Πλοήγηση ανά Θέμα "molecular model"
Αποτελέσματα 1-20 από 23
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Amino acid signatures in the HLA class II peptide-binding region associated with protection/susceptibility to the severe West Nile Virus disease
(2018)The MHC class II region in humans is highly polymorphic. Each MHC molecule is formed by an α and a β chain, produced by different genes, creating an antigen-binding groove. In the groove there are several pockets into which ... -
The architecture of hydrogen and sulfur σ-hole interactions explain differences in the inhibitory potency of C-β-D-glucopyranosyl thiazoles, imidazoles and an N-β-D glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design
(2020)C-Glucopyranosyl imidazoles, thiazoles, and an N-glucopyranosyl tetrazole were assessed in vitro and ex vivo for their inhibitory efficiency against isoforms of glycogen phosphorylase (GP; a validated pharmacological target ... -
Biochemical and in silico identification of the active site and the catalytic mechanism of the circadian deadenylase HESPERIN
(2022)The 24-h molecular clock is based on the stability of rhythmically expressed transcripts. The shortening of the poly(A) tail of mRNAs is often the first and rate-limiting step that determines the lifespan of a mRNA and is ... -
Cell migration leads to spatially distinct but clonally related airway cancer precursors
(2014)Background Squamous cell carcinoma of the lung is a common cancer with 95% mortality at 5 years. These cancers arise from preinvasive lesions, which have a natural history of development progressing through increasing ... -
Computer-simulation-based selection of optimal monomer for imprinting of tri-O-acetyl adenosine in a polymer matrix: calculations for benzene solution
(2016)Molecular imprinting is a promising way to create polymer materials that can be used as artificial receptors, and have anticipated use in synthetic imitation of natural antibodies. In case of successful imprinting, the ... -
Current status and future prospects of small–molecule protein–protein interaction (PPI) inhibitors of tumor necrosis factor (TNF) and receptor activator of NF-κB ligand (RANKL)
(2018)The overexpression of Tumor Necrosis Factor (TNF) is directly related to the development of several autoimmune diseases, such as rheumatoid and psoriatic arthritis, inflammatory bowel disease, Crohn’s disease, refractory ... -
Discovery of Small-Molecule Inhibitors of Receptor Activator of Nuclear Factor-κB Ligand with a Superior Therapeutic Index
(2020)Receptor activator of nuclear factor-κB ligand (RANKL) constitutes the master mediator of osteoclastogenesis, while its pharmaceutical inhibition by a monoclonal antibody has been approved for the treatment of postmenopausal ... -
Evidence for disulfide bonds in SR Protein Kinase 1 (SRPK1) that are required for activity and nuclear localization
(2017)Serine/arginine protein kinases (SRPKs) phosphorylate Arg/Ser dipeptide-containing proteins that play crucial roles in a broad spectrum of basic cellular processes. The existence of a large internal spacer sequence that ... -
Extending hidden Markov models to allow conditioning on previous observations
(2018)Hidden Markov Models (HMMs) are probabilistic models widely used in computational molecular biology. However, the Markovian assumption regarding transition probabilities which dictates that the observed symbol depends only ... -
Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography
(2019)Epimeric series of aryl-substituted glucopyranosylidene-spiro-imidazolinones, an unprecedented new ring system, were synthesized from the corresponding Schiff bases of O-perbenzoylated (gluculopyranosylamine)onamides by ... -
Glycogen phosphorylase revisited: Extending the resolution of the R- And T-state structures of the free enzyme and in complex with allosteric activators
(2021)The crystal structures of free T-state and R-state glycogen phosphorylase (GP) and of R-state GP in complex with the allosteric activators IMP and AMP are reported at improved resolution. GP is a validated pharmaceutical ... -
High consistency of structure-based design and X-ray crystallography: Design, synthesis, kinetic evaluation and crystallographic binding mode determination of biphenyl-n-acyl-β-d-glucopyranosylamines as glycogen phosphorylase inhibitors
(2019)Structure-based design and synthesis of two biphenyl-N-acyl-β-D-glucopyranosylamine derivatives as well as their assessment as inhibitors of human liver glycogen phosphorylase (hlGPa, a pharmaceutical target for type 2 ... -
A multidisciplinary study of 3-(β-D-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors
(2018)3-(β-D-Glucopyranosyl)-5-substituted-1,2,4-triazoles have been revealed as an effective scaffold for the development of potent glycogen phosphorylase (GP) inhibitors but with the potency very sensitive to the nature of the ... -
Nicotinic cholinergic system and COVID-19: In silico evaluation of nicotinic acetylcholine receptor agonists as potential therapeutic interventions
(2021)SARS-CoV-2 infection was announced as a pandemic in March 2020. Since then, several scientists have focused on the low prevalence of smokers among hospitalized COVID-19 patients. These findings led to our hypothesis that ... -
Nicotinic cholinergic system and COVID-19: In silico identification of interactions between α7 nicotinic acetylcholine receptor and the cryptic epitopes of SARS-Co-V and SARS-CoV-2 Spike glycoproteins
(2021)SARS-CoV-2 is the coronavirus that originated in Wuhan in December 2019 and has spread globally. Studies have shown that smokers are less likely to be diagnosed with or be hospitalized for COVID-19 but, once hospitalized, ... -
Predicting alpha helical transmembrane proteins using HMMs
(2017)Alpha helical transmembrane (TM) proteins constitute an important structural class of membrane proteins involved in a wide variety of cellular functions. The prediction of their transmembrane topology, as well as their ... -
Predicting beta barrel transmembrane proteins using HMMs
(2017)Transmembrane beta-barrels (TMBBs) constitute an important structural class of membrane proteins located in the outer membrane of gram-negative bacteria, and in the outer membrane of chloroplasts and mitochondria. They are ... -
Probing the β-pocket of the active site of human liver glycogen phosphorylase with 3-(C-β-D-glucopyranosyl)-5-(4-substituted-phenyl)-1, 2, 4-triazole inhibitors
(2018)Human liver glycogen phosphorylase (hlGP), a key enzyme in glycogen metabolism, is a valid pharmaceutical target for the development of new anti-hyperglycaemic agents for type 2 diabetes. Inhibitor discovery studies have ... -
Rare and common variants in extracellular matrix gene Fibrillin 2 (FBN2) are associated with macular degeneration
(2014)Neurodegenerative diseases affecting the macula constitute amajor cause of incurable vision loss and exhibit considerable clinical and genetic heterogeneity, from early-onset monogenic disease to multifactorial lateonset ... -
Similarity search of flexible 3d molecules combining local and global shape descriptors
(2016)In this paper, a framework for shape-based similarity search of 3D molecular structures is presented. The proposed framework exploits simultaneously the discriminative capabilities of a global, a local, and a hybrid ...