Targets looking for drugs: a multistep computational protocol for the development of structure-based pharmacophores and their applications for hit discovery

Pharmacophoresthree-dimensional (3D) arrangements of essential features enabling a molecule to exert a particular biological effectconstitute a very useful tool in drug design both in hit discovery and hit-to-lead optimization process. Two basic approaches for pharmacophoric model generation can be used by chemists, depending on the availability or not of the target 3D structure. In view of the rapidly growing number of protein structures that are now available, receptor-based pharmacophore generation methods are becoming more and more used. Since most of them require the knowledge of the 3D structure of the ligand-target complex, they cannot be applied when no compounds targeting the binding site of interest are known. Here, a GRID-based procedure for the generation of receptor-based pharmacophores starting from the knowledge of the sole protein structure is described and successfully applied to address three different tasks in the field of medicinal chemistry.     

Molecular basis of drug resistance in aurora kinases

Aurora kinases have emerged as potential targets in cancer therapy, and several drugs are currently undergoing preclinical and clinical validation. Whether clinical resistance to these drugs can arise is unclear. We exploited a hypermutagenic cancer cell line to select mutations conferring resistance to a well-studied Aurora inhibitor, ZM447439. All resistant clones contained dominant point mutations in Aurora B. Three mutations map to residues in the ATP-binding pocket that are distinct from the "gatekeeper" residue. The mutants retain wild-type catalytic activity and were resistant to all of the Aurora inhibitors tested. Our studies predict that drug-resistant Aurora B mutants are likely to arise during clinical treatment. Furthermore, because the plasticity of the ATP-binding pocket renders Aurora B insensitive to multiple inhibitors, our observations indicate that the drug-resistant Aurora B mutants should be exploited as novel drug targets.     

Isoelectronic series of oxygen deficient centers in silica: experimental estimation of homogeneous and inhomogeneous spectral widths

We report nanosecond time-resolved photoluminescence measurements on the isoelectronic series of oxygen deficient centers in amorphous silica related to silicon, germanium and tin atoms, which are responsible of fluorescence activities at approximately 4 eV under excitation at approximately 5 eV. The dependence of the first moment of their emission band on time and that of the radiative decay lifetime on emission energy are analyzed within a theoretical model able to describe the effects introduced by disorder on the optical properties of the defects. We obtain separate estimates of the homogeneous and inhomogeneous contributions to the measured emission line width, and we derive homogeneous spectroscopic features of the investigated point defects (Huang-Rhys factor, homogeneous width, oscillator strength, vibrational frequency). The results point to a picture in which an oxygen deficient center localized on a heavier atom features a higher degree of inhomogeneity due to stronger local distortion of the surrounding matrix. For Si, Ge, and Sn related defects, the parameter lambda, able to quantify inhomogeneity, is 65, 78, and 90%, respectively.     

On-line algorithms for networks of temporal constraints

We consider a semi-dynamic setting for the Temporal Constraint Satisfaction Problem (TCSP), where we are requested to maintain the path-consistency of a network under a sequence of insertions of new (further) constraints between pairs of variables. We show how to maintain the path-consistency in O(nR³) amortized time on a sequence of Θ(n²) insertions, where n is the number of vertices of the network and R is its range, defined as the maximum size of the minimum interval containing all the intervals of a single constraint.Furthermore we extend our algorithms to deal with more general temporal networks where variables can be points and/or intervals and constraints can also be defined on pairs of different kinds of variables. For such cases our algorithms maintain their performance. Finally, we adapt our algorithms to also maintain the arc-consistency of such generalized networks in O(R) amortized time for Θ(n²) insertions.     

Cortex-based independent component analysis of fMRI time series

The cerebral cortex is the main target of analysis in many functional magnetic resonance imaging (fMRI) studies. Since only about 20% of the voxels of a typical fMRI data set lie within the cortex, statistical analysis can be restricted to the subset of the voxels obtained after cortex segmentation. While such restriction does not influence conventional univariate statistical tests, it may have a substantial effect on the performance of multivariate methods.

Here, we describe a novel approach for data-driven analysis of single-subject fMRI time series that combines techniques for the segmentation and reconstruction of the cortical surface of the brain and the spatial independent component analysis (sICA) of the functional time courses (TCs). We use the mesh of the white matter/gray matter boundary, automatically reconstructed from high-spatial-resolution anatomical MR images, to limit the sICA decomposition of a coregistered functional time series to those voxels which are within a specified region with respect to the cortical sheet (cortex-based ICA, or cbICA). We illustrate our analysis method in the context of fMRI blocked and event-related experimental designs and in an fMRI experiment with perceptually ambiguous stimulation, in which an a priori specification of the stimulation protocol is not possible.

A comparison between cbICA and conventional hypothesis-driven statistical methods shows that cortical surface maps and component TCs blindly obtained with cbICA reliably reflect task-related spatiotemporal activation patterns. Furthermore, the advantages of using cbICA when the specification of a temporal model of the expected hemodynamic response is not straightforward are illustrated and discussed. A comparison between cbICA and anatomically unconstrained ICA reveals that — beside reducing computational demand — the cortex-based approach improves the fitting of the ICA model in the gray matter voxels, the separation of cortical components and the estimation of their TCs, particularly in the case of fMRI data sets with a complex spatiotemporal statistical structure.     

Correlation between shape and electronic states in nanostructures

We show how the electronic states of quantum wires and quantum dots can be evaluated exactly starting from the profile of the nanostructure observed by transmission electron microscopy, scanning tunneling microscopy and atomic force microscopy. The calculated quantization energies reproduce the energy position of the luminescence resonances in the optical spectra of different samples, without fitting parameters.     

A facile in situ microfluidic method for creating multivalent surfaces: toward functional glycomics

An in situ method of modifying the chemistry and topology of microfluidic surfaces in order to mimic the cellular environment is described. The binding of functionalised microbeads to microfluidic channels allows the surface-to-volume ratio of the system, and thus the number of biomolecules available for reaction, to be vastly increased, thereby enhancing the sensitivity of biochemical analyses. The sensitivity and specificity of the technique were first investigated via the study of carbohydrate-protein interactions. Beads featuring hydrazide moieties were adhered to the channel surface, after which carbohydrates (galactose and mannose) were bound to the beads in situ and reacted with fluorescently labelled proteins. Results showed a six-fold increase in fluorescent signal compared to the same process performed on a glass surface without the presence of beads, thereby demonstrating the increase in valence afforded by the method. In a subsequent study, beads, modified with galactose moieties via the in situ functionalisation technique, were used to perform studies of colon tumour cells from a cell sample. Here, the carcinoma cells exhibited superior adhesion than the normal cells due to an increased expression of active galactose receptors, thereby demonstrating the success of the biofunctionalisation method for investigating cellular mechanisms.