Repurposing the antihistamine terfenadine for antimicrobial activity against Staphylococcus aureus.

Staphylococcus aureus is a rapidly growing health threat in the U.S., with resistance to several commonly prescribed treatments. A high-throughput screen identified the antihistamine terfenadine to possess, previously unreported, antimicrobial activity against S. aureus and other Gram-positive bacteria. In an effort to repurpose this drug, structure-activity relationship studies yielded 84 terfenadine-based analogues with several modifications providing increased activity versus S. aureus and other bacterial pathogens, including Mycobacterium tuberculosis. Mechanism of action studies revealed these compounds to exert their antibacterial effects, at least in part, through inhibition of the bacterial type II topoisomerases. This scaffold suffers from hERG liabilities which were not remedied through this round of optimization; however, given the overall improvement in activity of the set, terfenadine-based analogues provide a novel structural class of antimicrobial compounds with potential for further characterization as part of the continuing process to meet the current need for new antibiotics.

Identification of Potent and Selective Inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (PfM18AAP) of Human Malaria via High-Throughput Screening.

The target of this study, the PfM18 aspartyl aminopeptidase (PfM18AAP), is the only AAP present in the genome of the malaria parasite Plasmodium falciparum. PfM18AAP is a metallo-exopeptidase that exclusively cleaves N-terminal acidic amino acids glutamate and aspartate. It is expressed in parasite cytoplasm and may function in concert with other aminopeptidases in protein degradation, of, for example, hemoglobin. Previous antisense knockdown experiments identified a lethal phenotype associated with PfM18AAP, suggesting that it is a valid target for new antimalaria therapies. To identify inhibitors of PfM18AAP function, a fluorescence enzymatic assay was developed using recombinant PfM18AAP enzyme and a fluorogenic peptide substrate (H-Glu-NHMec). This was screened against the Molecular Libraries Probe Production Centers Network collection of ~292,000 compounds (the Molecular Libraries Small Molecule Repository). A cathepsin L1 (CTSL1) enzyme-based assay was developed and used as a counter screen to identify compounds with nonspecific activity. Enzymology and phenotypic assays were used to determine mechanism of action and efficacy of selective and potent compounds identified from high-throughput screening. Two structurally related compounds, CID 6852389 and CID 23724194, yielded micromolar potency and were inactive in CTSL1 titration experiments (IC50>59.6 µM). As measured by the K(i) assay, both compounds demonstrated micromolar noncompetitive inhibition in the PfM18AAP enzyme assay. Both CID 6852389 and CID 23724194 demonstrated potency in malaria growth assays (IC504 µM and 1.3 µM, respectively).

Probing chemical space with alkaloid-inspired libraries.

Screening of small-molecule libraries is an important aspect of probe and drug discovery science. Numerous authors have suggested that bioactive natural products are attractive starting points for such libraries because of their structural complexity and sp(3)-rich character. Here, we describe the construction of a screening library based on representative members of four families of biologically active alkaloids (Stemonaceae, the structurally related cyclindricine and lepadiformine families, lupin and Amaryllidaceae). In each case, scaffolds were based on structures of the naturally occurring compounds or a close derivative. Scaffold preparation was pursued following the development of appropriate enabling chemical methods. Diversification provided 686 new compounds suitable for screening. The libraries thus prepared had structural characteristics, including sp(3) content, comparable to a basis set of representative natural products and were highly rule-of-five compliant.

Small-molecule pyrimidine inhibitors of the cdc2-like (Clk) and dual specificity tyrosine phosphorylation-regulated (Dyrk) kinases: development of chemical probe ML315.

Substituted pyrimidine inhibitors of the Clk and Dyrk kinases have been developed, exploring structure-activity relationships around four different chemotypes. The most potent compounds have low-nanomolar inhibitory activity against Clk1, Clk2, Clk4, Dyrk1A and Dyrk1B. Kinome scans with 442 kinases using agents representing three of the chemotypes show these inhibitors to be highly selective for the Clk and Dyrk families. Further off-target pharmacological evaluation with ML315, the most selective agent, supports this conclusion.

Distinct interactions of 2'- and 3'-O-(N-methyl)anthraniloyl-isomers of ATP and GTP with the adenylyl cyclase toxin of Bacillus anthracis, edema factor.

Anthrax disease is caused by the spore-forming bacterium, Bacillus anthracis. B. anthracis produces a calmodulin-activated adenylyl cyclase (AC) toxin, edema factor (EF). Through excessive cAMP accumulation EF disrupts host defence. In a recent study [Taha HM, Schmidt J, Göttle M, Suryanarayana S, Shen Y, Tang WJ, et al. Molecular analysis of the interaction of anthrax adenylyl cyclase toxin, edema factor, with 2'(3')-O-(N-(methyl)anthraniloyl)-substituted purine and pyrimidine nucleotides. Mol Pharmacol 2009;75:693-703] we showed that various 2'(3')-O-N-(methyl)anthraniloyl (MANT)-substituted nucleoside 5'-triphosphates are potent inhibitors (K(i) values in the 0.1-5 microM range) of purified EF. Upon interaction with calmodulin we observed efficient fluorescence resonance energy transfer (FRET) between tryptophan and tyrosine residues of EF and the MANT-group of MANT-ATP. Molecular modelling suggested that both the 2'- and 3'-MANT-isomers can bind to EF. The aim of the present study was to examine the effects of defined 2'- and 3'-MANT-isomers of ATP and GTP on EF. 3'-MANT-2'-deoxy-ATP inhibited EF more potently than 2'-MANT-3'-deoxy-ATP, whereas the opposite was the case for the corresponding GTP analogs. Calmodulin-dependent direct MANT fluorescence and FRET was much larger with 2'-MANT-3'-deoxy-ATP and 2'-MANT-3'-deoxy-GTP compared to the corresponding 3'-MANT-2'-deoxy-isomers and the 2'(3')-racemates. K(i) values of MANT-nucleotides for inhibition of catalysis correlated with K(d) values of MANT-nucleotides in FRET studies. Molecular modelling indicated different positioning of the MANT-group in 2'-MANT-3'-deoxy-ATP/GTP and 3'-MANT-2'-deoxy-ATP/GTP bound to EF. Collectively, EF interacts differentially with 2'- and 3'-MANT-isomers of ATP and GTP, indicative for conformational flexibility of the catalytic site and offering a novel approach for the development of potent and selective EF inhibitors. Moreover, our present study may serve as a general model of how to use MANT-nucleotide isomers for the analysis of the molecular mechanisms of nucleotide/protein interactions.

Ionic immobilization, diversification, and release: application to the generation of a library of methionine aminopeptidase inhibitors.

Development of an ionic immobilization, diversification, and release method for the generation of methionine aminopeptidase inhibitors is reported. This method involves the immobilization of 5-bromofuran-2-carboxylic acid and 5-bromothiophene-2-carboxylic acid onto PS-BEMP, followed by Suzuki reaction on a resin-bound intermediate and subsequent release to provide products in moderate yields and excellent purities. Compound potencies were evaluated on the Co(II), Mn(II), Ni(II), and Fe(II) forms of Escherichia coli MetAP1. The furoic-acid analogs were found to be Mn(II) selective with IC 50 values in the low micromolar range. Qualitative SAR analysis, supplemented by molecular modeling studies, provides valuable information on structural elements responsible for potency and selectivity.

Novel Algorithms for the Identification of Biologically Informative Chemical Diversity Metrics.

Despite great advances in the efficiency of analytical and synthetic chemistry, time and available starting material still limit the number of unique compounds that can be practically synthesized and evaluated as prospective therapeutics. Chemical diversity analysis (the capacity to identify finite diverse subsets that reliably represent greater manifolds of drug-like chemicals) thus remains an important resource in drug discovery. Despite an unproven track record, chemical diversity has also been used to posit, from preliminary screen hits, new compounds with similar or better activity. Identifying diversity metrics that demonstrably encode bioactivity trends is thus of substantial potential value for intelligent assembly of targeted screens. This paper reports novel algorithms designed to simultaneously reflect chemical similarity or diversity trends and apparent bioactivity in compound collections. An extensive set of descriptors are evaluated within large NCI screening data sets according to bioactivity differentiation capacities, quantified as the ability to co-localize known active species into bioactive-rich K-means clusters. One method tested for descriptor selection orders features according to relative variance across a set of training compounds, and samples increasingly finer subset meshes for descriptors whose exclusion from the model induces drastic drops in relative bioactive colocalization. This yields metrics with reasonable bioactive enrichment (greater than 50% of all bioactive compounds collected into clusters or cells with significantly enriched active/inactive rates) for each of the four data sets examined herein. A second method replaces variance by an active/inactive divergence score, achieving comparable enrichment via a much more efficient search process. Combinations of the above metrics are tested in 2D rectilinear diversity models, achieving similarly successful colocalization statistics, with metrics derived from the active/inactive divergence score typically outperforming those selected from the variance criterion and computed from the DiverseSolutions software.

On the Balance of Simplification and Reality in Molecular Modeling of the Electron Density.

Fused-sphere (van der Waals) surfaces and their variants such as solvent accessible surfaces and molecular surfaces are simple molecular models that are commonly used for many diverse purposes across a broad range of scientific disciplines due to their low computational resource demands. Fused-sphere models require atomic radii to be defined. Many different atomic radii have been proposed, with each set of radii being applicable to a relatively limited scope of molecular types or situations. The large number of differing radii sets actually serves to emphasize the simplicity of the model and its inability to accurately represent the reality of the molecule: its electron density. By measuring the similarity of fused-sphere, fuzzy fused-sphere, and calculated electron density representations of a set of small molecules via symmetric volume differences and the shape group method, it can be seen that fused-sphere models are very poor at representing the real electronic charge distribution of small molecules, especially where π bond systems, lone pair electrons, and aromatic rings are involved. Larger molecules, conceivably, will be even more poorly represented. With advances in computational power and modeling techniques to arrive at high-quality calculated electron density representations for large molecules already in existence, abandoning the use of fused-sphere models should be considered for many applications.

Whither combine? New opportunities for receptor-based QSAR.

Receptor based QSAR methods represent a computational marriage of structure activity relationship analysis and receptor structure based design that is providing valuable pharmacological insight to a wide range of therapeutic targets. One implementation, called Comparative Binding Energy (COMBINE) analysis, is particularly powerful by virtue of its explicit consideration of interatomic interactions between the ligand and receptor as the QSAR variable space. This review outlines the methodological basis for the COMBINE model, contrasts it relative to other 3D QSAR techniques, and discusses sample applications that illustrate recent key innovations. One major development discussed is the rigorous integration of multiple receptors into unified COMBINE models for probing bioactivity trends as a function of amino acid variation across a series of homologous protein receptors, and as a function of conformational variation within one single protein. Other important examples include a recent extension of the method to account for covalent effects arising from ligand binding, as well as successful application of a COMBINE model to high throughput virtual screening. This review concludes with discussions about possible future methodological refinements and their applications, including potential extensions to four-dimensional QSAR, and a potential role of quantum chemistry in addressing covalent bonding effects and parametric adaptivity.

A conformational transition in the adenylyl cyclase catalytic site yields different binding modes for ribosyl-modified and unmodified nucleotide inhibitors.

Adenylyl cyclases (ACs) are promising pharmacological targets for treating heart failure, cancer, and psychosis. Ribose-substituted nucleotides have been reported as a potent family of AC inhibitors. In silico analysis of the docked conformers of such nucleotides in AC permits assembly of a consistent, intuitive QSAR model with strong correlation relative to measured pK(i) values. Energy decomposition suggests that the MANT group effects an AC conformational transition upon ligand binding.

Stability and electronic properties of nitrogen nanoneedles and nanotubes.

The electronic structures and stability of nitrogen nanostructures, nanotubes, and fiberlike nanoneedles of various diameters, formed by units N2m (m = 2-6), were studied by quantum chemistry computational modeling methods. The geometrical structures with various cross-sections and terminal units, their energetic stability, and their rather peculiar electron density distributions were investigated. The tightest nitrogen nanoneedle (NNN) studied theoretically in this work is the structure (N4n with D2h symmetry, whereas the nitrogen nanotube (NNT) with the largest diameter discussed here is the structure (N12)n with D2 symmetry. These families of NNNs and NNTs can be considered as nanostructures not only for potential applications as devices in nanotechnology or as possible scaffold structures but also as ligands in synthetic chemistry and high-energy density materials (HEDMs). As a consequence of the lone-pair electrons present around the walls of these NNNs and NNTs, these nitrogen nanostructures and the nitrogen nano-bundles (NNB) formed by aligning and combining them using intermediate carbon atoms, can have highly variable electronic properties controlled by the changing charge environment. In particular, for extended systems based on the units studied here, the band gaps of each of these systems can be affected greatly by the local charge of the environment.

The electronic structures and properties of open-ended and capped carbon nanoneedles.

The existence of a family of very thin carbon needlelike nanostructures is predicted: the geometry and stability of several carbon nanoneedles (CNNs) formed by C4 and C6 units have been studied by quantum chemistry computational modeling methods. The structures of carbon nanoneedles are tighter than even the smallest single wall nanotubes (SWNTs) based on (4, 0) naphthacene. The electronic properties, energetic stability of geometrical structures with various terminal units are investigated. The relatively large band gaps, the strong bonding, and additional orbital interactions within the C4 rings and between the C4 layers make the H4(C4)(n)H4 type molecules nonmetallic. We have found indications that if the CNN (3, 0) structures are very long (in the limit of infinite-length), then they are likely to have semiconducting properties and could possibly be used as actual semiconductors. The studied families of CNNs can be considered as carbon nanostructures with unique structural and chemical properties and with possible potential for unusual electronic properties, with likely practical applications as nanomaterials and nanostructure devices.