Efficacious inhaled PDE4 inhibitors with low emetic potential and long duration of action for the treatment of COPD.

Oral phosphodiesterase 4 (PDE4) inhibitors, such as cilomilast and roflumilast, have been shown to be efficacious against chronic obstructive pulmonary disease (COPD). However, these drugs have been hampered by mechanism-related side effects such as nausea and emesis at high doses. Compounds administered by inhalation are delivered directly to the site of action and may improve the therapeutic index required to overcome side effects. This paper describes systematic and rational lead optimization to deliver highly potent, long-acting, and efficacious preclinical inhaled PDE4 inhibitors with low emetic potential.

Mitigating the inhibition of human bile salt export pump by drugs: opportunities provided by physicochemical property modulation, in silico modeling, and structural modification.

The human bile salt export pump (BSEP) is a membrane protein expressed on the canalicular plasma membrane domain of hepatocytes, which mediates active transport of unconjugated and conjugated bile salts from liver cells into bile. BSEP activity therefore plays an important role in bile flow. In humans, genetically inherited defects in BSEP expression or activity cause cholestatic liver injury, and many drugs that cause cholestatic drug-induced liver injury (DILI) in humans have been shown to inhibit BSEP activity in vitro and in vivo. These findings suggest that inhibition of BSEP activity by drugs could be one of the mechanisms that initiate human DILI. To gain insight into the chemical features responsible for BSEP inhibition, we have used a recently described in vitro membrane vesicle BSEP inhibition assay to quantify transporter inhibition for a set of 624 compounds. The relationship between BSEP inhibition and molecular physicochemical properties was investigated, and our results show that lipophilicity and molecular size are significantly correlated with BSEP inhibition. This data set was further used to build predictive BSEP classification models through multiple quantitative structure-activity relationship modeling approaches. The highest level of predictive accuracy was provided by a support vector machine model (accuracy = 0.87, κ = 0.74). These analyses highlight the potential value that can be gained by combining computational methods with experimental efforts in early stages of drug discovery projects to minimize the propensity of drug candidates to inhibit BSEP.

Prospective Prediction of Antitarget Activity by Matched Molecular Pairs Analysis.

Matched molecular pairs analysis (MMPA)1,2 is an inverse quantitative structure activity relationship (QSAR) technique that is rapidly gaining popularity in the retrospective analysis of large experimental datasets.3,4 While much of the recent focus has been on the differences in properties between structurally related groups of existing compounds, attempts to extend this methodology to the de-novo design of novel structures have been limited. To our knowledge the aggregate effect of multiple transformations, all suggesting the same molecular structure, has only ever being considered within a very limited dataset.5 We therefore sought to test this exciting new approach to the design (and absolute property prediction - effectively QSAR-by-MMPA) of novel chemical entities based on a larger, more diverse dataset, and couple these designs to MMPA-based predictions of antitarget activity.

The discovery of new spirocyclic muscarinic M3 antagonists.

The optimisation of a new series of high potency muscarinic M3 antagonists, derived from high throughput screening library hit is described.

WizePairZ: a novel algorithm to identify, encode, and exploit matched molecular pairs with unspecified cores in medicinal chemistry.

An algorithm to automatically identify and extract matched molecular pairs from a collection of compounds has been developed, allowing the learning associated with each molecular transformation to be readily exploited in drug discovery projects. Here, we present the application to an example data set of 11 histone deacetylase inhibitors. The matched pairs were identified, and corresponding differences in activity and lipophilicity were recorded. These property differences were associated with the chemical transformations encoded in the SMIRKS reaction notation. The transformations identified a subseries with the optimal balance of these two parameters. Enumeration of a virtual library of compounds using the extracted transformations identified two additional compounds initially excluded from the analysis with an accurate estimation of their biological activity. We describe how the WizePairZ system can be used to archive and apply medicinal chemistry knowledge from one drug discovery project to another as well as identify common bioisosteres.

Investigating the Conformational Preferences of Transforming Growth Factor-ß Isoforms using Targeted Molecular Dynamics Simulations.

We study the conformational preferences and mechanical properties of two isoforms of the cytokine transforming growth factor-ß (-ß1 and -ß3) with atomistic detail and including the effects of explicit water. Targeted molecular dynamics simulations are used to perturb experimental "closed" conformations of both proteins into an "open" conformation, thus far only observed crystallographically for one of the two isoforms. The artificial restraints imposed by the protocol are later released, allowing the two covalently bound units of each homodimer to relax. Homology models of the two proteins are also constructed using the other as a template; models that are later subjected to the same process of perturbation into the open conformation and relaxation. On release, both simulations of transforming growth factor-ß1 show a tendency to snap back toward the closed conformation, while those of transforming growth factor-ß3 remain open for the remainder of the simulation, apparently consistent with measurements from a variety of experimental sources. Duplication of the simulations affords confidence that this observation reflects a genuine effect of the sequence, as opposed to an artifact of the conformations selected at the outset. The study provides a previously unseen level of detail, describing the structural and dynamic behavior of these proteins in solution, and brings us a step closer to understanding the complex relationship between sequence, structure, and signaling in this family of cytokines.

Modelling the restoration of wild-type dynamic behaviour in DeltaF508-CFTR NBD1 by 8-cyclopentyl-1,3-dipropylxanthine.

Cystic fibrosis (CF) is the most frequently occurring severe, genetic disease in western populations with an incidence as high as 1 in 2500. The principal biochemical defect in CF is a mutation in a membrane transport protein, namely the cystic fibrosis transmembrane conductance regulator (CFTR), which is responsible for the conductance of chloride ions across cell membranes. In 70% of cases a single mutation in CFTR, namely the deletion of amino acid 508 (called DeltaF508) is sufficient to cause severe disease. This mutation manifests as a failure of the protein to be effectively targeted to the membrane. Recently, it has been shown that small molecule drug therapy can restore the membrane-targeting of DeltaF508-CFTR, where the mutant channel functions adequately. We have created models of the first nucleotide-binding domain (NBD1) region (which houses the proposed binding site of these restorative drugs) of the wild-type and mutant forms of human CFTR. We have simulated the dynamical behaviour of these proteins in the presence of drugs that restore trafficking of the protein. Our results indicate that there are particular modes of dynamic motion that are distinguishable between wild-type and mutant CFTR. These regions of motion are localized in the regions of the DeltaF508 mutation and the drug-binding regions. The simulations of drug binding indicate that wild-type dynamic motions are restored in these regions. We conclude therefore that these drugs are able to alter the dynamic properties of DeltaF508-CFTR such that the drug-bound mutant protein more closely resembles the wild-type protein dynamic behaviour, and hence we hypothesize that it is this that allows for correct targeting to the membrane.

Prevalence of pollen sensitization in younger children who have asthma.

It is commonly believed that young children are incapable of pollen sensitization; therefore, skin testing usually is not performed to these allergens. The purpose of this study was to identify the frequency of positive skin tests to outdoor allergens among younger children who have asthma. Patients who have asthma, aged 6 months to 10 years, were evaluated for pollen sensitization over a 10-year period. Skin-prick testing was performed to relevant individual aeroallergens including trees, grasses, and weeds. Testing for perennial indoor allergens such as dust mites, cats, dogs, cockroaches, and molds was performed also. A total of 687 children with asthma were evaluated. No child <12 months old was sensitized to pollens. Children between 12 and 24 months of age had a 29% incidence of pollen sensitization. Three-year-old children were as likely to be skin test positive to pollen as an indoor allergen. Notably, 49% of 3- and 4-year olds were sensitized to outdoor allergens. Primary sensitizing pollens in this age group were short ragweed, box elder, and June grass. In this population, pollen sensitization was not related to tobacco or wood smoke exposure. Although it is widely believed that young children with asthma are most commonly allergic to indoor allergens, almost 40% of our 1- to 3-year old children with asthma showed IgE-mediated sensitivity to outdoor allergens. Pediatric allergists should consider performing skin-prick testing to their local common aeroallergens in young children with asthma and seasonal symptoms.

Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water.

In the present study we examine the enthalpy of binding of 2-methoxy-3-isobutylpyrazine (IBMP) to the mouse major urinary protein (MUP), using a combination of isothermal titration calorimetry (ITC), NMR, X-ray crystallography, all-atom molecular dynamics simulations, and site-directed mutagenesis. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than a classical entropy-driven signature that might be expected given that the binding pocket of MUP-1 is very hydrophobic. The only ligand-protein hydrogen bond is formed between the side-chain hydroxyl of Tyr120 and the ring nitrogen of the ligand in the wild-type protein. ITC measurements on the binding of IBMP to the Y120F mutant demonstrate a reduced enthalpy of binding, but nonetheless binding is still enthalpy dominated. A combination of solvent isotopic substitution ITC measurements and all-atom molecular dynamics simulations with explicit inclusion of solvent water suggests that solvation is not a major contributor to the overall binding enthalpy. Moreover, hydrogen/deuterium exchange measurements suggest that there is no significant contribution to the enthalpy of binding derived from "tightening" of the protein structure. Data are consistent with binding thermodynamics dominated by favorable dispersion interactions, arising from the inequality of solvent-solute dispersion interactions before complexation versus solute-solute dispersion interactions after complexation, by virtue of poor solvation of the binding pocket.