keyword
https://read.qxmd.com/read/38537198/biokc-a-collaborative-platform-for-curation-and-annotation-of-molecular-interactions
#1
JOURNAL ARTICLE
Carlos Vega, Marek Ostaszewski, Valentin Grouès, Reinhard Schneider, Venkata Satagopam
Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in a format suitable for systems biology applications. Importantly, curation should capture the complexity of molecular interactions in such a format together with annotations of the involved elements and support stable identifiers and versioning...
March 27, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38537148/conformation-selection-by-atp-competitive-inhibitors-and-allosteric-communication-in-erk2
#2
JOURNAL ARTICLE
Jake W Anderson, David Vaisar, David N Jones, Laurel M Pegram, Guy P Vigers, Huifen Chen, John G Moffat, Natalie G Ahn
Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named 'L' and 'R,' where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site...
March 27, 2024: ELife
https://read.qxmd.com/read/38536765/autobench-v1-0-benchmarking-automation-for-electronic-structure-calculations
#3
JOURNAL ARTICLE
Rodrigo A Cormanich, Gabriel D da Silva
This work reports on new software for automatic conformer energy benchmarking calculations for flexible molecules. The software workflow consists of four parts: conformational search, preoptimization, optimization, and frequency calculations at a higher level and last calculations using several theoretical levels. The software was written to be user-friendly and versatile to be used by nonexperts in computational chemistry. Any theoretical levels available in either Gaussian 16 or ORCA 5 may be applied in the benchmarking study...
March 27, 2024: Journal of Chemical Information and Modeling
https://read.qxmd.com/read/38536023/tim3-and-ctla4-immune-checkpoint-polymorphisms-are-associated-with-acute-myeloid-leukemia-in-saudi-arabia
#4
JOURNAL ARTICLE
Mashael Alqahtani, Ali Aljuaimlani, Jameel Al-Tamimi, Suliman Alomar, Lamjed Mansour
BACKGROUND: Immune checkpoints are receptors on the surface of T cells that function crucially in suppressing the immune response, and they are implicated in autoimmunity and cancer diseases. AIM: The present study aimed to investigate the relationship between functional single nucleotide polymorphisms (SNPs) of two immune checkpoint molecules, CTLA-4 and TIM-3, and acute myeloid leukemia (AML) in a Saudi population. METHODS: Two SNPs in CTLA-4 (rs231775, A > G) and TIM-3 (rs10515746, A > C) were genotyped in 229 subjects, including 98 patients and 131 healthy controls, from the Saudi population using TaqMan assay methods...
December 2024: Hematology (Amsterdam, Netherlands)
https://read.qxmd.com/read/38536010/hydrophobic-functionalization-of-a-metal-organic-framework-as-an-ammonia-visual-sensing-material-under-high-humidity-conditions
#5
JOURNAL ARTICLE
Yuxin Wang, Zhengxuan Song, Yutao Liu, Yang Chen, Jinping Li, Libo Li, Jia Yao
Since exhaled ammonia (NH3 ) is one of the metabolic markers of liver and kidney diseases, ammonia visual sensing materials in humid environments have received extensive attention and investigation. Herein, through a tailor-made pore environment provided by metal-organic framework (MOF) materials (CH3 -Cu(BDC)), we achieved NH3 anti-interference sensing with apparent color changing under humid conditions. With methyl (CH3 -) functionalization, CH3 -Cu(BDC) demonstrated a strong response for trace ammonia and showed high selectivity under a humid environment...
March 27, 2024: Dalton Transactions: An International Journal of Inorganic Chemistry
https://read.qxmd.com/read/38535995/high-internal-phase-emulsion-for-constructing-chiral-helical-polymer-based-circularly-polarized-luminescent-porous-materials
#6
JOURNAL ARTICLE
Yanan Wang, Hai Zhong, Biao Zhao, Jianping Deng
Polymerized high internal phase emulsions (polyHIPEs) with circularly polarized luminescence (CPL), as an interesting class of porous materials, are of great significance for the development of CPL porous materials but have not been reported so far. Herein, we report the construction of polyHIPE-based CPL porous materials, taking advantage of an adsorption strategy. The pristine polyHIPEs constructed by chiral helical polymers, which acted as a chiral microenvironment, were fabricated by coordination polymerization of chiral acetylene monomers ( R / S -SA) using HIPEs as templates...
March 27, 2024: ACS Applied Materials & Interfaces
https://read.qxmd.com/read/38535991/photocatalytic-conversion-of-co-2-to-co-by-ru-ii-and-os-ii-octahedral-complexes-a-dft-tddft-study
#7
JOURNAL ARTICLE
Athanassios C Tsipis, Antonia A Sarantou
The reaction mechanisms of the photocatalytic reduction of CO2 to CO catalyzed by [(en)M(CO)3 Cl] complexes (M = Ru, Os, en = ethylenediamine) in the presence of triethanolamine (TEOA), R3 N (R = -CH2 CH2 OH), in DCM and DMF solvents, were studied by means of DFT/TDDFT electronic structure calculations. The geometric and free energy reaction profiles for two possible reaction pathways were calculated. Both reaction pathways studied, start with the 17e- , catalytically active intermediate, [(en)M(CO)3 ]˙+ generated from the first triplet excited state, T1 upon reductive quenching by TEOA which acts as a sacrificial electron donor...
March 27, 2024: Dalton Transactions: An International Journal of Inorganic Chemistry
https://read.qxmd.com/read/38535698/short-chain-sulfur-confined-into-nitrogen-doped-hollow-carbon-nanospheres-for-high-capacity-potassium-storage
#8
JOURNAL ARTICLE
Wenhan Liu, Tengfei Shi, Fang Liu, Chen Yang, Fan Qiao, Kang Han, Chunhua Han, Jiashen Meng, Xuanpeng Wang
Carbon-based materials are one of the ideal negative electrode materials for potassium ion batteries. However, the limited active sites and sluggish diffusion ion kinetics still hinder its commercialization process. To address these problems, we design a novel carbon composite anode, by confining highly reactive short-chain sulfur molecules into nitrogen-doped hollow carbon nanospheres (termed SHC-450). The formation process involves the controlled synthesis of hollow polyaniline (PANI) nanospheres as precursors via an Ostwald ripening mechanism and subsequent sulfuration treatment...
March 20, 2024: Nanomaterials
https://read.qxmd.com/read/38535621/emerging-trends-in-pathophysiology-insights-from-the-9th-international-congress-of-the-international-society-for-pathophysiology-isp-2023
#9
Anatolii Kubyshkin, Sergey Bolevich, Leonid Churilov, Vladimir Jakovljevic, Evgeniia Kovalenko, Aleksandr Korovin
This article provides a summary of the 9th International Congress of the International Society for Pathophysiology (ISP 2023) which took place in Belgrade, Serbia, from 4 to 6 July 2023. It describes the main trends and the most promising areas of research in current pathophysiology, including investigations of new pathogenic pathways, and the identification of cellular and molecular mechanisms, target molecules, genetic mechanisms, and new therapeutic strategies. The present article also highlights the research conducted by leading scientific teams and national pathophysiological societies from various countries that adds to our understanding of the pathogenesis of diseases and pathological processes...
March 4, 2024: Pathophysiology: the Official Journal of the International Society for Pathophysiology
https://read.qxmd.com/read/38535474/novel-1-3-4-thiadiazole-3-2-a-pyrimidin-5-ones-as-promising-biofilm-dispersal-agents-against-relevant-gram-positive-and-gram-negative-pathogens
#10
JOURNAL ARTICLE
Daniela Carbone, Camilla Pecoraro, Fabio Scianò, Valentina Catania, Domenico Schillaci, Barbara Manachini, Stella Cascioferro, Patrizia Diana, Barbara Parrino
Biofilm-associated infections pose significant challenges in healthcare settings due to their resistance to conventional antimicrobial therapies. In the last decade, the marine environment has been a precious source of bioactive molecules, including numerous derivatives with antibiofilm activity. In this study, we reported the synthesis and the biological evaluation of a new series of twenty-two thiadiazopyrimidinone derivatives obtained by using a hybridization approach combining relevant chemical features of two important classes of marine compounds: nortopsentin analogues and Essramycin derivatives...
March 15, 2024: Marine Drugs
https://read.qxmd.com/read/38535467/current-status-of-indole-derived-marine-natural-products-synthetic-approaches-and-therapeutic-applications
#11
REVIEW
Sergio Fernández, Virginia Arnáiz, Daniel Rufo, Yolanda Arroyo
Indole is a versatile pharmacophore widely distributed in bioactive natural products. This privileged scaffold has been found in a variety of molecules isolated from marine organisms such as algae and sponges. Among these, indole alkaloids represent one of the biggest, most promising family of compounds, having shown a wide range of pharmacological properties including anti-inflammatory, antiviral, and anticancer activities. The aim of this review is to show the current scenario of marine indole alkaloid derivatives, covering not only the most common chemical structures but also their promising therapeutic applications as well as the new general synthetic routes developed during the last years...
March 6, 2024: Marine Drugs
https://read.qxmd.com/read/38535442/natural-products-derived-from-marine-sponges-with-antitumor-potential-against-lung-cancer-a-systematic-review
#12
REVIEW
Alba Ortigosa-Palomo, Francisco Quiñonero, Raul Ortiz, Francisco Sarabia, Jose Prados, Consolación Melguizo
Non-small-cell lung cancer (NSCLC), the most commonly diagnosed cancer and the leading cause of cancer-related death worldwide, has been extensively investigated in the last decade in terms of developing new therapeutic options that increase patient survival. In this context, marine animals are a source of new, interesting bioactive molecules that have been applied to the treatment of different types of cancer. Many efforts have been made to search for new therapeutic strategies to improve the prognosis of lung cancer patients, including new bioactive compounds and cytotoxic drugs from marine sponges...
February 23, 2024: Marine Drugs
https://read.qxmd.com/read/38535286/numerical-simulation-of-mass-transfer-in-hollow-fiber-membrane-module-for-membrane-based-artificial-organs
#13
JOURNAL ARTICLE
Ziheng Wang, Shaofeng Xu, Yifan Yu, Wei Zhang, Xuechang Zhang
The mass transfer behavior in a hollow fiber membrane module of membrane-based artificial organs (such as artificial liver or artificial kidney) were studied by numerical simulation. A new computational fluid dynamics (CFD) method coupled with K-K equation and the tortuous capillary pore diffusion model (TCPDM) was proposed for the simulations. The urea clearance rate predicted by the use of the numerical model agrees well with the experimental data, which verifies the validity of our numerical model. The distributions of concentration, pressure, and velocity in the hollow fiber membrane module were obtained to analyze the mass transfer behaviors of bilirubin and bovine serum albumin (BSA), and the effects of tube-side flow rate, shell-side flow rate, and fiber tube length on the bilirubin or BSA clearance rate were studied...
March 10, 2024: Membranes
https://read.qxmd.com/read/38535180/innovations-in-antifungal-drug-discovery-among-cell-envelope-synthesis-enzymes-through-structural-insights
#14
REVIEW
Yue Zhou, Todd B Reynolds
Life-threatening systemic fungal infections occur in immunocompromised patients at an alarming rate. Current antifungal therapies face challenges like drug resistance and patient toxicity, emphasizing the need for new treatments. Membrane-bound enzymes account for a large proportion of current and potential antifungal targets, especially ones that contribute to cell wall and cell membrane biosynthesis. Moreover, structural biology has led to a better understanding of the mechanisms by which these enzymes synthesize their products, as well as the mechanism of action for some antifungals...
February 22, 2024: Journal of Fungi (Basel, Switzerland)
https://read.qxmd.com/read/38534886/drug-drug-interactions-of-fxi-inhibitors-clinical-relevance
#15
REVIEW
Nicola Ferri, Elisa Colombo, Alberto Corsini
Inhibitors of the factor FXI represent a new class of anticoagulant agents that are facing clinical approval for the treatment of acute coronary syndrome (ACS), venous thromboembolism (VTE), and stroke prevention of atrial fibrillation (AF). These new inhibitors include chemical small molecules (asundexian and milvexian), monoclonal antibodies (abelacimab, osocimab, and xisomab), and antisense oligonucleotides (IONIS-FXIRX and fesomersen), and thus, they have very peculiar and different pharmacokinetic and pharmacodynamic properties...
March 21, 2024: Hematology Reports
https://read.qxmd.com/read/38534687/navigating-the-chemical-space-of-enr-inhibitors-a-comprehensive-analysis
#16
JOURNAL ARTICLE
Vid Kuralt, Rok Frlan
Antimicrobial resistance is a global health threat that requires innovative strategies against drug-resistant bacteria. Our study focuses on enoyl-acyl carrier protein reductases (ENRs), in particular FabI, FabK, FabV, and InhA, as potential antimicrobial agents. Despite their promising potential, the lack of clinical approvals for inhibitors such as triclosan and isoniazid underscores the challenges in achieving preclinical success. In our study, we curated and analyzed a dataset of 1412 small molecules recognized as ENR inhibitors, investigating different structural variants...
March 11, 2024: Antibiotics
https://read.qxmd.com/read/38534647/synthesis-and-characterization-of-new-n-acyl-hydrazone-derivatives-of-carprofen-as-potential-tuberculostatic-agents
#17
JOURNAL ARTICLE
Ilinca Margareta Vlad, Diana Camelia Nuță, Miron Theodor Căproiu, Florea Dumitrașcu, Eleonóra Kapronczai, Georgiana Ramona Mük, Speranta Avram, Adelina Gabriela Niculescu, Irina Zarafu, Vanesa Alexandra Ciorobescu, Ana Maria Brezeanu, Carmen Limban
N-acyl hydrazone (NAH) is recognized as a promising framework in drug design due to its versatility, straightforward synthesis, and attractive range of biological activities, including antimicrobial, antitumoral, analgesic, and anti-inflammatory properties. In the global context of increasing resistance of pathogenic bacteria to antibiotics, NAHs represent potential solutions for developing improved treatment alternatives. Therefore, this research introduces six novel derivatives of ( EZ )-N'-benzylidene-2-(6-chloro-9 H -carbazol-2-yl)propanehydrazide, synthesized using a microwave-assisted method...
February 23, 2024: Antibiotics
https://read.qxmd.com/read/38534407/rna-interference-in-insects-from-a-natural-mechanism-of-gene-expression-regulation-to-a-biotechnological-crop-protection-promise
#18
REVIEW
Beltrán Ortolá, José-Antonio Daròs
Insect pests rank among the major limiting factors in agricultural production worldwide. In addition to direct effect on crops, some phytophagous insects are efficient vectors for plant disease transmission. Large amounts of conventional insecticides are required to secure food production worldwide, with a high impact on the economy and environment, particularly when beneficial insects are also affected by chemicals that frequently lack the desired specificity. RNA interference (RNAi) is a natural mechanism gene expression regulation and protection against exogenous and endogenous genetic elements present in most eukaryotes, including insects...
February 21, 2024: Biology
https://read.qxmd.com/read/38534362/repurposing-drugs-for-senotherapeutic-effect-potential-senomorphic-effects-of-female-synthetic-hormones
#19
JOURNAL ARTICLE
Laura R Bramwell, Ryan Frankum, Lorna W Harries
Repurposing previously approved drugs may fast track the route to the clinic for potential senotherapeutics and improves the inefficiency of the clinical drug development pipeline. We performed a repurposing screen of 240 clinically approved molecules in human primary dermal fibroblasts for their effects on CDKN2A expression. Molecules demonstrating effects on CDKN2A expression underwent secondary screening for senescence-associated beta galactosidase (SAB) activity, based on effect size, direction, and/or molecule identity...
March 15, 2024: Cells
https://read.qxmd.com/read/38534324/functional-selectivity-of-cannabinoid-type-1-g-protein-coupled-receptor-agonists-in-transactivating-glycosylated-receptors-on-cancer-cells-to-induce-epithelial-mesenchymal-transition-metastatic-phenotype
#20
JOURNAL ARTICLE
David A Bunsick, Jenna Matsukubo, Rashelle Aldbai, Leili Baghaie, Myron R Szewczuk
Understanding the role of biased G protein-coupled receptor (GPCR) agonism in receptor signaling may provide novel insights into the opposing effects mediated by cannabinoids, particularly in cancer and cancer metastasis. GPCRs can have more than one active state, a phenomenon called either 'biased agonism', 'functional selectivity', or 'ligand-directed signaling'. However, there are increasing arrays of cannabinoid allosteric ligands with different degrees of modulation, called 'biased modulation', that can vary dramatically in a probe- and pathway-specific manner, not from simple differences in orthosteric ligand efficacy or stimulus-response coupling...
March 8, 2024: Cells
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