Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors.

Protein lysine methyltransferases (KMTs) have emerged as important regulators of epigenetic signaling. These enzymes catalyze the transfer of donor methyl groups from the cofactor S-adenosylmethionine to specific acceptor lysine residues on histones, leading to changes in chromatin structure and transcriptional regulation. These enzymes also methylate an array of nonhistone proteins, suggesting additional mechanisms by which they influence cellular physiology. SMYD2 is reported to be an oncogenic methyltransferase that represses the functional activity of the tumor suppressor proteins p53 and RB. HTS screening led to identification of five distinct substrate-competitive chemical series. Determination of liganded crystal structures of SMYD2 contributed significantly to "hit-to-lead" design efforts, culminating in the creation of potent and selective inhibitors that were used to understand the functional consequences of SMYD2 inhibition. Taken together, these results have broad implications for inhibitor design against KMTs and clearly demonstrate the potential for developing novel therapies against these enzymes.

An improved model for fragment-based lead generation at AstraZeneca.

Modest success rates in fragment-based lead generation (FBLG) projects at AstraZeneca (AZ) prompted operational changes to improve performance. In this review, we summarize these changes, emphasizing the construction and composition of the AZ fragment library, screening practices and working model. We describe the profiles of the screening method for specific fragment subsets and statistically assess our ability to follow up on fragment hits through near-neighbor selection. Performance analysis of our second-generation fragment library (FL2) in screening campaigns illustrates the complementary nature of flat and 3D fragments in exploring protein-binding pockets and highlights our ability to deliver fragment hits using multiple screening techniques for various target classes. The new model has had profound impact on the successful delivery of lead series to drug discovery projects.

Discovery of 6-aryl-azabenzimidazoles that inhibit the TBK1/IKK-ε kinases.

The discovery and optimization of a series of 6-aryl-azabenzimidazole inhibitors of TBK1 and IKK-ε is described. Various internal azabenzimidazole leads and reported TBK1/IKK-ε inhibitors were docked into a TBK1 homology model. The resulting overlays inspired a focused screen of 6-substituted azabenzimidazoles against TBK1/IKK-ε. This screen resulted in initial hit compound 3. The TBK1/IKK-ε enzyme and cell potency of this compound was further improved using structure guided drug design. Systematic exploration of the C6 aryl group led to compound 19, a potent inhibitor of TBK1 with selectivity against cell cycle kinases CDK2 and Aurora B. Further elaboration and optimization gave compound 25, a single digit nM inhibitor of TBK1. These compounds may serve as in vitro probes to evaluate TBK1/IKK-ε as an oncology target.

Discovery of azabenzimidazole derivatives as potent, selective inhibitors of TBK1/IKKε kinases.

The design, synthesis and biological evaluation of a series of azabenzimidazole derivatives as TBK1/IKKε kinase inhibitors are described. Starting from a lead compound 1a, iterative design and SAR exploitation of the scaffold led to analogues with nM enzyme potencies against TBK1/IKKε. These compounds also exhibited excellent cellular activity against TBK1. Further structure-based design to improve selectivity over CDK2 and Aurora B resulted in compounds such as 5b-e. These probe compounds will facilitate study of the complex cancer biology of TBK1 and IKKε.

Structural basis of substrate methylation and inhibition of SMYD2.

Protein lysine methyltransferases are important regulators of epigenetic signaling. These enzymes catalyze the transfer of donor methyl groups from S-adenosylmethionine to specific acceptor lysines on histones, leading to changes in chromatin structure and transcriptional regulation. These enzymes also methylate nonhistone protein substrates, revealing an additional mechanism to regulate cellular physiology. The oncogenic protein SMYD2 represses the functional activities of the tumor suppressor proteins p53 and Rb, making it an attractive drug target. Here we report the discovery of AZ505, a potent and selective inhibitor of SMYD2 that was identified from a high throughput chemical screen. We also present the crystal structures of SMYD2 with p53 substrate and product peptides, and notably, in complex with AZ505. This substrate competitive inhibitor is bound in the peptide binding groove of SMYD2. These results have implications for the development of SMYD2 inhibitors, and indicate the potential for developing novel therapies targeting this target class.

DRIFTS studies on the photodegradation of tannic acid as a model for HULIS in atmospheric aerosols.

Humic like substances (HULIS) are important components of atmospheric aerosols, yet little is known about their photochemical transformation and the role of adsorbed water in this photochemistry. We report herein in situ and surface-sensitive spectroscopic studies on (1) the photodegradation of solid tannic acid, (2) structure of adsorbed water before and after photodegradation, and (3) the change in the hydrophilicity of tannic acid as a result of this photochemistry. Tannic acid (TA) was chosen as a synthetic proxy for HULIS because it has a defined molecular structure. Photochemical studies were conducted using diffuse reflectance infrared spectroscopy (DRIFTS) as a function of time (3 h), relative humidity (5-30%) and total irradiance (7, 20, 290 W m(-2) at 555 nm). Water adsorption isotherm measurements were recorded before and after photodegradation, which provided information on the structure of interfacial water and the thermodynamics of adsorption. The structure of water adsorbed on TA resembles that of water at the interface with polar organic solvents. Difference spectral data collected during irradiation shows loss features in the 1700-1000 cm(-1) range and growth in carbonyl features that are blue shifted relative to the starting material, suggesting oxidative photodegradation of TA and formation of aryl aldehydes. Under our experimental conditions, we observed no enhancement in water uptake after photodegradation relative to that on unirradiated samples. The implications of our results to the understanding of heterogeneous photochemistry of HULIS and the role of adsorbed water in these reactions are discussed.

Identification of amidoheteroaryls as potent inhibitors of mutant (V600E) B-Raf kinase with in vivo activity.

A series of amidoheteroaryl compounds were designed and synthesized as inhibitors of B-Raf kinase. Several compounds from the series show excellent potency in biochemical, phenotypic and mode of action cellular assays. Potent examples from the series have also demonstrated good plasma exposure following an oral dose in rodents and activity against the Ras-Raf pathway in tumor bearing mice.

Adsorption thermodynamics of p-arsanilic acid on iron (oxyhydr)oxides: in-situ ATR-FTIR studies.

The organoarsenical p-arsanilic acid (p-AsA) is used in the U.S. poultry industry as a feed additive and its structure resembles one of the stable biodegradation products of Roxarsone (ROX) in anaerobic environments. With the implementation of recent EPA MCL of total arsenic in drinking water (10 ppb), thereareconcernsaboutthefate of organoarsenicals introduced to the environment through the application of arsenic-contaminated manure. We report herein, for the first time, the thermodynamics of p-AsA binding to Fe-(oxyhydr)oxides using ATR-FTIR. ATR-FTIR spectra were used to quantify surface coverage of p-AsA, p-AsA(ads), by analyzing the broadband assigned to v(As-O) at 837 cm(-1). Adsorption isotherms were measured in situ at 298 K and pH 7 in the concentration range 1 microM to 40 mM. Values of Keq were obtained from Langmuir model fits and they range from 1411 to 3228 M(-1). We also determined the maximum adsorption capacities of Fe-(oxyhydr)oxides to p-AsA, and they range from 1.9 x 10(13) to 2.6 x 10(13) molecules/cm2. Our results suggest that p-AsA is more mobile than methylated and inorganic forms of arsenic and that the transport of nanoparticles with p-AsA(ads) might play a role in its mobility in geochemical environments.

N-arylaminonitriles as bioavailable peptidomimetic inhibitors of cathepsin B.

To improve the pharmacokinetics of a previously reported series of dipeptidyl nitrile cathepsin B inhibitors, the P(2)-P(3) amide group was replaced with an arylamine. Further optimization of this template resulted in highly potent and selective inhibitors with excellent oral availability.