Discovery and Synthesis of C-Nucleosides as Potential New Anti-HCV Agents.

Nucleoside analogues have long been recognized as prospects for the discovery of direct acting antivirals (DAAs) to treat hepatitis C virus because they have generally exhibited cross-genotype activity and a high barrier to resistance. C-Nucleosides have the potential for improved metabolism and pharmacokinetic properties over their N-nucleoside counterparts due to the presence of a strong carbon-carbon glycosidic bond and a non-natural heterocyclic base. Three 2'CMe-C-adenosine analogues and two 2'CMe-guanosine analogues were synthesized and evaluated for their anti-HCV efficacy. The nucleotide triphosphates of four of these analogues were found to inhibit the NS5B polymerase, and adenosine analogue 1 was discovered to have excellent pharmacokinetic properties demonstrating the potential of this drug class.

Discovery of BI 224436, a Noncatalytic Site Integrase Inhibitor (NCINI) of HIV-1.

An assay recapitulating the 3' processing activity of HIV-1 integrase (IN) was used to screen the Boehringer Ingelheim compound collection. Hit-to-lead and lead optimization beginning with compound 1 established the importance of the C3 and C4 substituent to antiviral potency against viruses with different aa124/aa125 variants of IN. The importance of the C7 position on the serum shifted potency was established. Introduction of a quinoline substituent at the C4 position provided a balance of potency and metabolic stability. Combination of these findings ultimately led to the discovery of compound 26 (BI 224436), the first NCINI to advance into a phase Ia clinical trial.

Preclinical profile of BI 224436, a novel HIV-1 non-catalytic-site integrase inhibitor.

BI 224436 is an HIV-1 integrase inhibitor with effective antiviral activity that acts through a mechanism that is distinct from that of integrase strand transfer inhibitors (INSTIs). This 3-quinolineacetic acid derivative series was identified using an enzymatic integrase long terminal repeat (LTR) DNA 3'-processing assay. A combination of medicinal chemistry, parallel synthesis, and structure-guided drug design led to the identification of BI 224436 as a candidate for preclinical profiling. It has antiviral 50% effective concentrations (EC50s) of <15 nM against different HIV-1 laboratory strains and cellular cytotoxicity of >90 µM. BI 224436 also has a low, ∼2.1-fold decrease in antiviral potency in the presence of 50% human serum and, by virtue of a steep dose-response curve slope, exhibits serum-shifted EC95 values ranging between 22 and 75 nM. Passage of virus in the presence of inhibitor selected for either A128T, A128N, or L102F primary resistance substitutions, all mapping to a conserved allosteric pocket on the catalytic core of integrase. BI 224436 also retains full antiviral activity against recombinant viruses encoding INSTI resistance substitutions N155S, Q148H, and E92Q. In drug combination studies performed in cellular antiviral assays, BI 224436 displays an additive effect in combination with most approved antiretrovirals, including INSTIs. BI 224436 has drug-like in vitro absorption, distribution, metabolism, and excretion (ADME) properties, including Caco-2 cell permeability, solubility, and low cytochrome P450 inhibition. It exhibited excellent pharmacokinetic profiles in rat (clearance as a percentage of hepatic flow [CL], 0.7%; bioavailability [F], 54%), monkey (CL, 23%; F, 82%), and dog (CL, 8%; F, 81%). Based on the excellent biological and pharmacokinetic profile, BI 224436 was advanced into phase 1 clinical trials.

Atmospheric pressure chemical ionization Fourier transform ion cyclotron resonance mass spectrometry for complex thiophenic mixture analysis.

RATIONALE: Polycyclic aromatic sulfur heterocycles (PASHs) are detrimental species for refining processes in petroleum industry. Current mass spectrometric methods that determine their composition are often preceded by derivatization and dopant addition approaches. Different ionization methods have different impact on the molecular assignment of complex PASHs. The analysis of such species under atmospheric pressure chemical ionization (APCI) is still considered limited due to uncontrolled ion generation with low- and high-mass PASHs. METHODS: The ionization behavior of a model mixture of five selected PASH standards was investigated using an APCI source with nitrogen as the reagent gas. A complex thiophenic fraction was separated from a vacuum gas oil (VGO) and injected using the same method. The samples were analyzed using Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). RESULTS: PASH model analytes were successfully ionized and mainly [M + H](+) ions were produced. The same ionization pattern was observed for the real thiophenic sample. It was found that S1 class species were the major sulfur-containing species found in the VGO sample. These species indicated the presence of alkylated benzothiophenic (BT), dibenzothiophenic (DBT) and benzonaphthothiophenic (BNT) series that were detected by APCI-FTICR MS. CONCLUSIONS: This study provides an established APCI-FTICR MS method for the analysis of complex PASHs. PASHs were detected without using any derivatization and without fragmentation. The method can be used for the analysis of S-containing crude oil samples.

Dehydrodimerization of pterostilbene during electrospray ionization mass spectrometry.

RATIONALE: Pterostilbene is a member of the hydroxystilbene family of compounds commonly found in plants such as blueberry and grapes. During the analysis of this compound by electrospray ionization mass spectrometry (ESI-MS), an ion was observed that corresponds to the dehydrodimer of pterostilbene in mass-to-charge ratio. Since such unexpected dimerization may lead to decreased monomer signal during quantitative analysis, it was of interest to identify the origin and structure of the observed pterostilbene dimer and examine the experimental conditions that influence its formation. METHODS: Liquid Chromatography/Mass Spectrometry (LC/MS), Nuclear Magnetic Resonance (NMR), and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) were used to examine the origin of the dimerization products. The structure of the formed pterostilbene dimer was examined by performing MS(n) analysis on the dimer ion. Effects of solvent composition, analyte concentration, radical scavenger, and other experimental conditions on the dimerization were also studied. RESULTS: LC/MS and NMR analyses clearly showed that the starting solution did not contain the pterostilbene dimer. Solvent type and radical scavenger concentration were found to have pronounced effects on the dimer formation. Particularly, presence of acetonitrile or ammonium acetate had favorable effects on the extent of dimerization during ESI-MS analysis whereas hydroquinone and butylated hydroquinone had negative effects. Dimer formation decreased at high flow rates and when fused-silica capillary was used as the spray needle. CONCLUSIONS: The data indicate that this dimerization occurs as a result of solution-phase electrochemical reactions taking place during the electrospray process. A possible structure for this dimer was proposed based on the MS(n) analysis and was similar to that of the enzymatically derived pterostilbene dehydrodimer already reported in the literature.

Optimization of a 1,5-dihydrobenzo[b][1,4]diazepine-2,4-dione series of HIV capsid assembly inhibitors 2: structure-activity relationships (SAR) of the C3-phenyl moiety.

Detailed structure-activity relationships of the C3-phenyl moiety that allow for the optimization of antiviral potency of a series of 1,5-dihydrobenzo[b][1,4]diazepine-2,4-dione inhibitors of HIV capsid (CA) assembly are described. Combination of favorable substitutions gave additive SAR and allowed for the identification of the most potent compound in the series, analog 27. Productive SAR also transferred to the benzotriazepine and spirobenzodiazepine scaffolds, providing a solution to the labile stereocenter at the C3 position. The molecular basis of how compound 27 inhibits mature CA assembly is rationalized using high-resolution structural information. Our understanding of how compound 27 may inhibit immature Gag assembly is also discussed.

Development of a piezoelectric inkjet dopant delivery device for an atmospheric pressure photoionization source with liquid chromatography/mass spectrometry.

This paper describes a simple, robust and integrated piezoelectric actuated printhead as a dopant delivery system for atmospheric pressure photoionization with liquid chromatography/mass spectrometry. The newly designed dopant delivery system avoids problems associated with traditional liquid delivery systems such as solvent immiscibility, backpressure and increased post-column dead volume issues. The performance of the new device was tested and evaluated using chlorobenzene as a dopant with a test mixture consisting of 18 different polycyclic aromatic hydrocarbons (PAHs). The results show that the new system works robustly at low dopant consumption level (1.6 uL min(-1)), consuming only approximately 5% of the amount used by conventional sources. The low dopant consumption has resulted in up to a 20-fold reduction in signal intensity of tested PAH molecules, but has led to less presence of background cluster ions and dopant trace contaminant background ions in the source area. Consequently, all tested PAHs were detected with excellent signal-to-noise ratio with at least two- to ten-fold improvements in the limit of detection and quantification compared to those obtained with traditional dopant assistance using a post-column addition method.

Investigation of the ionization mechanism of polycyclic aromatic hydrocarbons using an ethanol/bromobenzene/chlorobenzene/anisole mixture as a dopant in liquid chromatography/atmospheric pressure photoionization mass spectrometry.

RATIONALE: An ethanol-based multicomponent dopant consisting of ethanol/chlorobenzene/bromobenzene/anisole (98.975:0.1:0.9:0.025, v/v/v/v) has been used as a dopant for atmospheric pressure photoionization (APPI) of polycyclic aromatic hydrocarbons (PAHs). In this study the mechanism of ionization of PAHs assisted by the ethanol-based multicomponent dopant is investigated. METHODS: The reactant background cluster ions of the ethanol-based multicomponent dopant observed in the positive ion APPI were studied. These studies were performed to investigate the mechanism behind the generation of a molecular radical cation (M(+•)) for PAHs by APPI assisted by the ethanol-based multicomponent dopant. Full scan and MS/MS analyses were conducted using an LTQ Orbitrap mass spectrometer. The effect of acidification of the mobile phase on the dopant cluster ion formation was also investigated. RESULTS: With the ethanol-based multicomponent dopant, a single type of molecular radical cation M(+•) was observed for the studied PAHs. The characteristic ion signal of the multicomponent dopant mixture consisted of mainly anisole photoions at m/z 108.05697 and its adduct ions at m/z 124.05188 and 164.07061. The anisole ion response at m/z 108.05697 was stable in the presence of acetonitrile, methanol, water and 0.1% formic acid mobile phase composition. CONCLUSIONS: The abundance formation of anisole photoions shows the universality of this multicomponent dopant in ionizing compounds with ionization energy ranging from 7.1-8.2 eV. Since the ionization energy of anisole is 8.2 eV and is lower than those of chlorobenzene (9.07 eV) and bromobenzene (9.0 eV), the mechanism of formation of anisole photoions even with its very minute amounts was not only governed by its photoionization by the krypton lamp photon energy (10.0 eV and 10.6 eV), but also by charge transfer from bromobenzene and chlorobenzene radical cations. PAH molecules were mainly ionized by charge transfer reaction from photoionized anisole and oxidized anisole radical cations as well as by the krypton lamp.

Fullerene-catalyzed reduction of azo derivatives in water under UV irradiation.

Metal-free fullerene (C(60)) was found to be an effective catalyst for the reduction of azo groups in basic aqueous solution under UV irradiation in the presence of NaBH(4). Use of NaBH(4) by itself is not sufficient to reduce the azo dyes without the assistance of a metal catalyst such as Pd and Ag. Experimental and theoretical results suggest that C(60) catalyzes this reaction by using its vacant orbital to accept the electron in the bonding orbital of azo dyes, which leads to the activation of the N=N bond. UV irradiation increases the ability of C(60) to interact with electron-donor moieties in azo dyes.

The liver partition coefficient-corrected inhibitory quotient and the pharmacokinetic-pharmacodynamic relationship of directly acting anti-hepatitis C virus agents in humans.

Pharmacokinetic-pharmacodynamic (PK-PD) data analyses from early hepatitis C virus (HCV) clinical trials failed to show a good correlation between the plasma inhibitory quotient (IQ) and antiviral activity of different classes of directly acting antiviral agents (DAAs). The present study explored whether use of the liver partition coefficient-corrected IQ (LCIQ) could improve the PK-PD relationship. Animal liver partition coefficients (Kp(liver)) were calculated from liver to plasma exposure ratios. In vitro hepatocyte partition coefficients (Kp(hep)) were determined by the ratio of cellular to medium drug concentrations. Human Kp(liver) was predicted using an in vitro-in vivo proportionality method: the species-averaged animal Kp(liver) multiplied by the ratio of human Kp(hep) over those in animals. LCIQ was calculated using the IQ multiplied by the predicted human Kp(liver). Our results demonstrated that the in vitro-in vivo proportionality approach provided the best human Kp(liver) prediction, with prediction errors of <45% for all 5 benchmark drugs evaluated (doxorubicin, verapamil, digoxin, quinidine, and imipramine). Plasma IQ values correlated poorly (r(2) of 0.48) with maximum viral load reduction and led to a corresponding 50% effective dose (ED(50)) IQ of 42, with a 95% confidence interval (CI) of 0.1 to 148534. In contrast, the LCIQ-maximum VLR relationship fit into a typical sigmoidal curve with an r(2) value of 0.95 and an ED(50) LCIQ of 121, with a 95% CI of 83 to 177. The present study provides a novel human Kp(liver) prediction model, and the LCIQ correlated well with the viral load reductions observed in short-term HCV monotherapy of different DAAs and provides a valuable tool to guide HCV drug discovery.

Multicomponent mixed dopant optimization for rapid screening of polycyclic aromatic hydrocarbons using ultra high performance liquid chromatography coupled to atmospheric pressure photoionization high-resolution mass spectrometry.

RATIONALE: To enhance the ionization efficiencies in atmospheric pressure photoionization mass spectrometry a dopant with favorable ionization energy such as chlorobenzene is typically used. These dopants are typically toxic and difficult to mix with water-soluble organic solvents. In order to achieve a more efficient and less toxic dopant, a multicomponent mixed dopant was explored. METHODS: A multicomponent mixed dopant for non-targeted rapid screening of polycyclic aromatic hydrocarbons (PAHs) was developed and optimized using ultra high performance liquid chromatography (UPLC) coupled to atmospheric pressure photoionization high-resolution mass spectrometry. Various single and multicomponent mixed dopants consisting of ethanol, chlorobenzene, bromobenzene, anisole and toluene were evaluated. RESULTS: Fourteen out of eighteen PAHs were successfully separated and detected at low pg/µL levels within 5 min with high mass accuracy ≤4 ppm. The optimal mixed multicomponent dopant consisted of ethanol/chlorobenzene/bromobenzene/anisole (98.975:0.1:0.9:0.025, v/v %) and it improved the limit of detection (LOD) by 2- to 10-fold for the tested PAHs compared to those obtained with pure chlorobenzene. CONCLUSIONS: A novel multicomponent dopant that contains 99% ethanol and 1% mixture of chlorobenzene, bromobenzene and anisole was found to be an effective dopant mixture to ionize PAHs. The developed UPLC multicomponent dopant assisted atmospheric pressure photoionization high-resolution mass spectrometry offered a rapid non targeted screening method for detecting the PAHs at low pg/µL levels within a 5 min run time with high mass accuracy ≤4 ppm.

Cross-species absorption, metabolism, distribution and pharmacokinetics of BI 201335, a potent HCV genotype 1 NS3/4A protease inhibitor.

The present study describes the cross-species absorption, metabolism, distribution and pharmacokinetics of BI 201335, a potent HCV protease inhibitor currently in phase III clinical trials. BI 201335 showed a good Caco-II permeability (8.7 × 10(-6) cm/sec) and in vitro metabolic stability (predicted hepatic clearence (CL(hep)) <19% Q(h) in all species tested). Single dose PK revealed a clearance of 17, 3.0 and 2.6 mL/min/kg in rat, monkey and dog respectively, with a corresponding oral bioavailability of 29.1, 25.5 and 35.6%. Comparative plasma and liver PK profile in rodents showed a high liver Kp in the rat (42-fold), suggesting high target tissue distribution. Simple allometry based on animal PK predicted a human oral CL/F of 168 mL/min, within two-fold of the observed value (118 mL/min) at 240 mg in healthy volunteers. Allometry of volume of distribution generated a low exponent of 0.59, and a much lower predicted Vss/F (5-fold less than observed). Several different approaches of Vss/F prediction were evaluated and compared with the value observed in human. The averaged Vss/F from preclinical animals provides the best estimation of the observed human value (169 L vs. 175 L). Corresponding human "effective" t(1/2) values were also compared. The predicted human t(1/2) based on the CL from allometry with metabolic corrections and the averaged animal Vss represented the best estimation of the clinical data (12.1 vs. 17.2 hr). The present study demonstrated that the good preclinical ADMEPK profile of BI 201335 is consistent with that observed in the clinic. While preclinical data accurately predicted the human CL, the prediction of human Vss seems to be more challenging. The averaged Vss/F from all tested preclinical animals provided the best prediction of human Vss and the resulting "effective" t(1/2).

Preclinical characterization of BI 201335, a C-terminal carboxylic acid inhibitor of the hepatitis C virus NS3-NS4A protease.

BI 201335 is a hepatitis C virus (HCV) NS3-NS4A (NS3 coexpressed with NS4A) protease inhibitor that has been shown to have potent clinical antiviral activity. It is a highly optimized noncovalent competitive inhibitor of full-length NS3-NS4A proteases of HCV genotypes 1a and 1b with K(i) values of 2.6 and 2.0 nM, respectively. K(i) values of 2 to 230 nM were measured against the NS3-NS4A proteases of HCV genotypes 2 to 6, whereas it was a very weak inhibitor of cathepsin B and showed no measurable inhibition of human leukocyte elastase. BI 201335 was also shown to be a potent inhibitor of HCV RNA replication in vitro with 50% effective concentrations (EC(50)s) of 6.5 and 3.1 nM obtained in genotype 1a and 1b replicon assays. Combinations of BI 201335 with either interferon or ribavirin had additive effects in replicon assays. BI 201335 had good permeability in Caco-2 cell assays and high metabolic stability after incubation with human, rat, monkey, and dog liver microsomes. Its good absorption, distribution, metabolism, and excretion (ADME) profile in vitro, as well as in rat, monkey, and dog, predicted good pharmacokinetics (PK) in humans. Furthermore, drug levels were significantly higher in rat liver than in plasma, suggesting that distribution to the target organ may be especially favorable. BI 201335 is a highly potent and selective NS3-NS4A protease inhibitor with good in vitro and animal ADME properties, consistent with its good human PK profile, and shows great promise as a treatment for HCV infection.

Thiotetrazole alkynylacetanilides as potent and bioavailable non-nucleoside inhibitors of the HIV-1 wild type and K103N/Y181C double mutant reverse transcriptases.

A series of aryl thiotetrazolylacetanilides were synthesized and found to be potent inhibitors of the HIV-1 wild type and K103N/Y181C double mutant reverse transcriptases. The incorporation of an alkynyl fragment on the aniline provided inhibitors with excellent cellular activity and extensive SAR led to the identification of one inhibitor having good oral bioavailability in rats.

A novel human cytochrome P450, CYP26C1, involved in metabolism of 9-cis and all-trans isomers of retinoic acid.

Retinoids are potent regulators of cell proliferation, cell differentiation, and morphogenesis and are important therapeutic agents in oncology and dermatology. The gene regulatory activity of endogenous retinoids is effected primarily by retinoic acid isomers (all-trans and 9-cis) that are synthesized from retinaldehyde precursors in a broad range of tissues and act as ligands for nuclear retinoic acid receptors. The catabolism of all-trans-retinoic acid (atRA) is an important mechanism of controlling RA levels in cell and tissues. We have previously identified two cytochrome P450s, P450RAI-1 and P450RAI-2 (herein named CYP26A1 and CYP26B1), which were shown to be responsible for catabolism of atRA both in the embryo and the adult. In this report, we describe the identification, molecular cloning, and substrate characterization of a third member of the CYP26 family, named CYP26C1. Transiently transfected cells expressing CYP26C1 convert atRA to polar water-soluble metabolites similar to those generated by CYP26A1 and -B1. Competition studies with all-trans, 13-cis, and 9-cis isomers of retinoic acid demonstrated that atRA was the preferred substrate for CYP26C1. Although CYP26C1 shares extensive sequence similarity with CYP26A1 and CYP26B1, its catalytic activity appears distinct from those of other CYP26 family members. Specifically, CYP26C1 can also recognize and metabolize 9-cis-RA and is much less sensitive than the other CYP26 family members to the inhibitory effects of ketoconazole. CYP26C1 is not widely expressed in the adult but is inducible by RA in HPK1a, transformed human keratinocyte cell lines. This third CYP26 member may play a specific role in catabolizing both all-trans and 9-cis isomers of RA.

CYP2U1, a novel human thymus- and brain-specific cytochrome P450, catalyzes omega- and (omega-1)-hydroxylation of fatty acids.

Long chain fatty acids have recently emerged as critical signaling molecules in neuronal, cardiovascular, and renal processes, yet little is presently known about the precise mechanisms controlling their tissue distribution and bioactivation. We have identified a novel cytochrome P450, CYP2U1, which may play an important role in modulating the arachidonic acid signaling pathway. Northern blot and real-time PCR analysis demonstrated that CYP2U1 transcripts were most abundant in the thymus and the brain (cerebellum), indicating a specific physiological role for CYP2U1 in these tissues. Recombinant human CYP2U1 protein, expressed in baculovirus-infected Sf9 insect cells, was found to metabolize arachidonic acid exclusively to two region-specific products as determined by liquid chromatography-mass spectrometry. These metabolites were identified as 19- and 20-hydroxy-modified arachidonic acids by liquid chromatography-tandem mass spectrometry analysis. In addition to omega/omega-1 hydroxylation of arachidonic acid, CYP2U1 protein also catalyzed the hydroxylation of structurally related long chain fatty acid (docosahexaenoic acid) but not fatty acids such as lauric acid or linoleic acid. This is the first report of the cloning and functional expression of a new human member of P450 family 2, CYP2U1, which metabolizes long chain fatty acids. Based on the ability of CYP2U1 to generate bioactive eicosanoid derivatives, we postulate that CYP2U1 plays an important physiological role in fatty acid signaling processes in both cerebellum and thymus.

High-sensitivity quantitation of cabergoline and pergolide using a triple-quadrupole mass spectrometer with enhanced mass-resolution capabilities.

Quantitative analysis of pharmaceuticals with low systemic plasma levels requires the utmost in sensitivity and selectivity from the analytical method used. A recently introduced triple-quadrupole mass spectrometer with unique enhanced mass-resolution capability was evaluated in the analysis of two such drugs, cabergoline and pergolide, in plasma. Liquid chromatographic/electrospray ionization selected reaction monitoring determination of cabergoline in plasma at unit mass-resolution demonstrated improved sensitivity (50 fg on-column), coupled with suitable accuracy and precision over a broad linear dynamic range covering five orders of magnitude (50 fg to 5 ng on-column). Liquid chromatographic/atmospheric pressure chemical ionization selective reaction monitoring determination of pergolide in plasma also attained a high level of sensitivity (500 fg on-column) at unit mass-resolution, with accuracy and precision values well within pharmaceutical industry standards. Again, a linear dynamic range covering five orders of magnitude (500 fg to 50 ng on-column) was achieved for the assay. Utility of the enhanced mass-resolution feature of the triple-quadrupole mass spectrometer in the determination of pergolide resulted in an improvement in analyte sensitivity (250 fg on-column) and linear dynamic range (250 fg to 50 ng on-column).

Investigation of an enhanced resolution triple quadrupole mass spectrometer for high-throughput liquid chromatography/tandem mass spectrometry assays.

Triple quadrupole mass spectrometers, when operated in multiple reaction monitoring (MRM) mode, offer a unique combination of sensitivity, specificity, and dynamic range. Consequently, the triple quadrupole is the workhorse for high-throughput quantitation within the pharmaceutical industry. However, in the past, the unit mass resolution of quadrupole instruments has been a limitation when interference from matrix or metabolites cannot be eliminated. With recent advances in instrument design, triple quadrupole instruments now afford mass resolution of less than 0.1 Dalton (Da) full width at half maximum (FWHM). This paper describes the evaluation of an enhanced resolution triple quadrupole mass spectrometer for high-throughput bioanalysis with emphasis on comparison of selectivity, sensitivity, dynamic range, precision, accuracy, and stability under both unit mass (1 Da FWHM) and enhanced (