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Journal of Molecular Recognition: JMR

Vanessa R A Ferreira, Manuel A Azenha, M Teresa Mêna, Cosme Moura, Carlos M Pereira, Ricardo I Pérez-Martín, José A Vázquez, A Fernando Silva
Imprinting chondroitin sulfate (CS)/silica composites with Pb(II) and Cu(II) cations was explored with CS of bovine and different fish species origin. The process was based on the assumption that particular arrangements of the linear CS chains in aqueous solution, induced so as to accommodate cross complexation with the cations, would be embodied into a tridimensional matrix created through an organoalkoxysilane sol-gel scheme. The presence of Cu(II) in the synthesis of the composites did not result in the production of significantly stronger Cu(II)-oriented binding arrangements, and therefore, the imprinting was not successful...
February 3, 2017: Journal of Molecular Recognition: JMR
Guangxin Liu, Pei Wang, Chan Li, Jing Wang, Zhenyu Sun, Xinfeng Zhao, Xiaohui Zheng
Drug-protein interaction analysis is pregnant in designing new leads during drug discovery. We prepared the stationary phase containing immobilized β2 -adrenoceptor (β2 -AR) by linkage of the receptor on macroporous silica gel surface through N,N'-carbonyldiimidazole method. The stationary phase was applied in identifying antiasthmatic target of protopine guided by the prediction of site-directed molecular docking. Subsequent application of immobilized β2 -AR in exploring the binding of protopine to the receptor was realized by frontal analysis and injection amount-dependent method...
January 26, 2017: Journal of Molecular Recognition: JMR
Yves Claude Guillaume, Claire André
TRAIL is a member of the tumor necrosis factor family of cytokines, which induces apoptosis of cancer cells, thanks to its binding to its cognate receptors DR5 and DR4. We have recently demonstrated that nanovectorization of TRAIL with single-walled carbon nanotubes enhanced TRAIL affinity to DR5. In this paper, 1-pyrenebutyric acid N-hydroxysuccinimide ester functionalized boron nitride nanotubes (BNNTs) were used to anchor the TRAIL protein. The resulting BNNT/1-pyrenebutyric acid N-hydroxysuccinimide ester nanotubes were mixed with methoxy-poly(ethylene glycol)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-conjugates so as to allow a good dispersion of these nanoparticle TRAIL (NPT) in aqueous solution...
January 25, 2017: Journal of Molecular Recognition: JMR
B Zapotoczny, K Owczarczyk, K Szafranska, E Kus, S Chlopicki, M Szymonski
Liver sinusoidal endothelial cells (LSECs) represent unique type of endothelial cells featured by their characteristic morphology, ie, lack of a basement membrane and presence of fenestrations-transmembrane pores acting as a dynamic filter between the vascular space and the liver parenchyma. Delicate structure of LSECs membrane combined with a submicron size of fenestrations hinders their visualization in live cells. In this work, we apply atomic force microscopy contact mode to characterize fenestrations in LSECs...
January 25, 2017: Journal of Molecular Recognition: JMR
Jacob J Terracina, Susan T Sharfstein, Magnus Bergkvist
A 2-step molecular mechanical and quantum mechanical geometry optimization scheme (MM ➔ QM) was used to "computationally imprint" chiral molecules. Using a docking technique, we show the imprinted binding sites to exhibit an enantioselective preference for the imprinted molecule over its enantiomer. Docking of structurally similar chiral molecules showed that the sites computationally imprinted with R- or S-tBOC-tyrosine were able to differentiate between R- and S-forms of other tyrosine derivatives. The cross-enantioselectivity did not hold for chiral molecules that did not share the tyrosine H-bonding functional group orientations...
January 25, 2017: Journal of Molecular Recognition: JMR
Rami Yankelov, Irena Yungerman, Simcha Srebnik
Polymer-based protein recognition systems have enormous potential within clinical and diagnostic fields due to their reusability, biocompatibility, ease of manufacturing, and potential specificity. Imprinted polymer matrices have been extensively studied and applied as a simple technique for creating artificial polymer-based recognition gels for a target molecule. Although this technique has been proven effective when targeting small molecules (such as drugs), imprinting of proteins have so far resulted in materials with limited selectivity due to the large molecular size of the protein and aqueous environment...
January 23, 2017: Journal of Molecular Recognition: JMR
Somnath Das, Md Maidul Islam, Gopal Chandra Jana, Anirudha Patra, Pradeep K Jha, Maidul Hossain
In this paper, the comparative binding behavior of antimalarial drug azure A, azure B and azure C with bovine serum albumin (BSA) has been studied. The interaction has been confirmed by multispectroscopic (UV, fluorescence, Fourier transform infrared (FT-IR), and circular dichroism) and molecular docking techniques. The experimental results show that azure B has the highest BSA binding affinity followed by azure A and azure C. The experimental evidence of binding showed a static quenching mechanism in the interaction azures with BSA...
January 19, 2017: Journal of Molecular Recognition: JMR
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
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
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
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
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
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
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
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
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
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
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
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
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
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