Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

Eg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop 5/helix α2 (L5/α2). Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to explore this hydrophobic pocket with our MED-SuMo fragment-based protocol, and thus discover novel chemical structures that might bind as inhibitors. The MED-SuMo software is able to compare and superimpose similar interaction surfaces upon the whole protein data bank (PDB). In a fragment-based protocol, MED-SuMo retrieves MED-Portions that encode protein-fragment binding sites and are derived from cross-mining protein-ligand structures with libraries of small molecules. Furthermore we have excluded intra-family MED-Portions derived from Eg5 ligands that occupy the hydrophobic pocket and predicted new potential ligands by hybridization that would fill simultaneously both pockets. Some of the latter having original scaffolds and substituents in the hydrophobic pocket are identified in libraries of synthetically accessible molecules by the MED-Search software. Ksenia Oguievetskaia and Laetitia Martin-Chanas contributed equally to this work.     

KRAS Binders Hidden in Nature

Natural products have proven to be a rich source of molecular architectures for drugs. Here, an integrated approach to natural product screening is proposed, which uncovered eight new natural product scaffolds for KRAS—the most frequently mutated oncogenic driver in human cancers, which has remained thus far undrugged. The approach combines aspects of virtual screening, fragment-based screening, structure-activity relationships (SAR) by NMR, and structure-based drug discovery to overcome the limitations in traditional natural product approaches. By using our approach, a new “snugness of fit” scoring function and the first crystal-soaking system of the active form of KRAS^G12D, the protein–ligand X-ray structures of a tricyclic indolopyrrole fungal alkaloid and an indoloisoquinolinone have been successfully elucidated. The natural product KRAS hits discovered provide fruitful ground for the optimization of highly potent natural-product-based inhibitors of the active form of oncogenic RAS. This integrated approach for screening natural products also holds promise for other “undruggable” targets.     

Synergies between operations research and data mining: The emerging use of multi-objective approaches

Operations research and data mining already have a long-established common history. Indeed, with the growing size of databases and the amount of data available, data mining has become crucial in modern science and industry. Data mining problems raise interesting challenges for several research domains, and in particular for operations research, as very large search spaces of solutions need to be explored. Hence, many operations research methods have been proposed to deal with such challenging problems. But the relationships between these two domains are not limited to these natural applications of operations research approaches. The counterpart is also important to consider, since data mining approaches have also been applied to improve operations research techniques. The aim of this article is to highlight the interplay between these two research disciplines. A particular emphasis will be placed on the emerging theme of applying multi-objective approaches in this context.     

Synthesis and attachment of silver nanowires on atomic force microscopy cantilevers for tip‐enhanced Raman spectroscopy

Surface‐enhanced Raman spectroscopy is based on the absorption of light by nanometer‐sized metal particles, resulting in large enhancement of the Raman signal. By replacing the metal particles by a metallic nanotip, the enhancement can be localized. The resulting tip‐enhanced Raman spectroscopy is capable of measuring Raman spectra with high spatial resolution, effectively overcoming the diffraction limit. A successful tip‐enhanced Raman spectroscopy experiment depends heavily on the ability to fabricate tips of a definite metal with the appropriate shape and size, which is still a challenging process. We have prepared silver nanowires with a diameter of 200–300 nm by templated electrochemical deposition and attached them onto atomic force microscope cantilevers by focused electron beam induced deposition. We found that they produce a reproducible enhancement of the Raman signal intensity. Other metals and smaller nanostructures might also be produced, suggesting an interesting development potential for these novel nanoprobes. Copyright © 2011 John Wiley & Sons, Ltd.     

Growth and structural characterization of YMnO3 thin films grown by pulsed liquid injection MOCVD on Si and SrTiO3 substrates

Optimum parameters for the growing of YMnO₃ films by pulsed liquid injection metalorganic chemical vapor deposition have been studied. Si substrates were used for the optimization of the deposition process. X-ray diffraction (XRD) and transmission electron microscopy (TEM) results show that polycrystalline single phase YMnO₃ films can be obtained for an optimal ratio of Y and Mn on the injected solution and either amorphous, metastable orthorhombic, and/or hexagonal YMnO₃ phases can be obtained depending on the deposition temperature and precursors ratio. In a second stage, YMnO₃ films were grown on SrTiO₃ substrates. Pure epitaxial orthorhombic YMnO₃ phase was confirmed by XRD. The films microstructure, characterized by scanning electron microscopy and TEM, shows a columnar growth. Each columnar grain grows epitaxially with three possible orientations.     

The pattern of methylcyclopentane and n-hexane reactions on Rh/Al2O3 in catalytic runs of various length

Methylcyclopentane and n-hexane were reacted on a Rh/alumina catalyst in a closed-loop reactor. The product composition was analyzed at different moments of the run. In spite of a slow self-deactivation, the distribution of primary products and the depth of hydrogenolysis showed hardly any dependence on the sampling time in the conversion range of 1.5% and 50%. This is discussed in terms of accumulation of hydrocarbonaceous residues and the low readsorption probability of primary products on rhodium surface.     

A strategy for isotope containment during radiosynthesis--devolatilisation of bromobenzene by fluorous-tagging-Ir-catalysed borylation en route to the 4-phenylpiperidine pharmacophore

Syntheses of two 4-phenylpiperidines from bromobenzene have been developed involving anchoring to a fluorous-tag, Ir-catalysed borylation, Pd- and Co-catalysed elaboration then traceless cleavage. Although performed using 'cold' (i.e. unlabelled) bromobenzene as the starting material, these routes have been designed to minimise material loss via volatile intermediates and expedite purification during radiosynthesis from 'hot' (i.e. [(14)C] labelled) bromobenzene.     

Synthesis and spectroscopic examination of various substituted 1,3-dibenzoylmethane, active agents for UVA/UVB photoprotection

We describe the synthesis of eighteen variously substituted 1,3- dibenzoylmethane (1,3-DBM) and their change in absorption spectra depending of the nature of donor or acceptor substituents on one or the two aromatic moieties. These compounds were prepared in two steps starting from the corresponding acetophenones, phenol and benzoyl chlorides. The phenyl benzoate was obtained by condensation of benzoyl chloride with phenol in a classical way. Stirring of the phenyl benzoate and acetophenone in DMSO with powdered sodium hydroxide for a few minutes gave the dibenzoylmethane in yields depending on substituents on the phenyl rings. Changes in absorption of UVA/UVB sunlight of these molecules were observed according to the nature and the position of substituents on the phenyl rings. Molecules 2b (1-phenyl-3-(3,4,5-trimethoxyphenyl)-1,3-propanedione), 2d (1-(3,4-dimethoxyphenyl)-3-phenyl-l,3-propanedione), 2e (1-(2,3-dimethoxyphenyl)-3-phenyl-l,3-propanedione) and 2f (1-(2,3,4-trimethoxyphenyl)-3-phenyl-l,3-propanedione) were the most interesting for cosmetic applications because even after irradiation, they preserve their absorptive in UVA range and also in UVB range The other compounds are too photounstable and so can lose their protective effects. These results showed the lack of phototoxicity of these compounds and the possibility to use them as solar filters. Therefore, variously di- or tri methoxy 1,3-DBM are interesting molecules in term of photoprotection and open new prospects for UVA photostable filters.     

High order variational numerical schemes with application to Nash–MFG vaccination games

This paper introduces high-order explicit Runge–Kutta numerical schemes in metric spaces. We show that our approach reduces to the corresponding Runge–Kutta schemes if the ambient space is Hilbert. We apply these schemes to compute the Nash equilibrium in a mean field vaccination game. Numerical simulations show improvement in the speed of convergence towards the Nash equilibrium; the numerical scheme has high order (2–4) in time.