Mild route to generate gaseous metal anions.

Gaseous metal anions such as Na(-), K(-), Cs(-), and Ag(-) can be generated at ambient temperatures by the collision-induced dissociation of the anions of several dicarboxylic acid salts, including oxalate, maleate, fumarate, succinate, and glutamate salts. The formation of gaseous metal anions in this way is unprecedented because the metal is initially present in its cationic form. The mild process described here could facilitate novel applications of metal anions as selective reagents for gas-phase ion-molecule and ion-ion reactions. Ab initio calculations were used to describe the dissociation process for anions of the oxalate salts. The formation of alkalides occurs via production of a metal-carbon dioxide anion intermediate with a bidentate three-center two-electron bond to the metal. The metal atom acquires a partial negative charge in the intermediate structure.

Reactivity of gaseous sodiated ions derived from benzene dicarboxylate salts toward residual water in the collision gas.

The sodium adduct of disodium salts of benzene dicarboxylic acids (m/z 233), when subjected to collision-induced dissociation (CID), undergoes a facile loss of CO(2) to produce an ion of m/z 189, which retains all the three sodium atoms of the precursor. The CID spectrum of this unusual m/z 189 ion shows significant peaks at m/z 167, 63 and 85. The enigmatic m/z 167 ion, which appeared to represent a loss of a 22-Da neutral fragment from the precursor ion is in fact a fragment produced by the interaction of the m/z 189 ion with traces of water present in the collision gas. The change of the m/z 167 peak to 168, when D(2)O vapor was introduced to the collision gas of a Q-ToF instrument, proved that such an intervention of water could occur even in collision cells of tandem-in-space mass spectrometers. The m/z 189 ion has such high affinity for water; it forms an ion/molecule complex even during the brief residence time of ions in collision cells of triple quadrupole instruments. The complex formed in this way then eliminates elements of NaOH to produce the ion observed at m/z 167. In an ion trap, the relative intensity of the m/z 167 peak increases with longer activation time even at the lowest possible collision energy setting. Similarly, the m/z 145 ion (which represents the sodium adduct of phenelenedisodium, formed by two consecutive losses of CO(2) from the m/z 233 ion of meta- and para-isomers) interacts with water to produce a fragment ion at m/z 123 for the sodium adduct of phenylsodium. Other uncommon ions that originate also from water/ion interactions are observed at m/z 85 and 63 for [Na(3)O](+) and [Na(2)OH](+), respectively. Tandem mass spectrometric experiments conducted with appropriately deuterium-labeled compounds confirmed that the proton required for the formation of the [Na(2)OH](+) ion originates from traces of water present in the collision gas and not from the ring protons of the aromatic moiety.

Discovery and SAR of novel pyrazole-based thioethers as cathepsin S inhibitors: part 1.

A series of pyrazole-based thioethers were prepared and found to be potent cathepsin S inhibitors. A crystal structure of 13 suggests that the thioether moiety may bind to the S3 pocket of the enzyme. Additional optimization led to the discovery of aminoethylthioethers with improved enzymatic activity and submicromolar cellular potency.

Generation of gas-phase sodiated arenes such as [(Na3(C6H4)+] from benzene dicarboxylate salts.

Upon collision-induced activation, gaseous sodium adducts generated by electrospray ionization of disodium salts of 1,2- 1,3-, and 1,4-benzene dicarboxylic acids (m/z 233) undergo an unprecedented expulsion of CO(2) by a rearrangement process to produce an ion of m/z 189 in which all three sodium atoms are retained. When isolated in a collision cell of a tandem-in-space mass spectrometer, and subjected to collision-induced dissociation (CID), only the m/z 189 ions derived from the meta and para isomers underwent a further CO(2) loss to produce a peak at m/z 145 for a sodiated arene of formula (Na(3)C(6)H(4))(+). This previously unreported m/z 145 ion, which is useful to differentiate meta and para benzene dicarboxylates from their ortho isomer, is in fact the sodium adduct of phenelenedisodium. Moreover, the m/z 189 ion from all three isomers readily expelled a sodium radical to produce a peak at m/z 166 for a radical cation [(*C(6)H(4)CO(2)Na(2))(+)], which then eliminated CO(2) to produce a peak at m/z 122 for the distonic cation (*C(6)H(4)Na(2))(+).

Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements.

A crystal structure of 1 bound to a Cys25Ser mutant of cathepsin S helped to elucidate the binding mode of a previously disclosed series of pyrazole-based CatS inhibitors and facilitated the design of a new class of arylalkyne analogs. Optimization of the alkyne and tetrahydropyridine portions of the pharmacophore provided potent CatS inhibitors (IC50=40-300 nM), and an X-ray structure of 32 revealed that the arylalkyne moiety binds in the S1 pocket of the enzyme.

Hydroxycarbonyl anion (m/z 45), a diagnostic marker for alpha-hydroxy carboxylic acids.

Collision-induced dissociation mass spectra of anions derived from alpha-hydroxy carboxylic acids (AHAs) show a diagnostic peak at m/z 45. Product ion spectra recorded from this m/z 45 ion confirm that it represents the hydroxycarbonyl anion [DIAGRAM: SEE TEXT], and not the formate anion [DIAGRAM: SEE TEXT] as sometimes described in the literature. For example, the formate anion is not only defiant to further fragmentation but is also unreactive toward CO2. In contrast, the hydroxycarbonyl anion easily fragments to produce a peak at m/z 17 for the hydroxyl anion, and also readily reacts with CO2 to produce a peak at m/z 61 for the bicarbonate anion. The hydrogen atom in the hydroxycarbonyl anion and that in the formate anion are not mobile within the skeletal framework of the ions, since the two ions did not manifest any interconversion under the conditions and time scales of our mass spectrometric experiments. The other significant product ion peak in the spectra of deprotonated AHAs represents a 46-Da loss. MS/MS data from appropriately deuteriated compounds confirmed that one hydrogen atom from the C-2 position, and the other from the hydroxy group are specifically removed for this loss of elements of formic acid. Moreover, the two oxygen atoms eliminated for the HCOOH loss originate exclusively from the carboxylate group.

Identification of a potent, selective, and orally active leukotriene a4 hydrolase inhibitor with anti-inflammatory activity.

LTA 4H is a ubiquitously distributed 69 kDa zinc-containing cytosolic enzyme with both hydrolase and aminopeptidase activity. As a hydrolase, LTA 4H stereospecifically catalyzes the transformation of the unstable epoxide LTA 4 to the diol LTB 4, a potent chemoattractant and activator of neutrophils and a chemoattractant of eosinophils, macrophages, mast cells, and T cells. Inhibiting the formation of LTB 4 is expected to be beneficial in the treatment of inflammatory diseases such as inflammatory bowel disease (IBD), asthma, and atherosclerosis. We developed a pharmacophore model using a known inhibitor manually docked into the active site of LTA 4H to identify a subset of compounds for screening. From this work we identified a series of benzoxazole, benzthiazole, and benzimidazole inhibitors. SAR studies resulted in the identification of several potent inhibitors with an appropriate cross-reactivity profile and excellent PK/PD properties. Our efforts focused on further profiling JNJ 27265732, which showed encouraging efficacy in a disease model relevant to IBD.

2-Aryl benzimidazoles featuring alkyl-linked pendant alcohols and amines as inhibitors of checkpoint kinase Chk2.

A series of benzimidazole compounds containing pendant alcohol and amine moieties was found to be active against checkpoint kinase Chk2. These compounds were prepared to examine a potential hydrogen bond interaction with an active site residue and to investigate replacement of a biaryl linker with an aliphatic system in an effort to improve solubility.

Three-dimensional models of histamine H3 receptor antagonist complexes and their pharmacophore.

Molecular modeling was used to analyze the binding mode and activities of histamine H3 receptor antagonists. A model of the H3 receptor was constructed through homology modeling methods based on the crystal structure of bovine rhodopsin. Known H3 antagonists were interactively docked into the putative antagonist binding pocket and the resultant model was subjected to molecular mechanics energy minimization and molecular dynamics simulations which included a continuum model of the lipid bilayer and intra- and extracellular aqueous environments surrounding the transmembrane helices. The transmembrane helices stayed well embedded in the dielectric slab representing the lipid bilayer and the intra- and extracellular loops remain situated in the aqueous solvent region of the model during molecular dynamics simulations of up to 200 ps in duration. A pharmacophore model was calculated by mapping the features common to three active compounds three-dimensionally in space. The 3D pharmacophore model complements our atomistic receptor/ligand modeling. The H3 antagonist pharmacophore consists of two protonation sites (i.e. basic centers) connected by a central aromatic ring or hydrophobic region. These two basic sites can simultaneously interact with Asp 114 (3.32) in helix III and a Glu 206 (5.46) in helix V which are believed to be the key residues that histamine interacts with to stabilize the receptor in the active state. The interaction with Glu 206 is consistent with the enhanced activity resulting from the additional basic site. In addition to these two salt bridging interactions, the central region of these antagonists contains a lipophilic group, usually an aromatic ring, that is found to interact with several nearby hydrophobic side chains. The picture of antagonist binding provided by these models is consistent with earlier pharmacophore models for H3 antagonists with some exceptions.

Novel non-benzimidazole chk2 kinase inhibitors.

In a recent paper, [Arienti, K. L.; Brunmark, A.; Axe, F. U.; McClure, K. M.; Lee, A.; Blevitt, J.; Neff, D. K.; Huang, L.; Crawford, S.; Chennagiri, R. P.; Karlsson, L.; Brietenbucher, J. G. J. Med. Chem.2005, 48, 1873], we described the discovery of a class of benzimidazole chk2 kinase inhibitors, exemplified by compound 1, which had radio-protective effects in human T-cells subjected to ionizing radiation. Here, a series of non-benzimidazole analogs intended to define the scope of the SAR about this new series of inhibitor, and allow for refinement of the binding model of these compounds to the chk2 kinase is described.

Checkpoint kinase inhibitors: SAR and radioprotective properties of a series of 2-arylbenzimidazoles.

The discovery of a series of novel, potent, and highly selective inhibitors of the DNA damage control kinase chk2 is disclosed. Here we report the first SAR study around inhibitors of this kinase. High-throughput screening of purified human chk2 led to the identification of a novel series of 2-arylbenzimidazole inhibitors of the kinase. Optimization was facilitated using homology models of chk2 and docking of inhibitors, leading to the highly potent 2-arylbenzimidazole 2h (IC(50) 15 nM). Compound 2h is an ATP-competitive inhibitor of chk2 that dose dependently protects human CD4(+) and CD8(+) T-cells from apoptosis due to ionizing radiation. This work suggests that a selective small molecule inhibitor of chk2 could be a useful adjuvant to radiotherapy, increasing the therapeutic window of such treatment.

Structure-based design of selective and potent inhibitors of protein-tyrosine phosphatase beta.

Protein-tyrosine phosphatases (PTPs) are considered important therapeutic targets because of their pivotal role as regulators of signal transduction and thus their implication in several human diseases such as diabetes, cancer, and autoimmunity. In particular, PTP1B has been the focus of many academic and industrial laboratories because it was found to be an important negative regulator of insulin and leptin signaling, and hence a potential therapeutic target in diabetes and obesity. As a result, significant progress has been achieved in the design of highly selective and potent PTP1B inhibitors. In contrast, little attention has been given to other potential drug targets within the PTP family. Guided by x-ray crystallography, molecular modeling, and enzyme kinetic analyses with wild type and mutant PTPs, we describe the development of a general, low molecular weight, non-peptide, non-phosphorus PTP inhibitor into an inhibitor that displays more than 100-fold selectivity for PTPbeta over PTP1B. Of note, our structure-based design principles, which are based on extensive bioinformatics analyses of the PTP family, are general in nature. Therefore, we anticipate that this strategy, here applied to PTPbeta, in principle can be used in the design and development of selective inhibitors of many, if not most PTPs.

Inhibition of fructose-1,6-bisphosphatase by a new class of allosteric effectors.

A highly constrained pseudo-tetrapeptide (OC252-324) further defines a new allosteric binding site located near the center of fructose-1,6-bisphosphatase. In a crystal structure, pairs of inhibitory molecules bind to opposite faces of the enzyme tetramer. Each ligand molecule is in contact with three of four subunits of the tetramer, hydrogen bonding with the side chain of Asp187 and the backbone carbonyl of residue 71, and electrostatically interacting with the backbone carbonyl of residue 51. The ligated complex adopts a quaternary structure between the canonical R- and T-states of fructose-1,6-bisphosphatase, and yet a dynamic loop essential for catalysis (residues 52-72) is in a conformation identical to that of the T-state enzyme. Inhibition by the pseudo-tetrapeptide is cooperative (Hill coefficient of 2), synergistic with both AMP and fructose 2,6-bisphosphate, noncompetitive with respect to Mg2+, and uncompetitive with respect to fructose 1,6-bisphosphate. The ligand dramatically lowers the concentration at which substrate inhibition dominates the kinetics of fructose-1,6-bisphosphatase. Elevated substrate concentrations employed in kinetic screens may have facilitated the discovery of this uncompetitive inhibitor. Moreover, the inhibitor could mimic an unknown natural effector of fructose-1,6-bisphosphatase, as it interacts strongly with a conserved residue of undetermined functional significance.

Non-imidazole heterocyclic histamine H3 receptor antagonists.

Continued exploration of the SAR around the lead imidazopyridine histamine H(3) antagonist 1 has led to the discovery of several related series of heterocyclic histamine H(3) antagonists. The synthesis and SAR of indolizine, indole and pyrazolopyridine based compounds are now described.