Adaptive optimization of focused compound libraries

Das Ziel des adaptiven Entwurfs von Substanzbibliotheken ist es, die vollständige biologische Testung einer molekularen Screeningbibliothek zu vermeiden. Stattdessen erfolgt, geleitet durch Optimierungsalgorithmen, eine "intelligente" Navigation durch den chemischen Raum, um so bevorzugt Substanzen mit gewünschten Eigenschaften auszuwählen. In einer retrospektiven Studie wurden die Optimierungsalgorithmen "Zufallssuche", "Simulated Annealing", "Evolutionsstrategie" und "Partikelschwarmoptimierung" im Hinblick auf den Entwurf von Bibliotheken von Serinproteaseinhibitoren systematischen verglichen. Die Gesamtzahl verfügbarer Substanztestungen wurde auf 300 beschränkt, um Laborbedingungen zu simulieren. Als Ergebnis zeigten sich besonders die Evolutionsstrategien für einen Einsatz in einer Niedrigdurchsatzscreening-Kampagne geeignet, da diese effizient mit großen Populationen und wenigen Iterationen arbeiteten. Der zweite Teil dieser Arbeit beschreibt den erfolgreichen Entwurf einer fokussierten Bibliothek von RNA-Liganden. In einer hybriden, prospektiven Optimierungsstudie wurden nach dem Vorbild einer iterativen Niedrigdurchsatzscreening-Kampagne vom Computer vorgeschlagene Moleküle im Labor getestet. Die Substanzen wurden auf Inhibition einer spezifischen molekularen Wechselwirkung im Replikationszyklus von HIV getestet (Tat-TAR-Interaktion). In vier Generationen wurden 9 von 170 untersuchten Verbindungen positiv auf Inhibition der Tat-TAR-Interaktion getestet (Trefferquote: 5,3%), wobei lediglich 0,089% der Verbindungen der Screeningbibliothek untersucht wurden. Die zwei potentesten Kandidaten wiesen einen IC50 von 51 uM bzw. 116 uM auf.The goal of adaptive library design is to avoid biological testing of a complete screening compound library. Instead, the idea is to navigate chemical space in an "intelligent" way, guided by optimization algorithms and "cherry-picking" primarily molecules with desired properties. In a retrospective study the optimization algorithms "random search", "simulated annealing", "evolution strategy", and "particle swarm optimization" were systematically compared with respect to the design of libraries of serine protease inhibitors. To simulate laboratory conditions the total number of compound tests was restricted to 300. As a result evolution strategies showed to be particularly suited for an employment in a low-throughput screening campaign as they operated efficiently with large populations and a small number of iterations. Next, the successful design of a focused library of RNA ligands is described. In a hybrid, prospective optimization study compounds were suggested by a computer program and tested in the lab in an iterative manner, following the spirit of a low-throughput screening campaign. The compounds were tested for inhibition of a specific molecular interaction in the replication cycle of HIV (Tat-TAR interaction). Within four generations 9 out of 170 screened compounds were found to inhibit the Tat-TAR interaction (hit rate: 5.3%) while only 0.089% of the screening library compounds were examined. The two most potent candidates exhibited an IC50 of 51 uM and 116 uM, respectively

Vor der Sommerpause: Zweimal kein Rechtsschutz gegen Vereinte Nationen

Innerhalb kurzer Zeit ergingen durch die Vereinten Nationen (UN) in New York und den Europäischen Gerichtshof für Menschenrechte (EGMR) zwei Entscheidungen, Betroffenen und Hinterbliebenen keinen Zugang zu Überprüfungsmechanismen für ihre geltend gemachten Ansprüche gegen die Vereinten Nationen zu gewähren. Die Ansprüche betrafen zum einen den Ausbruch von Cholera in Haiti und zum anderen den Völkermord in Srebrenica

Enhanced spin-orbit coupling in core/shell nanowires

The spin-orbit coupling (SOC) in semiconductors is strongly influenced by structural asymmetries, as prominently observed in bulk crystal structures that lack inversion symmetry. Here, we study an additional effect on the SOC: the asymmetry induced by the large interface area between a nanowire core and its surrounding shell. Our experiments on purely wurtzite GaAs/AlGaAs core/shell nanowires demonstrate optical spin injection into a single free-standing nanowire and determine the effective electron g-factor of the hexagonal GaAs wurtzite phase. The spin relaxation is highly anisotropic in time-resolved micro-photoluminescence measurements on single nanowires, showing a significant increase of spin relaxation in external magnetic fields. This behavior is counterintuitive compared to bulk wurtzite crystals. We present a model for the observed electron spin dynamics highlighting the dominant role of the interface-induced SOC in these core/shell nanowires. This enhanced SOC may represent an interesting tuning parameter for the implementation of spin-orbitronic concepts in semiconductor-based structures

Neutral and Charged Inter-Valley Biexcitons in Monolayer MoSe2_2

In atomically thin transition metal dichalcogenides (TMDs), reduced dielectric screening of the Coulomb interaction leads to strongly correlated many-body states, including excitons and trions, that dominate the optical properties. Higher-order states, such as bound biexcitons, are possible but are difficult to identify unambiguously using linear optical spectroscopy methods alone. Here, we implement polarization-resolved two-dimensional coherent spectroscopy to unravel the complex optical response of monolayer MoSe$_2$ and identify multiple higher-order correlated states. Decisive signatures of neutral and charged inter-valley biexcitons appear in cross-polarized two-dimensional spectra as distinct resonances with respective ~20 meV and ~5 meV binding energies--similar to recent calculations using variational and Monte Carlo methods. A theoretical model taking into account the valley-dependent optical selection rules reveals the specific quantum pathways that give rise to these states. Inter-valley biexcitons identified here, comprised of neutral and charged excitons from different valleys, offer new opportunities for creating exotic exciton-polariton condensates and for developing ultrathin biexciton lasers and polarization-entangled photon sources

Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function

Currently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for functional prediction of protein structures has emerged. Here we present an integrated bioinformatics method that combines sequence-based relationships and three-dimensional (3D) structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members of this family with known 3D structure but unknown function were identified for which a probable functional classification is provided. Our bioinformatics analyses suggest that they could be involved in plant cell wall degradation (Lin2118 protein from Listeria innocua, PDB code 3oou), symbiotic nitrogen fixation (protein from Chromobacterium violaceum, PDB code 3oio), and either metabolism of plant-derived biomass or nitrogen fixation (protein from Rhodopseudomonas palustris, PDB code 3mn2)

Candida glabrata environmental stress response involves Saccharomyces cerevisiae Msn2/4 orthologous transcription factors

We determined the genome-wide environmental stress response (ESR) expression profile of Candida glabrata, a human pathogen related to Saccharomyces cerevisiae. Despite different habitats, C. glabrata, S. cerevisiae, Schizosaccharomyces pombe and Candida albicans have a qualitatively similar ESR. We investigate the function of the C. glabrata syntenic orthologues to the ESR transcription factor Msn2. The C. glabrata orthologues CgMsn2 and CgMsn4 contain a motif previously referred to as HD1 (homology domain 1) also present in Msn2 orthologues from fungi closely related to S. cerevisiae. We show that regions including this motif confer stress-regulated intracellular localization when expressed in S. cerevisiae. Site-directed mutagenesis confirms that nuclear export of CgMsn2 in C. glabrata requires an intact HD1. Transcript profiles of CgMsn2/4 mutants and CgMsn2 overexpression strains show that they regulate a part of the CgESR. CgMsn2 complements a S. cerevisiae msn2 null mutant and in stressed C. glabrata cells, rapidly translocates from the cytosol to the nucleus. CgMsn2 is required for full resistance against severe osmotic stress and rapid and full induction of trehalose synthesis genes (TPS1, TPS2). Constitutive activation of CgMsn2 is detrimental for C. glabrata. These results establish an Msn2-regulated general stress response in C. glabrata

Rational Design of Resveratrol O-methyltransferase for the Production of Pinostilbene

Pinostilbene is a monomethyl ether analog of the well-known nutraceutical resveratrol. Both compounds have health-promoting properties, but the latter undergoes rapid metabolization and has low bioavailability. O-methylation improves the stability and bioavailability of resveratrol. In plants, these reactions are performed by O-methyltransferases (OMTs). Few efficient OMTs that monomethylate resveratrol to yield pinostilbene have been described so far. Here, we report the engineering of a resveratrol OMT from Vitis vinifera (VvROMT), which has the highest catalytic efficiency in di-methylating resveratrol to yield pterostilbene. In the absence of a crystal structure, we constructed a three-dimensional protein model of VvROMT and identified four critical binding site residues by applying different in silico approaches. We performed point mutations in these positions generating W20A, F24A, F311A, and F318A variants, which greatly reduced resveratrol’s enzymatic conversion. Then, we rationally designed eight variants through comparison of the binding site residues with other stilbene OMTs. We successfully modified the native substrate selectivity of VvROMT. Variant L117F/F311W showed the highest conversion to pinostilbene, and variant L117F presented an overall increase in enzymatic activity. Our results suggest that VvROMT has potential for the tailor-made production of stilbenes.This research was funded by PROYECTO INTERDISCIPLINA-VRI-UC-II160020, number 3514-913, Pontificia Universidad Católica de Chile (to L.P.P. and A.S.) and BECA DE DOCTORADO NACIONAL 2016, number 21161084, National Agency for Research and Development (ANID), Chile (to D.P.H.), for which we are grateful. The APC was funded by Pontificia Universidad Católica de Chile