DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for Docking and Molecular Dynamics analysis.

Abstract Motivation The ligand/protein binding interaction is typically investigated by docking and molecular dynamics (MD) simulations. In particular, docking-based virtual screening (VS) is used to select the best ligands from database of thousands of compounds, while MD calculations assess the energy stability of the ligand/protein binding complexes. Considering the broad use of these techniques, it is of great demand to have one single software that allows a combined and fast analysis of VS and MD results. With this in mind, we have developed the Drug Discovery Tool (DDT) that is an intuitive graphics user interface able to provide structural data and physico-chemical information on the ligand/protein interaction. Results DDT is designed as a plugin for the Visual Molecular Dynamics (VMD) software and is able to manage a large number of ligand/protein complexes obtained from AutoDock4 (AD4) docking calculations and MD simulations. DDT delivers four main outcomes: i) ligands ranking based on an energy score; ii) ligand ranking based on a ligands' conformation cluster analysis; iii) identification of the aminoacids forming the most occurrent interactions with the ligands; iv) plot of the ligands' center-of-mass coordinates in the Cartesian space. The flexibility of the software allows saving the best ligand/protein complexes using a number of user-defined options. Availability and implementation DDT_site_1 (alternative DDT_site_2); the DDT tutorial movie is available here. Supplementary information Supplementary data are available at Bioinformatics online

Retrograde Positive Contrast Urethrocystography of the Fish Urogenital System

The radiological differences between the urinary tract of  Dicentrarchus labrax, Sparus aurata, Tinca tinca, and Cyprinus carpio are shown. In fresh water teleosts the urinary bladder is sigmoid and a short urethra leads to the urinary pore. Genital and anal pores are present. In Sparus aurata the urinary bladder has a globoid shape. In Dicentrarchus labrax the urinary bladder is smaller and elongate. In both marine teleosts a single urogenital pore is visible. Positive contrast was used to survey the urogenital system and evaluate shape and size of the bladder, urethra, ureter, and gonadal ducts. Results demonstrate the morphological variability of the urinary bladder and the craniodorsal entry of the ureters into the bladder. It is envisaged that this work will provide baseline information for further imaging studies for investigating the urogenital morphology and can be applied to identify disorders in fishes. Furthermore, the main interest of this study is that it demonstrates the morphological variability of the lower urinary system that exists between different species of fishes

A literature review of hypertensive retinopathy: systemic correlations and new technologies

OBJECTIVE: Hypertensive retinopathy (HR) is the most common ocular manifestation of systemic arterial hypertension. This paper aims to summarize the current knowledge of HR, reviewing its classical features, such as epidemiology, pathophysiology, clinical manifestations, classifications, management and the most significant systemic correlations. We also provide an update on the latest advances in new technologies focusing on novel instrumental classifications. MATERIALS AND METHODS: A literature search was performed to identify articles regarding HR listed in Embase, PubMed, Medline (Ovid) and Scopus database up to 1 December 2021. The reference lists of the analyzed articles were also considered a source of literature information. The following keywords were used in various combinations: hypertensive retinopathy, hypertension and eye, hypertensive retinopathy and systemic correlations, optical coherence tomography (OCT) and hypertensive retinopathy, optical coherence tomography angiography (OCTA) and hypertensive retinopathy, adaptive optics (AO) and hypertensive retinopathy. The authors analyzed all English articles found using the aforementioned Keywords. All the publications were thoroughly reviewed to create a detailed overview of this issue. RESULTS: HR signs have a significative association with cardiovascular, cerebrovascular and other systemic diseases. Patients with arteriosclerotic changes and, at the same time, severe HR, are at increased risk for coronary disease, peripheral vascular disease, stroke and dementia. HR is even now diagnosed and classified by its clinical appearance on a fundoscopic exam that is limited by interobserver variability. New technologies, like OCT, OCTA, AO and artificial intelligence may be used to develop a new instrumental classification that could become an objective and quantitative method for the evaluation of this disease. They could be useful to evaluate the subclinical retinal microvascular changes due to hypertension that may reflect the involvement of other vital organs. CONCLUSIONS: The eye is the only organ in the human body where changes in the blood vessels due to systemic hypertension can be studied in vivo. All doctors should be familiar with this disease because it has been largely demonstrated that signs of HR are correlated to patient’s health and mortality. Researchers should develop a new common, standardized, and objective method to assess hypertensive retinal changes; new technologies may have a significant role in this field. This review takes most of the literature published so far, including the OCTA studies in order to stimulate new points of reference to standardize parameters and new diagnostic markers of this disease

Evidence of Presynaptic Localization and Function of the c-Jun N-Terminal Kinase

The c-Jun N-terminal kinase (JNK) is part of a stress signalling pathway strongly activated by NMDA-stimulation and involved in synaptic plasticity. Many studies have been focused on the post-synaptic mechanism of JNK action, and less is known about JNK presynaptic localization and its physiological role at this site. Here we examined whether JNK is present at the presynaptic site and its activity after presynaptic NMDA receptors stimulation. By using N-SIM Structured Super Resolution Microscopy as well as biochemical approaches, we demonstrated that presynaptic fractions contained significant amount of JNK protein and its activated form. By means of modelling design, we found that JNK, via the JBD domain, acts as a physiological effector on T-SNARE proteins; then using biochemical approaches we demonstrated the interaction between Syntaxin-1-JNK, Syntaxin-2-JNK, and Snap25-JNK. In addition, taking advance of the specific JNK inhibitor peptide, D-JNKI1, we defined JNK action on the SNARE complex formation. Finally, electrophysiological recordings confirmed the role of JNK in the presynaptic modulation of vesicle release. These data suggest that JNK-dependent phosphorylation of T-SNARE proteins may have an important functional role in synaptic plasticity

Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation

SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that the globally invasive G614 spike variant i) underwent a significant demographic expansion in most countries not explained by stochastic effects nor by overrepresentation in clinical samples; ii) increases the spike S1/S2 furin-like site conformational plasticity (short-range effect), and iii) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our results support the hypothesis of a selective advantage at the basis of the spread of the G614 variant, which we suggest may be due to structural modification of the spike protein at the S1/S2 proteolytic site, and provides structural information to guide the design of variant-specific drugs

Enhancing a Transition to a Circular Economy in the Water Sector: The EU Project WIDER UPTAKE

Wastewater treatment plants (WWTPs) require an urgent transition from a linear to a circular economy operation/design concept with a consequent resource recovery and more sustainable waste management. Natural resources have to be preserved, and wastes have to become an opportunity for recovering resources and materials (water reuse, energy, sludge reuse). However, the transition toward a circular economy is a complex and long process due to the existence of technical, economic, social and regulatory barriers. These existing barriers are critical challenges for a modern and sustainable WWTP concept. The recovery of resources must be considered a strategic target from the earliest process-design phase. In this context, the European Union’s Horizon 2020 project “Achieving wider uptake of water-smart solutions—WIDER UPTAKE” aims to overcome the existing barriers (technological, regulatory, organizational, social and economic) toward the transition from a linear to a circular economy model for WWTPs. This study is aimed at increasing the awareness of the existing barriers to a circular economy and summarizes the key contributions of the WIDER UPTAKE project in terms of water reuse, sludge reuse and nutrient recovery

Genomic landscape and survival analysis of ctDNA “neo-RAS wild-type” patients with originally RAS mutant metastatic colorectal cancer

Background: The term “neo-RAS wild-type” refers to the switch to RAS wild-type disease in plasma circulating tumor DNA (ctDNA) from originally RAS mutant colorectal cancers. Consistently, the hypothesis to re-determine RAS mutational status in ctDNA at disease progression in RAS mutant mCRC opened to a new perspective for clinically-based selection of patients to be treated with EGFR inhibitors. Currently, the genomic landscape of “neo-RAS wild-type” is unknown. This is a prospective study aimed to investigate clinical and genomic features associated with RAS mutation clearance in a large cohort of RAS mutant mCRC patients who converted to RAS wild- type in liquid biopsy at failure of first-line treatments. Secondary aim was to investigate the long term prognostic significance of “true neo-RAS wild- type”. Patients and methods: 70 patients with stage IV RAS mutant colorectal cancer were prospectively enrolled. Plasma samples were collected at progression from first-line treatment. RAS/BRAF mutations in plasma were assessed by RT-PCR. In RAS/BRAF wild-type samples, ctDNA was used to generate libraries using a 17 genes panel whose alteration has clinical relevance. To investigate the prognostic significance of RAS mutation clearance, test curves for PFS and OS were represented by Kaplan-Meier estimator plot and Log-rank test. Results: The most commonly detected actionable mutations in “neo-RAS wild-type” were: PIK3CA (35.7%); RET (11.9%); IDH1 (9.5%); KIT (7%); EGFR (7%); MET (4.7%); ERBB2 (4.7%); FGFR3 (4.7%). Both OS and post-progression survival were longer in patients with “neo-RAS wild-type” compared to those who remained RAS mutant (p<0.001 for both). Conclusions: De-novo-targetable mutations occured in a large percentage of “neo-RAS wild-type”, being PIK3CA the most commonly detected. RAS mutation clearance in ctDNA is associated with long- term improvement of overall survival

CAP2 dimerization regulates cofilin in synaptic plasticity and Alzheimer's disease

Abstract Regulation of actin cytoskeleton dynamics in dendritic spines is crucial for learning and memory formation. Hence, defects in the actin cytoskeleton pathways are a biological trait of several brain diseases, including Alzheimer's Disease. Here, we describe a novel synaptic mechanism governed by the cyclase-associated protein 2 (CAP2), which is required for structural plasticity phenomena and completely disrupted in Alzheimer's Disease. We report that the formation of CAP2 dimers through its Cys32 is important for CAP2 binding to cofilin and for actin turnover. The Cys32-dependent CAP2 homodimerization and association to cofilin are triggered by long-term potentiation and are required for long-term potentiation-induced cofilin translocation into spines, spine remodelling and the potentiation of synaptic transmission. This mechanism is specifically affected in the hippocampus, but not in the superior frontal gyrus, of both Alzheimer's Disease patients and APP/PS1 mice, where CAP2 is down-regulated and CAP2 dimer synaptic levels are reduced. Notably, CAP2 levels in the cerebrospinal fluid are significantly increased in Alzheimer's Disease patients but not in subjects affected by frontotemporal dementia. In Alzheimer's Disease hippocampi, cofilin association to CAP2 dimer/monomer is altered and cofilin is aberrantly localized in spines. Taken together, these results provide novel insights into structural plasticity mechanisms that are defective in Alzheimer's Disease

Constrained Spherical Deconvolution Tractography reveals a direct cerebello-ventro tegmental pathway in humans

Introduction. In addition to its role in motor control, reflex adaption and motor learning in the past years numerous studies demonstrated the role of the cerebellum in non-motor functions. Furthermore, lesional animal and neuroimaging in vivo human studies demonstrated connections of the cerebellum with brain regions involved in cognitive, emotional, motivation linguistic processing [1, 2]. Although, studies suggest the role of the cerebellum in neuropsychiatric disorders of the mesocorticolimbic structure (i.e. schizophrenia), at the present time the existence cerebello-ventro tegmental pathway has been demonstrated in only in rodents and only hypothesized in humans. Aim. The goal of this in vivo constrained spherical deconvolution (CSD) tractography study is the investigation on the presence of a direct cerebello-ventro tegmental pathway in the human brain. Material and Methods. We recruited 15 human subjects with no previous history of neurological or psychiatric disorders. The entire study was performed using a 3T Achieva Philips scanner; a SENSE 8 channels head coil, acquiring T1 weighted 3D TFE, DTI sequence; data were analyzed by using constrained spherical deconvolution techniques (CDS). Results. We demonstrated with CSD dentate-ventral midbrain connections. In particular, we found a direct route linking between the dentate nucleus and the ventro tegmental area. Conclusions. This study provides for the first time the existence of a human dentate nucleus connections with the ventro tegmental area, moreover the existence of this cerebello-midbrain pathway suggest that the cerebellum may be involved in the modulation of the mesocorticolimbic system and in related neuropsychiatric disorders such as the schizophrenia

Investigation into the Use of Encorafenib to Develop Potential PROTACs Directed against BRAFV600E Protein

BRAF is a serine/threonine kinase frequently mutated in human cancers. BRAF(V600E) mutated protein is targeted through the use of kinase inhibitors which are approved for the treatment of melanoma; however, their long-term efficacy is hampered by resistance mechanisms. The PROTAC-induced degradation of BRAF(V600E) has been proposed as an alternative strategy to avoid the onset of resistance. In this study, we designed a series of compounds where the BRAF kinase inhibitor encorafenib was conjugated to pomalidomide through different linkers. The synthesized compounds maintained their ability to inhibit the kinase activity of mutated BRAF with IC(50) values in the 40–88 nM range. Selected compounds inhibited BRAF(V600E) signaling and cellular proliferation of A375 and Colo205 tumor cell lines. Compounds 10 and 11, the most active of the series, were not able to induce degradation of mutated BRAF. Docking and molecular dynamic studies, conducted in comparison with the efficient BRAF degrader P5B, suggest that a different orientation of the linker bearing the pomalidomide substructure, together with a decreased mobility of the solvent-exposed part of the conjugates, could explain this behavior