FLAP - American Chemical Society

Chapter 4

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Discovery of the Novel Oxadiazole-Containing 5-Lipoxygenase Activating Protein (FLAP) Inhibitor BI 665915 Hidenori Takahashi,*,1 Alessandra Bartolozzi,1 and Thomas Simpson2 1Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States 2Department of Chemistry, West Chester University, 700 South High Street, West Chester, Pennsylvania 19383, United States *E-mail: [email protected].

This is a brief review of the discovery of FLAP inhibitor BI 665915 (Takahashi, H., et al. J. Med. Chem. 2015, 58, 1669−1690). The chapter summarizes the discovery efforts including structure-activity relationship (SAR), drug metabolism and pharmacokinetics (DMPK) profile and medicinal chemistry synthetic route towards oxadiazolecontaining 5-lipoxygenase-activating protein (FLAP) inhibitors. A knowledge-based lead generation followed by lead optimization using a structure-based drug design provided compounds that demonstrated excellent FLAP binding potency (IC50 < 10 nM) and potent inhibition of LTB4 synthesis in human whole blood (hWB) (IC50 < 100 nM). Optimization of the binding, functional potencies and physicochemical properties resulted in the identification of a amino-pyrimidinyl molecule (BI 665915) that significantly inhibited LTB4 production in a murine ex vivo whole blood study in a dose-dependent manner. This also significantly inhibited atherosclerosis progression in a rabbit disease model. Based on the high quality of its overall profile and in vivo activity, the compound was advanced into preclinical development.

© 2016 American Chemical Society Abdel-Magid et al.; Comprehensive Accounts of Pharmaceutical Research and Development: From Discovery to Late-Stage ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


Introduction 5-Lipoxygenase-activating protein (FLAP) was discovered in the early 1990s as an essential accessory protein that is involved in the cellular biosynthesis of leukotrienes (LTs) in the 5-lipoxygenase (5-LO) pathway (1, 2). FLAP and 5-LO are primarily expressed in neutrophils, monocytes, macrophages, eosinophils and mast cells. LTs are a family of eicosanoid pro-inflammatory mediators that are biosynthesized from arachidonic acid (AA) (3–6). The LT pathway is initiated upon inflammatory stimuli which activates phospholipase A2 (PLA2) which hydrolyzes phospholipid to release AA from the cell membrane. AA then binds to membrane-attached FLAP and interacts with 5-LO, leading to the oxidation of AA to the unstable intermediate leukotriene A4 (LTA4) (7). LTA4 is the common precursor for the biosynthesis of leukotriene B4 (LTB4) and the cysteinyl leukotriene C4 (LTC4) that can be further transformed into leukotrienes D4 and E4 (i.e., LTD4 and LTE4, respectively). These lipid mediators activate G protein-coupled transmembrane receptors (GPCRs). For example, LTB4 activates BLT1 and BLT2 while CysLTs stimulate CysLT1, CysLT2, and CysLTER that further trigger the pro-inflammatory signaling pathway (Figure 1). Through the course of research on LTs (8–10). it has become clear that they play important pathophysiological roles across a wide range of respiratory, allergic (11, 12), and cardiovascular diseases (13–17) such as asthma, allergic rhinitis, chronic obstructive pulmonary disease (COPD), arthritis, inflammatory bowel disease, psoriasis, liver fibrosis, cancer, endothelial dysfunction, intimal hyperplasia, atherosclerosis, myocardial dysfunction, ischemic stroke and aortic aneurysms. This chapter describes the structure-guided design, structure-activity relationships (SAR) and biological evaluation of a novel class of oxadiazole-containing FLAP inhibitors, as well as their divergent synthesis for the SAR development.

Discovery and SAR of the Novel Oxadiazole Containing Flap Inhibitors The first FLAP inhibitor, MK-886, was reported by Merck-Frosst in 1989 (18). In addition to MK-886, four other selective FLAP inhibitors have advanced to clinical trials (Figure 2) (19–21). These compounds share a common structural feature that comprises a carboxylic acid moiety that is tethered to a heteroaryl (i.e., an indole in MK-886, MK-591 and AM-803) or an aryl (i.e., a phenyl in BAY X1005 and ABT-080) scaffold via an alkyl linker (22, 23). The clinical progression of ABT-080 was stopped after phase I. MK-886 (24), MK-591 (25) and BAY X1005 (26) showed efficacy in asthmatic patients without adverse hepatotoxic events in contrast to the 5-LO inhibitor Zileuton© (27). Further development of MK-591 was discontinued because the degree of improvement observed in the clinical studies was not as good as expected given the biochemical potency (28), and deCODE stopped the development of BAY X1005 due to formulation issues. Finally, Amira’s FLAP inhibitor AM-803 (GSK-2190915) displayed good safety and tolerability, as well as efficacy on 102

Abdel-Magid et al.; Comprehensive Accounts of Pharmaceutical Research and Development: From Discovery to Late-Stage ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


the allergen-induced asthmatic response in patients with mild asthma in phase II clinical trials (29, 30). Genetic, pharmacological, and clinical studies support the use of LT modulators beyond the treatment of asthma. Specifically, pre-clinical studies have shown that LTs play pathophysiological roles in cardiovascular diseases (31). The FLAP inhibitors MK-886 and BAY X1005 have demonstrated statistically significant reduction of the aortic atherosclerotic lesions in the apoE/LDLR double knockout mice model (32–34).

Figure 1. Leukotriene pathway. (Reproduced from reference (41). Copyright 2015 Americam Chemical Society). 103 Abdel-Magid et al.; Comprehensive Accounts of Pharmaceutical Research and Development: From Discovery to Late-Stage ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


In a Swedish nationwide population-based analysis of a large number of patients, the occurrence of cardiovascular endpoints in asthmatic patients treated with the CysLT1 antagonist Montelukast© revealed a modest decrease in the risk of recurrent stroke and myocardial infarction (35). Additionally, the 5-LO inhibitor VIA-2291 (Atreleuton©) has displayed a statistically significant reduction in noncalcified plaque volume at 24 weeks in the treated patients as compared to the placebo group (36). Recently, the drug discovery efforts on LT pathway inhibitors have been directed towards demonstrating a proof of clinical concept in cardiovascular diseases. For instance, AstraZeneca recently advanced FLAP inhibitor, AZD5718, into phase I clinical trials for cardiovascular disorders (37).

Figure 2. FLAP inhibitors advanced into clinical trials. (Reproduced from reference (41). Copyright 2015 Americam Chemical Society).

Based on the data in support of the therapeutic value of FLAP inhibitors, we decided to pursue FLAP as a target for the treatment of atherosclerosis. Although we initially applied high throughput screening for identifying lead chemical series, the method didn’t provide robust lead series. Then, we implemented a knowledge-based drug design approach to identify new lead chemical series using the X-ray co-crystal structure of human FLAP/MK-591 complex (PDB ID: 2Q7M) (38) in combination with published SAR on bis-aryl FLAP inhibitors (34, 39). The X-ray co-crystal structure of human FLAP/MK-591 complex revealed that FLAP crystallized as a homotrimer with MK-591 bound in a groove located at the interface of adjacent monomers and exposed to the lipid bilayer. Through computer-assisted drug design, we identified a series of substituted oxadiazoles, which were predicted by docking studies to occupy the same binding pocket as MK-591 (Figure 3). Indeed, the initial FLAP inhibition SAR of these oxadiazoles supported the predicted binding mode. 104



Figure 3. Proposed binding mode for the oxadiazole series of FLAP inhibitors: (A) Overlay of a docking pose generated for 6 (dark gray sticks) with the crystal structure of FLAP in complex with MK-591 (2) (light gray sticks; PDB ID: 2Q7M). Key amino acids are labeled in the binding site and the inhibitors are shown as sticks. (B) The docking pose of 6 (dark gray sticks) in the FLAP binding site shown on semi-transparent rendering of solvent accessible protein surface for the binding site defined by labeled amino acids that are within 3.5 Å sphere of the inhibitor. (Reproduced from reference (41). Copyright 2015 Americam Chemical Society).

The SAR development in this series was initially driven by: • •

The FLAP binding assay that measured the ability of a test compound to displace the radio-labeled ligand [125I]-L-691831 (PE NEX084) (40). The FLAP functional assay that determined the inhibition of LTB4 synthesis in human whole blood (hWB) (41). 105



The SAR summary of a select group of oxadiazole substituents is shown in Table 1. The amino-containing compound 7 showed a robust FLAP binding potency (IC50 = 20 nM) and served as a good starting point for further SAR development. The strong binding activity of 7 translated into potent inhibition of LTB4 synthesis in the hWB assay (IC50 = 440 nM). Although alkylation of the amino group (e.g., -NHEt) retained the binding and cellular potency, polar substituents on the amine moiety such as the sulfonyl group were not tolerated (data not shown). To explore the available space, a phenyl derivative 8 was synthesized and tested, which showed > 10-fold boost in the FLAP binding potency (IC50 = 1.4 nM) as compared to 7. Unfortunately, the improved binding affinity of 8 did not translate into higher potency in the hWB assay (IC50 = 470 nM). Compound 8 has high clogP (4.07) (42) and low topological polar surface area (TPSA: 91 Å2) (43). We hypothesized that highly lipophilic compounds such as 8 may be highly protein bound in human plasma (i.e., low free fraction) leading to low activity in hWB. To test this hypothesis, the phenyl substituent was systematically replaced with more polar 5- and 6-membered hetero-aromatic groups. Generally, the FLAP binding SAR of these analogs was relatively flat. For instance, the 3-pyridine 9, the 4-imidazole (11), the 3-pyrazole (12) and the 4-pyrazole (13) derivatives showed comparable FLAP binding potency (IC50 < 10 nM) to the phenyl analog 8. However, in line with our hypothesis, these less lipophilic hetero-aromatic compounds were two- to four-fold more potent in the hWB assay (9, 11-13: IC50 =110-270 nM) than 8. In contrast, pyridone derivative 10 displayed a good binding potency (IC50 = 2.9 nM) but did not inhibit the LTB4 production in the hWB assay at the highest tested concentration of 5 μM. Our analysis of a larger set of compounds in this series had revealed a relationship between the FLAP binding or hWB potency and TPSA (Figure 4). Although no clear correlation between TPSA and FLAP binding IC50 was observed, generally, compounds with high TPSA (> 120 Å2) showed diminished hWB activities, which could be attributed to lower cell penetration. Indeed, the lower activity of 10 (TPSA = 124 Å2) in the hWB assay was consistent with the findings from this analysis. Based on its attractive binding and functional potencies, 13 was selected for further optimization. Table 2 shows the SAR summary of the 4-pyrazole substitutions. Methyl substituted compound 14 showed comparable binding potency (IC50 = 1.9 nM) to 13 and approximately two-fold improvement in hWB activity (IC50 = 45 nM). Although 13 and 14 showed good FLAP binding and functional potencies, they were both highly crystalline and displayed low aqueous solubility at pH 6.8 (0.4 and 0.03 μg/mL, respectively).

106 Abdel-Magid et al.; Comprehensive Accounts of Pharmaceutical Research and Development: From Discovery to Late-Stage ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


Table 1. SAR of Substituted Oxadiazoles



Figure 4. Correlation between TPSA (Å2) and FLAP binding IC50 (nM) (A) or hWB IC50 (nM) (B).

To improve the aqueous solubility, we decided to substitute the methyl group of 14 with polar solubilizing groups. The N,N-dimethylethylamine analog 15 showed good binding and functional potencies, as well as high aqueous solubility (270 μg/mL at pH 6.8). However, 15 has an embedded basic moiety (i.e., the –NMe2 group) that was believed to be the source of cytochrome P450 (CYP450) enzymes 2C9 and 2D6 inhibition (IC50 = 7 and 10 μM, respectively). In contrast, compound 16, which was substituted with a neutral N,N-dimethylacetamide group, did not inhibit the CYP450 enzymes at the highest tested concentrations (30 μM) while maintaining the FLAP binding and hWB activities (IC50 = 3.6 and 81 nM, respectively). The carboxymethyl derivative 17, de-protonated and negatively charged under physiological and assay conditions, was five-fold less potent in FLAP binding than 16, and did not inhibit the LTB4 production in the hWB assay. However, a hindered and neutral hydroxyl containing analog 18 showed good binding potency and functional activity (IC50s of 3.5 and 69 nM, respectively). Apparently, removal of the charged group (i.e., -COO– → -OH) and shielding of the polar hydroxyl moiety with the methyl groups provided a good balance of functional activity and aqueous solubility (e.g., 18: hWB IC50 = 69 nM, pH 6.8 sol = 8.1 μg/mL). Docking studies with N-substituted 4-pyrazoles suggested that the N-1 substituent pointed out of the FLAP binding pocket towards the lipophilic center of the phospholipid bilayer (Figure 3B). The observed loss of binding potency associated with 17 (i.e., an analog bearing a charged group) and potent binding activity of 18 (i.e., a derivative containing a neutral and shielded polar functional group) was consistent with this modeling hypothesis.



Table 2. SAR of N-Substituents on 4-Pyrazole



Table 3 shows the SAR at the benzylic carbon group. The unsubstituted compound 19 showed lack of FLAP binding and hWB potencies at the highest tested concentrations (1 μM and 5 μM, respectively). However, the dimethyl analog 20 showed good FLAP binding activity (IC50 = 6.7 nM) and a robust functional inhibition in the hWB assay (IC50 = 93 nM). This SAR suggests that the substitution on the C-8 position is crucial for the FLAP binding activity. Interestingly, replacing the gem-dimethyl group with a cyclopropane ring, as in 21, resulted in a 15-fold loss of binding potency (cf. 21 binding IC50 = 100 nM vs. 20 binding IC50 = 6.7 nM) while increasing the ring size to cyclobutane ring restored the binding and functional activities (e.g., 14: binding IC50 = 1.9 nM; hWB IC50 = 45 nM). We calculated the torsional angle between the bis-aryl groups for various R1 and R2 substituents. These calculations suggested that the cyclopropane ring of 21 caused the maximal distortion of the bis-aryl angle (119.0°). In contrast, the geminal methyls of compound 20 (104.2°) and the cyclobutane ring in compound 14 (109.0°) affected smaller deviations from the tetrahedral bond angle. In view of the observed binding potencies of these compounds, it appears that the bond angle between the two aryl groups has a profound impact on the FLAP binding potency. A bond angle of < 119° seemed to be required for achieving a good binding potency (IC50 < 100 nM). Docking studies indicated that the benzylic carbon occupied a small hydrophobic space that was at the interface of the α4 and α1 helices of two adjacent FLAP monomers and lined with the side chains of a collection of hydrophobic amino acid residues such as V20, V21, I119, L120, and F123 (Figure 3A and B). The binding pose showed that the linker substituents pointed towards the inner part of this small pocket. A closer examination of the docking model indicated that the R2 substituent occupied a smaller hydrophobic cavity closer to the I119, L120 and F123 cluster of residues, while R1 was pointing towards a slightly larger space near the V20, and the V21 residues of the two adjacent monomer (Figure 3B), which suggested a potential stereochemical preference. To validate the modeling prediction and to assess the impact of various substituents on the FLAP binding and functional potencies, additional SAR on the benzylic carbon group was performed. The racemate of the iso-propyl/methyl analog 22 showed similar binding potency as compared to the germinal dimethyl compound 20 (cf. IC50 = 2.0 nM vs. IC50 = 6.7 nM, respectively). Compound 22 was resolved to provide the (R) and the (S) enantiomers, (23 and 24, respectively). The (R)-enantiomer 23 showed potent FLAP binding and functional activities with IC50 values of 1.6 and 33 nM, respectively. In fact, the (R)-enantiomer 23 was approximately five-fold more potent in FLAP binding and ten-fold more potent in hWB activity than the corresponding (S)-enantiomer 24. A similar pattern was also observed with enantiomers 25 and 26. These data confirmed that the substitution on the benzylic carbon of the bis-aryl core required an optimal size and chirality for maximal FLAP inhibition.



Table 3. SAR of Substitutions on the Methylene Linker



Table 4. SAR of Left Hand Side Phenyl Substitutions

The docking studies also suggested that the substituents on the left-hand side phenyl occupied a small cavity inside of the FLAP helices (Figure 3B); hence, it was predicted that groups occupying this binding pocket would have size limitation. Our initial SAR in this area had indicated that para-amino substituted nitrogen-containing 6-membered heteroaryls were preferred. Table 4 shows the SAR of a select group of these 6-membered heteroaromatic groups. For example, the amino-pyridyl analog 27 and the amino-pyrimidinyl analog (28: BI 665915) 112 Abdel-Magid et al.; Comprehensive Accounts of Pharmaceutical Research and Development: From Discovery to Late-Stage ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.

displayed good binding potencies (IC50 = 1.1 and 1.7 nM, respectively) and hWB activities (IC50 = 66 and 45 nM, respectively). Introduction of an alkyl chain on the amino substituent did modulate both the binding and the functional potencies. For instance, the aminomethyl analog 29 retained both binding and functional activities as compared to the non-alkylated derivative 28. However, larger substituents such as iso-propyl amine (e.g., 29) eroded the FLAP binding and cellular potencies.


Table 5. Overall Profile of BI 665915

Overall, the SAR indicated several favorable structural features to achieve potent FLAP binding and functional inhibition. For instance, the most favorable effects were obtained when the C-8 benzylic carbon was a part of cyclobutane ring or carries (R)-cyclopropyl/methyl groups. Also, N,N-dimethylacetamide, N,N-dimethylaminoethyl and 1,1-dimethyl-ethanol moieties were preferred 113 Abdel-Magid et al.; Comprehensive Accounts of Pharmaceutical Research and Development: From Discovery to Late-Stage ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


as the substituents on the pyrazole ring. Thus, an array of compounds that combined these preferred groups were synthesized and evaluated. Compound 28 that featured the N,N-dimethylacetamide substituted pyrazole and the (R)-cyclopropyl/methyl central substituents showed good FLAP potencies and a favorable off-target profile (Table 5). This compound was also very selective for FLAP as compared to other enzymes and receptors in the leukotriene pathway such as 5-LO, cycloxygenease (COX)-1 and -2, PLA2, LTA4 hydrolase, BLT1, and BLT2 (< 50 % inhibition at 10 μM). Based on its overall profile, 28 was selected for in vitro and in vivo DMPK assessment. Compound 28 showed a modest human hepatocyte clearance (41 percent of hepatic blood flow (% Qh)) and relatively high plasma protein binding (unbound fraction = 4.7 %). It displayed high membrane permeability in Caco-2 cell line with a low efflux ratio (AB = 34 x 10-6 cm/s, efflux ratio = 1.9). Weak CYP450 3A4 induction was detected (~2-fold at 30 µM) for 28; however, there was no evidence of time-dependent inhibition (highest tested concentration = 100 µM) suggesting a low risk for potential drug-drug interactions. The pharmacokinetic properties of 28 were evaluated in rat, dog, and cynomolgus monkey. It showed low iv plasma clearance in all three species (CL = 7 % Qh in rat, 2.8 % Qh in dog, and 3.6 % Qh in cynomolgus monkey). The volumes of distribution (Vss) across the tested species were in the range of 0.5 to 1.2 L/kg, and the bioavailabilities were moderate to good (F = 45 to 63 %). The overall DMPK profile of 28 was very attractive and qualified it for advancement into the ex vivo stimulated LTB4 production in mice whole blood study. Compound 28 demonstrated a dose-dependent inhibition of an ex vivo stimulated LTB4 production in mice whole blood after a single oral dose (LTB4 production inhibition = 94.9 % at 100 mg/kg dose, 77.8 % at 30 mg/kg dose and 9.0 % at 10 mg/kg dose as compared to the vehicle treated group) (41). Compound 28 was also found to significantly inhibit atherosclerosis progression in a rabbit disease model (44, 45), that qualified it as a pre-clinical development candidate.

Medicinal Chemistry Synthetic Route The general synthetic strategy that was implemented for the SAR development of the oxadiazole-containing FLAP inhibitors is shown in Scheme 1. According to this approach, dialkylation of 4-bromophenylacetonitrile 31 would generate a quaternary nitrile of formula 32, which could be converted to the amidoxime 33 by treatment with hydroxylamine. Cyclization of 33 with a compound bearing an activated carboxylic acid moiety could produce an oxadiazole of formula 34, which could be further functionalized via Suzuki-Miyaura cross-coupling reaction to generate the FLAP inhibitors 35. For some examples, the synthetic protocol was modified as follows: the phenyl group of 32 was functionalized via SuzukiMiyaura cross-coupling reaction and followed by an oxadiazole cyclization and installation of oxadiazole functional group. The representative synthetic route for 23 and 24 using the later synthetic protocol is summarized in Scheme 2. 114



Scheme 1. General synthesis of oxadiazole-containing FLAP inhibitors. (Reproduced from reference (41). Copyright 2015 Americam Chemical Society).

Sequential dialkylation of 4-bromophenylacetonitrile 31 with 2-bromopropane and methyl iodide generated a racemic mixture of structure 36. Compound 36 was coupled with 2-aminopyrimidine-5-boronic acid pinacol ester via Suzuki-Miyaura cross-coupling reaction afforded 37. Then 37 was reacted with hydroxylamine to form the amidoxime, and the amidoxime intermediate was coupled with 1-methyl-1H-pyrazole-4-carboxylic acid to afford the racemate 22; which was separated into pure enantiomers 23 and 24 using chiral supercritical fluid chromatography (SFC). The absolute configuration at the C-8 of 23 and 24 were assigned based on single-crystal X-ray diffraction studies of representative compounds.

Scheme 2. Representative synthesis of chiral compounds 23 and 24 using chiral SFC separation

In conclusion, a series of oxadiazole-containing FLAP inhibitors was identified from the knowledge-based drug design. The series was successfully optimized for FLAP binding and funcational hWB activities, selectivity and in vivo efficacy through the structure-based rational drug design. The compound 28 demonstrated desired potency and overall drug-like properties, and 28 was nominated for a preclinical development candidate. 115 Abdel-Magid et al.; Comprehensive Accounts of Pharmaceutical Research and Development: From Discovery to Late-Stage ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.

For the SAR development, we applied the SFC chiral separation to synthesize enatiomercally pure compounds. The asymmetric synthetic route for large scale preparation of 28 (BI 665915) was successfully developed by the chemical development, and the details are discussed in the following chapter.

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