Identification and optimisation of a pyrimidopyridone series of IRAK4 inhibitors.

In this article, we report the discovery of a series of pyrimidopyridones as inhibitors of IRAK4 kinase. From a previously disclosed 5-azaquinazoline series, we found that switching the pyridine ring for an N-substituted pyridone gave a novel hinge binding scaffold which retained potency against IRAK4. Importantly, introduction of the carbonyl established an internal hydrogen bond with the 4-NH, establishing a conformational lock and allowing truncation of the large basic substituent to a 1-methylcyclopyl group. Subsequent optimisation, facilitated by X-ray crystal structures, allowed identification of preferred substituents at both the pyridone core and pyrazole. Subsequent combinations of optimal groups allowed control of lipophilicity and identification of potent and selective inhibitors of IRAK4 with better in vitro permeability and lower clearance.

Potent and Selective Inhibitors of the Epidermal Growth Factor Receptor to Overcome C797S-Mediated Resistance.

The epidermal growth factor receptor (EGFR) harboring activating mutations is a clinically validated target in non-small-cell lung cancer, and a number of inhibitors of the EGFR tyrosine kinase domain, including osimertinib, have been approved for clinical use. Resistance to these therapies has emerged due to a variety of molecular events including the C797S mutation which renders third-generation C797-targeting covalent EGFR inhibitors considerably less potent against the target due to the loss of the key covalent-bond-forming residue. We describe the medicinal chemistry optimization of a biochemically potent but modestly cell-active, reversible EGFR inhibitor starting point with sub-optimal physicochemical properties. These studies culminated in the identification of compound 12 that showed improved cell potency, oral exposure, and in vivo activity in clinically relevant EGFR-mutant-driven disease models, including an Exon19 deletion/T790M/C797S triple-mutant mouse xenograft model.

Discovery of a Series of 5-Azaquinazolines as Orally Efficacious IRAK4 Inhibitors Targeting MyD88L265P Mutant Diffuse Large B Cell Lymphoma.

In this article, we report the discovery of a series of 5-azaquinazolines as selective IRAK4 inhibitors. From modestly potent quinazoline 4, we introduced a 5-aza substitution to mask the 4-NH hydrogen bond donor (HBD). This allowed us to substitute the core with a 2-aminopyrazole, which showed large gains in cellular potency despite the additional formal HBD. Further optimization led to 6-cyanomethyl-5-azaquinazoline 13, a selective IRAK4 inhibitor, which proved efficacious in combination with ibrutinib, while showing very little activity as a single agent up to 100 mg/kg. This contrasted to previously reported IRAK4 inhibitors that exhibited efficacy in the same model as single agents and was attributed to the enhanced specificity of 13 toward IRAK4.

Optimization of permeability in a series of pyrrolotriazine inhibitors of IRAK4.

We have developed a series of orally efficacious IRAK4 inhibitors, based on a scaffold hopping strategy and using rational structure based design. Efforts to tackle low permeability and high efflux in our previously reported pyrrolopyrimidine series (Scott et al., 2017) led to the identification of pyrrolotriazines which contained one less formal hydrogen bond donor and were intrinsically more lipophilic. Further optimisation of substituents on this pyrrolotriazine core culminated with the discovery of 30 as a promising in vivo probe to assess the potential of IRAK4 inhibition for the treatment of MyD88 mutant DLBCL in combination with a BTK inhibitor. When tested in an ABC-DLBCL model with a dual MyD88/CD79 mutation (OCI-LY10), 30 demonstrated tumour regressions in combination with ibrutinib.

Expanding the Armory: Predicting and Tuning Covalent Warhead Reactivity.

Targeted covalent inhibition is an established approach for increasing the potency and selectivity of potential drug candidates, as well as identifying potent and selective tool compounds for target validation studies. It is evident that identification of reversible recognition elements is essential for selective covalent inhibition, but this must also be achieved with the appropriate level of inherent reactivity of the reactive functionality (or "warhead"). Structural changes that increase or decrease warhead reactivity, guided by methods to predict the effect of those changes, have the potential to tune warhead reactivity and negate issues related to potency and/or toxicity. The half-life to adduct formation with glutathione (GSH t1/2) is a useful assay for measuring the reactivity of cysteine-targeting covalent warheads but is limited to synthesized molecules. In this manuscript we assess the ability of several experimental and computational approaches to predict GSH t1/2 for a range of cysteine targeting warheads, including a novel method based on pKa. Furthermore, matched molecular pairs analysis has been performed against our internal compound collection, revealing structure-activity relationships between a selection of different covalent warheads. These observations and methods of prediction will be valuable in the design of new covalent inhibitors with desired levels of reactivity.

Methanol adducts leading to the identification of a reactive aldehyde metabolite of CPAQOP in human liver microsomes by ultra-high-performance liquid chromatography/mass spectrometry.

RATIONALE: The incubation of CPAQOP (1-[(2R)-2-[[4-[3-chloro-4-(2-pyridyloxy)anilino]quinazolin-5-yl]oxymethyl]-1-piperidyl]-2-hydroxy) with human liver microsomes generated several metabolites that highlighted the hydroxyacetamide side chain was a major site of metabolism for the molecule. The metabolites were derived predominantly from oxidative biotransformations; however, two unexpected products were detected by liquid chromatography/ultraviolet/mass spectrometry (LC/UV/MS) and identified as methanol adducts. This observation prompted further LC/MS investigations into their formation. METHODS: Three separate incubations of CPAQOP were conducted in human liver microsomes; Naïve, fortified with methoxyamine and fortified with glutathione. Separation was achieved via ultra-high-performance liquid chromatography with either methanol or acetonitrile gradients containing formic acid. MS analysis was conducted by electrospray ionisation LTQ Orbitrap mass spectrometry acquiring accurate mass full scan, data-dependent MS2 and all ion fragmentation. RESULTS: No methanol adducts were detected by MS when acetonitrile was used in the mobile phase instead of methanol, verifying that a metabolite was reacting with methanol on column. Although this reactive metabolite could not be isolated or structurally characterised by LC/MS directly, product ion spectra of the methanol adducts confirmed addition of methanol on the hydroxyacetamide side chain. Additional experiments using methoxyamine showed the disappearance of the two methanol adducts and appearance of a methoxyamine adduct, confirming the presence of an aldhyde. Product ion spectra of the methoxyamine adduct confirmed addition of methoxyamine to the hydroxyacetamide side chain. CONCLUSIONS: The proposed bioactivation of CPAQOP occurred via the reactive aldehyde intermediate, which readily reacted with methanol in the mobile phase to form a pair of isomeric hemiacetal methanol adducts. In acidified methanol the equilibrium favoured the methanol adduct and in acidified acetonitrile it favoured the hydrate; therefore, the reactive aldehyde metabolite was not detected and could not be structurally characterised directly. Copyright © 2016 John Wiley & Sons, Ltd.

Discovery of a Potent, Selective, Orally Bioavailable, and Efficacious Novel 2-(Pyrazol-4-ylamino)-pyrimidine Inhibitor of the Insulin-like Growth Factor-1 Receptor (IGF-1R).

Optimization of cellular lipophilic ligand efficiency (LLE) in a series of 2-anilino-pyrimidine IGF-1R kinase inhibitors led to the identification of novel 2-(pyrazol-4-ylamino)-pyrimidines with improved physicochemical properties. Replacement of the imidazo[1,2-a]pyridine group of the previously reported inhibitor 3 with the related pyrazolo[1,5-a]pyridine improved IGF-1R cellular potency. Substitution of the amino-pyrazole group was key to obtaining excellent kinase selectivity and pharmacokinetic parameters suitable for oral dosing, which led to the discovery of (2R)-1-[4-(4-{[5-chloro-4-(pyrazolo[1,5-a]pyridin-3-yl)-2-pyrimidinyl]amino}-3,5-dimethyl-1H-pyrazol-1-yl)-1-piperidinyl]-2-hydroxy-1-propanone (AZD9362, 28), a novel, efficacious inhibitor of IGF-1R.

Identification of the reactive metabolites of fenclozic acid in bile duct cannulated rats.

Fenclozic acid (Myalex) was developed by ICI pharmaceuticals in the 1960s for the treatment of rheumatoid arthritis and was a promising compound with a good preclinical safety profile and efficacy. While it did not show adverse hepatic effects in preclinical animal tests or initial studies in man [ Chalmers et al. Ann. Rheum. Dis. 1969 , 28 , 595 and Chalmers et al. Ann. Rheum. Dis. 1969 , 28 , 590 ], it was later withdrawn from clinical development. Hepatotoxicity was observed in humans at daily doses of 400 mg but was not replicated in any of the animal species tested. Rodrigues et al. [ Arch. Toxicol. 2013 , 87 , 1569 ] published a mechanistic investigation using modern in vitro assays/techniques in order to investigate the hepatotoxicity; however, only the covalent binding in rat, dog, and human microsomes was identified as a potential indicator for hepatoxicity. Metabolites associated with or responsible for covalent binding could not be detected, likely due to the low in vitro metabolic turnover of fenclozic acid in microsomes. Foulkes [ J. Pharmacol. Exp. Ther. 1970 , 172 , 115 ] investigated the in vivo metabolism of fenclozic acid which included a rat bile duct cannulated (BDC) study characterizing the biliary and urinary metabolites; however, no reactive metabolites were identified. This study aimed to reinvestigate the in vivo metabolism of fenclozic acid in rat, with a focus on identifying any reactive metabolites that could explain the in vitro covalent binding in microsomes observed across the species. Using modern analytical techniques, we were successful in identifying an epoxide reactive metabolite, which upon conjugation with glutathione (GSH), formed up to 16 GSH-related products including positional and diastereoisomers. Not including the GSH related conjugates, 7 additional metabolites were identified compared to these previous metabolism studies.

Reactive metabolite trapping screens and potential pitfalls: bioactivation of a homomorpholine and formation of an unstable thiazolidine adduct.

Successful early attrition of potential problematic compounds is of great importance in the pharmaceutical industry. The lead compound in a recent project targeting neuropathic pain was susceptible to metabolic bioactivation, which produced reactive metabolites and showed covalent binding to protein. Therefore, as a part of the backup series for this compound several structural modifications were explored to mediate the reactive metabolite and covalent binding risk. A homomorpholine containing series of compounds was identified without compromising potency. However, when these compounds were incubated with human liver microsomes in the presence of GSH, Cys-Gly adducts were identified, instead of intact GSH conjugates. This article examines the formation of the Cys-Gly adduct with AZX ([M+H]+ 486) as a representative compound for this series. The AZX-Cys-Gly-adduct ([M+H]+ 662) showed evidence of ring contraction by formation of a thiazolidine-glycine and was additionally shown to be unstable. During its isolation for structural characterization by 1H NMR spectroscopy, it was found to have decomposed to a product with [M+H]+ 446. The characterization and identification of this labile GSH-derived adduct using LC-MS/MS and 1H NMR are described, along with observations around stability. In addition, various structurally related trapping reagents were employed in an attempt to further investigate the reaction mechanism along with a methoxylamine trapping experiment to confirm the structure of the postulated reactive intermediate.

Reaction of homopiperazine with endogenous formaldehyde: a carbon hydrogen addition metabolite/product identified in rat urine and blood.

Drug reactivity and bioactivation are of major concern to the development of potential drug candidates in the pharmaceutical industry (Chem Res Toxicol 17:3-16, 2004; Chem Res Toxicol 19:889-893, 2006). Identifying potentially problematic compounds as soon as possible in the discovery process is of great importance, so often early in vitro screening is used to speed up attrition. Identification of reactive moieties is relatively straightforward with appropriate in vitro trapping experiments; however, on occasion unexpected reactive intermediates can be found later during more detailed in vivo studies. Here, we present one such example involving a series of compounds from an early drug discovery campaign. These compounds were found to react with endogenous formaldehyde from a rat in vivo study, resulting in the formation of novel +13-Da bridged homopiperazine products (equivalent to the addition of one carbon and one hydrogen atom), which were detected in urine and blood. The identification of these +13-Da products and their origin and mechanism of formation are described in detail through analyses of a representative homopiperazine compound [N-(3-(3-fluorophenyl)-1,2,4-thiadiazol-5-yl)-4-(4-isopropyl-1,4-diaze-pane-2-carbonyl)piperazine-1-carboxamide (AZX)] by liquid chromatography-UV-mass spectrometry, (1)H NMR, and chemical tests.

Disposition and metabolism of the specific endothelin A receptor antagonist zibotentan (ZD4054) in healthy volunteers.

Zibotentan (ZD4054) is a specific endothelin A (ET(A)) receptor antagonist that is in clinical development for the treatment of castration-resistant prostate cancer (CRPC) and has shown a promising signal for improvement in overall survival compared with placebo in a Phase II study of patients with metastatic CRPC. In this study, the pharmacokinetics, disposition and metabolism of zibotentan were evaluated following administration of a single oral dose of [(14)C]-zibotentan 15 mg to six healthy subjects. Zibotentan was rapidly absorbed, with the maximum zibotentan plasma concentration being observed 1 hour after administration. Excretion was rapid with the majority of the dose being excreted in the urine (71-94%). Total recovery of radioactivity over the 5 days of the study was high (mean 93%), with 78% of the dose being recovered within 24 hours. Concentrations of radioactivity in the plasma were similar up to 12 hours post dose, and diverged thereafter, indicating the presence of circulating metabolites. The main circulating component was zibotentan with a number of metabolites being identified in excreta. Zibotentan was well absorbed and was cleared via metabolism and urinary excretion with zibotentan-related material predominantly excreted via the urine.

The metabolism of [14C]-zibotentan (ZD4054) in rat, dog and human, the loss of the radiolabel and the identification of an anomalous peak, derived from the animal feed.

This paper presents an overview of a cross-species investigation of the metabolic fate of [(14)C]-zibotentan (ZD4054), with particular focus on the main analytical challenges encountered during the study. A combination of detection methods were used including HPLC coupled to UV, RAD and/or MS(MS), and (1)H NMR spectroscopy. The objective was to characterise and identify the major metabolites found in the circulation and excreta of rat and dog for comparison with those produced in human. Initial investigations in rat, using [(14)C]-labelled zibotentan positioned on the oxadiazole ring and HPLC-UV-RAD analysis, revealed seven labelled resolved metabolite peaks. Parallel analysis by HPLC-UV-MS (with in-source fragmentation) uncovered two additional metabolites, indicating loss of the radiolabel during biotransformation. Hence, in subsequent studies in rat, dog and human, dual-radiolabelled zibotentan was employed with the (14)C-label positioned on the pyridine ring, which was shown to be less prone to metabolism. A total of 12 metabolites were found in the excreta and plasma in all species. One of these metabolites was found in the circulation in humans, which warranted further investigations. Characterisation of the isolated human circulating metabolite by (1)H NMR was complicated by the co-extraction of a matrix component with a similar UV-chromophore to zibotentan, which was identified as daidzein, an isoflavone derived from the animal feed.

Nuclear magnetic resonance (NMR)-based drug metabolite profiling.

The identification of drug metabolites in biofluids such as urine, plasma and bile is an important step in drug discovery and development. Proton nuclear magnetic resonance ((1)H-NMR) spectroscopy can provide detailed information regarding the structural transformation of a compound as a consequence of metabolism. However, successful identification of drug metabolites by (1)H-NMR spectroscopy is generally compromised by the presence of endogenous metabolites, which can obscure the signals of the drug metabolites in question. Hence, sample clean-up and separation of the metabolites from the biofluid matrix is crucial. This is generally achieved by extraction of the biofluid, solid-phase extraction (SPE), high-performance liquid chromatography (HPLC) or any combination of these. Apart from (1)H, other NMR-active nuclei, such as (19)F, can provide a useful handle for metabolite profiling, provided they are not naturally present in the biofluid. Successful studies have shown that the presence of a fluorine-handle on the drug and its metabolites can provide additional qualitative and quantitative data by (19)F-NMR spectroscopy. This chapter provides guidelines and examples of NMR-based drug metabolite profiling.

Characterisation and identification of the human N+-glucuronide metabolite of cediranib.

Cediranib (4-[(4-fluoro-2-methyl-1H-indol-5-yl)oxy]-6-methoxy-7-[3-(1-pyrrolidinyl)propoxy]quinazoline; RECENTIN), a vascular endothelial growth factor (VEGF) tyrosine kinase inhibitor (TKI) of all three VEGF receptors, is currently in Phase III clinical trials for the first-line treatment of colorectal cancer and the treatment of recurrent glioblastoma. During its clinical development a unique human metabolite, an N(+)-glucuronide, was identified as a major circulating metabolite and one of the major metabolites excreted into faeces. Given the possibility of four sites for the conjugation of the glucuronic acid moiety, determination of the location of the conjugation site on cediranib was warranted. A small quantity of the N(+)-glucuronide metabolite of cediranib was initially generated using recombinant human uridine glucuronosyltransferase 1A4 (UGT1A4) enzymes. The metabolite generated was characterised by HPLC-UV and mass spectrometric (HPLC-MS(n)) detection and confirmed by (1)H NMR spectroscopy. However, the exact site of conjugation could not be determined without generating more of the metabolite. Hence a subsequent biosynthetic scale-up experiment was devised to generate a sufficiently large quantity for full structural characterisation by (1)H NMR spectroscopy. The identity of the N(+)-glucuronide metabolite generated in the UGT1A4 scale-up experiment was confirmed by HPLC-MS(n) and displayed the same retention time, molecular mass and mass fragmentation data as the metabolite generated in previous human liver microsomal and hepatocyte incubations. (1)H NMR spectroscopy clearly showed the characteristic anomeric doublet at approximately 4.7 ppm, which, following irradiation during selective Rotating frame Overhauser Effect Spectroscopy (ROESY) experiments, enabled the site of glucuronidation to be confirmed on the pyrrolidine nitrogen. With the exception of the N(+)-glucuronide metabolite, all other human metabolites of cediranib were observed following incubation with hepatocytes from rat and cynomolgus monkey, the species used for toxicology testing of the drug [6]. As the N(+)-glucuronide was not detected in the preclinical species, it is suggested that its formation is more likely in human and higher primates (great apes), a finding widely supported in the literature.

Analysis of time course 1H NMR metabolomics data by multivariate curve resolution.

Modeling NMR-based metabolomics data often involves linear methods such as principal component analysis (PCA) and partial least squares (PLS). These methods have the objective of describing the main variance in the data and maximum covariance between the predictor variables and some response variable respectively. If the experiment is designed to investigate temporal biological fluctuations, however, the factors obtained become difficult to interpret in a biological context. Moreover, when these methods are applied to analyze data, an implicit assumption is made that the measurement errors exhibit an iid-normal distribution, often limiting the extent of the information recovered. A method for the linear decomposition of NMR-based metabolomics data by multivariate curve resolution (MCR), which has been used elsewhere for time course transcriptomics applications, is introduced and implemented via a weighted alternating least squares (ALS) approach. Measurement of error information is incorporated in the modeling process, allowing the least squares projections to be performed in a maximum likelihood fashion. As a result, noise heteroscedasticity resulting from pH-induced peak shifts can be modeled, eliminating the need for binning/bucketing. The utility of the method is demonstrated using two sets of temporal NMR metabolomics data, HgCl(2)-induced nephrotoxicity in rat, and fish (Japanese medaka, Oryzias latipes) embryogenesis. Profiles extracted for the nephrotoxicity data exhibit strong correlations with metabolites consistent with temporal fluctuations in glucosuria. The concentration of metabolites such as acetate, glucose, and alanine exhibit a steady increase, which peaks at Day 3 post dose and returns to basal levels at Day 8. Other metabolites including citrate and 2-oxoglutarate exhibit the opposite characteristics. Although the fish embryogenesis data are more complex, the profiles extracted by the algorithm display characteristics that depict temporal variation consistent with processes associated with embryogenesis.

A metabonomic study of strain- and age-related differences in the Zucker rat.

Ultra-performance liquid chromatography (UPLC) coupled to orthogonal acceleration time-of-flight mass spectrometry (oa-TOFMS) in positive electrospray ionization mode was used to obtain metabolite profiles for urine obtained from three strains of Zucker rat. These were the Zucker lean, the Zucker (fa/fa) obese and the Zucker lean/(fa) cross. Clear age- and strain-related differences were noted with the leptin-deficient (fa/fa) obese animal showing significant differences from both the other Zucker rat strains with respect to metabolite profiles.

Superheated water chromatography-nuclear magnetic resonance spectroscopy of kava lactones.

Three kava lactone constituents of Piper methysticum, namely, kawain, methysticin and desmethoxyyangonin, have been separated and identified by reversed-phase HPLC using superheated deuterium oxide as the mobile phase and on-line 1H-NMR detection. The method avoids the use of organic solvents in the mobile phase and hence interferences in the NMR analysis are minimised.

A combined (1)H NMR and HPLC-MS-based metabonomic study of urine from obese (fa/fa) Zucker and normal Wistar-derived rats.

(1)H NMR and HPLC-MS were used to generate metabolite fingerprints for the metabonomic analysis of urine obtained from both male and female Zucker obese (fa/fa) rats, used as a model of type II diabetes, and normal male Wistar-derived animals. The resulting data were subjected to chemometric analysis (principal components analysis and partial least squares discriminant analysis) to investigate the effects of strain, diurnal variation is strain, diurnal variation and gender and gender on metabolite profiles. In the case of strain, (1)H NMR spectroscopic analysis revealed increased taurine, hippurate and formate and decreased betaine, alpha-ketoglutarate, succinate and acetate in samples from Zucker-obese compared to Wistar-derived rats. HPLC-MS analysis detected increased hippurate and ions at m/z 255.0640 and 285.0770 in positive, and 245.0122 and 261.0065 in negative electrospray ionisation (ESI), respectively, for the Zucker obese samples. Both techniques enable the detection of diurnal variation in the urine of male and female Zucker rats, marked by increases in taurine, creatinine, allantoin and alpha-ketoglutarate by (1)H NMR, and ions at m/z 285.0753, 291.0536 and 297.1492 (positive ESI) and 461.1939 (negative ESI) using HPLC-MS, in the evening samples. Differences between male and female Zucker rats were also observed. Compared to samples from male rats hippurate, succinate, alpha-ketoglutarate and dimethylglycine ((1)H NMR) were elevated in the urine of female animals together with ions at, e.g., m/z 431.1047, 325.0655, 271.0635 and 447.0946 (positive ESI) and m/z 815.5495 and 459.0985 (negative ESI) by HPLC-MS. Both analytical techniques used in this study were able to detect differences between normal and Zucker obese rats, which may provide markers of metabolic disease.

HPLC-MS-based methods for the study of metabonomics.

The development and use of HPLC-MS for the study of metabonomics is reviewed. To date the technique has been applied to the analysis of urine samples obtained from studies in rodents in investigations of physiological variation (e.g., factors such as strain, gender, diurnal variation, etc.) and toxicity. Examples are provided of the use of conventional HPLC, capillary methods and the recently introduced high-resolution systems based on a combination of high pressure and small particle size ("UPLC"). Comparison is also made of the use of 1H NMR spectroscopy and HPLC-MS for the analysis of biofluid samples and the advantages and limitations of the two approaches are assessed. Likely future developments are considered.

Superheated water chromatography-nuclear magnetic resonance spectroscopy and mass spectrometry of vitamins.

The water-soluble vitamins, pyridoxine, riboflavin, and thiamine, were separated by reversed-phase liquid chromatography using hot or superheated water as the mobile phase and were detected using a range of detectors, including ultraviolet and fluorescence spectroscopy and mass spectrometry. By using deuterium oxide as the eluent, direct on-line nuclear magnetic resonance spectra could be obtained with minimal spectral interference from the mobile phase. Some of the compounds showed deuterium exchange of alkyl-protons when separated at high temperatures.