disclose prominent alterations of metabolic signatures in NCI N87/R and MKN45/R cells when compared with the parent cells which are crucial for understanding of underlying mechanisms of resistance and for developing strategies to overcome trastuzumab resistance.

Resistance mechanism exploration has become an urgent need owing to the widespread trastuzumab resistance in gastric cancer.     

Relation between chloroguanide bioactivation to cycloguanil and the genetically determined metabolism of mephenytoin in humans.

It has been suggested recently that the bioactivation of chloroguanide hydrochloride (proguanil) to its active antimalarial metabolite cycloguanil cosegregates with the genetically determined polymorphism of mephenytoin hydroxylation. We determined the chloroguanide to cycloguanil ratio in urine after oral administration of a single dose of 200 mg proguanil either alone or together with 100 mg racemic mephenytoin or 40 mg dextromethorphan in a randomized crossover study performed in 24 healthy subjects. The mephenytoin hydroxylation index was also determined after administration of 100 mg racemic mephenytoin either alone or together with 200 mg proguanil. Two subjects were poor metabolizers and one subject was an intermediate metabolizer of mephenytoin. These three subjects had chloroguanide to cycloguanil ratios of more than 50. The 21 subjects with the extensive metabolizer phenotype for mephenytoin hydroxylation had chloroguanide to cycloguanil ratios of less than 10. The chloroguanide to cycloguanil ratio was not significantly altered by mephenytoin or dextromethorphan coadministration. The trend toward a correlation between chloroguanide/cycloguanil ratio and log mephenytoin hydroxylation index did not reach statistical significance. Inclusion of the dextromethorphan metabolic ratio into the model did not improve the relationship. These findings confirm that the bioactivation of chloroguanide to cycloguanil cosegregates with the genetically determined activity of the CYP2C family. However, the chloroguanide to cycloguanil ratio and the mephenytoin hydroxylation index do not similarly reflect the variable activity of CYP2C.     

Murine Kupffer cells. Mononuclear phagocytes deficient in the generation of reactive oxygen intermediates

Murine Kupffer cells (KC) were isolated by a high yield collagenase perfusion technique. The morphology, surface markers, and secretory products were typical of macrophages in other tissues. However, KC released negligible levels of H2O2 and O-2, in contrast to peritoneal macrophages. KC oxygen consumption was not increased by agents triggering a respiratory burst in peritoneal cells. Moreover, KC capacity to secrete reactive oxygen intermediates (ROI), in contrast to Ia antigen expression, was not enhanced by exposure to lymphokines or recombinant gamma interferon. The selective defect in KC oxidative response was paralleled by impaired in vitro killing of Toxoplasma gondii trophozoites and Leishmania donovani promastigotes and amastigotes. Deficient secretion of ROI by KC might protect hepatocytes and erythrocytes from injury during endocytosis by KC, but might render the liver more susceptible to parasitization by organisms that are primarily killed through oxygen-dependent mechanisms.     

Cytochrome P-450-dependent bioactivation of 1,1-dichloroethylene to a reactive epoxide in human lung and liver microsomes

We investigated the cytochrome P-450-dependent metabolism of 1, 1-dichloroethylene (DCE) by human lung and liver microsomes and compared the results from analogous experiments in mice. Metabolites were identified by HPLC analysis of their glutathione conjugates and/or hydrolyzed products and were detected by using [14C]DCE. The role of human CYP2E1 in the metabolic reactions was examined by comparing p-nitrophenol hydroxylase activities with levels of metabolites formed and by using the CYP2E1-selective inhibitor diallyl sulfone. The major products formed in microsomal incubations containing NADPH were the DCE-epoxide-derived glutathione conjugates 2-(S-glutathionyl)acetyl glutathione and 2-S-glutathionyl acetate. Lower levels of the acetal of 2,2-dichloroacetaldehyde were also detected. In lung samples from eight patients, the amounts of epoxide-derived conjugates formed ranged from 15.6 +/- 4.23 to 34.9 +/- 12.75 pmol/mg protein/min. The levels in murine lung were higher at 40.0 +/- 3.8 pmol/mg protein/min. In liver samples from five patients, conjugate levels ranged from 46.5 +/- 8.3 to 240.0 +/- 10. 5 pmol/mg protein/min, whereas levels in murine liver were 83.0 +/- 6.2 pmol/mg protein/min. Conjugate levels formed in human liver correlated with the relative levels of p-nitrophenol hydroxylase activity present, but this relationship was equivocal in human lung. Diallyl sulfone inhibited the formation of the glutathione conjugates (20-65%) in liver samples from all four patients, whereas only one of five human lung samples exhibited this inhibition (27%). These results demonstrated that the DCE-epoxide is a major metabolite formed by human microsomes and is mediated by CYP2E1 in liver and in some individuals in lung.     

Interaction of antimycobacterial drugs with the anti-Mycobacterium avium complex effects of antimicrobial effectors, reactive oxygen intermediates, reactive nitrogen intermediates, and free fatty acids produced by macrophages

The profiles of the interaction of antimycobacterial drugs with macrophage (MPhi) antimicrobial mechanisms have yet to be elucidated in detail. We examined the effects of various antimycobacterial drugs on the anti-Mycobacterium avium complex (MAC) antimicrobial activity of reactive oxygen intermediates (ROIs), especially of an H(2)O(2)-halogen (H(2)O(2)-Fe(2+)-NaI)-mediated bactericidal system, reactive nitrogen intermediates (RNIs), and free fatty acids (FFAs), which are known as central antimicrobial effectors of host MPhis against mycobacterial pathogens. We have found that certain drugs, such as rifampin (RIF), rifabutin (RFB), isoniazid (INH), clofazimine (CLO), and some fluoroquinolones, strongly or moderately reduced the anti-MAC activity of the H(2)O(2)-Fe(2+)-NaI system, primarily by inhibiting the generation of hypohalite ions and in part by interfering with the halogenation reaction of bacterial cell components due to the H(2)O(2)-Fe(2+)-NaI system. This phenomenon is specific to the H(2)O(2)-Fe(2+)-NaI system, since these drugs did not reduce the anti-MAC activity of RNIs and FFAs. From the perspective of the chemotherapy of MAC infections, the present findings indicate an important possibility that certain antimycobacterial drugs, such as rifamycins (RIF and RFB), INH, CLO, and also some types of fluoroquinolones, may interfere with the ROI-mediated antimicrobial mechanisms of host MPhis against intracellular MAC organisms.     

串联质谱和高效液相色谱-串联质谱二次筛查联合应用于新生儿MMA筛查

目的探讨串联质谱和高效液相色谱-串联质谱二次筛查联合应用在甲基丙二酸血症(MMA)中的筛查价值。方法收集新生儿串联质谱初筛结果中C3、C3/C2、C3/C0单一或多个指标异常的新生儿干血滤纸片标本,用高效液相色谱-串联质谱的方法定量检测原始血片中甲基丙二酸、甲基枸橼酸和高半胱氨酸,对二次筛查后疑似阳性的新生儿进行召回复查,并进行尿气相色谱/质谱检测。临床诊断患儿进一步予以基因检测进行确诊。结果共收集423例C3、C3/C2、C3/C0单一或多个指标异常的新生儿筛查标本,初筛阳性率约为1%,行联合筛查检测结果发现8例标本中甲基丙二酸和同型半胱氨酸表达水平明显升高,召回复查尿气相色谱质谱提示甲基丙二酸轻度升高。结论串联质谱和高效液相色谱-串联质谱联合应用可以提高新生儿MMA筛查的阳性预测值、降低假阳性率,在新生儿遗传代谢病筛查中具有重要价值。     

LC-MS/MS systematic toxicological analysis: comparison of MS/MS spectra obtained with different instruments and settings

OBJECTIVES: To compare the mass spectra obtained using a linear-ion-trap (LIT) tandem mass spectrometer (QTRAP) operated in the "enhanced product ion scan" (EPI) mode with those obtained in the classical triple-quadrupole product ion scan (PIS) mode run on the same as well as on two other instruments (TSQ-Quantum and Quattro-Micro). DESIGN AND METHODS: After tentative standardization of ion fragmentation and transmission in both polarities using a reference compound (glafenine) on the three instruments, eight test compounds detected in the positive mode and five in the negative mode were systematically infused in different ionization sources and spectral acquisition performed over approximately 5 s. The relative intensity of the ions present in the resulting spectra was quantitatively and statistically compared. Also, the intra-day and inter-day variabilities of these relative intensities, as well as the effect of increasing compound concentration, were studied using QTRAP operated in EPI mode. RESULTS: The EPI and PIS modes operated on a single LIT MS/MS instrument resulted in significant differences in relative ion intensities in both polarities, and so did the other two instruments despite prior standardization with glafenine. Some fragments could be absent in certain spectra, but no unexpected or unique fragments showed up. Intra-day variability was smaller in the LIT EPI than in the regular PIS mode and in the positive than in the negative polarity. In EPI mode, both intra- and inter-day variabilities increased when the relative intensity decreased. The effect of increasing concentration on the relative intensity of major and minor ions was small but significant in both polarities. Finally, contamination and cleansing of the ionization source also had noticeable effects on MS/MS spectra, though the cause is unclear. CONCLUSIONS: MS/MS spectra do not offer the expected inter-instrument reproducibility despite an attempt at standardizing the fragmentation conditions using a reference compound. However, although the inter-instrument differences in ion relative intensity were significant, the spectra obtained looked almost similar. This suggests that in library searching algorithms, higher weight should be assigned for the m/z ratios than for their relative intensity in the spectra.     

Carbohydrate metabolism genes and pathways in insects: insights from the honey bee genome

Carbohydrate-metabolizing enzymes may have particularly interesting roles in the honey bee, Apis mellifera, because this social insect has an extremely carbohydrate-rich diet, and nutrition plays important roles in caste determination and socially mediated behavioural plasticity. We annotated a total of 174 genes encoding carbohydrate-metabolizing enzymes and 28 genes encoding lipid-metabolizing enzymes, based on orthology to their counterparts in the fly, Drosophila melanogaster, and the mosquito, Anopheles gambiae. We found that the number of genes for carbohydrate metabolism appears to be more evolutionarily labile than for lipid metabolism. In particular, we identified striking changes in gene number or genomic organization for genes encoding glycolytic enzymes, cellulase, glucose oxidase and glucose dehydrogenases, glucose-methanol-choline (GMC) oxidoreductases, fucosyltransferases, and lysozymes.     

Characterization of insulin cross-seeding: the underlying mechanism reveals seeding and denaturant-induced insulin fibrillation proceeds through structurally similar intermediates

Insulin rapidly fibrillates in the presence of amyloid seeds from different sources. To address its cross-reactivity we chose the seeds of seven model proteins and peptides along with the seeds of insulin itself. Model candidates were selected/designed according to their size, amino acid sequence, and hydrophobicity. We found while some seeds provided catalytic ends for inducing the formation of non-native insulin conformers and increase fibrillation, others attenuated insulin fibrillation kinetics. We also observed competition between the intermediate insulin conformers which formed with urea and amyloid seeds in entering the fibrillogenic pathway. Simultaneous incubation of insulin with urea and amyloid seeds resulted in the formation of nearly similar insulin intermediate conformers which synergistically enhance insulin fibrillation kinetics. Given these results, it is highly likely that, structurally, there is a specific intermediate in different pathways of insulin fibrillation that governs fibrillation kinetics and morphology of the final mature fibril. Overall, this study provides a novel mechanistic insight into insulin fibrillation and gives new information on how seeds of different proteins are capable of altering insulin fibrillation kinetics and morphology. This report, for the first time, tries to answer an important question that why fibrillation of insulin is either accelerated or attenuated in the presence of amyloid fibril seeds from different sources.

Native insulins in the presence of low urea concentrations or seeds with low hydrophobicity form ordered aggregates (amyloid fibrils), while high urea concentrations or the seeds with high level of hydrophobicity can induce the amorphous aggregation.