Toward quantitative estimates of binding affinities for protein-ligand systems involving large inhibitor compounds: a steered molecular dynamics simulation route.

Understanding binding mechanisms between enzymes and potential inhibitors and quantifying protein-ligand affinities in terms of binding free energy is of primary importance in drug design studies. In this respect, several approaches based on molecular dynamics simulations, often combined with docking techniques, have been exploited to investigate the physicochemical properties of complexes of pharmaceutical interest. Even if the geometric properties of a modeled protein-ligand complex can be well predicted by computational methods, it is still challenging to rank with chemical accuracy a series of ligand analogues in a consistent way. In this article, we face this issue calculating relative binding free energies of a focal adhesion kinase, an important target for the development of anticancer drugs, with pyrrolopyrimidine-based ligands having different inhibitory power. To this aim, we employ steered molecular dynamics simulations combined with nonequilibrium work theorems for free energy calculations. This technique proves very powerful when a series of ligand analogues is considered, allowing one to tackle estimation of protein-ligand relative binding free energies in a reasonable time. In our cases, the calculated binding affinities are comparable with those recovered from experiments by exploiting the Michaelis-Menten mechanism with a competitive inhibitor.

Hydrogenated amorphous silicon high flux x-ray detectors for synchrotron microbeam radiation therapy.

Objective. Microbeam radiation therapy (MRT) is an alternative emerging radiotherapy treatment modality which has demonstrated effective radioresistant tumour control while sparing surrounding healthy tissue in preclinical trials. This apparent selectivity is achieved through MRT combining ultra-high dose rates with micron-scale spatial fractionation of the delivered x-ray treatment field. Quality assurance dosimetry for MRT must therefore overcome a significant challenge, as detectors require both a high dynamic range and a high spatial resolution to perform accurately.Approach. In this work, a series of radiation hard a-Si:H diodes, with different thicknesses and carrier selective contact configurations, have been characterised for x-ray dosimetry and real-time beam monitoring applications in extremely high flux beamlines utilised for MRT at the Australian Synchrotron.Results. These devices displayed superior radiation hardness under constant high dose-rate irradiations on the order of 6000 Gy s-1, with a variation in response of 10% over a delivered dose range of approximately 600 kGy. Dose linearity of each detector to x-rays with a peak energy of 117 keV is reported, with sensitivities ranging from (2.74 ± 0.02) nC/Gy to (4.96 ± 0.02) nC/Gy. For detectors with 0.8µm thick active a-Si:H layer, their operation in an edge-on orientation allows for the reconstruction of micron-size beam profiles (microbeams). The microbeams, with a nominal full-width-half-max of 50µm and a peak-to-peak separation of 400µm, were reconstructed with extreme accuracy. The full-width-half-max was observed as 55 ± 1µm. Evaluation of the peak-to-valley dose ratio and dose-rate dependence of the devices, as well as an x-ray induced charge (XBIC) map of a single pixel is also reported.Significance. These devices based on novel a-Si:H technology possess a unique combination of accurate dosimetric performance and radiation resistance, making them an ideal candidate for x-ray dosimetry in high dose-rate environments such as FLASH and MRT.

High-Resolution Photoemission Study of Neutron-Induced Defects in Amorphous Hydrogenated Silicon Devices.

In this paper, by means of high-resolution photoemission, soft X-ray absorption and atomic force microscopy, we investigate, for the first time, the mechanisms of damaging, induced by neutron source, and recovering (after annealing) of p-i-n detector devices based on hydrogenated amorphous silicon (a-Si:H). This investigation will be performed by mean of high-resolution photoemission, soft X-Ray absorption and atomic force microscopy. Due to dangling bonds, the amorphous silicon is a highly defective material. However, by hydrogenation it is possible to reduce the density of the defect by several orders of magnitude, using hydrogenation and this will allow its usage in radiation detector devices. The investigation of the damage induced by exposure to high energy irradiation and its microscopic origin is fundamental since the amount of defects determine the electronic properties of the a-Si:H. The comparison of the spectroscopic results on bare and irradiated samples shows an increased degree of disorder and a strong reduction of the Si-H bonds after irradiation. After annealing we observe a partial recovering of the Si-H bonds, reducing the disorder in the Si (possibly due to the lowering of the radiation-induced dangling bonds). Moreover, effects in the uppermost coating are also observed by spectroscopies.

Intraoperative Lung Ultrasound (ILU) for the Assessment of Pulmonary Nodules.

BACKGROUND: The primary aim of this study was to confirm the validity of intraoperative lung ultrasound (ILU) as a safe and effective method of localization for difficult to visualize pulmonary nodules during Video-Assisted Thoracoscopic Surgery (VATS) and open thoracotomy. The secondary aim was to enhance knowledge on the morphological patterns of presentation of pulmonary nodules on direct ultrasound examination. MATERIALS AND METHODS: 131 patients with lung nodule and indication for surgery were enrolled. All patients underwent pre-operative imaging of the chest, including Chest Computed Tomography (CT) and Transthoracic Ultrasound (TUS), and surgical procedures for histological assessment of pulmonary nodules (VATS or open thoracotomy). RESULTS: The identification of 100.00% of lung nodules was allowed by ILU, while the detection rate of digital palpation was 94.66%. It was not possible to associate any specific ILU echostructural pattern to both benign or malignant lesions. However, the actual histological margins of the lesions in the operating samples were corresponding to those visualized at ILU in 125/131 (95.42%) cases. No complications have been reported with ILU employment. CONCLUSIONS: In our experience, ILU performed during both open surgery and VATS demonstrated to be a reliable and safe method for visualization and localization of pulmonary nodules non previously assessed on digital palpation. In addition, ILU showed to allow a clear nodule's margins' definition matching, in most cases, with the actual histological margins.

Whole-Transcriptome Analysis Unveils the Synchronized Activities of Genes for Fructans in Developing Tubers of the Jerusalem Artichoke.

Helianthus tuberosus L., known as the Jerusalem artichoke, is a hexaploid plant species, adapted to low-nutrient soils, that accumulates high levels of inulin in its tubers. Inulin is a fructose-based polysaccharide used either as dietary fiber or for the production of bioethanol. Key enzymes involved in inulin biosynthesis are well known. However, the gene networks underpinning tuber development and inulin accumulation in H. tuberous remain elusive. To fill this gap, we selected 6,365 expressed sequence tags (ESTs) from an H. tuberosus library to set up a microarray platform and record their expression across three tuber developmental stages, when rhizomes start enlarging (T0), at maximum tuber elongation rate (T3), and at tuber physiological maturity (Tm), in "VR" and "K8-HS142"clones. The former was selected as an early tuberizing and the latter as a late-tuberizing clone. We quantified inulin and starch levels, and qRT-PCR confirmed the expression of critical genes accounting for inulin biosynthesis. The microarray analysis revealed that the differences in morphological and physiological traits between tubers of the two clones are genetically determined since T0 and that is relatively low the number of differentially expressed ESTs across the stages shared between the clones (93). The expression of ESTs for sucrose:sucrose 1-fructosyltransferase (1-SST) and fructan:fructan 1-fructosyltransferase (1-FFT), the two critical genes for fructans polymerization, resulted to be temporarily synchronized and mirror the progress of inulin accumulation and stretching. The expression of ESTs for starch biosynthesis was insignificant throughout the developmental stages of the clones in line with the negligible level of starch into their mature tubers, where inulin was the dominant polysaccharide. Overall, our study disclosed candidate genes underpinning the development and storage of carbohydrates in the tubers of two H. tuberosus clones. A model according to which the steady-state levels of 1-SST and 1-FFT transcripts are developmentally controlled and might represent a limiting factor for inulin accumulation has been provided. Our finding may have significant repercussions for breeding clones with improved levels of inulin for food and chemical industry.

Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations.

We present a new computational strategy for calculating the absolute binding free energy for protein ligand association in the context of atomistic simulation in explicit solvent. The method is based on an appropriate definition of a solute tempering scheme enforced via Hamilton replica exchange method (HREM). The definition of "solute" includes both the ligand and the active site, with the remainder of the systems defined as "solvent". The hydrophilicity of the solute and the solute torsional plus nonbonded intrasolute interactions are increased and decreased, respectively, along the replica progression, thus favoring the extrusion of the drug form the active site in the scaled states of the generalized ensemble. The proposed technique, named "Energy Driven Undocking" (EDU-HREM), completely bypasses the need for defining and/or identifying the relevant reaction coordinates in a ligand receptor interactions and allows the calculation of the absolute binding free energy in one single generalized simulation of the drug-receptor system. The methodology is applied, with encouraging results, to the calculation of the absolute binding free energy of some FK506-related ligands of the peptidyl prolyl cis-trans isomerase protein (FKBP12) with known dissociation constants. Aspects of the binding/inhibition mechanism in FKBP12 are also analyzed and discussed.

The precise chemical-physical nature of the pharmacore in FK506 binding protein inhibition: ElteX, a New class of nanomolar FKBP12 ligands.

Due to its central role in immunosuppression and cell proliferation and due to its specific peptidyl-prolyl-isomerase (PPI) function, the FKBP protein family is at the crossroad of several important metabolic pathways. Members of this family, and notably FK506 binding protein (FKBP12), are thought to be involved in neurodegenerative diseases such as Alzheimer disease, Parkinson disease, multiple sclerosis, amyotrophic lateral sclerosis, as well as in proliferation disorders and cancer. Using an interdisciplinary approach based on computational, synthetic, and experimental techniques, we show that the best potential binders for FKBP proteins optimally expose the two contiguous carbonyl oxygen in the proline-mimetic chain for FKBP docking and are characterized by the abundance of rigid quasi-cyclic structures stabilized in aqueous solution by intraligand hydrophobic interactions mimicking the macrolide structure of the natural FKBP binders FK506 and Rapamycin. These peculiar structural and chemical-physical features define at the same time an ElteX compound and the minimal pharmacore in the FKBP family, shedding new light on the isomerization mechanism of the PPI domain. On the basis of the above hypothesis, we have successfully designed and synthesized several nanomolar ElteX FKBP12 ligands. Among these, ElteN378 is a new low atomic weight ligand with affinity comparable to that of the macrolide Rapamycin.

Intraligand hydrophobic interactions rationalize drug affinities for peptidyl-prolyl cis-trans isomerase protein.

The conformational landscape of three FK506-related drugs with disparate inhibition constants is determined in bulk solution using a replica exchange simulation method with solute torsional tempering. Energetic fitness of important drug conformations with respect to the FKBP12 protein is evaluated by molecular mechanics. Results show that the experimental affinity toward peptidyl-prolyl cis-trans isomerase protein (FKBP12) of the analyzed ligands appears to be positively correlated to the observed population of specific chair structures of the drug piperidinic ring in bulk solution. This observation is rationalized on the basis that such structures, stabilized by stereospecific intramolecular hydrophobic interactions, allows the formation of a pair of protein-ligand hydrogen bonds upon binding.