A discovery biotransformation strategy: combining in silico tools with high-resolution mass spectrometry and software-assisted data analysis for high-throughput metabolism.

Understanding compound metabolism in early drug discovery aids medicinal chemistry in designing molecules with improved safety and ADME properties. While advancements in metabolite prediction brings increased confidence, structural decisions require experimental data. In vitro metabolism studies using liquid chromatography and high-resolution mass spectrometry (LC-MS) are generally resource intensive and performed on very few compounds, limiting the chemical space that can be examined.Here, we describe a novel metabolism strategy increasing compound throughput using residual in vitro clearance samples conducted at drug concentrations of 0.5 µM. Analysis by robust ultra high-performance liquid chromatography separation and accurate-mass MS detection ensures major metabolites are identified from a single injection. In silico prediction (parent cLogD) tailors chromatographic conditions, with data-dependent tandem mass spectroscopy targeting predicted metabolites. Software-assisted data mining, structure elucidation and automatic reporting are used.Confidence in the globally aligned workflow is demonstrated with 16 marketed drugs. The approach is now implemented routinely across our laboratories. To date, the success rate for identification of at least one major metabolite is 85%. The utility of these data has been demonstrated across multiple projects, allowing earlier medicinal chemistry decisions to increase efficiency and impact of the design-make-test cycle thus improving the translatability of early in vitro metabolism data.

Using Gas Phase Reactions of Hexamethylene Triperoxide Diamine (HMTD) to Improve Detection in Mass Spectrometry.

Our efforts to lower the detection limits of hexamethylene triperoxide diamine (HMTD) have uncovered previously unreported gas-phase reactions of primary and secondary amines with one of the six methylene carbons. The reaction occurs primarily in the atmospheric pressure chemical ionization (APCI) source and is similar to the behavior of alcohols with HMTD [1]. However, unlike alcohols, the amine reaction conserves the hydrogen peroxide on the intact product. Furthermore, with or without amines, HMTD is oxidized to tetramethylene diperoxide diamine dialdehyde (TMDDD) in a temperature-dependent fashion in the APCI source. Synthesized TMDDD forms very strong adducts (not products) to ammonium and amine ions in the electrospray ionization (ESI) source. Attempts to improve HMTD detection by generating TMDDD in the APCI source with post-column addition of amines were not successful. Signal intensity of the solvent related HMTD product in methanol, [HMTD+MeOH2-H2O2]+ (m/z 207.0975), was understandably related to the amount of methanol in the HMTD environment as it elutes into the source. With conditions optimized for this product, the detection of 100 pg on column was accomplished with a robust analysis of 300 pg (1.44 pmol) routinely performed on the Orbitrap mass spectrometers. Graphical Abstract ᅟ.

Reactions of Organic Peroxides with Alcohols in Atmospheric Pressure Chemical Ionization-the Pitfalls of Quantifying Triacetone Triperoxide (TATP).

Over the last several decades, mass spectrometry has become one of the principle methods for compound identification and quantification. While for analytical purposes, fragments which are not fully characterized in terms of origin and intensity as a function of experimental conditions have been used, understanding the nature of those species is very important. Herein we discuss such issues relative to triacetone triperoxide (TATP) and its frequently observed fragment at m/z 89. This "fragment" has been identified as the gas-phase reaction product of TATP with one or two methanol molecules/ions. Additionally, the origin and conditions of other fragments at m/z 91, 75, and 74 associated with TATP will be addressed. Similar analytical issues associated with other multi-peroxide organic compounds [hexamethylene triperoxide diamine (HMTD), methyl ethyl ketone peroxides (MEKP)] will also be discussed. Solution storage conditions for TATP, HMTD, and tetramethylene diperoxide diamine dialdehyde have been determined. Graphical Abstract ᅟ.

Acetonitrile Ion Suppression in Atmospheric Pressure Ionization Mass Spectrometry.

Efforts to analyze trace levels of cyclic peroxides by liquid chromatography/mass spectrometry gave evidence that acetonitrile suppressed ion formation. Further investigations extended this discovery to ketones, linear peroxides, esters, and possibly many other types of compounds, including triazole and menadione. Direct ionization suppression caused by acetonitrile was observed for multiple adduct types in both electrospray ionization and atmospheric pressure chemical ionization. The addition of only 2% acetonitrile significantly decreased the sensitivity of analyte response. Efforts to identify the mechanism were made using various nitriles. The ion suppression was reduced by substitution of an acetonitrile hydrogen with an electron-withdrawing group, but was exacerbated by electron-donating or steric groups adjacent to the nitrile. Although current theory does not explain this phenomenon, we propose that polar interactions between the various functionalities and the nitrile may be forming neutral aggregates that manifest as ionization suppression. Graphical Abstract ᅟ.

Gas-phase reactions of alcohols with hexamethylene triperoxide diamine (HMTD) under atmospheric pressure chemical ionization conditions.

RATIONALE: Hexamethylene triperoxide diamine (HMTD) is a sensitive peroxide explosive first synthesized in 1885. HMTD exhibits an unusual gas-phase phenomenon in the presence of alcohols that has been previously observed, but incorrectly resolved. We are attempting to determine this specific mechanism. METHODS: We used positive ion mode atmospheric pressure chemical ionization (APCI) as the interface to the mass spectrometer. HMTD was infused with various solvents including (18) O- and (2) H-labeled methanol in order to determine gas-phase reaction mechanisms. RESULTS: Based on these labeled experiments, it was determined that, under APCI conditions, the alcohol oxygen attacks a methylene carbon of HMTD and releases H2 O2 . This was attempted with nine different alcohols and, in each case, the alcohol is fully incorporated into the molecule with the peroxide release. A mechanism for this reaction has been proposed. CONCLUSIONS: This work appears to have confirmed the gas-phase reaction mechanism of HMTD with alcohols. As we continue efforts to characterize this unusual molecule, the information may prove useful in determining formation and degradation mechanism(s). In addition, this property of HMTD may find use in other fields of science.

In vitro metabolism of the 5-hydroxytryptamine1B receptor antagonist elzasonan.

The metabolism of elzasonan has been examined in vitro using hepatic microsomes from human and recombinant heterologously expressed P450 enzymes (rCYP). Metabolism occurs primarily via oxidative N-demethylation to form M4 and oxidation reactions to form elzasonan N-oxide (M5) and 5-hydroxyelzasonan metabolite (M3). Additionally, elzasonan was shown to be metabolized to the novel cyclized indole metabolite (M6) which undergoes subsequent oxidation to form the iminium ion metabolite (M3a). The rCYP data was normalized relative to the levels of each CYP form in native human liver microsomes to better assess the contribution of each rCYP in the metabolism of elzasonan. Results demonstrated the involvement of CYP3A4 in the pathways leading to M3a, M3, M5 and M6 and CYP2C8 in the formation of M4. Kinetic constants for the formation of M3 were determined and correlation and inhibition studies suggested that CYP3A4 is primarily responsible for the formation of M3 and CYP2C19 plays a very minor role in its formation. Cytochrome b5 has shown to be an essential component in P450 3A4 catalyzed 5-hydroxyelzasonan formation and provides insights on the disconnect between human liver microsomes data and that of rCYP. Furthermore, rCYP3A4 containing b5 are useful models for predicting the rates for liver microsomes P450-dependent drug oxidations and should be utilized routinely.

Oxidative ipso substitution of 2,4-difluoro-benzylphthalazines: identification of a rare stable quinone methide and subsequent GSH conjugate.

In vitro metabolite identification and GSH trapping studies in human liver microsomes were conducted to understand the bioactivation potential of compound 1 [2-(6-(4-(4-(2,4-difluorobenzyl)phthalazin-1-yl)piperazin-1-yl)pyridin-3-yl)propan-2-ol], an inhibitor of the Hedgehog pathway. The results revealed the formation of a unique, stable quinone methide metabolite (M1) via ipso substitution of a fluorine atom and subsequent formation of a GSH adduct (M2). The stability of this metabolite arises from extensive resonance-stabilized conjugation of the substituted benzylphthalazine moiety. Cytochrome P450 (P450) phenotyping studies revealed that the formation of M1 and M2 were NADPH-dependent and primarily catalyzed by CYP3A4 among the studied P450 isoforms. In summary, an unusual and stable quinone methide metabolite of compound 1 was identified, and a mechanism was proposed for its formation via an oxidative ipso substitution.

In vitro-in vivo correlation for intrinsic clearance for CP-409,092 and sumatriptan: a case study to predict the in vivo clearance for compounds metabolized by monoamine oxidase.

Oxidative deamination of the GABA(A) partial agonist CP-409,092 and sumatriptan represents a major metabolic pathway and seems to play an important role for the clearance of these two compounds. Similar to sumatriptan, human mitochondrial incubations with deprenyl and clorgyline, probe inhibitors of monoamine oxidase B and monoamine oxidase A (MAO-B and MAO-A), respectively, showed that CP-409,092 was metabolized to a large extent by the enzyme MAO-A. The metabolism of CP-409,092 and sumatriptan was therefore studied in human liver mitochondria and in vitro intrinsic clearance (CL(int)) values were determined and compared to the corresponding in vivo oral clearance (CL(PO)) values. The overall objective was to determine whether an in vitro-in vivo correlation (IVIVC) could be described for compounds cleared by MAO-A. The intrinsic clearance, CL(int), of CP-409,092 was approximately 4-fold greater than that of sumatriptan (CL(int), values were calculated as 0.008 and 0.002 ml/mg/min for CP-409,092 and sumatriptan, respectively). A similar correlation was observed from the in vivo metabolic data where the unbound oral clearance, CL(u)(PO), values in humans were calculated as 724 and 178 ml/min/kg for CP-409,092 and sumatriptan, respectively. The present work demonstrates that it is possible to predict in vivo metabolic clearance from in vitro metabolic data for drugs metabolized by the enzyme monoamine oxidase.

Metabolism, pharmacokinetics, and excretion of the 5-hydroxytryptamine1b receptor antagonist elzasonan in humans.

The metabolism, pharmacokinetics, and excretion of a potent and selective 5-hydroxytryptamine(1B) receptor antagonist elzasonan have been studied in six healthy male human subjects after oral administration of a single 10-mg dose of [(14)C]elzasonan. Total recovery of the administered dose was 79% with approximately 58 and 21% of the administered radioactive dose excreted in feces and urine, respectively. The average t(1/2) for elzasonan was 31.5 h. Elzasonan was extensively metabolized, and excreta and plasma were analyzed using mass spectrometry and NMR spectroscopy to elucidate the structures of metabolites. The major component of drug-related material in the excreta was in the feces and was identified as 5-hydroxyelzasonan (M3), which accounted for approximately 34% of the administered dose. The major human circulating metabolite was identified as the novel cyclized indole metabolite (M6) and accounted for ∼65% of the total radioactivity. A mechanism for the formation of M6 is proposed. Furthermore, metabolism-dependent covalent binding of drug-related material was observed upon incubation of [(14)C]elzasonan with liver microsomes, and data suggest that an indole iminium ion is involved. Overall, the major metabolic pathways of elzasonan were due to aromatic hydroxylation(s) of the benzylidene moiety, N-oxidation at the piperazine ring, N-demethylation, indirect glucuronidation, and oxidation, ring closure, and subsequent rearrangement to form M6.

Mechanism of [m+h]+ formation in atmospheric pressure photoionization mass spectrometry: identification of propionitrile in acetonitrile with high mass accuracy measurement and tandem mass spectrometry and evidence for its involvement in the protonation phenomenon.

The role of propionitrile in the production of [M+H]+ under atmospheric pressure photoionization (APPI) was investigated. In dopant-assisted APPI using acetone and anisole, protonated acetone and anisole radical cations were the most prominent ions observed. In dopant-free or direct APPI in acetonitrile, however, a major ion in acetonitrile was detected and identified as propionitrile, using high accuracy mass measurement and collision induced dissociation studies. Vaporizing ca. 10(-5) M althiazide and bendroflumethazide under direct APPI in acetonitrile produced their corresponding protonated species [M+H]+. In addition to protonated acetonitrile, its dimers, and acetonitrile/water clusters, protonated propionitrile, propionitrile dimer, and propionitrile/water clusters were also observed. The role of propionitrile, an impurity in acetonitrile and/or a possible product of ion-molecule reaction, in the production of [M+H]+ of althiazide and bendroflumethazide was further investigated in the absence of dopant using propionitrile-d5. The formation of [M+D]+ species was observed, suggesting a possible role of propionitrile in the protonation process. Additionally, an increase in the [M+H]+ signal of althiazide and bendroflumethazide was observed as a function of propionitrile concentration in acetonitrile. Theoretical data from the literature supported the assumption that one possible mechanism, among others, for the formation of [M+H]+ could be attributed to photo-initiated isomerization of propionitrile. The most stable isomers of propionitrile, based on their calculated ionization energy (IE) and relative energy (DeltaE), were assumed to undergo proton transfer to the analytes, and mechanisms were proposed.

Characterization of metabolites of a NK1 receptor antagonist, CJ-11,972, in human liver microsomes and recombinant human CYP isoforms by liquid chromatography/tandem mass spectrometry.

The in vitro metabolism of CJ-11,972, (2-benzhydryl-1-aza-bicyclo[2.2.2]oct-3-yl)-(5-tert-butyl-2-methoxybenzyl)amine, an NK1 receptor antagonist, was studied in human liver microsomes and recombinant human CYP isoforms. Liquid chromatography/mass spectrometry (LC/MS) and tandem mass spectrometry (LC/MS/MS) coupled to radioactive detection were used to detect and identify the metabolites. CJ-11,972 was extensively metabolized in human liver microsomes and recombinant human CYP 3A4/3A5 isoforms. A total of fourteen metabolites were identified by a combination of various MS techniques. The major metabolic pathways were due to oxidation of the tert-butyl moiety to form an alcohol (M6) and/or O-demethylation of the anisole moiety. The alcohol metabolite M6 was further oxidized to the corresponding aldehyde (M7) and carboxylic acid (M4). Two unusual metabolites (M13, M17), formed by C-demethylation of the tert-butyl group, were identified as 2-{3-[(2-benzhydryl-1-aza-bicyclo[2.2.2]oct-3-ylamino)methyl]-4-methoxyphenyl}propan-2-ol and (2-benzhydryl-1-aza-bicyclo[2.2.2]oct-3-yl)-(5-isopropenyl-2-methoxybenzyl)amine. A plausible mechanism for C-demethylation may involve oxidation of M6 to form an aldehyde metabolite (M7), followed by cytochrome P450-mediated deformylation leaving an unstable carbon-centered radical, which would quickly form either the alcohol metabolite M13 and the olefin metabolite M17.

Metabolism, pharmacokinetics, and excretion of the substance P receptor antagonist CP-122,721 in humans: structural characterization of the novel major circulating metabolite 5-trifluoromethoxy salicylic acid by high-performance liquid chromatography-tandem mass spectrometry and NMR spectroscopy.

The metabolism, pharmacokinetics, and excretion of a potent and selective substance P receptor antagonist, CP-122,721 [(+)-(2S,3S)-3-(2-methoxy-5-trifluoromethoxybenzylamino)-2-phenylpiperidine], have been studied in six healthy male human subjects [four extensive metabolizers (EMs) and two poor metabolizers (PMs) of CYP2D6) following oral administration of a single 30-mg dose of [14C]CP-122,721. Approximately 84% of the administered radioactivity was recovered from the urine and feces of the subjects over a period of 312 h. Approximately 80% of the dose for EM subjects was recovered within 48 h. PM subjects, however, excreted only about 45% of the dose in 48 h and required the full 312 h to achieve nearly 80% recovery. Absorption of CP-122,721 was rapid in both extensive and poor metabolizers, as indicated by the rapid appearance of radioactivity in serum. The serum concentrations of total radioactivity were always much greater than those of unchanged drug indicating early formation of metabolites. The average CP-122,721 t1/2 was 6.7 h and 45.0 h for EM and PM subjects, respectively. The serum concentrations of CP-122,721 reached a peak of 7.4 and 69.8 ng/ml for extensive and poor metabolizers, respectively. The major metabolic pathways of CP-122,721 were due to O-demethylation, aromatic hydroxylation, and indirect glucuronidation. The minor metabolic pathways included aliphatic oxidation at the piperidine moiety, O-dealkylation of the trifluoromethoxy group, N-dealkylation, and oxidative deamination. In addition to the major human circulating metabolite 5-trifluoromethoxy salicylic acid (TFMSA), all other circulating metabolites of CP-122,721 were glucuronide conjugates of oxidized metabolites. TFMSA was identified using high pressure liquid chromatography/tandem mass spectrometry and NMR and mechanisms were proposed for its formation. There are no known circulating active metabolites of CP-122,721.

Novel CCR1 antagonists with improved metabolic stability.

The synthesis, biological activity, and pharmacokinetic profile of novel CCR1 antagonists are described.