scholarly journals Study of the binding mechanisms between palytoxin and its aptamer by docking and molecular simulation

2018 ◽  
Author(s):  
Bo Hu ◽  
Rong Zhou ◽  
Zhengang Li ◽  
Jiaxiang Qin ◽  
Shengqun Ouyang ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Specific Binding ◽  
Interaction Mechanism ◽  
Computational Results ◽  
Therapeutic Application ◽  
High Affinity ◽  
Ssdna Aptamer ◽  
Molecular Structure Analysis ◽  
Binding Mechanisms

This paper provides a feasible model for aptamer and its target in molecular structure analysis and interaction mechanism. In this study, modeling and dynamic simulation of ssDNA aptamer (P-18S2) and target (Palytoxin,PTX) were performed separately. Then, the combination mechanism of DNA and PTX were predicted, and docking results showed that PTX can combine steadily in the groove at the top of DNA model trough strong hydrogen-bonds and electrostatic interaction. Therefore, we have further truncated and optimized to P-18S2 by simulating, at the same time, we also confirmed the reliability of simulative results by experimenting. Combining with the experimental and computational results, we provide a more reasonable interpretation for the high affinity and specific binding of P-18S2 and PTX and offer the basis for aptamer development in molecular diagnostics and therapeutic application.

scholarly journals Study of the binding mechanism of aptamer to palytoxin by docking and molecular simulation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bo Hu ◽  
Rong Zhou ◽  
Zhengang Li ◽  
Shengqun Ouyang ◽  
Zhen Li ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Specific Binding ◽  
Complex Structure ◽  
Interaction Mechanism ◽  
Computational Results ◽  
Binding Mechanism ◽  
High Affinity ◽  
Ssdna Aptamer ◽  
Simulation Results ◽  
Molecular Structure Analysis

Abstract This paper provides a feasible model for molecular structure analysis and interaction mechanism of aptamer and micromolecule. In this study, modeling and dynamic simulation of ssDNA aptamer (P-18S2) and target (Palytoxin, PTX) were performed separately. Then, the complex structure between DNA and PTX was predicted, and docking results showed that PTX could combine steadily at the groove’s top of DNA model by strong hydrogen-bonds and electrostatic interaction. Thus, we truncated and optimized P-18S2 by simulating. At the same time, we also confirmed the reliability of simulation results by experiments. With the experimental and computational results, the study provided a more reasonable interpretation for the high affinity and specific binding of P-18S2 and PTX, which laid the foundation for further optimization and development of aptamers in molecular diagnostics and therapeutic applications.

Conformation as the Therapeutic Target for Neurodegenerative Diseases

2017 ◽  
Vol 14 (4) ◽  
pp. 393-402 ◽  
Author(s):  
Rajaraman Krishnan ◽  
Franz Hefti ◽  
Haim Tsubery ◽  
Michal Lulu ◽  
Ming Proschitsky ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Neurodegenerative Diseases ◽  
Protein Misfolding ◽  
Specific Binding ◽  
Drug Candidate ◽  
High Affinity ◽  
Novel Approach ◽  
Multiple Protein ◽  
Clinical Benefits ◽  
Effective Drugs

Therapeutic strategies that target pathways of protein misfolding and the toxicity of intermediates along these pathways are mainly at discovery and early development stages, with the exception of monoclonal antibodies that have mainly failed to produce convincing clinical benefits in late stage trials. The clinical failures represent potentially critical lessons for future neurodegenerative disease drug development. More effective drugs may be achieved by pursuing the following two strategies. First, conformational targeting of aggregates of misfolded proteins, rather than less specific binding that includes monomer subunits, which vastly outnumber the toxic targets. Second, since neurodegenerative diseases frequently include more than one potential protein pathology, generic targeting of aggregates by shape might also be a crucial feature of a drug candidate. Incorporating both of these critical features into a viable drug candidate along with high affinity binding has not been achieved with small molecule approaches or with antibody fragments. Monoclonal antibodies developed so far are not broadly acting through conformational recognition. Using GAIM (General Amyloid Interaction Motif) represents a novel approach that incorporates high affinity conformational recognition for multiple protein assemblies, as well as recognition of an array of assemblies along the misfolding pathway between oligomers and fibers. A GAIM-Ig fusion, NPT088, is nearing clinical testing.

scholarly journals Interaction mechanism of aloe-emodin with trypsin: molecular structure–affinity relationship and effect on biological activities

RSC Advances ◽  
2020 ◽  
Vol 10 (35) ◽  
pp. 20862-20871
Author(s):  
Guoyan Ren ◽  
He Sun ◽  
Gen Li ◽  
Jinling Fan ◽  
Lin Du ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Biological Activity ◽  
Biological Activities ◽  
Interaction Mechanism ◽  
Mechanism Of Interaction ◽  
Development And Utilization ◽  
Aloe Emodin

The mechanism of interaction between AE and trypsin was studied firstly. The biological activity of both decreased after the interaction. These results provide a basis for the development and utilization of AE.

scholarly journals Potential for imaging the high-affinity state of the 5-HT1B receptor: a comparison of three PET radioligands with differing intrinsic activity

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Anton Lindberg ◽  
Ryosuke Arakawa ◽  
Tsuyoshi Nogami ◽  
Sangram Nag ◽  
Magnus Schou ◽  
...  
Keyword(s):  
Pet Imaging ◽  
Specific Binding ◽  
Occipital Cortex ◽  
Intrinsic Activity ◽  
High Affinity ◽  
G Protein Coupled ◽  
Dose Dependent ◽  
The Brain ◽  
Agonist Affinity States ◽  
Different Doses

Abstract Background Over the last decade, a few radioligands have been developed for PET imaging of brain 5-HT1B receptors. The 5-HT1B receptor is a G-protein-coupled receptor (GPCR) that exists in two different agonist affinity states. An agonist ligand is expected to be more sensitive towards competition from another agonist, such as endogenous 5-HT, than an antagonist ligand. It is of interest to know whether the intrinsic activity of a PET radioligand for the 5-HT1B receptor impacts on its ability to detect changes in endogenous synaptic 5-HT density. Three high-affinity 11C-labeled 5-HT1B PET radioligands with differing intrinsic activity were applied to PET measurements in cynomolgus monkey to evaluate their sensitivity to be displaced within the brain by endogenous 5-HT. For these experiments, fenfluramine was pre-administered at two different doses (1.0 and 5.0 mg/kg, i.v.) to induce synaptic 5-HT release. Results A dose-dependent response to fenfluramine was detected for all three radioligands. At the highest dose of fenfluramine (5.0 mg/kg, i.v.), reductions in specific binding in the occipital cortex increased with radioligand agonist efficacy, reaching 61% for [11C]3. The most antagonistic radioligand showed the lowest reduction in specific binding. Conclusions Three 5-HT1B PET radioligands were identified with differing intrinsic activity that could be used in imaging high- and low-affinity states of 5-HT1B receptors using PET. From this limited study, radioligand sensitivity to endogenous 5-HT appears to depend on agonist efficacy. More extensive studies are required to substantiate this suggestion.

Molecular structure analysis of ascending aorta aneurysm upon atherosclerosis

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
I Mamarelis ◽  
V Mamareli ◽  
M Kyriakidou ◽  
O Tanis ◽  
C Mamareli ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Raman Spectra ◽  
Molecular Level ◽  
Ascending Aorta ◽  
Ir And Raman Spectra ◽  
Aggregate Formation ◽  
Aorta Aneurysm ◽  
Ft Ir ◽  
Molecular Structure Analysis ◽  
Ir And Raman

Abstract Background The atherosclerotic ascending aorta could represent a potential source of emboli or could be an indicator of atherosclerosis in general with high mortality. The mechanism of aneurysm formation and atherosclerosis of the ascending aorta at the molecular level has not yet been clarified. To approach the mechanism of ascending aortic lesions and mineralization at a molecular level, we used the non-destructive FT-IR, Raman spectroscopy, SEM and Hypermicroscope. Methods Six ascending aorta biopsies were obtained from patients who underwent aortic valve replacement (AVR) cardiac surgery. CytoViva (einst inc) hyperspectral microscope was used to obtain the images of ascending aorta. The samples were dissolved in hexane on a microscope glass plate. The FT-IR and Raman spectra were recorded with Nicolet 6700 thermoshintific and micro-Raman Reinshaw (785nm, 145 mwatt), respectively. The architecture of ascending aorta biopsies was obtained by using scanning electron microscope (SEM of Fei Co) without any coating. Results FT-IR and Raman spectra showed changes arising from the increasing of lipophilic environment and aggregate formation (Fig. 1). The band at 1744 cm–1 is attributed to aldehyde CHO mode due to oxidation of lipids. The shifts of the bands of the amide I and amide II bands to lower are associated with protein damage, in agreement with SEM data. The bands at about 1170–1000 cm–1 resulted from the C-O-C of advanced glycation products as result of connecting tissues fragmentations and polymerization. The spectroscopic data were analogous with the lesions observed with SEM and hypermicroscopic images. Conclusions The present innovate molecular structure analysis showed that upon ascending aorta aneurysm development an excess of lipophilic aggregate formation and protein lesions, changing the elasticity of the aorta's wall. The released Ca2+ interacted mostly with carbonate-terminal of cellular protein chains accelerated the ascending aorta calcifications. Figure 1. FT-IR and Raman spectra Funding Acknowledgement Type of funding source: None

Synthesis, crystal and molecular structure, and vibrational spectra of the complex (COOH)2•2H2O•18-crown-6

1986 ◽  
Vol 64 (1) ◽  
pp. 142-147 ◽  
Author(s):  
Suzanne Deguire ◽  
François Brisse ◽  
Jacques Ouellet ◽  
Rodrigue Savoie
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Oxalic Acid ◽  
Raman Spectra ◽  
Vibrational Spectra ◽  
Crystal And Molecular Structure ◽  
Unit Cell ◽  
Infrared And Raman Spectra ◽  
O 18 ◽  
Stoichiometric Complex

A stoichiometric complex of formula (COOH)2•2H2O•18-crown-6 has been obtained from oxalic acid and the macrocyclic polyether 18-crown-6. The crystals of the complex have a monoclinic unit cell and belong to the P21/c space group. The components in the adduct are linked through hydrogen bonds in a polymer-like fashion: -crown–H2O–HOOCCOOH–OH2–crown–, where the oxalic acid molecules are present in two distinct disordered orientations. The infrared and Raman spectra of the complex are also reported and interpreted.

Crystal and molecular structure of diorganoammonium oxalatotrimethylstannate, [R2NH2][Me3Sn(C2O4)] (R=i-Bu, cyclohexyl)

2011 ◽  
Vol 34 (5-6) ◽  
pp. 127-130 ◽  
Author(s):  
Yaya Sow ◽  
Libasse Diop ◽  
Kieran C. Molloy ◽  
Gabrielle Kociok-Köhn
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonds ◽  
Diffraction Study ◽  
Crystal And Molecular Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Trigonal Bipyramidal ◽  
Trans Complex ◽  
A Chain ◽  
Distorted Trigonal Bipyramidal

Abstract The title compounds [R2NH2][C2O4SnMe3](R=i-Bu, Cy), in which tin atoms adopt a distorted trigonal bipyramidal configuration, have been prepared and submitted to an X-ray diffraction study. These compounds have been obtained from the reaction of (Cy2NH2)2C2O4·H2O or (i-Bu2NH2)2C2O4 with SnMe3Cl. In both [R2NH2][C2O4SnMe3] compounds, the trans complex has an almost regular trigonal bipyramidal geometry around the tin atom. The SnMe3 residues are connected as a chain with bridging oxalate anions in a trans-SnC3O2 framework, the oxygen atoms being in axial positions. The cations connect linear adjacent chains through NH…O hydrogen bonds giving layered structures.

scholarly journals Adenosine Receptors of Cerebral Microvessels and Choroid Plexus

1986 ◽  
Vol 6 (4) ◽  
pp. 463-470 ◽  
Author(s):  
Rajesh N. Kalaria ◽  
Sami I. Harik
Keyword(s):  
Cerebral Cortex ◽  
Ligand Binding ◽  
Choroid Plexus ◽  
Adenosine Receptors ◽  
Binding Sites ◽  
Specific Binding ◽  
Cerebral Microvessels ◽  
High Affinity ◽  
Receptor Sites ◽  
Ligand Binding Sites

We studied, by ligand binding methods, the two adenosine receptors, A, and A2, in rat and pig cerebral microvessels and pig choroid plexus. Ligand binding to cerebral microvessels was compared with that to membranes of the cerebral cortex. [3H]Cyclohexyladenosine and [3H]l-phenylisopropyladenosine were the ligands used for A1-receptors, and [3H]5'- N-ethylcarboxamide adenosine ([3H]NECA) was used to assess A2-receptors. We report that cerebral microvessels and choroid plexus exhibit specific [3H]NECA binding, but have no appreciable A1-receptor ligand binding sites. Specific binding of [3H]NECA to cerebral microvessels, choroid plexus, and cerebral cortex was saturable and suggested the existence of two classes of A2-receptor sites: high-affinity ( Kd ∼ 250 n M) and low-affinity ( Kd ∼ 1–2 μ M) sites. The Kd and Bmax of NECA binding to cerebral microvessels and cerebral cortex were similar within each species. Our results, indicating the existence of A2-receptors in cerebral microvessels, are consistent with results of increased adenylate cyclase activity by adenosine and some of its analogues in these microvessels.

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