Discovery of (4-Pyrazolyl)-2-aminopyrimidines as Potent and Selective Inhibitors of Cyclin-Dependent Kinase 2.

CDK2 is a critical regulator of the cell cycle. For a variety of human cancers, the dysregulation of CDK2/cyclin E1 can lead to tumor growth and proliferation. Historically, early efforts to develop CDK2 inhibitors with clinical applications proved unsuccessful due to challenges in achieving selectivity over off-target CDK isoforms with associated toxicity. In this report, we describe the discovery of (4-pyrazolyl)-2-aminopyrimidines as a potent class of CDK2 inhibitors that display selectivity over CDKs 1, 4, 6, 7, and 9. SAR studies led to the identification of compound 17, a kinase selective and highly potent CDK2 inhibitor (IC50 = 0.29 nM). The evaluation of 17 in CCNE1-amplified mouse models shows the pharmacodynamic inhibition of CDK2, measured by reduced Rb phosphorylation, and antitumor activity.

Discovery of 5,7-Dihydro-6H-pyrrolo[2,3-d]pyrimidin-6-ones as Highly Selective CDK2 Inhibitors.

A series of exceptionally selective CDK2 inhibitors are described. Starting from an HTS hit, we successfully scaffold hopped to a 5,7-dihydro-6H-pyrrolo[2,3-d]pyrimidin-6-one core structure, which imparted a promising initial selectivity within the CDK family. Extensive further SAR identified additional factors that drove selectivity to above 200× for CDKs 1/4/6/7/9. General kinome selectivity was also greatly improved. Finally, use of in vivo metabolite identification allowed us to pinpoint sulfonamide dealkylation as the primary metabolite, which was ameliorated through the deuterium effect.

Discovery of Novel Pyrazolopyrimidines as Potent, Selective, and Orally Bioavailable Inhibitors of ALK2.

Activin receptor-like kinase 2 (ALK2) is a transmembrane kinase receptor that mediates the signaling of the members of the TGF-ß superfamily. The aberrant activation of ALK2 has been linked to the rare genetic disorder fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG) that are associated with severely reduced life expectancy in pediatric patients. ALK2 has also been shown to play an essential role in iron metabolism by regulating hepcidin levels and affecting anemia of chronic disease. Thus, selective inhibition of ALK2 has emerged as a promising strategy for the treatment of multiple disorders. Herein, we report the discovery of a novel pyrazolopyrimidines series as highly potent, selective, and orally bioavailable inhibitors of ALK2. Structure-based drug design and systematic structure-activity relationship studies were employed to identify potent inhibitors displaying high selectivity against other ALK subtypes with good pharmacokinetic profiles.

Characterization of INCB086550: A Potent and Novel Small-Molecule PD-L1 Inhibitor.

Blocking the activity of the programmed cell death protein 1 (PD-1) inhibitory receptor with therapeutic antibodies against either the ligand (PD-L1) or PD-1 itself has proven to be an effective treatment modality for multiple cancers. Contrasting with antibodies, small molecules could demonstrate increased tissue penetration, distinct pharmacology, and potentially enhanced antitumor activity. Here, we describe the identification and characterization of INCB086550, a novel, oral, small-molecule PD-L1 inhibitor. In vitro, INCB086550 selectively and potently blocked the PD-L1/PD-1 interaction, induced PD-L1 dimerization and internalization, and induced stimulation-dependent cytokine production in primary human immune cells. In vivo, INCB086550 reduced tumor growth in CD34+ humanized mice and induced T-cell activation gene signatures, consistent with PD-L1/PD-1 pathway blockade. Preliminary data from an ongoing phase I study confirmed PD-L1/PD-1 blockade in peripheral blood cells, with increased immune activation and tumor growth control. These data support continued clinical evaluation of INCB086550 as an alternative to antibody-based therapies. SIGNIFICANCE: We have identified a potent small-molecule inhibitor of PD-L1, INCB086550, which has biological properties similar to PD-L1/PD-1 monoclonal antibodies and may represent an alternative to antibody therapy. Preliminary clinical data in patients demonstrated increased immune activation and tumor growth control, which support continued clinical evaluation of this approach. See related commentary by Capparelli and Aplin, p. 1413. This article is highlighted in the In This Issue feature, p. 1397.

Inhibition of ALK2 with bicyclic pyridyllactams.

Activin receptor-like kinase 2 (ALK2) has been implicated as a key target in multiple rare diseases. Herein, we describe the design of a novel bicyclic lactam series of potent and selective ALK2 inhibitors. This manuscript details an improvement in potency of two orders of magnitude from the initial bicyclic structure as well as a two-fold improvement in cellular potency from the original monocyclic inhibitor. Furthermore, we provide a detailed strategy for progressing this project in the future.

Discovery of Pemigatinib: A Potent and Selective Fibroblast Growth Factor Receptor (FGFR) Inhibitor.

Aberrant activation of FGFR has been linked to the pathogenesis of many tumor types. Selective inhibition of FGFR has emerged as a promising approach for cancer treatment. Herein, we describe the discovery of compound 38 (INCB054828, pemigatinib), a highly potent and selective inhibitor of FGFR1, FGFR2, and FGFR3 with excellent physiochemical properties and pharmacokinetic profiles. Pemigatinib has received accelerated approval from the U.S. Food and Drug Administration for the treatment of adults with previously treated, unresectable locally advanced or metastatic cholangiocarcinoma with a FGFR2 fusion or other rearrangement. Additional clinical trials are ongoing to evaluate pemigatinib in patients with FGFR alterations.

INCB054828 (pemigatinib), a potent and selective inhibitor of fibroblast growth factor receptors 1, 2, and 3, displays activity against genetically defined tumor models.

Alterations in fibroblast growth factor receptor (FGFR) genes have been identified as potential driver oncogenes. Pharmacological targeting of FGFRs may therefore provide therapeutic benefit to selected cancer patients, and proof-of-concept has been established in early clinical trials of FGFR inhibitors. Here, we present the molecular structure and preclinical characterization of INCB054828 (pemigatinib), a novel, selective inhibitor of FGFR 1, 2, and 3, currently in phase 2 clinical trials. INCB054828 pharmacokinetics and pharmacodynamics were investigated using cell lines and tumor models, and the antitumor effect of oral INCB054828 was investigated using xenograft tumor models with genetic alterations in FGFR1, 2, or 3. Enzymatic assays with recombinant human FGFR kinases showed potent inhibition of FGFR1, 2, and 3 by INCB054828 (half maximal inhibitory concentration [IC50] 0.4, 0.5, and 1.0 nM, respectively) with weaker activity against FGFR4 (IC50 30 nM). INCB054828 selectively inhibited growth of tumor cell lines with activation of FGFR signaling compared with cell lines lacking FGFR aberrations. The preclinical pharmacokinetic profile suggests target inhibition is achievable by INCB054828 in vivo with low oral doses. INCB054828 suppressed the growth of xenografted tumor models with FGFR1, 2, or 3 alterations as monotherapy, and the combination of INCB054828 with cisplatin provided significant benefit over either single agent, with an acceptable tolerability. The preclinical data presented for INCB054828, together with preliminary clinical observations, support continued investigation in patients with FGFR alterations, such as fusions and activating mutations.

Rosamines targeting the cancer oxidative phosphorylation pathway.

Reprogramming of energy metabolism is pivotal to cancer, so mitochondria are potential targets for anticancer therapy. A prior study has demonstrated the anti-proliferative activity of a new class of mitochondria-targeting rosamines. This present study describes in vitro cytotoxicity of second-generation rosamine analogs, their mode of action, and their in vivo efficacies in a tumor allografted mouse model. Here, we showed that these compounds exhibited potent cytotoxicity (average IC50<0.5 µM), inhibited Complex II and ATP synthase activities of the mitochondrial oxidative phosphorylation pathway and induced loss of mitochondrial transmembrane potential. A NCI-60 cell lines screen further indicated that rosamine analogs 4 and 5 exhibited potent antiproliferative effects with Log10GI50 = -7 (GI50 = 0.1 µM) and were more effective against a colorectal cancer sub-panel than other cell lines. Preliminary in vivo studies on 4T1 murine breast cancer-bearing female BALB/c mice indicated that treatment with analog 5 in a single dosing of 5 mg/kg or a schedule dosing of 3 mg/kg once every 2 days for 6 times (q2d×6) exhibited only minimal induction of tumor growth delay. Our results suggest that rosamine analogs may be further developed as mitochondrial targeting agents. Without a doubt proper strategies need to be devised to enhance tumor uptake of rosamines, i.e. by integration to carrier molecules for better therapeutic outcome.

High-contrast fluorescence imaging in fixed and living cells using optimized optical switches.

We present the design, synthesis and characterization of new functionalized fluorescent optical switches for rapid, all-visible light-mediated manipulation of fluorescence signals from labelled structures within living cells, and as probes for high-contrast optical lock-in detection (OLID) imaging microscopy. A triazole-substituted BIPS (TzBIPS) is identified from a rational synthetic design strategy that undergoes robust, rapid and reversible, visible light-driven transitions between a colorless spiro- (SP) and a far-red absorbing merocyanine (MC) state within living cells. The excited MC-state of TzBIPS may also decay to the MC-ground state emitting near infra-red fluorescence, which is used as a sensitive and quantitative read-out of the state of the optical switch in living cells. The SP to MC transition for a membrane-targeted TzBIPS probe (C12-TzBIPS) is triggered at 405 nm at an energy level compatible with studies in living cells, while the action spectrum of the reverse transition (MC to SP) has a maximum at 650 nm. The SP to MC transition is complete within the 790 ns pixel dwell time of the confocal microscope, while a single cycle of optical switching between the SP and MC states in a region of interest is complete within 8 ms (125 Hz) within living cells, the fastest rate attained for any optical switch probe in a biological sample. This property can be exploited for real-time correction of background signals in living cells. A reactive form of TzBIPS is linked to secondary antibodies and used, in conjunction with an enhanced scope-based analysis of the modulated MC-fluorescence in immuno-stained cells, for high-contrast immunofluorescence microscopic analysis of the actin cytoskeleton.

Energy transfer cassettes in silica nanoparticles target intracellular organelles.

Lipophilic energy transfer cassettes like 1 and 2 are more conveniently synthesized than the corresponding hydrophilic compounds, but they are not easily used in aqueous media. To overcome the latter issue, cassettes 1 and 2 were separately encapsulated in silica nanoparticles (ca. 22 nm) which freely disperse in aqueous media. Photophysical properties of the encapsulated dyes 1-SiO(2) and 2-SiO(2) were recorded. The nanoparticles 1-SiO(2) permeated into Clone 9 rat liver cells and targeted only the ER. A high degree of energy transfer was observed in this organelle such that most of the light fluoresced from the acceptor part, i.e. the particles appeared red. Silica nanoparticles 2-SiO(2) also permeated into Clone 9 rat liver cells and they targeted mitochondria but were also observed in endocytic vesicles (lysosomes or endosomes). In these organelles they fluoresced red and red/green respectively. Thus the cargo inside the nanoparticles influences where they localize in cells, and the environment of the nanoparticles in the cells changes the fluorescent properties of the encapsulated dyes. Neither of these findings were anticipated given that silica nanoparticles of this type are generally considered to be non-porous.

Optical control of calcium affinity in a spiroamido-rhodamine based calcium chelator.

An optically controlled Ca(2+)-chelator 1 was developed to mimic natural calcium oscillations. Compound 1, a spiroamido-rhodamine derivative of 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), underwent cycles of reversible transitions between a colorless closed state and a fluorescent open form. The closed-state exhibited a high affinity for Ca(2+) (K(d): 509 nM) with excellent selectivity over Mg(2+) (K(d): 19 mM). The open isomer had a 350-fold lower Ca(2+) affinity (K(d): 181 µM), while the Mg(2+) affinity was not significantly affected (K(d): 14 mM).

Organelle-selective energy transfer: a fluorescent indicator of intracellular environment.

A dye cassette fluoresces green (ca 520 nm) in the cytoplasm, endoplasmic reticulum (ER), and lysosomes, but red in mitochondria, that is, it illustrates 'organelle specific energy transfer'. This phenomenon may open new horizons in intracellular imaging.

Fluorescent cassettes for monitoring three-component interactions in vitro and in living cells.

Two water-soluble "through-bond energy transfer cassettes" (TBET-cassettes) were prepared. They have good extinction coefficients at the donor part and transfer energy to the acceptor parts with good "overall quantum yields" (0.30 and 0.24 in pH 7.4 phosphate buffer). Fluorescence resonance energy transfer from one protein functionalized with an appropriate donor can be used to excite the TBET-cassettes on different proteins to probe protein-protein interactions under conditions that would not be possible for single-dye acceptor systems.

New cytotoxic rosamine derivatives selectively accumulate in the mitochondria of cancer cells.

Conventional cytotoxic anticancer drugs that target all rapidly dividing cells are nonselective in their mechanism of action, because they disrupt essential components that are crucial to both malignant and proliferating normal cells. Instead, targeting cellular functions that are distinctly different between normal and cancer cells may provide a basis for selective killing of tumor cells. One such strategy that is still largely unexplored is to utilize the relatively higher negative mitochondrial membrane potential in carcinoma cells compared with adjacent normal epithelial cells to enhance accumulation and retention of cytotoxic lipophilic cations in the former. In this study, the anticancer activities of a new class of rosamines with cyclic amine substituents and their structure-activity relationships were investigated. From an in-vitro cell growth inhibition assay, 14 of the rosamines inhibited the growth of human leukemia HL-60 cells by 50% at micromolar or lower concentrations. Derivatives containing hydrophilic substituents had less potent activity, whereas aryl substitution at the meso position conferred extra activity with thiofuran and para-iodo aryl substitutions being the most potent. In addition, both compounds were at least 10-fold more cytotoxic than rhodamine 123 against a panel of cell lines of different tissue origin and similar to rhodamine 123, exhibited more cytotoxicity against cancer cells compared with immortalized normal epithelial cells of the same organ type. In subsequent experiments, the para-iodo aryl substituted rosamine was found to localize exclusively within the mitochondria and induced apoptosis as the major mode of cell death. Our results suggest that these compounds offer potential for the design of mitochondria-targeting agents that either directly kill or deliver cytotoxic drugs to selectively kill cancer cells.

Synthesis and spectroscopic properties of rosamines with cyclic amine substituents.

There is a close structural similarity between rosamines A and rhodamines B, yet a diversity of structures in the rosamine class and their spectral properties have yet to be explored in depth. This manuscript describes a concise, scalable, solution-phase method to obtain rosamines 1-5 and 12-15, which include some water-soluble derivatives. In one test case (for 15) an illustrative protein conjugate was also formed. Throughout these products were isolated and purified, and the syntheses were found to be scalable. Further, the rosamines with these cyclic amine substituents display solvent-dependent fluorescence intensities, and high quantum yields in chlorinated hydrocarbons. In some cases the nature of the cyclic amine substituent was shown to modulate the fluorescence of the parent molecules in pH-dependent ways. The ring size of those amine substituents also correlated with some of their spectroscopic properties. Several water-soluble rosamines were prepared from some of the addition products 1-5, and one of these, 15, was efficiently conjugated to avidin via an amide linkage. The spectroscopic properties of 15 and 15-avidin in aqueous media were very similar.

A new synthesis of symmetric boraindacene (BODIPY) dyes.

BODIPY dyes were synthesized from pyrrole-2-carbaldehyde derivatives in high yields; this constitutes a new approach to this dye framework.

Fluorescent amino- and thiopyronin dyes.

Highly fluorescent rhodamine/rosamine analogues 2 were prepared from ketone 1.

Syntheses of highly fluorescent GFP-chromophore analogues.

Eight B-containing compounds, i.e., 1a-h, were prepared as mimics of the green fluorescent protein (GFP) fluorophore. The underlying concept was that synthetic GFP chromophore analogues are not fluorescent primarily because of free rotation about an aryl-alkene bond (Figure 1b). This rotation is not possible in the beta-barrel of GFP; hence, the molecule is strongly fluorescent. In compounds 1a-h, radiationless decay via this mechanism is prevented by complexation of the BF2 entity. The target materials were prepared via two methods; most were obtained according to the novel route shown in Scheme 1b, but compound 1f was made via the procedure described in Scheme 2. Both syntheses involved formation of undesired compounds E-4a-h that formed simultaneously with the desired isomeric intermediates Z-4a-h. Both compounds form BF2 adducts, i.e., 1a-h and 5a-h, respectively. Methods used for spectroscopic characterization and differentiation of compounds in the series 1 and 5 are discussed, and these are supported by single-crystal X-ray diffraction analyses for compounds 1c, 5c, 1f, and 5f. Electronic spectra of compounds 1a-h and 5a-h were studied in detail. Those in the 5 series were shown to be only weakly fluorescent, but the 1 series were strongly fluorescent compounds (comparable to the boraindacene, BODIPY, dyes). Compounds 1g and 1h are water soluble, and 1h has particularly significant potential as a probe, since it also has a carboxylic acid group for attachment to biomolecules.

Functionalized BF(2) Chelated Azadipyrromethene Dyes.

Fluorescent molecules that emit in the near infra-red are potentially useful as probes for biotechnology. A relatively under-explored design for probes of this type are the aza-BODIPY dyes; this study was performed to enhance our understanding of these materials and ways in which they may be used in dye cassette systems. Thus, the aza-BODIPY dyes 1a - g were prepared. An advanced intermediate towards an eighth compound in the series, 6h, was made but it could not be complexed with boron effectively to give 1h. Spectroscopic properties of these compounds were recorded, and correlations between substituent effects, UV absorbance, fluorescence emissions, and quantum yields were made. Compound 1a was coupled with a fluorescein-alkyne derivative to give the energy transfer cassettes 2 and 3. Both these compounds gave poor energy transfer, and the possible reasons for this were discussed.

Degradation of calcium lignosulfonate using gamma-ray irradiation.

Gamma-ray irradiation was proven to be a promising means for the removal of calcium lignosulfonate (CaLS). At a dose rate of 55Gy min(-1), over 90% of CaLS was mineralized to CO(2), H(2)O and sulfates within 3-d irradiation. The degradation of CaLS with the initial CaLS concentrations ranging from 40 to 200mg l(-1) followed zero-order kinetics at the dose rates of 16-150Gy min(-1). The zero-order degradation rate constant was functionally related with irradiation dose rate. Experiments performed with or without addition of radical scavengers demonstrated that the role of *OH was predominant in CaLS degradation and the reductive species made minor contributions to CaLS degradation. Addition of appropriate amounts of H(2)O(2) significantly enhanced the mineralization of CaLS, e.g., addition of 10mM H(2)O(2) at a dose rate of 55Gy min(-1) elevated the mineralization rate constant by five times. The addition of Fenton's reagent to irradiated CaLS solutions facilitated the degradation of CaLS, but no obviously synergistic effect was observed.