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Journal of Molecular Recognition: JMR

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https://www.readbyqxmd.com/read/28083885/preparation-of-diclofenac-imprinted-polymer-beads-for-selective-molecular-separation-in-water
#1
Tongchang Zhou, Tripta Kamra, Lei Ye
Molecular imprinting technique is an attractive strategy to prepare materials for target recognition and rapid separation. In this work, a new type of diclofenac (DFC)-imprinted polymer beads was synthesized by Pickering emulsion polymerization using 2-(dimethylamino)ethyl methacrylate as the functional monomer. The selectivity and capacity of the molecularly imprinted polymers (MIPs) were investigated in aqueous solution. Equilibrium binding results show that the MIPs have a high selectivity to bind DFC in a wide range of pH values...
January 13, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28058739/comparative-study-of-the-binding-of-3-flavonoids-to-the-fat-mass-and-obesity-associated-protein-by-spectroscopy-and-molecular-modeling
#2
Lijiao Zhang, Ting Ren, Zechun Wang, Ruiyong Wang, Junbiao Chang
This study aims to investigate the interaction between 3 flavonoids (quercetin, apigenin, and naringenin) and fat mass and obesity-associated protein by fluorescence, ultraviolet-visible absorption spectroscopy, and molecular modeling. Results indicate that the intrinsic fluorescence of fat mass and obesity-associated protein can be quenched by the 3 flavonoids through a static quenching procedure. Thermodynamic analysis and molecular modeling results suggest that hydrophobic interaction and hydrogen bond forces play the major roles in the binding process...
January 6, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28054415/characterizing-the-effect-of-polymyxin-b-antibiotics-to-lipopolysaccharide-on-escherichia%C3%A2-coli-surface-using-atomic-force-microscopy
#3
Yoo Jin Oh, Birgit Plochberger, Markus Rechberger, Peter Hinterdorfer
Lipopolysaccharide (LPS) on gram-negative bacterial outer membranes is the first target for antimicrobial agents, due to their spatial proximity to outer environments of microorganisms. To develop antibacterial compounds with high specificity for LPS binding, the understanding of the molecular nature and their mode of recognition is of key importance. In this study, atomic force microscopy (AFM) and single molecular force spectroscopy were used to characterize the effects of antibiotic polymyxin B (PMB) to the bacterial membrane at the nanoscale...
January 5, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28008676/direct-mapping-of-melanoma-cell-endothelial-cell-interactions
#4
Béla Varga, Csilla Fazakas, Judit Molnár, Imola Wilhelm, Réka A Domokos, István A Krizbai, Zsolt Szegletes, György Váró, Attila G Végh
The most life-threatening aspect of cancer is metastasis; cancer patient mortality is mainly due to metastasis. Among all metastases, presence of brain metastasis is one with the poorest prognosis; the median survival time can be counted in months. Therefore, prevention or decreasing their incidence would be highly desired both by patients and physicians. Metastatic cells invading the brain must breach the cerebral vasculature, primarily the blood-brain barrier. The key step in this process is the establishment of firm adhesion between the cancer cell and the cerebral endothelial layer...
December 23, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28008665/discovery-of-novel-potent-nuclear-factor-kappa-b-inhibitors-ikk-%C3%AE-via-extensive-ligand-based-modeling-and-virtual-screening
#5
Mahmoud A Al-Sha'er, Inas S Almazari, Mutasem O Taha
Inhibitor kappa-B kinase-beta (IKK-β) controls the activation of nuclear transcription factor kappa-B and has been linked to inflammation and cancer. Therefore, inhibitors of this kinase should have potent anti-inflammatory and anticancer properties. Accordingly, we explored the pharmacophoric space of 218 IKK-β inhibitors to identify high-quality binding models. Subsequently, genetic algorithm-based quantitative structure activity relationship (QSAR) analysis was employed to select the best possible combination of pharmacophoric models and physicochemical descriptors that explain bioactivity variation among training compounds...
December 23, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27995655/phenotypic-assays-for-analyses-of-pluripotent-stem-cell-derived-cardiomyocytes
#6
Martin Pesl, Jan Pribyl, Guido Caluori, Vratislav Cmiel, Ivana Acimovic, Sarka Jelinkova, Petr Dvorak, Zdenek Starek, Petr Skladal, Vladimir Rotrekl
Stem cell-derived cardiomyocytes (CMs) hold great hopes for myocardium regeneration because of their ability to produce functional cardiac cells in large quantities. They also hold promise in dissecting the molecular principles involved in heart diseases and also in drug development, owing to their ability to model the diseases using patient-specific human pluripotent stem cell (hPSC)-derived CMs. The CM properties essential for the desired applications are frequently evaluated through morphologic and genotypic screenings...
December 20, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27943449/investigation-and-comparison-of-the-binding-between-tolvaptan-and-pepsin-and-trypsin-multi-spectroscopic-approaches-and-molecular-docking
#7
Xiangling Ma, Jiawei He, Yanmei Huang, Ying Xiao, Qing Wang, Hui Li
Tolvaptan (TF), a selective arginine vasopressin V2 receptor antagonist, was approved by the Food and Drug Administration in 2009. This study mainly investigated the differences between the binding of TF with pepsin and trypsin by using a series of spectroscopy and molecular modeling methods. Thermodynamic parameters and molecular docking results suggested that the binding of TF to pepsin and trypsin were both spontaneous but driven by different forces. For pepsin, the binding was driven by hydrogen bonds and van der Waals forces; but for trypsin, it was driven by electrostatic forces and hydrophobic forces...
December 12, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27933673/a-biophysical-and-computational-study-unraveling-the-molecular-interaction-mechanism-of-a-new-janus-kinase-inhibitor-tofacitinib-with-bovine-serum-albumin
#8
Ali Saber Abdelhameed, Saima Nusrat, Mohammad Rehan Ajmal, Syed Mohammad Zakariya, Masihuz Zaman, Rizwan Hasan Khan
The interaction of a recently certified kinase inhibitor Tofacitinib (TFB) with bovine serum albumin (BSA) has been studied, by spectroscopic and molecular docking studies. Spectrofluorimetric measurements at 3 different temperatures (288, 298, and 310 K) showed that TFB quench the intrinsic fluorescence of BSA upon forming a nonfluorescent complex. The intrinsic fluorescence data showed that TFB binds to BSA with binding constant (Kb ) of approximately 10(4) M(-1) , affirming a significant affinity of TFB with BSA...
December 9, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27921334/synacton-and-individual-activity-of-synthetic-and-natural-corticotropins
#9
T V Vyunova, L A Andreeva, K V Shevchenko, N F Myasoedov
Short endogenous peptides represent one of the most important constituents of the mammalian body's general regulatory system. Some synthesized analogs and modified natural peptides (eg, corticotropins) also show high biological activity. Nevertheless, the mechanism of action of regulatory peptides remains unclear. To explain the effects of peptides of intermolecular processes, the hypothesis that a synactonal mechanism underlies the action of regulatory peptides, exemplified by the heptapeptide Semax, has been proposed...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27921323/the-application-of-strand-invasion-phenomenon-directed-by-peptide-nucleic-acid-pna-and-single-stranded-dna-binding-protein-ssb-for-the-recognition-of-specific-sequences-of-human-endogenous-retroviral-herv-w-family
#10
Grzegorz Machnik, Łukasz Bułdak, Jarosław Ruczyński, Tomasz Gąsior, Małgorzata Huzarska, Dariusz Belowski, Magdalena Alenowicz, Piotr Mucha, Piotr Rekowski, Bogusław Okopień
The HERV-W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV-W-derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin-1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV-W members is highly desirable...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27917590/antichaperone-activity-and-heme-degradation-effect-of-methyl-tert-butyl-ether-mtbe-on-normal-and-diabetic-hemoglobins
#11
Ismaeil Hossein Najdegerami, Parvaneh Maghami, Vahid Sheikh-Hasani, Ghader Hosseinzadeh, Nader Sheibani, Ali A Moosavi-Movahedi
Because of the extensive use of methyl tert-butyl ether (MTBE) as an additive to increase the octane quality of gasoline, the environmental pollution by this compound has increased in recent decades. Environmental release of MTBE may lead to its entry to the blood stream through inhalation or drinking of contaminated water, and its interactions with biological molecules such as proteins. The present study was proposed to comparatively investigate the interactions of MTBE with hemoglobin (Hb) from diabetic and nondiabetic individuals using various spectroscopic methods including UV-visible, fluorescence, chemiluminescence, and circular dichroism...
December 5, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27917540/interaction-of-procarbazine-with-calf-thymus-dna-a-biophysical-and-molecular-docking-study
#12
Razique Anwer, Nazia Ahmad, Khalid I Al Qumaizi, Osama A Al Khamees, Waleed Mohammed Al Shaqha, Tasneem Fatma
Interaction of procarbazine (PCZ) with calf thymus DNA was studied using biophysical and molecular docking studies. Procarbazine was to interact with DNA with a binding constant of 6.52 × 10(3)  M(-1) as calculated using ultraviolet-visible spectroscopy. To find out the binding mode, molecular docking was performed that predicted PCZ to interact with DNA through groove binding mode with binding affinity of -6.7 kcal/mole. To confirm the groove binding nature, different experiments were performed. Dye displacement assays confirmed the non-intercalative binding mode...
December 5, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27891685/the-dna-aptamer-binds-stemness-enriched-cancer-cells-in-pancreatic-cancer
#13
Yoon-Jin Kim, Hee Seung Lee, Dawoon E Jung, Jeong Mi Kim, Si Young Song
Pancreatic cancer remains one of the most common and lethal cancers. Most patients (80%) present with inoperable advanced pancreatic cancer at initial diagnosis, and their early diagnosis is a significant unmet challenge. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). CSCs are responsible not only for the pathogenesis of cancer but also for the heterogeneity, malignant degree, anticancer therapy resistance, and recurrence of tumors...
November 28, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27891677/staurosporine-scaffold-based-rational-discovery-of-the-wild-type-sparing-reversible-inhibitors-of-egfr-t790m-gatekeeper-mutant-in-lung-cancer-with-analog-sensitive-kinase-technology
#14
Xiaoyun Song, Xingcai Liu, Xi Ding
The human epidermal growth factor receptor (EGFR) has been established as an attractive target for lung cancer therapy. However, an acquired EGFR T790M gatekeeper mutation is frequently observed in patients treated with first-line anticancer agents such as gefitinib and erlotinib to cause drug resistance, largely limiting the application of small-molecule kinase inhibitors in EGFR-targeted chemotherapy. Previously, the reversible pan-kinase inhibitor staurosporine and its several analogs such as Gö6976 and K252a have been reported to selectively inhibit the EGFR T790M mutant (EGFR(T790M) ) over wild-type kinase (EGFR(WT) ), suggesting that the staurosporine scaffold is potentially to develop the wild-type sparing reversible inhibitors of EGFR(T790M) ...
November 28, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27885734/simultaneous-determination-of-thermodynamic-and-kinetic-parameters-of-aminopolycarbonate-complexes-of-cobalt-ii-and-nickel-ii-based-on-isothermal-titration-calorimetry-data
#15
Aleksandra Tesmar, Dariusz Wyrzykowski, Eva Muñoz, Bogusław Pilarski, Joanna Pranczk, Dagmara Jacewicz, Lech Chmurzyński
The influence of the different side chain residues on the thermodynamic and kinetic parameters for complexation reactions of the Co(2)(+) and Ni(2)(+) ions has been investigated by using the isothermal titration calorimetry (ITC) technique supported by potentiometric titration data. The study was concerned with the 2 common tripodal aminocarboxylate ligands, namely, nitrilotriacetic acid and N-(2-hydroxyethyl) iminodiacetic acid. Calorimetric measurements (ITC) were run in the 2-(N-morpholino)ethanesulfonic acid hydrate (2-(N-morpholino) ethanesulfonic acid), piperazine-N,N'-bis(2-ethanesulfonic acid), and dimethylarsenic acid buffers (0...
November 25, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27885729/new-biosourced-chiral-molecularly-imprinted-polymer-synthesis-characterization-and-evaluation-of-the-recognition-capacity-of-methyltestosterone
#16
Asma Saadaoui, Corinne Sanglar, Raouf Medimagh, Anne Bonhomme, Robert Baudot, Saber Chatti, Sylvain Marque, Damien Prim, Mongia Saïd Zina, Herve Casabianca
New biosourced chiral cross-linkers were reported for the first time in the synthesis of methyltestosterone (MT) chiral molecularly imprinted polymers (cMIPs). Isosorbide and isomannide, known as 1,4:3,6-dianhydrohexitols, were selected as starting diols. The cMIPs were synthesized following a noncovalent approach via thermal radical polymerization and monitored by Raman spectroscopy. These cross-linkers were fully characterized by (1) H and (13) C nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry...
November 25, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27859846/molecularly-imprinted-core-shell-magnetic-nanoparticles-for-selective-extraction-of-triazines-in-soils
#17
María José Patiño-Ropero, Myriam Díaz-Álvarez, Antonio Martín-Esteban
In this work, a propazine-imprinted polymer was synthesized on the surface of modified magnetic nanoparticles to be used in the solid-phase extraction of triazines in soil samples. The effect of different solvents on the selective extraction of target analytes was assessed to establish the optimum rebinding conditions. The obtained magnetic molecularly imprinted particles exhibited high selectivity for triazines and were easily collected and separated by an external magnetic field without additional centrifugation or filtration steps...
November 18, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27862476/analysis-of-the-binding-loops-configuration-and-surface-adaptation-of-different-crystallized-single-domain-antibodies-in-response-to-various-antigens
#18
Mohammed M Al Qaraghuli, Valerie A Ferro
Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies...
November 16, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27859766/structural-and-molecular-analysis-of-a-protective-epitope-of-lyme-disease-antigen-ospa-and-antibody-interactions
#19
Shivender Shandilya, Nese Kurt Yilmaz, Andrew Sadowski, Ejemel Monir, Zachary A Schiller, William D Thomas, Mark S Klempner, Celia A Schiffer, Yang Wang
The murine monoclonal antibody LA-2 recognizes a clinically protective epitope on outer surface protein (OspA) of Borrelia burgdorferi, the causative agent of Lyme disease in North America. Human antibody equivalence to LA-2 is the best serologic correlate of protective antibody responses following OspA vaccination. Understanding the structural and functional basis of the LA-2 protective epitope is important for developing OspA-based vaccines and discovering prophylactic antibodies against Lyme disease. Here, we present a detailed structure-based analysis of the LA-2/OspA interaction interface and identification of residues mediating antibody recognition...
November 16, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27862500/antibodies-to-h1-histone-from-the-sera-of-hiv-infected-patients-recognize-and-catalyze-site-specific-degradation-of-this-histone
#20
Svetlana V Baranova, Pavel S Dmitrienok, Nikita V Ivanisenko, Valentina N Buneva, Georgy A Nevinsky
Histones and their posttranslational modifications have key roles in chromatin remodeling and gene transcription. Besides intranuclear functions, histones act as damage-associated molecules when they are released into the extracellular space. Administration of histones to animals leads to systemic inflammatory and toxic responses. Autoantibodies with enzymatic activities (abzymes) are distinctive feature of some autoimmune and viral diseases. Electrophoretically and immunologically homogeneous IgGs containing no canonical enzymes were isolated from sera of human immunodeficiency virus-infected patients by chromatography on several affinity sorbents...
November 10, 2016: Journal of Molecular Recognition: JMR
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