A hidden active site in the potential drug target Mycobacterium tuberculosis dUTPase is accessible through small-amplitude protein conformational changes

dUTPases catalyze the hydrolysis of dUTP into dUMP and pyrophosphate to maintain the proper nucleotide pool for DNA metabolism. Recent evidence suggests that dUTPases may also represent a selective drug target in mycobacteria because of the crucial role of these enzymes in maintaining DNA integrity. Nucleotide-hydrolyzing enzymes typically harbor a buried ligand-binding pocket at interdomain or intersubunit clefts, facilitating proper solvent shielding for the catalyzed reaction. The mechanism by which substrate binds this hidden pocket and product is released in dUTPases is unresolved because of conflicting crystallographic and spectroscopic data. We sought to resolve this conflict by using a combination of random acceleration molecular dynamics (RAMD) methodology and structural and biochemical methods to study the dUTPase from Mycobacterium tuberculosis. In particular, the RAMD approach used in this study provided invaluable insights into the nucleotide dissociation process that reconciles all previous experimental observations. Specifically, our data suggest that nucleotide binding takes place as a small stretch of amino acids transiently slides away and partially uncovers the active site. The in silico data further revealed a new dUTPase conformation on the pathway to a relatively open active site. To probe this model, we developed the Trp21 reporter and collected crystallographic, spectroscopic, and kinetic data that confirmed the interaction of Trp21 with the active site shielding C-terminal arm, suggesting that the RAMD method is effective. In summary, our computational simulations and spectroscopic results support the idea that small loop movements in dUTPase allow the shuttlingof the nucleotides between the binding pocket and the solvent

Polythelia: still a marker of urinary tract anomalies in children

OBJECTIVE: Supernumerary nipples (SNN), or polythelia, are the most common form of the accessory mammary tissue malformation. The frequency of this condition ranges from 0.2% to 5.6% depending on various factors. This condition is associated with several anomalies, although this association is often controversial. The aim of this study was to evaluate the association between SNN and kidney/urinary tract (K/UT) anomalies, where anomalies is taken to mean functional disorders, malformations and diseases. MATERIAL AND METHODS: A case-control study was performed. The study evaluated 166 children (case group) referred to the Pediatric Nephrology Unit of the Department of Pediatrics of the Catholic University of Rome and 182 children (control group) admitted to the Department of Pediatrics because of pathologies not involving the urinary tract. RESULTS: There were 11 children with SNN in the case group, and only two patients in the control group (6.62% vs 1.09%, p<0.05). CONCLUSION: The results show a high incidence of K/UT anomalies in children with SNN, and therefore K/UT should be investigated in this specific population

Spectrally tunable ultrashort monochromatized extreme ultraviolet pulses at 100 kHz

We present the experimental realization of spectrally tunable, ultrashort, quasi-monochromatic extreme ultraviolet (XUV) pulses generated at 100 kHz repetition rate in a user-oriented gas high harmonic generation beamline of the Extreme Light Infrastructure—Attosecond Light Pulse Source facility. Versatile spectral and temporal shaping of the XUV pulses is accomplished with a double-grating, time-delay compensated monochromator accommodating the two composing stages in a novel, asymmetrical geometry. This configuration supports the achievement of high monochromatic XUV flux (2.8 ± 0.9 × 1010 photons/s at 39.7 eV selected with 700 meV full width at half maximum bandwidth) combined with ultrashort pulse duration (4.0 ± 0.2 fs using 12.1 ± 0.6 fs driving pulses) and small spot size (sub-100 µm). Focusability, spectral bandwidth, and overall photon flux of the produced radiation were investigated, covering a wide range of instrumental configurations. Moreover, complete temporal (intensity and phase) characterization of the few-femtosecond monochromatic XUV pulses—a goal that is difficult to achieve by conventional reconstruction techniques—has been realized using a ptychographic algorithm on experimentally recorded XUV-infrared pump-probe traces. The presented results contribute to in situ, time-resolved experiments, accessing direct information on the electronic structure dynamics of novel target materials

Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands

Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered

Amorphization of Atorvastatin Calcium by Mechanical Process: Characterization and Stabilization Within Polymeric Matrix

International audienc

Molecular basis of binding and stability of curcumin in diamide-linked y-cyclodextrin dimers

Curcumin is a naturally occurring molecule with medicinal properties that is unstable in water, whose efficacy as a drug can potentially be enhanced by encapsulation inside a host molecule. In this work, the thermodynamics and mechanism of binding of curcumin to succinamide- and urea-linked γ-cyclodextrin (γ-CD) dimers in water are investigated by molecular dynamics simulations. The simulated binding constants of curcumin to succinamide- and urea-linked γ-CD dimers at 310 K are 11.3 × 10⁶ M ⁻¹ and 1.6 × 10⁶ M ⁻¹, respectively, matching well with previous experimental results of 8.7 × 10⁶ M ⁻¹ and 2.0 × 10⁶ M ⁻¹. The simulations reveal structural information about the encapsulation of curcumin inside the diamide-linked γ-CD dimers, with distinct qualitative differences observed for the two dimers. In particular, (1) the predominant orientation of curcumin inside the urea-linked γ-CD dimer is perpendicular to that in the succinamide-linked γ-CD dimer; (2) the magnitude of the angle between the planes of the cyclodextrins is larger for the succinamide-linked γ-CD dimer; and (3) curcumin exhibits greater configurational freedom inside the urea-linked γ-CD dimer. A consequence of some of these structural differences is that the dimer interior is more accessible to water in the succinamide-linked γ-CD dimer. These observations explain the higher stability and lower binding constant observed experimentally for curcumin in the urea-linked cyclodextrin γ-CD dimer compared with the succinamide-linked γ-CD dimer. More generally, the results demonstrate how stability and binding strength can be decoupled and thus separately optimized in host–guest systems used for drug delivery.Samuel J. Wallace, Tak W. Kee, and David M. Huan