Tjeerd Barf

Irreversible protein kinase inhibitors: balancing the benefits and risks.

■ INTRODUCTION In the relatively young but expanding field of irreversible kinase inhibitor drug discovery, there are two main developments that are of central importance. First, the patients have watched the first wave of low molecular weight protein kinase inhibitors becoming available to them over the past decade. These kinase inhibitors have been approved by the U.S. Food and Drug Administration (FDA) for therapeutic use in oncology indications and constitute an important addition to the arsenal of drugs to combat cancer (Table 1). Without exception, these marketed protein kinase inhibitors have been identified and developed using conventional approaches, i.e., reversible inhibitors that (partly) occlude the ATP pocket in the catalytic domain of the kinase. Although protein kinases are regarded as an attractive drug target family, it took (and still takes) huge efforts to master the human kinome, which comprises more than 500 protein kinases. The search for clinically applicable kinase inhibitors that target the highly conserved ATP pocket has been thwarted by a couple of well-known hurdles. Selectivity, cellular potency, and an increasingly crowded intellectual property arena are major points of attention. The second important development is the renewed interest in covalent binding drugs (reviewed by Potashman and Duggan and by Singh et al). This recent revival results from a better understanding of the benefits of the covalent binding principle and the approval of effective and safe covalent drugs. Historically, drug discoverers have been taught to stay away from small molecular entities that harbor reactive electrophilic groups because these used to be equivalent to promiscuity. Promiscuous hits that relied on reactive groups were traditionally hard to optimize toward leads, since these were more than often interfering with the biochemical assay rather than truly modifying the activity of the target of interest. Even if the target modulation was real, indiscriminant reactivity was believed to trigger insurmountable toxic events that may surface in late stage clinical trials when larger patient populations are involved. As a consequence, “suicide inhibitors”, “warheads”, and covalent irreversible inhibitors developed a negative flavor over time and became almost synonymous with toxicity in some organizations. The skepticism toward irreversible drugs may evaporate as more examples of irreversible drugs progress clinically that demonstrate good efficacy and safety margins. In a nutshell, the therapeutic applicability or the success of irreversible binding kinase inhibitors is dependent on whether or not the covalent bond can be confined solely to the protein kinase of interest. So this approach is in essence a story about two T’s: treatment and toxicity. When relying on the covalent binding principle, it is important to discern adduct-based toxicity and adduct-based treatment, since the adducting molecular entities in question obey overlapping fundamental rules in terms of reactivity. The only key difference is the nature and the function of the proteins that are covalently modified. Covalent kinase inhibitors with well-balanced recognition and reactivity should provide efficacy, selectivity, and ultimately the safety margins that are required for regulatory approval. If we strike the right balance, a third “T” will give enough comfort: therapeutic window. This Perspective aims to give a comprehensive account from a medicinal chemists point of view on the progress of irreversible kinase inhibitor drug discovery. The “state of the art” is reviewed by means of reported irreversible kinase inhibitors profiles and their chemical structures. The potential upsides and pitfalls that are associated with this concept are highlighted to provide a general understanding of the differences with respect to conventional drug discovery, as well as the future potential of this approach.

N-Benzyl-indolo carboxylic acids: Design and synthesis of potent and selective adipocyte fatty-acid binding protein (A-FABP) inhibitors.

Small molecule inhibitors of adipocyte fatty-acid binding protein (A-FABP) have gained renewed interest following the recent publication of pharmacologically beneficial effects of such inhibitors. Despite the potential utility of selective A-FABP inhibitors within the fields of metabolic disease, inflammation and atherosclerosis, there are few examples of useful A-FABP inhibitors in the public domain. Herein, we describe the optimization of N-benzyl-tetrahydrocarbazole derivatives through the use of co-crystal structure guided medicinal chemistry efforts. This led to the identification of a potent and selective class of A-FABP inhibitors as illustrated by N-benzyl-hexahydrocyclohepta[b]indole 30.

Active site variability of type 1 11beta-hydroxysteroid dehydrogenase revealed by selective inhibitors and cross-species comparisons.

The NADPH-dependent enzyme type 1 11beta-hydroxysteroid dehydrogenase (11beta-HSD1) activates in a tissue-specific manner circulating pro-glucocorticoid hormones (cortisone in humans) to the 11beta-OH ligand (cortisol in humans), which is able to bind to its cognate receptor and regulate gene transcription. Modulation of this pre-receptor activation mechanism by selective enzyme inhibitors is a desirable goal in the treatment of insulin resistance and related metabolic disorders. Like most other hydroxysteroid dehydrogenases 11beta-HSD1 belongs to the evolutionarily conserved enzyme superfamily of short-chain dehydrogenases/reductases (SDR). The enzyme is anchored within the endoplasmic reticulum through an N-terminal transmembrane domain. In this study we aimed to characterize the active site of mammalian 11beta-HSD1 by determining primary structures from several mammalian lines (cat, hamster, cynomolgus, chimpanzee, dog) thus increasing substantially available sequence information, and allowing us to determine highly variable and constant parts within the primary structure. These regions were mapped to the recently determined three-dimensional structure and are mostly found around the substrate binding site. Furthermore we performed inhibition studies by using different series of inhibitors, comprising 11beta-HSD1 selective arylsulfonamidothiazoles and the unselective steroid-based compound carbenoxolone. The different arylsulfonamidothiazoles display distinct inhibition profiles versus the mammalian species tested, with several tight binding inhibitors for the human enzyme (Ki approximately 50 nM), intermediate for mouse, and weak or not binding inhibitors for rat and guinea pig (Ki>3 microM). Analysis of the inhibition mode reveals that the tight binding inhibitor BVT.528 is a competitive inhibitor for the human form, whereas the related compound BVT.2733 displays a mixed-type inhibition pattern versus the mouse enzyme. Taken together, this structure-activity study provides increased insight into active site complexity and catalytic mechanism of 11beta-HSD1, useful for further inhibitor design.

Characterization of irreversible kinase inhibitors by directly detecting covalent bond formation: a tool for dissecting kinase drug resistance

Targeting protein kinases in cancer therapy with irreversible small‐molecule inhibitors is moving to the forefront of kinase‐inhibitor research and is thought to be an effective means of overcoming mutation‐associated drug resistance in epidermal growth factor receptor kinase (EGFR). We generated a detection technique that allows direct measurements of covalent bond formation without relying on kinase activity, thereby allowing the straightforward investigation of the influence of steric clashes on covalent inhibitors in different resistant kinase mutants. The obtained results are discussed together with structural biology and biochemical studies of catalytic activity in both wild‐type and gatekeeper mutated kinase variants to draw conclusions about the impact of steric hindrance and increased catalytic activity in drug‐resistant kinase variants.

Structure-based lead identification of ATP-competitive MK2 inhibitors.

MK2 kinase is a promising drug discovery target for the treatment of inflammatory diseases. Here, we describe the discovery of novel MK2 inhibitors using X-ray crystallography and structure-based drug design. The lead has in vivo efficacy in a short-term preclinical model.

Discovery of selective and orally available spiro-3-piperidyl ATP-competitive MK2 inhibitors

The identification of a potent, selective, and orally available MK2 inhibitor series is described. The initial absence of oral bioavailability was successfully tackled by moving the basic nitrogen of the spiro-4-piperidyl moiety towards the electron-deficient pyrrolepyridinedione core, thereby reducing the pK(a) and improving Caco-2 permeability. The resulting racemic spiro-3-piperidyl analogues were separated by chiral preparative HPLC, and the activity towards MK2 inhibition was shown to reside mostly in the first eluting stereoisomer. This led to the identification of new MK2 inhibitors, such as (S)-23, with low nanomolar biochemical inhibition (EC(50) 7.4 nM) and submicromolar cellular target engagement activity (EC(50) 0.5 μM).

Abstract 2596: ACP-196: a novel covalent Bruton's tyrosine kinase (Btk) inhibitor with improved selectivity and in vivo target coverage in chronic lymphocytic leukemia (CLL) patients

Ibrutinib, a first generation Btk inhibitor, is approved for the treatment of CLL and mantle cell lymphoma; known toxicities include atrial fibrillation, diarrhea, rash, arthralgia and bleeding events (1). Recent reports show ibrutinib9s off target effects may negatively impact its potential for combined therapy with anti-CD20 antibodies (2,3). Here we describe the pharmacologic characterization of ACP-196 a potent, novel second generation Btk inhibitor, which binds covalently to Cys481 with improved selectivity and in vivo target coverage. Compared to ibrutinib and CC-292, ACP-196 demonstrated higher selectivity for Btk when profiled against a panel of 395 non-mutant kinases (1 μM) in a competitive binding assay. IC50 determinations on 9 kinases with a Cys in the same position as Btk showed ACP-196 to be the most selective. The improved selectivity is related to the reduced intrinsic reactivity of ACP-1969s electrophile. Importantly, unlike ibrutinib, ACP-196 did not inhibit EGFR, Itk or Txk. Phosphoflow assays on EGFR expressing cell lines confirmed ibrutinib9s EGFR inhibition (EC50: 47-66 nM) with no inhibition observed for ACP-196 at 10 μM. These data may explain the ibrutinib-related incidence of diarrhea and rash. Ibrutinib9s potency on Itk and Txk may explain why it interferes with cell-mediated anti-tumor activities of therapeutic CD20 antibodies and immune-mediated killing in the tumor microenvironment (2,3). In human whole blood, ACP-196 and ibrutinib showed robust and equipotent inhibitory activity on B-cell receptor induced responses in the low nM range, whereas CC-292 was 10-20 fold less potent. In vivo, oral administration of ACP-196 in mice resulted in dose-dependent inhibition of anti-IgM-induced CD86 expression in CD19+ splenocytes with an ED50 of 0.34 mg/kg compared to 0.91 mg/kg for ibrutinib. A similar model was used to compare the duration of Btk inhibition after a single oral dose of 25 mg/kg. ACP-196 and ibrutinib inhibited CD86 expression >90% at 3h and ∼50% at 24h postdose. In contrast, CC-292 inhibited ∼50% at 3h and ∼20% at 24h postdose. An ELISA based Btk target occupancy assay was developed to measure target coverage in preclinical and clinical studies. In healthy volunteers, ACP-196 at an oral dose of 100 mg QD showed >90% target coverage over a 24h period. Btk occupancy and regulation of the PD markers (CD69 and CD86) correlated with PK parameters for exposure. In CLL patients, after 7 days of dosing with ACP-196 at 200 mg QD, 94% Btk target occupancy was observed compared with ∼80% reported for ibrutinib at 420 mg QD (4). In conclusion, ACP-196 is a novel Btk inhibitor with key pharmacologic differentiators versus ibrutinib and CC-292. ACP-196 is currently being evaluated in clinical trials. 1. IMBRUVICA package insert 2014 2. Rajasekaran Blood 2014 Abstr # 3118 3. Da Roit Haematologica 2014 4. Byrd NEJM 2013 Citation Format: Todd Covey, Tjeerd Barf, Michael Gulrajani, Fanny Krantz, Bart van Lith, Elena Bibikova, Bas van de Kar, Edwin de Zwart, Ahmed Hamdy, Raquel Izumi, Allard Kaptein. ACP-196: a novel covalent Bruton9s tyrosine kinase (Btk) inhibitor with improved selectivity and in vivo target coverage in chronic lymphocytic leukemia (CLL) patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2596. doi:10.1158/1538-7445.AM2015-2596

Acalabrutinib (ACP-196): A Covalent Bruton Tyrosine Kinase Inhibitor with a Differentiated Selectivity and In Vivo Potency Profile

Several small-molecule Bruton tyrosine kinase (BTK) inhibitors are in development for B cell malignancies and autoimmune disorders, each characterized by distinct potency and selectivity patterns. Herein we describe the pharmacologic characterization of BTK inhibitor acalabrutinib [compound 1, ACP-196 (4-[8-amino-3-[(2S)-1-but-2-ynoylpyrrolidin-2-yl]imidazo[1,5-a]pyrazin-1-yl]-N-(2-pyridyl)benzamide)]. Acalabrutinib possesses a reactive butynamide group that binds covalently to Cys481 in BTK. Relative to the other BTK inhibitors described here, the reduced intrinsic reactivity of acalabrutinib helps to limit inhibition of off-target kinases having cysteine-mediated covalent binding potential. Acalabrutinib demonstrated higher biochemical and cellular selectivity than ibrutinib and spebrutinib (compounds 2 and 3, respectively). Importantly, off-target kinases, such as epidermal growth factor receptor (EGFR) and interleukin 2-inducible T cell kinase (ITK), were not inhibited. Determination of the inhibitory potential of anti-immunoglobulin M–induced CD69 expression in human peripheral blood mononuclear cells and whole blood demonstrated that acalabrutinib is a potent functional BTK inhibitor. In vivo evaluation in mice revealed that acalabrutinib is more potent than ibrutinib and spebrutinib. Preclinical and clinical studies showed that the level and duration of BTK occupancy correlates with in vivo efficacy. Evaluation of the pharmacokinetic properties of acalabrutinib in healthy adult volunteers demonstrated rapid absorption and fast elimination. In these healthy individuals, a single oral dose of 100 mg showed approximately 99% median target coverage at 3 and 12 hours and around 90% at 24 hours in peripheral B cells. In conclusion, acalabrutinib is a BTK inhibitor with key pharmacologic differentiators versus ibrutinib and spebrutinib and is currently being evaluated in clinical trials.

Novel ATP competitive MK2 inhibitors with potent biochemical and cell-based activity throughout the series.

Optimization of our previously described pyrrolopiperidone series led to the identification of a new benzamide sub-series, which exhibits consistently high potency in biochemical and cell-based assays throughout the series. Strong inhibition of LPS-induced production of the cytokine TNFα is coupled to the regulation of HSP27 phosphorylation, indicating that the observed cellular effects result from the inhibition of MK2. X-ray crystallographic and computational analyses provide a rationale for the high potency of the series.