Structure-Activity Relationship of Synthetic Linear KTS-Peptides Containing Meta-Aminobenzoic Acid as Antagonists of α1β1 Integrin with Anti-Angiogenic and Melanoma Anti-Tumor Activities.

To develop peptide drugs targeting integrin receptors, synthetic peptide ligands endowed with well-defined selective binding motifs are necessary. The snake venom KTS-containing disintegrins, which selectively block collagen α1β1 integrin, were used as lead compounds for the synthesis and structure-activity relationship of a series of linear peptides containing the KTS-pharmacophore and alternating natural amino acids and 3-aminobenzoic acid (MABA). To ensure a better stiffness and metabolic stability, one, two and three MABA residues, were introduced around the KTS pharmacophore motif.

Statistical analysis of sequential motifs at biologically relevant protein-protein interfaces.

Understanding protein-protein interactions (PPIs) at the molecular level may lead to innovations in medicine and biochemistry. The assumption that there are certain "hot spots" on protein surfaces that mediate their interactions with other proteins has led to a search for specific sequences involved in protein-protein contacts. In this work, we analyze sequential amino acid motifs, both at the single motif and at the motif-motif level, across a large and diverse dataset of biologically relevant protein-protein interfaces retrieved from the PDB, comparing their presence at interfaces and surfaces in a statistically rigorous manner.

Inhibition of AcrAB-TolC enhances antimicrobial activity of phytochemicals in .

Introduction: The eons-long co-evolvement of plants and bacteria led to a plethora of interactions between the two kingdoms, in which bacterial pathogenicity is counteracted by plant-derived antimicrobial defense molecules. In return, efflux pumps (EP) form part of the resistance mechanism employed by bacteria to permit their survival in this hostile chemical environment. In this work we study the effect of combinations of efflux pump inhibitors (EPIs) and plant-derived phytochemicals on bacterial activity using 1692 (Pb1692) as a model system.

A comparison between 2D and 3D descriptors in QSAR modeling based on bio-active conformations.

QSAR models are widely and successfully used in many research areas. The success of such models highly depends on molecular descriptors typically classified as 1D, 2D, 3D, or 4D. While 3D information is likely important, e.

Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments.

Glass fragments found in crime scenes may constitute important forensic evidence when properly analyzed, for example, to determine their origin. This analysis could be greatly helped by having a large and diverse database of glass fragments and by using it for constructing reliable machine learning (ML)-based glass classification models. Ideally, the samples that make up this database should be analyzed by a single accurate and standardized analytical technique.

Towards an Enrichment Optimization Algorithm (EOA)-based Target Specific Docking Functions for Virtual Screening.

Docking-based virtual screening (VS) is a common starting point in many drug discovery projects. While ligand-based approaches may sometimes provide better results, the advantage of docking lies in its ability to provide reliable ligand binding modes and approximated binding free energies, two factors that are important for hit selection and optimization. Most docking programs were developed to be as general as possible and consequently their performances on specific targets may be sub-optimal.

Inter-laboratory workflow for forensic applications: Classification of car glass fragments.

The International Atomic Energy Agency (IAEA) has coordinated a research project titled "Enhancing Nuclear Analytical Techniques to Meet the Needs of Forensics Sciences" (CRP F11021) with the aim of empowering accelerator and reactor based techniques for applications in forensic sciences. One of the key topics of this project was the analysis and classification of forensic glass specimens using Ion Beam Analysis (IBA) techniques and in particular, Particle Induced X-ray Emission (PIXE). To this end, glass fragments from car windows from different car models and manufacturers provided by the Israeli police force were subjected to PIXE measurements at three laboratories to determine their elemental compositions and possible glass corrosion.

A Comparison between Enrichment Optimization Algorithm (EOA)-Based and Docking-Based Virtual Screening.

Virtual screening (VS) is a well-established method in the initial stages of many drug and material design projects. VS is typically performed using structure-based approaches such as molecular docking, or various ligand-based approaches. Most docking tools were designed to be as global as possible, and consequently only require knowledge on the 3D structure of the biotarget.

The Spliced Leader RNA Silencing (SLS) Pathway in Trypanosoma brucei Is Induced by Perturbations of Endoplasmic Reticulum, Golgi Complex, or Mitochondrial Protein Factors: Functional Analysis of SLS-Inducing Kinase PK3.

In the parasite Trypanosoma brucei, the causative agent of human African sleeping sickness, all mRNAs are -spliced to generate a common 5' exon derived from the spliced leader (SL) RNA. Perturbations of protein translocation across the endoplasmic reticulum (ER) induce the spliced leader RNA silencing (SLS) pathway. SLS activation is mediated by a serine-threonine kinase, PK3, which translocates from the cytosolic face of the ER to the nucleus, where it phosphorylates the TATA-binding protein TRF4, leading to the shutoff of SL RNA transcription, followed by induction of programmed cell death.

PIXE based, Machine-Learning (PIXEL) supported workflow for glass fragments classification.

This paper presents a structured workflow for glass fragment analysis based on a combination of Elemental Analysis using PIXE and Machine Learning tools, with the ultimate goal of standardizing and helping forensic efforts. The proposed workflow was implemented on glass fragments received from the Israeli DIFS (Israeli Police Force's Division of Identification and Forensic Sciences) that were collected from various vehicles, including glass fragments from different manufacturers and years of production. We demonstrate that this workflow can produce models with high (>80%) accuracy in identifying glass fragment's origins and provide a test-case demonstrating how the model can be applied in real-life forensic events.

Phloretin, an Apple Phytoalexin, Affects the Virulence and Fitness of by Interfering With Quorum-Sensing.

The effects of phloretin a phytoalexin from apple, was tested on (Pb1692), an emerging soft-rot pathogen of potato. Exposure of Pb1692 to 0.2 mM phloretin a concentration that does not affect growth, or to 0.

The CFTR P67L variant reveals a key role for N-terminal lasso helices in channel folding, maturation, and pharmacologic rescue.

Patients with cystic fibrosis (CF) harboring the P67L variant in the cystic fibrosis transmembrane conductance regulator (CFTR) often exhibit a typical CF phenotype, including severe respiratory compromise. This rare mutation (reported in <300 patients worldwide) responds robustly to CFTR correctors, such as lumacaftor and tezacaftor, with rescue in model systems that far exceed what can be achieved for the archetypical CFTR mutant F508del. However, the specific molecular consequences of the P67L mutation are poorly characterized.

Stability Prediction for Mutations in the Cytosolic Domains of Cystic Fibrosis Transmembrane Conductance Regulator.

Cystic Fibrosis (CF) is caused by mutations to the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) chloride channel. CFTR is composed of two membrane spanning domains, two cytosolic nucleotide-binding domains (NBD1 and NBD2) and a largely unstructured R-domain. Multiple CF-causing mutations reside in the NBDs and some are known to compromise the stability of these domains.

Discovery and Design of Novel Small Molecule GSK-3 Inhibitors Targeting the Substrate Binding Site.

The serine/threonine kinase, GSK-3, is a promising drug discovery target for treating multiple pathological disorders. Most GSK-3 inhibitors that were developed function as ATP competitive inhibitors, with typical limitations in specificity, safety and drug-induced resistance. In contrast, substrate competitive inhibitors (SCIs), are considered highly selective, and more suitable for clinical practice.

Evaluation of QSAR Equations for Virtual Screening.

Quantitative Structure Activity Relationship (QSAR) models can inform on the correlation between activities and structure-based molecular descriptors. This information is important for the understanding of the factors that govern molecular properties and for designing new compounds with favorable properties. Due to the large number of calculate-able descriptors and consequently, the much larger number of descriptors combinations, the derivation of QSAR models could be treated as an optimization problem.

Dynamic Classification for Materials-Informatics: Mining the Solar Cell Space.

The ever-growing data acquisition speed represents a challenge for data analysis in materials sciences in general and the field of solar cells in particular. This is because many unsupervised and supervised learning algorithms require model re-derivation when presented with new samples which are markedly different from those used for model construction. Dynamic segmentation addresses this problem by continuously updating the clusters structure, for example, by splitting old clusters or opening new ones, as new samples are presented.

Phenotypic and molecular characteristics of CF patients carrying the I1234V mutation.

Background: The Mutation I1234V is a CF causing mutation; however the mechanisms leading to loss of function are not fully understood. In this study, we aimed to characterize phenotypically individuals with the I1234V variant, and to gain a structural point of view of the mutant CFTR using computational studies.

Methods: We conducted a retrospective descriptive study, reviewing the clinical records of 9 Israeli patients.

Improving the Potency of -Aryl-2,5-dimethylpyrroles against Multidrug-Resistant and Intracellular Mycobacteria.

A series of -phenyl-2,5-dimethylpyrrole derivatives, designed as hybrids of the antitubercular agents BM212 and SQ109, have been synthesized and evaluated against susceptible and drug-resistant mycobacteria strains. Compound , bearing a cyclohexylmethylene side chain, showed high potency against including MDR-TB strains at submicromolar concentrations. The new compound shows bacteriostatic activity and low toxicity and proved to be effective against intracellular mycobacteria too, showing an activity profile similar to isoniazid.

Direct Binding of Salicylic Acid to -Acyl-Homoserine Lactone Synthase.

Salicylic acid (SA) is a hormone that mediates systemic acquired resistance in plants. We demonstrated that SA can interfere with group behavior and virulence of the soft-rot plant pathogen spp. through quorum sensing (QS) inhibition.

An Ancient CFTR Ortholog Informs Molecular Evolution in ABC Transporters.

The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel central to the development of secretory diarrhea and cystic fibrosis. The oldest CFTR ortholog identified is from dogfish shark, which retains similar structural and functional characteristics to the mammalian protein, thereby highlighting CFTR's critical role in regulating epithelial ion transport in vertebrates. However, the identification of an early CFTR ortholog with altered structure or function would provide critical insight into the evolution of epithelial anion transport.

Structure-activity relationship study of NPP1 inhibitors based on uracil-N1-(methoxy)ethyl-β-phosphate scaffold.

Overexpression of ecto-nucleotide pyrophosphatase-1 (NPP1) is associated with diseases such as calcium pyrophosphate dihydrate deposition disease, calcific aortic valve disease, and type 2 diabetes. In this context, NPP1 inhibitors are potential drug candidates for the treatment of these diseases. The present study focuses on the analysis of the structure-activity relationship of NPP1 inhibitors based on acyclic uracil-nucleotides.

Novel inhibitors of leukocyte transendothelial migration.

Leukocyte transendothelial migration is one of the most important step in launching an inflammatory immune response and chronic inflammation can lead to devastating diseases. Leukocyte migration inhibitors are considered as promising and potentially effective therapeutic agents to treat inflammatory and auto-immune disorders. In this study, based on previous trioxotetrahydropyrimidin based integrin inhibitors that suboptimally blocked leukocyte adhesion, twelve molecules with a modified scaffold were designed, synthesized, and tested in vitro for their capacity to block the transendothelial migration of immune cells.

Nrf2 Activation by SK-119 Attenuates Oxidative Stress, UVB, and LPS-Induced Damage.

Background/aims: The Nrf2 signaling pathway plays a pivotal role in neutralizing excess reactive oxygen species formation and therefore enhancing the endogenous cellular protection mechanism. Thus, activating this pathway may provide therapeutic options against oxidative stress-related disorders. We have recently applied a computer-aided drug design approach to the design and synthesis of novel Nrf2 enhancers.