Interactive exploration of chemical space with Scaffold Hunter

We describe Scaffold Hunter, a highly interactive computer-based tool for navigation in chemical space that fosters intuitive recognition of complex structural relationships associated with bioactivity. The program reads compound structures and bioactivity data, generates compound scaffolds, correlates them in a hierarchical tree-like arrangement, and annotates them with bioactivity. Brachiation along tree branches from structurally complex to simple scaffolds allows identification of new ligand types. We provide proof of concept for pyruvate kinase.

Bioactivity-guided mapping and navigation of chemical space

The structure- and chemistry-based hierarchical organization of library scaffolds in tree-like arrangements provides a valid, intuitive means to map and navigate chemical space. We demonstrate that scaffold trees built using bioactivity as the key selection criterion for structural simplification during tree construction allow efficient and intuitive mapping, visualization and navigation of the chemical space defined by a given library, which in turn allows correlation of this chemical space with the investigated bioactivity and further compound design. Brachiation along the branches of such trees from structurally complex to simple scaffolds with retained yet varying bioactivity is feasible at high frequency for the five major pharmaceutically relevant target classes and allows for the identification of new inhibitor types for a given target. We provide proof of principle by identifying new active scaffolds for 5-lipoxygenase and the estrogen receptor ERalpha.

Impact of stent design on intra-aneurysmal flow. A computer simulation study

SUMMARY

In addition to providing a skeleton for vessel reconstruction, stent implantation as used for cerebral aneurysm treatment can induce flow redirection, thus reducing vortical flow velocities within the aneurysm cavity. Further, stent characteristics such as strut size, porosity and cell shape influence the changes in intra-aneurysmal flow by analog simulations. The purpose of this computer simulation study was to visualize the flow pattern over the entire neck area of a side wall aneurysm while changing the stent parameters. A 3-D computer model aneurysm was constructed to have a parent artery of 5 mm diameter and an aneurysm of 10 mm diameter. The distance between the midline of main artery and center point of the aneurysm was 6.8 mm, providing a neck length of 5 mm, a width of 3.6 mm, and a neck area of 14 mm 2. The simulations were carried out with a Finite Element Method based flow simulation package. The incompressible Navier-Stokes equation was solved for a steady flow with a mean speed of 290 mm/s, steady viscosity of 3.83 cp, and density of 1.0 g/cm3. Two parallel stent struts (dimensions: 100 mum m 100 mum m 2.0 mm) were introduced into the plane of the aneurysm neck. The fraction of the aneurysm neck cross-section occupied by the stent was 2.83% in all cases. The velocity distribution through the neck of the aneurysm was calculated for three different choices of separation between the struts for each of two orientations of the struts (parallel and perpendicular) relative to the vessel axis. The flow pattern in the aneurysm was composed of an inflow zone at the distal neck and of an outflow zone at the proximal neck. The placement of stent struts at the aneurysm neck resulted in a decrease in the mean speed in the aneurysm. The degree of reduction and the distribution of flow through the neck did depend on the orientation of the stent struts. The struts, when placed parallel or perpendicular to the parent vessel axis affected the mean speed through the aneurysm neck differently.

Biology-inspired synthesis of compound libraries

Biologically active small molecules represent the basis for chemical biology applications in which small molecules are used as chemical tools to probe biological processes. In this report, we review two approaches to design and synthesize compound libraries for biological screenings, i.e., diversity-oriented synthesis (DOS) and biology-oriented synthesis (BIOS).

ATP competitive inhibitors of D-alanine-D-alanine ligase based on protein kinase inhibitor scaffolds

D-Alanine-D-alanine ligase (DDl) is an essential enzyme in bacterial cell wall biosynthesis and an important target for developing new antibiotics. Here, we describe a new approach to identify new inhibitor scaffolds for DDl based on similarity in the ATP binding region of different kinases and DDl. After an initial screening of several protein kinase inhibitors, we found that the Brutons's tyrosine kinase inhibitor LFM-A13, an analog of the Leflunomide metabolite A771726, inhibits DDl with a K(i) of 185 microM. A series of malononitrilamide and salicylamide derivatives of LFM-A13 has been synthesized to confirm the validity of this scaffold as an inhibitor of DDl.

The scaffold tree--visualization of the scaffold universe by hierarchical scaffold classification

A hierarchical classification of chemical scaffolds (molecular framework, which is obtained by pruning all terminal side chains) has been introduced. The molecular frameworks form the leaf nodes in the hierarchy trees. By an iterative removal of rings, scaffolds forming the higher levels in the hierarchy tree are obtained. Prioritization rules ensure that less characteristic, peripheral rings are removed first. All scaffolds in the hierarchy tree are well-defined chemical entities making the classification chemically intuitive. The classification is deterministic, data-set-independent, and scales linearly with the number of compounds included in the data set. The application of the classification is demonstrated on two data sets extracted from the PubChem database, namely, pyruvate kinase binders and a collection of pesticides. The examples shown demonstrate that the classification procedure handles robustly synthetic structures and natural products.

In vivo assessment and visualization of intracranial arterial hemodynamics with flow-sensitized 4D MR imaging at 3T

SUMMARY

We evaluated electrocardiogram-synchronized flow-sensitized 4-dimensional MR imaging at 3T in combination with advanced 3D visualization strategies to ascertain its feasibility for the assessment of local intracranial blood-flow patterns in vivo. In large arteries of healthy volunteers, the temporal and spatial evolution of blood flow was successfully visualized and revealed--for example, a helical flow pattern in the carotid siphon. In a patient with steno-occlusive neurovascular disease, stagnant and retrograde flow patterns were readily visible.

Charting biologically relevant chemical space: a structural classification of natural products (SCONP)

The identification of small molecules that fall within the biologically relevant subfraction of vast chemical space is of utmost importance to chemical biology and medicinal chemistry research. The prerequirement of biological relevance to be met by such molecules is fulfilled by natural product-derived compound collections. We report a structural classification of natural products (SCONP) as organizing principle for charting the known chemical space explored by nature. SCONP arranges the scaffolds of the natural products in a tree-like fashion and provides a viable analysis- and hypothesis-generating tool for the design of natural product-derived compound collections. The validity of the approach is demonstrated in the development of a previously undescribed class of selective and potent inhibitors of 11beta-hydroxysteroid dehydrogenase type 1 with activity in cells guided by SCONP and protein structure similarity clustering. 11beta-hydroxysteroid dehydrogenase type 1 is a target in the development of new therapies for the treatment of diabetes, the metabolic syndrome, and obesity.

Traumatic vertical atlantoaxial dislocation

We present a case of traumatic vertical atlantoaxial dislocation of 16 millimetres with a fatal outcome. We hypothesize that this extremely rare traumatic vertical atlantoaxial dislocation results from insufficiency of the C1/C2 facet capsules after rupture of the tectorial membrane and the alar ligaments.

Eczema herpeticatum

Patients affected by atopic dermatitis tend to develop viral infections. Probably the most feared complication of atopic dermatitis is eczema herpeticum, a disseminated infection with herpes simplex virus. A monomorphic eruption of dome-shaped blisters, pustules and erosions in the eczematous skin lesions along with severe systemic illness leads to the diagnosis. The clinical diagnosis may be confirmed by polymerase chain reaction, viral culture, electron microscopy with negative staining, Tzanck test, immunofluorescence tests or serology. While intravenous acyclovir is still regarded as standard treatment of eczema herpeticum, several recently-developed antiviral drugs provide therapeutic options.

ADC mapping of the aging frontal lobes in mild cognitive impairment

Normal aging, leukoaraiosis (LA) and vascular disease particularly involve the human frontal lobes. We decided to investigate a population of elderly patients referred for neuroimaging because of progressive minor cognitive deficits but no dementia. They underwent conventional Magnetic resonance imaging (MRI) using axial T1 and T2-weighted imaging as well as coronal FLAIR sequences in addition to the axial diffusion-weighted MRI. MRI allowed us to differentiate patients with leukoaraïosis (LA+) from those without it (LA-) and mapping of the apparent diffusion coefficient (ADC) to investigate local tissular water motion. We observed an increase in the ADC in all investigated patients with increasing age (r=0.326, p=0.002). This increase was observed in both patients groups (LA+ and LA-). In addition, the LA+ group had significant higher ADC values than the LA- group after controlling for age (p<0.0001).

Multiplex RT-PCR detection of four aphid-borne strawberry viruses in Fragaria spp. in combination with a plant mRNA specific internal control

The principal aphid-borne viruses infecting Strawberry (Fragaria spp.) Strawberry crinkle virus (SCV), Strawberry mild yellow edge virus (SMYEV), Strawberry mottle virus (SMoV) and Strawberry vein banding virus (SVBV) can cause serious crop losses. In this paper, a multiplex reverse transcriptase polymerase chain reaction (RT-PCR) method is described for the simultaneous detection of all four viruses in combination with a plant mRNA specific internal control which can be used as an indicator of the effectiveness of the extraction and RT-PCR. In total, 18 strawberry isolates infected naturally were analysed by this method. Every combination of RNA virus was able to be detected and a full complement of all four viruses were found together in three isolates, all taken from wild strawberry (Fragaria chiloensis (L.) Duch.) in Chile. The upper detection limit for the four viruses was at an extract dilution of 1/200. The broad applicability of the RNA specific internal control primers-which produced a PCR fragment of the expected size in 25 of 27 plant species tested-combined with improvements, made in extraction methods described provides potentially a standard method for comparable RT-PCR analyses in a wide variety of plant species.