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1
Giragossian, Craig, Maria Pellegrini, and Dale F. Mierke. "NMR studies of CCK-8/CCK1 complex support membrane-associated pathway for ligand-receptor interaction." Canadian Journal of Physiology and Pharmacology 80, no. 5 (2002): 383–87. http://dx.doi.org/10.1139/y02-031.
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The interaction of peptide ligands with their associated G-protein-coupled receptors has been examined by a number of different experimental approaches over the years. We have been developing an approach utilizing high-resolution NMR to determine the structural features of the peptide ligand, well-designed fragments of the receptor, and the ligandreceptor complexes formed upon titration of the peptide hormone. The results from these investigations provide evidence for a membrane-associated pathway for the initial interaction of peptide ligands with the receptor. Here, our results from the investigation of the interaction of CCK-8 with the CCK1 receptor are described. Our spectroscopic results clearly show that both CCK-8 and the regions of CCK1 with which it interacts are closely associated with the zwitterionic interface of the lipids utilized in our solution spectroscopic studies.Key words: G-protein-coupled receptors, NMR structural characterization, cholecystokinin, CCK-8, cholecystokinin receptor, subtype 1, CCK1, peptide hormones.
2
Ruan, Ke-He. "High resolution nuclear magnetic resonance spectroscopy-guided mutagenesis for characterization of membrane-bound proteins: Experimental designs and applications." Spectroscopy 18, no. 1 (2004): 13–29. http://dx.doi.org/10.1155/2004/802728.
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High resolution Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for determining the solution structures of peptides and small proteins, and their ligand binding functions. Molecular biology mutagenesis is a widely used and powerful approach for identification of the protein functions. We have developed a strategy integrating NMR experiments with mutagenesis studies to advance and extend the approaches used for structure/function relationship studies of proteins, especially for membrane-bound proteins, which play important roles in physiopathological processes. The procedures include the design of the functional protein domain, identification of the solution structure and intermolecular contacts between the protein segment and its ligand. These determinations are resolved by high-resolution 2D NMR spectroscopy, and followed by site-directed mutagenesis of the residues suggested from the NMR experiment for the membrane-bound proteins. The residues important to the protein functions, identified by the mutagenesis, were further used to re-assign the NMR spectra and finalize the docking of the protein with its ligand. A structural model of the protein/ligand interaction can be constructed at an atomic level based on the NMR spectroscopy and mutagenesis results. As an application, the strategy has enhanced our knowledge in the understanding of the structure/function relationship for a membrane-bound G protein coupling receptor, the thromboxane A2receptor (TP receptor), interacting with its ligand, and a microsomal P450, prostacyclin synthase (PGIS), docking with its substrate in the endoplasmic reticulum (ER) membrane. In this review, we have summarized the principles and applications for this newly developed technique.
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Fitri, Tengku Anggia, Rudi Hendra, and Adel Zamri. "One-pot synthesis and molecular docking study of pyrazoline derivatives as an anticancer agent." Pharmacy Education 23, no. 2 (2023): 260–65. http://dx.doi.org/10.46542/pe.2023.232.260265.
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Background: Pyrazoline is a series of heterocyclics with an N–N bond linkage, which is the determining factor in their biological activities, including anticancer. Objectives: This research aims to synthesise pyrazoline derivative compounds with anticancer potential. Method: 4-Metoxyacetophenon, halogen-substituted benzaldehyde, and phenylhydrazine were used to prepare pyrazoline derivatives (4a, b) under basic conditions using a microwave-assisted, one-pot, three-component reaction method. UV, FTIR, 1H-NMR, and HRMS spectrometers were used to confirm the molecular structure of pyrazolines (4a, b) using their UV, FTIR, 1H-NMR, and HRMS spectra. The anticancer activity of the compounds (4a, b) was evaluated using molecular docking studies to observe the receptor-ligand interaction of the compounds with the Estrogen Receptor Erα. Result: The pyrazoline (4a, b) produced positive results, with approximately 40% yield. It can be used as an anticancer agent due to its binding free energy values of -9.74 and -9.29 respectively, and a receptor-ligan interaction. Discussion and Conclusion: New pyrazolines (4a, b) have been successfully synthesised with good yields through the one-pot three-component reaction and have potential as anti-breast cancer agents because of their good affinity for the ERα evidenced by the negative binding free energy values and receptor-ligand interactions that are similar to natural ligand, 4OHT.
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Assadi-Porter, Fariba, James Radek, Hongyu Rao, and Marco Tonelli. "Multimodal Ligand Binding Studies of Human and Mouse G-Coupled Taste Receptors to Correlate Their Species-Specific Sweetness Tasting Properties." Molecules 23, no. 10 (2018): 2531. http://dx.doi.org/10.3390/molecules23102531.
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Taste signaling is a complex process that is linked to obesity and its associated metabolic syndromes. The sweet taste is mediated through a heterodimeric G protein coupled receptor (GPCR) in a species-specific manner and at multi-tissue specific levels. The sweet receptor recognizes a large number of ligands with structural and functional diversities to modulate different amplitudes of downstream signaling pathway(s). The human sweet-taste receptor has been extremely difficult to study by biophysical methods due to the difficulty in producing large homogeneous quantities of the taste-receptor protein and the lack of reliable in vitro assays to precisely measure productive ligand binding modes that lead to activation of the receptor protein. We report here a multimodal high throughput assay to monitor ligand binding, receptor stability and conformational changes to model the molecular ligand-receptor interactions. We applied saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR) complemented by differential scanning calorimetry (DSC), circular dichroism (CD) spectroscopy, and intrinsic fluorescence spectroscopy (IF) to characterize binding interactions. Our method using complementary NMR and biophysical analysis is advantageous to study the mechanism of ligand binding and signaling processes in other GPCRs.
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Braitsch, Michaela, Hanspeter Kählig, Georg Kontaxis, et al. "Synthesis of fluorinated maltose derivatives for monitoring protein interaction by 19F NMR." Beilstein Journal of Organic Chemistry 8 (March 27, 2012): 448–55. http://dx.doi.org/10.3762/bjoc.8.51.
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A novel reporter system, which is applicable to the 19F NMR investigation of protein interactions, is presented. This approach uses 2-F-labeled maltose as a spy ligand to indirectly probe protein–ligand or protein–protein interactions of proteins fused or tagged to the maltose-binding protein (MBP). The key feature is the simultaneous NMR observation of both 19F NMR signals of gluco/manno-type-2-F-maltose-isomers; one isomer (α-gluco-type) binds to MBP and senses the protein interaction, and the nonbinding isomers (β-gluco- and/or α/β-manno-type) are utilized as internal references. Moreover, this reporter system was used for relative affinity studies of fluorinated and nonfluorinated carbohydrates to the maltose-binding protein, which were found to be in perfect agreement with published X-ray data. The results of the NMR competition experiments together with the established correlation between 19F chemical shift data and molecular interaction patterns, suggest valuable applications for studies of protein–ligand interaction interfaces.
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Morales, Paula, Marta Bruix та M. Angeles Jiménez. "Structural Insights into β-arrestin/CB1 Receptor Interaction: NMR and CD Studies on Model Peptides". International Journal of Molecular Sciences 21, № 21 (2020): 8111. http://dx.doi.org/10.3390/ijms21218111.
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Activation of the cannabinoid CB1 receptor induces different cellular signaling cascades through coupling to different effector proteins (G-proteins and β-arrestins), triggering numerous therapeutic effects. Conformational changes and rearrangements at the intracellular domain of this GPCR receptor that accompany ligand binding dictate the signaling pathways. The GPCR-binding interface for G proteins has been extensively studied, whereas β-arrestin/GPCR complexes are still poorly understood. To gain knowledge in this direction, we designed peptides that mimic the motifs involved in the putative interacting region: β-arrestin1 finger loop and the transmembrane helix 7-helix 8 (TMH7-H8) elbow located at the intracellular side of the CB1 receptor. According to circular dichroism and NMR data, these peptides form a native-like, helical conformation and interact with each other in aqueous solution, in the presence of trifluoroethanol, and using zwitterionic detergent micelles as membrane mimics. These results increase our understanding of the binding mode of β-arrestin and CB1 receptor and validate minimalist approaches to structurally comprehend complex protein systems.
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Pintilie, Lucia, Amalia Stefaniu, Alina Ioana Nicu, Maria Maganu, and Miron Teodor Caproiu. "Design, Synthesis and Docking Studies of Some Novel Fluoroquinolone Compounds with Antibacterial Activity." Revista de Chimie 69, no. 4 (2018): 815–22. http://dx.doi.org/10.37358/rc.18.4.6207.
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A new series of fluoroquinolone compounds have been obtained by Gould-Jacobs method. The compounds have been characterized by physic-chemical methods (elemental analysis, FTIR, NMR, UV-Vis) and by antimicrobial activity against Gram-positive and Gram-negative microorganisms. For the synthesized compounds have been performed calculations of characteristics and molecular properties, using Spartan�14 Software from Wavefunction, Inc. Irvine, CA. and molecular docking studies using CLC Drug Discovery Workbench 2.4 software, to identify and visualize the most likely interaction ligand (fluoroquinolone) with the receptor protein.
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Nguyen, Hoa, Tianwei Jing та Xu Wang. "The Q163C/Q309C mutant of αMI-domain is an active variant suitable for NMR characterization". PLOS ONE 18, № 1 (2023): e0280778. http://dx.doi.org/10.1371/journal.pone.0280778.
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Integrin αMβ2 (Mac-1, CD11b/CD18, CR3) is an important adhesion receptor expressed on monocytes. Mac-1 is responsible for mediating cell migration, phagocytosis, degranulation as well as cell-cell fusion. It is also the most promiscuous integrin in terms of ligand specificity with over 100 ligands, most of which use the αMI-domain as their binding site. Despite the importance of αMI-domain in defining ligand interactions of Mac-1, structural studies of αMI-domain’s interactions with ligands are lacking. In particular, solution NMR studies of αMI-domain’s interaction with ligands have not been possible because the most commonly used active αMI-domain mutants (I316G and ΔK315) are not sufficiently stable and soluble to be used in solution NMR. The goal of this study is to identify an αMI-domain active mutant that’s amenable to NMR characterization. By screening known activating mutations of αMI-domain, we determined that the Q163C/Q309C mutant, which converts the αMI-domain into its active form through the formation of an intramolecular disulfide bond, can be produced with a high yield and is more stable than other active mutants. In addition, the Q163C/Q309C mutant has better NMR spectral quality than other active mutants and its affinity for ligands is comparable to other active mutants. Analysis of the Co2+-induced pseudocontact shifts in the Q163C/Q309C mutant showed the structure of the mutant is consistent with the active conformation. Finally, we show that the minor fraction of the Q163C/Q309C mutant without the disulfide bond can be removed through the use of carboxymethyl sepharose chromatography. We think the availability of this mutant for NMR study will significantly enhance structural characterizations of αMI-domain-ligand interactions.
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Bhat, Ishwar K. "SYNTHESIS, DOCKING STUDY AND ANTI-INFLAMMATORY STUDIES OF SOME FLAVANONES." INDIAN DRUGS 58, no. 02 (2021): 54–60. http://dx.doi.org/10.53879/id.58.02.12228.
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In this work, a series of flavanones (P1-P9) was synthesized by cyclization of substituted (hydroxyphenyl)- 3-(phenyl) prop-2-en-1-ones (S1-S9). The structures of the synthesized compounds were characterized by IR, 1 H NMR and mass spectral data. These derivatives were evaluated for anti-inflammatory activity. Compounds P1, P3, P6 and P7 showed excellent anti-inflammatory activity as compared to standard drug diclofenac sodium. Molecular docking of these flavanones (P1-P9) was also performed with receptor phosphoinositide-3-kinase PI3Kδ (PDB code: 5ITD). All the flavanones (P1-P9) were docked into same groove of the binding site of native co-crystallized (5-{4-[3-(4-acetylpiperazine-1-carbonyl) phenyl] quinazolin-6-yl}-2-methoxypyridine carbonitrile) ligand for activity explanation and exhibited good ligand interaction and binding affinity were of range -4.57 to -8.79kcal/mol.
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Kharche, Shalmali, Manali Joshi, Amitabha Chattopadhyay, and Durba Sengupta. "Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1." PLOS Computational Biology 17, no. 5 (2021): e1008593. http://dx.doi.org/10.1371/journal.pcbi.1008593.
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The dynamic interactions between G protein-coupled receptors (GPCRs) and their cognate protein partners are central to several cell signaling pathways. For example, the association of CXC chemokine receptor 1 (CXCR1) with its cognate chemokine, interleukin-8 (IL8 or CXCL8) initiates pathways leading to neutrophil-mediated immune responses. The N-terminal domain of chemokine receptors confers ligand selectivity, but unfortunately the conformational dynamics of this intrinsically disordered region remains unresolved. In this work, we have explored the interaction of CXCR1 with IL8 by microsecond time scale coarse-grain simulations, complemented by atomistic models and NMR chemical shift predictions. We show that the conformational plasticity of the apo-receptor N-terminal domain is restricted upon ligand binding, driving it to an open C-shaped conformation. Importantly, we corroborated the dynamic complex sampled in our simulations against chemical shift perturbations reported by previous NMR studies and show that the trends are similar. Our results indicate that chemical shift perturbation is often not a reporter of residue contacts in such dynamic associations. We believe our results represent a step forward in devising a strategy to understand intrinsically disordered regions in GPCRs and how they acquire functionally important conformational ensembles in dynamic protein-protein interfaces.
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Beglova, Natalia, and Chang-Jin Lee. "Mapping Interactions Between B2GPI and the Lipoprotein Receptors by Solution NMR Spectroscopy." Blood 112, no. 11 (2008): 2018. http://dx.doi.org/10.1182/blood.v112.11.2018.2018.
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Abstract Antiphospholipid syndrome (APS) is an autoimmune disease characterized by venous or arterial thrombosis and recurrent pregnancy loss. Beta2 glycoprotein I (B2GPI) is the major target for these antibodies. Current evidence suggests that B2GPI acquires pathological properties leading to APS after association with antibodies. It was demonstrated that APS related antibodies induce activation of endothelial cells, monocytes and platelets, although the identity of a cell-surface receptors that transmit the antibody-induced signaling inside cells remain unclear. Biochemical studies have shown that the receptors of the low-density lipoprotein receptor (LDLR) family are all capable to bind B2GPI/antibody complexes. These receptors are abundantly expressed by many cell types. The ligand-binding activity of the lipoprotein receptors is confined primarily to structurally homologous LA modules, which are arranged in sequence to form a ligand-binding domain. We investigated at the atomic level the features of the ligand-binding LA modules required for interaction with B2GPI. We sought to determine whether the same residues that form the ligand-binding pocket on the LA modules in the crystal structure of a RAP/LA3-4 complex also recognize B2GPI. We demonstrated that the same residues that form the ligand-binding pocket on LA4 in the crystal structure of the RAP/LA3-4 complex comprise the contact site for B2GPI. The domain 5 from B2GPI (B2GPI-D5) was expressed and labeled for NMR studies. The residues of B2GPI-D5 that are perturbed when B2GPI-D5 was titrated with LA4 are located at the C-terminus of domain 5. Using NMR relaxation measurements, we determined that B2GPI-D5 binds LA4 with 1:1 stoichiometry. The estimated Kd of the B2GPI-D5/LA4 complex is about 30 uM. NMR experimental data was used to build a docking model of the complex.
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Pistolesi, Sara, Nico Tjandra, and Guillermo A. Bermejo. "Solution NMR studies of periplasmic binding proteins and their interaction partners." BioMolecular Concepts 2, no. 1-2 (2011): 53–64. http://dx.doi.org/10.1515/bmc.2011.005.
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AbstractPeriplasmic binding proteins (PBPs) are a crucial part of ATP-binding cassette import systems in Gram-negative bacteria. Central to their function is the ability to undergo a large-scale conformational rearrangement from open-unliganded to closed-liganded, which signals the presence of substrate and starts its translocation. Over the years, PBPs have been extensively studied not only owing to their essential role in nutrient uptake but also because they serve as excellent models for both practical applications (e.g., biosensor technology) and basic research (e.g., allosteric mechanisms). Although much of our knowledge at atomic level has been inferred from the detailed, static pictures afforded by crystallographic studies, nuclear magnetic resonance (NMR) has been able to fill certain gaps in such body of work, particularly with regard to dynamic processes. Here, we review NMR studies on PBPs, and their unique insights on conformation, dynamics, energetics, substrate binding, and interactions with related transport proteins. Based on the analysis of recent paramagnetic NMR results, as well as crystallographic and functional observations, we propose a mechanism that could explain the ability of certain PBPs to achieve a closed conformation in absence of ligand while others seem to remain open until ligand-mediated closure.
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Mittag, Tanja, Stephen Orlicky, Wing-Yiu Choy, et al. "Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor." Proceedings of the National Academy of Sciences 105, no. 46 (2008): 17772–77. http://dx.doi.org/10.1073/pnas.0809222105.
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Intrinsically disordered proteins play critical but often poorly understood roles in mediating protein interactions. The interactions of disordered proteins studied to date typically entail structural stabilization, whether as a global disorder-to-order transition or minimal ordering of short linear motifs. The disordered cyclin-dependent kinase (CDK) inhibitor Sic1 interacts with a single site on its receptor Cdc4 only upon phosphorylation of its multiple dispersed CDK sites. The molecular basis for this multisite-dependent interaction with a single receptor site is not known. By NMR analysis, we show that multiple phosphorylated sites on Sic1 interact with Cdc4 in dynamic equilibrium with only local ordering around each site. Regardless of phosphorylation status, Sic1 exists in an intrinsically disordered state but is surprisingly compact with transient structure. The observation of this unusual binding mode between Sic1 and Cdc4 extends the understanding of protein interactions from predominantly static complexes to include dynamic ensembles of intrinsically disordered states.
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Kumar, Manish, Poonam Jangra Darolia, Nidhi Antil, et al. "Spectral, Theoretical and Biological Studies of 3-((4-Mercaptophenyl)imino)- 1-phenylindolin-2-one Schiff Base and Its Organotellurium(IV) Complexes." Asian Journal of Chemistry 33, no. 8 (2021): 1749–56. http://dx.doi.org/10.14233/ajchem.2021.23214.
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Schiff base ligand (3-((4-mercaptophenyl)imino)-1-phenylindolin-2-one) of 1-phenylindoline-2,3-dione and 4-aminothiophenol was synthesized by refluxing. Organotellurium(IV) complexes of type (RTeCl3.NPhIATP and R2TeCl2.NPhIATP, where R = 4-hydroxyphenyl, 4-methoxyphenyl and 3-methyl-4-hydroxyphenyl, NPhIATP = Schiff base ligand). The ligand and its organotellurium(IV) complexes (9a-f) were characterized by FT-IR, molar conductance, elemental analyses, UV-vis, mass, 1H & 13C NMR spectral studies. Geometry of all the compounds were optimized and octahedral geometry have been proposed for all the tellurium(IV) complexes. Molecular docking was studied to find the binding interactions between ligand (NPhIATP) and receptor proteins: E. coli (3t88) and S. aureus (3ty7). The antimicrobial activity of ligand and its tellurium(IV) complexes have been screened against bacteria and fungi. All the organotellurium(IV) complexes complexes showed good activity to ligand towards different studied microorganisms.
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Pintilie, Lucia, Constantin Tanase, Maria Maganu, and Miron Teodor Caproiu. "Design, Synthesis, Molecular Docking and Antibacterial Screening of some Quinolone Compounds." Revista de Chimie 71, no. 11 (2020): 10–21. http://dx.doi.org/10.37358/rc.20.11.8369.
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Some 6,8-dichloro-quinolone compounds were designed and synthesized; by comparing with 6-fluoro-8-chloro-quinolone compounds, the influence of the nature of the halogen atom from six position of the quinolone ring on the molecular properties and on the antimicrobial activity was studied. The DFT/B3LYP/6-311G* level of basis set was used for the computation of molecular structure of optimized compounds. The calculations of characteristics and molecular properties were performed using Spartan�14 Software from Wavefunction, Inc. Irvine, CA. The HOMO-LUMO energies and orbitals, global reactivity descriptors, various thermodynamic parameters, and dipole moment (i) were calculated to determine the molecular properties of quinolone compounds. Molecular docking studies were realized to identify and visualize the most likely interaction ligand (quinolone/fluoroquinolone compounds) with the protein receptor. The score and hydrogen bonds formed with the amino acids from group interaction atoms are used to predict the binding modes, the binding affinities, and the orientation of the docked quinolone/fluoroquinolone derivatives in the active site of the protein receptor. The protein-ligand complex was realized based on the X-ray structure of Bacillus cereus (PDB ID: 1VEN) using CLC Drug Discovery Workbench 2.4 software. The quinolone compounds were characterized by physical-chemical methods (elemental analysis, IR spectral analysis, 1H-NMR, 13C-NMR spectra, UV-Vis, thin layer chromatography) and by antimicrobial activity against some Gram-positive and Gram-negative microorganisms: Staphylococcus aureus, Bacillus cereus, Bacillus subtilis, Micrococcus luteus, Escherichia coli and Pseudomonas aeruginosa.
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Rahim, Shermin, and John Milne. "Studies on the interaction of selenite and selenium with sulphur donors. Part 4. Thiosulfate." Canadian Journal of Chemistry 74, no. 5 (1996): 753–59. http://dx.doi.org/10.1139/v96-082.
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Raman and Se-77 NMR spectroscopy confirm that when selenous acid is reduced by thiosulfate in water selenopentathionate and tetrathionate are formed.[Formula: see text]Depending upon the stoichiometry and pH, two isomers of the selenopentathionate ion, O- and S-bonded, are formed. Insufficiently acid solutions cause decomposition to selenium and tetrathionate ion.[Formula: see text]Fresh solutions prepared from crystalline sodium selenopentathionate and water undergo slow decompositon. NMR and Raman spectra show the presence of both the O-bonded and S-bonded linkage isomers. The O-bonded isomer facilitates the formation of tetrathionate. Addition of thiosulfate to selenotrithionate solution or sulfite to selenopentathionate solution yields trithionate with no indication of dithionate or tetrathionate formation. This suggests that simple S—S bond formation at selenium does not occur but that there may be direct attack of the incoming ligand on the attached ligand. Key words: selenite, thiosulfate, selenopentathionate, Se-77 NMR, Raman spectroscopy, linkage isomerism.
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Oktay, Ferit, and Sümeyra Tuna Yıldırım. "Synthesis, Characterization and Docking Studies of a Schiff Base Ligand and Some Metal Complexes." Pharmata 5, no. 1 (2025): 16–21. https://doi.org/10.62425/pharmata.1549830.
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Objective: To synthesize a Schiff base ligand and some metal complexes, perform characterization studies and elucidate the action mechanisms of the synthesized compounds with the Schrödinger Suite computer aided molecular modeling program. Methods: A Schiff base ligand has been synthesized by the reaction of a salicylaldehyde derivate with an aminophenol. With using this ligand, metal complexes were prepared from Co(II), Ni(II), Cu(II) and Zn(II) acetate salts. The structures of the synthesized compounds were confirmed by different spectroscopic and microscopic techniques such as Elemental Analysis, FT-IR, 1H-NMR, 13C-NMR, UV-Vis, XRD, SEM and TGA. In order to elucidate the mechanism of action of the synthesized compounds, some descriptive molecular properties were calculated using the Schrödinger Suite computer aided molecular modeling program. Results: Within the scope of the study, a ligand and its complexes were synthesized. The structures of compounds were elucidated and molecular docking studies showed that Zn(II) complex had the highest scores obtained. Conclusion: Structural characterization showed that ligand at the metal complexes act as bidentate chelates by binding to the metal ion from the imine nitrogen and phenolic oxygen. The mechanism of action of the synthesized compounds and the active site where the coupling will take place were determined, and the interactions of possible drug molecule candidates synthesized with the target receptor site were calculated.
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Ghosh, Ruchira, Donald S. Thomas, and Jayashree Arcot. "Molecular Recognition Patterns between Vitamin B12 and Proteins Explored through STD-NMR and In Silico Studies." Foods 12, no. 3 (2023): 575. http://dx.doi.org/10.3390/foods12030575.
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Ligand–receptor molecular recognition is the basis of biological processes. The Saturation Transfer Difference–NMR (STD–NMR) technique has been recently used to gain qualitative and quantitative information about physiological interactions at an atomic resolution. The molecular recognition patterns between the cyanocobalamin (CNBL)/aqua cobalamin (OHBL) and different plant and animal proteins were investigated via STD–NMR supplemented by molecular docking. This study demonstrates that myoglobin has the highest binding affinity and that gluten has the lowest affinity. Casein also shows a higher binding affinity for cyanocobalamin when compared with that of plant-based proteins. STD–NMR results showed the moderate binding capability of casein with both CNBL and OHBL. Computer simulation confirmed the recognition mode in theory and was compared with the experiments. This work is beneficial for understanding the binding affinity and biological action of cyanocobalamin and will attract researchers to use NMR technology to link the chemical and physiological properties of nutrients.
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Dey, Shuchismita, Md Zakir Sultan, and Md Abdus Salam. "Synthesis, Characterization and Biological Studies of Gemifloxacin Mesylate with Nickel(II) and Copper(II)." Asian Journal of Chemistry 36, no. 11 (2024): 2609–14. http://dx.doi.org/10.14233/ajchem.2024.32589.
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Gemifloxacin mesylate, a fourth-generation fluoroquinolone-type antibiotic, is widely used for community treatment of acquired pneumonia and severe bacterial infections. The Cu(II) and Ni(II) complexes of gemifloxacin mesylate were synthesized by refluxing an aqueous solution of the ligand with the required amount of metal(II) salts in a round bottom flask with 2:1 (L:M) ratio in an oil bath at 90 ºC with a continuous stirring for 4 h. The mixture was kept overnight to obtain a coloured solid complex. The synthesized metal(II) complexes were characterized by physico-chemical parameters and spectral analyses, including UV-Vis, FT-IR and 1H NMR. The structures of the complexes were further confirmed by elemental (CHNS) and TG-DTA analyses. The spectral findings revealed that metal-ligand interaction has successfully occurred where the ligand acted as a bidentate chelate in the synthesized metal(II) complexes. The IR studies showed that upon complexation the characteristic carboxylic stretching frequency at 1714 cm-1 disappeared and the pyridone stretching frequency shifted to a lower frequency region. The 1H NMR data of the complexes confirm the effective interaction between the metal and the ligand via 3-carboxyl group and 4-oxo groups. The thermal and elemental analyses data were also in agreement with the proposed interaction. The ligand as well as its metal(II) complexes showed significant activity against all the studied 11 bacterial strains and one of the fungal strains, Candida sp.
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Alam, Yusuf Syaril, Pratiwi Pudjiastuti, Saipul Maulana, et al. "Synthesis and Antidiabetic Evaluation of <i>N</i>’-Benzylidenebenzohydrazide Derivatives by <i>In Silico</i> Studies." Indonesian Journal of Chemistry 23, no. 4 (2023): 1061. http://dx.doi.org/10.22146/ijc.82073.
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Two new of N’-benzylidenebenzohydrazide (NBB) derivatives were successfully synthesized and yielded 50–58%. FTIR, ESI-MS, 1H-NMR and 13C-NMR were used to investigate the characteristic of NBB derivates. The structure and relationship of NBB derivatives into α-glucosidase and α-amylase as good targets for diabetes treatment were evaluated using in silico screening. Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB/GBSA) was used to calculate the free binding energy (ΔGbind (MM-GBSA)) of NBB to α-glucosidase and α-amylase receptors showed that the results of −0.45 and −20.79 kcal/mol respectively. In the ortho position, NBB derivatives exhibited electron donating groups (EDG like -OCH3, -OH and -Cl with binding free energies of −21.94, −6.71 and 21.94, respectively, and acarbose, a native ligand energy of 32.62 kcal/mol. In addition, the binding free energy of N-2-(-OCH3, -OH and -Cl)-NBB to the α-amylase receptor showed the number of −39.33, −43.96, −42.81, respectively and −46.51 kcal/mol in comparing with a native ligand. As a result, it was found that all the NBB derivatives were able to interact with several amino acids in the α-glucosidase cavity as well as the native ones, including Ala281, Asp282, and Asp616. NBB and native ligand showed similar interaction between α-amylase with Gly110 amino acid residue.
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Gossert, Alvar D., Sebastian Hiller, and César Fernández. "Automated NMR Resonance Assignment of Large Proteins for Protein−Ligand Interaction Studies." Journal of the American Chemical Society 133, no. 2 (2011): 210–13. http://dx.doi.org/10.1021/ja108383x.
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Fatisa, Yuni, Arif Yasthophi, Elviyenti Elviyenti та ін. "A Novel Benzenesulfonylurea-Substituted Pyridazinone Derivative with Antidiabetic Effect as the Peroxisome Proliferator-activated Receptor (PPAR-γ) Agonist". Jurnal Kimia Valensi 11, № 1 (2025): 18–29. https://doi.org/10.15408/jkv.v11i1.42187.
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Peroxisome Proliferator-activated Receptor (PPAR-γ) protein is one of the target proteins for insulin sensitivity therapy in Type 2 DM. PPAR-γ has a key role as a nuclear receptor that regulates the expression of several metabolism-related genes. This research aims to synthesize a novel benzenesulfonylurea-substituted pyridazinone derivative, namely (E)-N'-(1-(4-(3-(4-methoxyphenyl)-6-oxopyridazin-1(6H)- yl)phenyl)ethylidene)-4-methylbenzenesulfonohydrazide (8) and predicted it activity as the PPAR-γ agonist using a molecular docking approach and ADMET profiles. The compound 8 was obtained through a Schiff base condensation reaction between compound 6, p-tosyl hydrazine, and a glacial acetic acid catalyst using monowave. The purity of the compound was determined by TLC test, and melting point measurement. The structure was confirmed through FTIR, 1H-NMR, C-NMR and HRMS analysis. Molecular docking studies were carried out on the crystal structure of the human PPAR-γ Ligand Binding Domain target protein in complex with the α-aryloxyphenyl acetic acid agonist (PDB ID 1ZEO). The results of the docking show that compound 8 has a lower binding free energy than rosiglitazone (positive control) with a free energy value (S score) = -13.513 kcal/mol and -8.3089 kcal/mol, respectively. Compound 8 can form two hydrogen bonds with residues His323 and Ser289, π-π interactions with Phe363 and π-H interactions with Cys285. The interactions are similar to the interaction between the native ligand agonists α-aryloxyphenyl acetic acid and rosiglitazone with the target protein. Furthermore, compound 8 is predicted to have a moderate ADME profile. The results support that compound 8 can be developed as a PPAR-γ agonist candidate for the antidiabetic therapeutic agent.
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Abdul-Khaleq Mohammed, Baraa, Sahbaa Ali Ahmed, and Fanar Al-Healy. "Design, characterizations, DFT, molecular docking and antibacterial studies of some complexes derived from 4-aminpantipyrine with glycine amino acid and ligand." Bulletin of the Chemical Society of Ethiopia 38, no. 6 (2024): 1609–24. http://dx.doi.org/10.4314/bcse.v38i6.9.
Texte intégralRésumé :
The synthesis of the heterocyclic ligand (LK) involved the combination of 4-amino antipyrine, 4-nitroacetophenone, and glycine. A new series of transition metal complexes of Ni(II), Co(II), Cu(II), and Zn(II) have been synthesized from the Schiff base (LK). It was characterized by micro elemental analysis, FT-IR, UV-Vis, and 1H-NMR spectroscopy. The prepared complexes were characterized using (CHN) analysis, flame atomic absorption, as well as conductivity measurements and magnetic susceptibility. From the obtained data, the octahedral structure was suggested for all complexes. The ligand showed tridentate nature by binding to metal ions through the N atom of antipyrine and the N,O atom of glycine. The exhibited excellent electrolytic properties, except for the Cu(II) and Zn(II) complex which exhibited non-electrolytic behavior. Theoretical calculations with DFT were conducted for all complexes. The antibacterial activity of the ligand and its complexes against (S. aureus, B. subtilis) was evaluated through the disc diffusion method. Additionally, molecular docking analysis was conducted to gain more insights into the ligand's binding energy and interaction with the S. aureus receptor. KEY WORDS: 4-Amino antipyrine, Heterocyclic ligand, Glycine, Molecular docking Bull. Chem. Soc. Ethiop. 2024, 38(6), 1609-1624. DOI: https://dx.doi.org/10.4314/bcse.v38i6.9
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Kharwar, Ruby, and Ritu B. Dixit. "Transition Metal Complexes of N-(4-(N-(8-Hydroxyquinolin-5-yl)sulfamoyl)phenyl)acetamide ligand: Synthesis, Characterization, in silico, in vitro Antimicrobial and DNA Binding Studies." Asian Journal of Organic & Medicinal Chemistry 5, no. 1 (2020): 20–29. http://dx.doi.org/10.14233/ajomc.2020.ajomc-p238.
Texte intégralRésumé :
A new, N-(4-(N-(8-hydroxyquinolin-5-yl)sulfamoyl)phenyl)acetamide (8HQSPA) ligand and its metal chelates with transition metal salts of Cu(II), Ni(II), Zn(II), Co(II), Fe(II) and Mn(II) was synthesized. The synthesized 8HQSPA ligand was characterized by mass, FT-IR, 1H NMR, 13C NMR and its metal chelates by studying their physico-chemical properties, elemental analysis, FT-IR, thermogravimetric (TG) analysis, UV-visible absorption spectroscopy and magnetic susceptibility. Thermogravimetric analysis result evident presence of two water molecules in the coordination which gives the idea of octahedral geometry and also electronic spectra showed transitions in ligand field and charge transfer bands. in silico ADMET studies was carried out to know the biological potential of synthesized compounds as it helps in development of drug candidate with fewer side effects. Molecular docking studies was carried out on bacterial proteins (PDB ID: 5h67, 3ty7, 3t88 and 5i39) and DNA helix (PDB ID: 1BNA) to predict its inhibitory effect and role on integration of DNA helix. Results showed least binding energy score (kcal/mol), which indicate that their potential of binding is greater in receptor of proteins and binds DNA through intercalation mode, which was further assessed by in vitro experiments. Antibacterial studies were carried out in the form of minimum inhibitory concentration (MIC), the results showed increased biological activity of free ligand on metal complexation in the following order: Cu > Fe > Zn > Ni > Co > Mn > 8HQSPA. Also interaction of complexes with CT-DNA was carried out by viscosity measurement, electronic absorption titration and gel electrophoresis, showed intercalation mode of binding.
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Bernini, Andrea, Arianna Ciutti, Ottavia Spiga та ін. "NMR and MD Studies on the Interaction Between Ligand Peptides and α-Bungarotoxin". Journal of Molecular Biology 339, № 5 (2004): 1169–77. http://dx.doi.org/10.1016/j.jmb.2004.04.041.
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Porta, Francesca, Željka Krpetić, Laura Prati, Aureliano Gaiassi, and Giorgio Scarì. "Gold-Ligand Interaction Studies of Water-Soluble Aminoalcohol Capped Gold Nanoparticles by NMR." Langmuir 24, no. 14 (2008): 7061–64. http://dx.doi.org/10.1021/la8008392.
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Dallavalle, Sabrina, Roberto Artali, Salvatore Princiotto, Loana Musso, Gigliola Borgonovo, and Stefania Mazzini. "Investigation of the Interaction between Aloe vera Anthraquinone Metabolites and c-Myc and C-Kit G-Quadruplex DNA Structures." International Journal of Molecular Sciences 23, no. 24 (2022): 16018. http://dx.doi.org/10.3390/ijms232416018.
Texte intégralRésumé :
G-quadruplexes are nucleotide sequences present in the promoter region of numerous oncogenes, having a key role in the suppression of gene transcription. Recently, the binding of anthraquinones from Aloe vera to G-quadruplex structures has been studied through various physico-chemical techniques. Intrigued by the reported results, we investigated the affinity of aloe emodin, aloe emodin-8-glucoside, and aloin to selected G-quadruplex nucleotide sequences by NMR spectroscopy. The structural determinants for the formation of the ligand/nucleotide complexes were elucidated and a model of the interactions between the tested compounds and C-Kit and c-Myc G-quadruplex DNA structures was built by integrated NMR and molecular modeling studies. Overall, the obtained results confirmed and implemented the previously reported findings, pointing out the complementarity of the different approaches and their contribution to a more detailed overview of the ligand/nucleotide complex formation. Furthermore, the proposed models of interaction could pave the way to the design of new nature-derived compounds endowed with increased G-quadruplex stabilizing activity.
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Murugan, T., Rangaswamy Venkatesh, Kannappan Geetha, and Aly Abdou. "Synthesis, Spectral Investigation, DFT, Antibacterial, Antifungal and Molecular Docking Studies of Ni(II), Zn(II), Cd(II) Complexes of Tetradentate Schiff-Base Ligand." Asian Journal of Chemistry 35, no. 6 (2023): 1509–17. http://dx.doi.org/10.14233/ajchem.2023.27808.
Texte intégralRésumé :
By refluxing 4-nitro-o-phenylenediamine and 5-nitro salicylaldehyde, a new Schiff base ligand was synthesized. By reacting the appropriate precursor with the tetradentate Schiff base ligand, three nitro-substituted nickel(II), zinc(II) and cadmium(II) complexes were synthesized. UV-Visible, FTIR and 1H NMR spectral investigations were used to characterize the ligand. Molar conductance, LC-MS, UV-visible and FTIR spectrum analysis were used to characterize the synthesized metal(II) complexes. The ligand and metal(II) complexes were also tested for antibacterial activity. DFT simulations were performed at the B3LYP/6-311G (d,p) and LanL2dz levels of theory were utilized to study the geometry of the Schiff base ligand and the metal(II) complexes. In addition, the molecular orbital occupancy of HOMO and LUMO, as well as the molecular electrostatic potential (MEP), were computed. Molecular docking investigation were conducted utilizing the active sites of the E. coli FabH-CoA complex (PDB ID: 1HNJ) receptor in order to detect the interactions between metal(II) complexes and define their likely binding locations.
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Abdalrazaq, Eid, Abdel Aziz Qasem Jbarah, Taghreed Hashim Al-Noor, Gassan Thabit Shinain, and Mohammed Mahdi Jawad. "Synthesis, DFT Calculations, DNA Interaction, and Antimicrobial Studies of Some Mixed Ligand Complexes of Oxalic Acid and Schiff Base Trimethoprim with Various Metal Ions." Indonesian Journal of Chemistry 22, no. 5 (2022): 1348. http://dx.doi.org/10.22146/ijc.74020.
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Mixed ligand metal complexes are synthesized from oxalic acid with Schiff base, and the Schiff base was obtained from trimethoprim and acetylacetone. The synthesized complexes were of the type [M(L1)(L2)], where the metal, M, is Ni(II), Cu(II), Cr(III), and Zn(II), L1 corresponds to the trimethoprim ((Z)-4-((4-amino-5-(3,4,5-trimethoxybenzyl)pyrimidine-2-yl)imino)pentane-2-one) as the first ligand and L2 represent the oxalate anion ( ) as a second ligand. Characterization of the prepared compounds was performed by elemental analysis, molar conductivity, magnetic measurements, 1H-NMR, 13C-NMR, FT-IR, and Ultraviolet-visible (UV-Vis) spectral studies. The recorded infrared data is reinforced with density functional theory (DFT) calculations. Also, the recorded and calculated IR spectra of the complexes suggested that the coordination of Schiff base is a bidentate ligand with Cu and Ni complexes and a tridentate ligand with Co, Cr, and Zn complexes. The electronic structures of the complexes were investigated by DFT calculations, showing several degrees of HOMO-LUMO energy gaps between complexes. The complexes were studied for their DNA interaction activities. The synthesized ligand and its metal complexes were evaluated for antimicrobial properties against bacterial strains of Bacillus subtilis (G+), Enterobacter cloacae (G-), and Staphylococcus aureus (G+). These complexes considered in this study showed good antimicrobial activity.
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Yusof, Enis Nadia Md, Mohammad Azam, Siti Syaida Sirat, et al. "Dithiocarbazate Ligand-Based Cu(II), Ni(II), and Zn(II) Complexes: Synthesis, Structural Investigations, Cytotoxicity, DNA Binding, and Molecular Docking Studies." Bioinorganic Chemistry and Applications 2022 (July 31, 2022): 1–13. http://dx.doi.org/10.1155/2022/2004052.
Texte intégralRésumé :
S-4-methylbenzyl-β-N-(2-methoxybenzylmethylene)dithiocarbazate ligand, 1, prepared from S-(4-methylbenzyl)dithiocarbazate, was used to produce a novel series of transition metal complexes of the type, [M (L)2] [M = Cu(II) (2), Ni(II) (3), and Zn(II) (4), L = 1]. The ligand and its complexes were investigated by elemental analysis, FTIR, 1H and 13C-NMR, MS spectrometry, and molar conductivity. In addition, single X-ray crystallography was also performed for ligand, 1, and complex 3. The Hirshfeld surface analyses were also performed to know about various bonding interactions in the ligand, 1, and complex 3. The investigated compounds were also tested to evaluate their cytotoxic behaviour. However, complex 2 showed promising results against MCF-7 and MDA-MB-213 cancer cell lines. Furthermore, the interaction of CT-DNA with ligand, 1, and complex 2 was also studied using the electronic absorption method, revealing that the compounds have potential DNA-binding ability via hydrogen bonding and hydrophobic and van der Waals interactions. A molecular docking study of complex 2 was also carried out, which revealed that free binding free energy value was −7.39 kcal mol−1.
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Khalaf, Mai M., Hany M. Abd El-Lateef, Abdulrahman Alhadhrami, et al. "Synthesis, Spectroscopic, Structural and Molecular Docking Studies of Some New Nano-Sized Ferrocene-Based Imine Chelates as Antimicrobial and Anticancer Agents." Materials 15, no. 10 (2022): 3678. http://dx.doi.org/10.3390/ma15103678.
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The newly synthesized organometallic acetyl ferrocene imine ligand (HL) was obtained by the direct combination of 2-acetyl ferrocene with 2-aminothiophenol. The electronic and molecular structure of acetyl ferrocene imine ligand (HL) was refined theoretically and the chemical quantum factors were computed. Complexes of the acetyl ferrocene imine ligand with metal(II)/(III) ions (Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and Cd(II)) were fabricated. They were inspected by thermal (DTG /TG), spectroscopic techniques (FT-IR, 1H NMR, mass, UV–Vis), molar conductivity, and CHNClM to explicate their structures. Studies using scanning electron microscope (SEM) were conducted on the free acetyl ferrocene imine ligand and its Cd(II) chelate to confirm their nano-structure. To collect an idea about the effect of metal ions on anti-pathogenic properties upon chelation, the newly synthesized acetyl ferrocene imine ligand and some of its metal chelates were tested against a variety of microorganisms, including Bacillus subtilis, Staphylococcus aureus, Salmonella typhimurium, Escherichia coli, Aspergillus fumigatus, and Candida albicans. The ligand and its metal chelate were tested for cytotoxic activity in human cancer (MCF-7 cell viability) and human melanocyte cell line HBF4. It was discovered that the Cd(II) chelate had the lowest IC50 of the three and thus had the prior activity. Molecular docking was utilized to investigate the interaction of acetyl ferrocene imine ligand (HL) with the receptors of the vascular endothelial growth factor receptor VEGFR (PDB ID: 1Y6a), human Topo IIA-bound G-segment DNA crystal structure (PDB ID: 2RGR), and Escherichia coli crystal structure (PDB ID: 3T88).
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Ben Nasr, Mahjouba, Emmanuel Aubert, Enrique Espinosa, Frederic Lefebvre, and Cherif Ben Nasr. "Synthesis and physico-chemical studies of a novel coordination compound ZnCl2(C6H4FNH2)2." JOURNAL OF ADVANCES IN CHEMISTRY 10, no. 3 (2014): 2502–11. http://dx.doi.org/10.24297/jac.v10i3.2292.
Texte intégralRésumé :
A new Zn(II) complex with the monodentate ligand 3-fluoroaniline, ZnCl2(C6H4FNH2)2, has been prepared and characterized by single crystal X-ray diffraction, Solid state NMR, IR and UV-visible spectroscopies. The Zn(II) ion, located on a special position, is tetracoordinated by two nitrogen atoms of two 3-fluoroaniline monodentate ligands and two chlorine ligands. In the atomic arrangement, the ZnCl2(NH2)2 entities are interconnected via N-H…Cl hydrogen bonds to form inorganic layers parallel to the (b, c) plane. The organic 3-fluorophenyl groups are located between these layers and connect each other via C-H…F hydrogen bonds to perform an infinite three-dimensional network. The F atom of the 3-fluoroaniline ligand is disordered over two positions. An F-F interaction between neighboring fluorine atoms contributes also to the structure cohesion. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. DFT calculations allow the attribution of the carbon peaks to the different independent atoms. Solid-state UV-Vis spectrum of the complex has been assigned to ligand and charge transfer transitions.
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Li, Yan, Shuang Liu, Elizabeth Yihui Ng, et al. "Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4." Biochemical Journal 475, no. 12 (2018): 2043–55. http://dx.doi.org/10.1042/bcj20180225.
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The oncoprotein YAP (Yes-associated protein) requires the TEAD family of transcription factors for the up-regulation of genes important for cell proliferation. Disrupting YAP–TEAD interaction is an attractive strategy for cancer therapy. Targeting TEADs using small molecules that either bind to the YAP-binding pocket or the palmitate-binding pocket is proposed to disrupt the YAP–TEAD interaction. There is a need for methodologies to facilitate robust and reliable identification of compounds that occupy either YAP-binding pocket or palmitate-binding pocket. Here, using NMR spectroscopy, we validated compounds that bind to these pockets and also identify the residues in mouse TEAD4 (mTEAD4) that interact with these compounds. Flufenamic acid (FA) was used as a positive control for validation of palmitate-binding pocket-occupying compounds by NMR. Furthermore, we identify a hit from a fragment screen and show that it occupies a site close to YAP-binding pocket on the TEAD surface. Our results also indicate that purified mTEAD4 can catalyze autopalmitoylation. NMR studies on mTEAD4 revealed that exchanges exist in TEAD as NMR signal broadening was observed for residues close to the palmitoylation site. Mutating the palmitoylated cysteine (C360S mutant) abolished palmitoylation, while no significant changes in the NMR spectrum were observed for the mutant which still binds to YAP. We also show that FA inhibits TEAD autopalmitoylation. Our studies highlight the utility of NMR spectroscopy in identifying small molecules that bind to TEAD pockets and reinforce the notion that both palmitate-binding pocket and YAP-binding pocket are targetable.
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AL-RAQA, Shaya, İpek ÖMEROĞLU, Doğan ERBAHAR, and Mahmut DURMUŞ. "A novel selective fluorescent chemosensor for Fe3+ ions based on phthalonitrile dimer: synthesis, analysis, and theoretical studies." TURKISH JOURNAL OF CHEMISTRY 44, no. 5 (2020): 1254–64. http://dx.doi.org/10.3906/kim-2004-68.
Texte intégralRésumé :
Phenyl-4,4-di(3,6-dibutoxyphthalonitrile) (3) was synthesized by the reaction of 1,4-phenylenebisboronic acid (1) and 4-bromo-3,6-dibutoxyphthalonitrile (2), using Suzuki cross-coupling reaction. The newly synthesized compound (3) was characterized by FT-IR, MALDI-MS, ESI-MS, 1H-NMR, 13C-NMR, and 13C-DEPT-135-NMR. The fluorescence property of phenyl-4,4-di(3,6- dibutoxyphthalonitrile) (3) towards various metal ions was investigated by fluorescence spectroscopy, and it was observed thatthe compound (3) displayed a significantly ‘turn-off’ response to Fe3+, which was referred to 1:2 complex formation between ligand (3) and Fe3+. The compound was also studied via density functional theory calculations revealing the interaction mechanism of the molecule with Fe3+ ions.
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Swarnalatha, K., P. Rathnamala, A. A. Babu, and N. Bhuvanesh. "Structural characterization, photophysical and BSA binding interaction studies of 4,4'-bis(benzimidazolyl)-2,2'-bipyridine." Журнал структурной химии 57, no. 8 (2016): 1649. http://dx.doi.org/10.26902/jsc20160809.
Texte intégralRésumé :
The title compound is synthesized from the precursors 1,2-diaminobenzene and 2,2'-bipyridine-4,4'-dicarboxylic acid (dcbpy) and characterized using ESI-Mass, 1H NMR, FT-IR and single crystal X-ray analysis. We are the first to report the crystal structure of the 4,4'-bis(benzimidazolyl)-2,2'-bipyridine (bimbpy) ligand. The photophysical properties of the compound in dimethyl sulfoxide and in the aqueous medium are studied. The interaction studies of bimbpy with bovine serum albumin (BSA) were performed with the fluorescence technique and it strongly binds with BSA.
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., Ereshanaik, M. C. Prabhakara, Naik H. S. Bhojya, H. M. Kumaraswamy, and Shafeeulla R. Mohammed. "Computational, Experimental and Pharmacological Studies of Cu(II), Co(II) and Ni(II) Metal Complexes containing Azo Schiff base Ligand." Research Journal of Chemistry and Environment 26, no. 11 (2022): 11–27. http://dx.doi.org/10.25303/2611rjce011027.
Texte intégralRésumé :
The metal complexes containing Cu(II), Co(II) and Ni(II) metal ions were synthesised in the molar ratio of 1:2 [M:L] and azo Schiff base ligand as a primary ligand. The synthesized metal complexes were confirmed by the different analytical and spectroscopic techniques like UV-Visible, FT-IR, NMR, LC-MS and P-XRD techniques. The binding interaction of synthesized metal chelates with CT-DNA has been investigated by absorption spectra, viscosity measurements and thermal denaturation techniques. The mode of binding of the metal complexes with calf-thymus DNA has been explored. The metal complexes [Cu(II), Co(II) and Ni(II)] intercalated between the base pairs of the CT-DNA tightly with intrinsic binding constant (Kb) in Tris - HCl buffer containing 50 mMNaCl buffer. The DNA cleavage activities of the complexes were clearly assayed by using pUC-18 DNA which was monitored by the gel electrophoresis method. The antibacterial activity was carried out by a well-diffusion method against gram-positive bacteria S. aureus and gram-negative bacteria Shigella. Amylase inhibitory activity of pooled fractions was carried out according to the standard method with minor modification (antidiabetic activity). The in silico molecular docking was achieved with the DNA binding receptor PDB ID: 1E3Y taken from RCSB Protein Data Bank (www.rcsb.org/pdb). The receptor structre was prepared before use in docking study using protein preparation module of HEX 8.2 modelling package.
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Prasad Ratnala, V. R., F. B. Hulsbbergen, H. J. M. de Groot, and W. J. de Grip. "Analysis of histamine and modeling of ligand-receptor interactions in the histamine H 1 receptor for Magic Angle Spinning NMR studies." Inflammation Research 52, no. 10 (2003): 417–23. http://dx.doi.org/10.1007/s00011-003-1195-3.
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Baligar, Rajesh, and Vidyanand Revankar. "Coordination diversity of new mononucleating hydrazone in 3d metal complexes: synthesis, characterization and structural studies." Journal of the Serbian Chemical Society 71, no. 12 (2006): 1301–10. http://dx.doi.org/10.2298/jsc0612301b.
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The mononucleating hydrazone ligand LH3, a condensation product of salicyloylhydrazine and (2-formylphenoxy)acetic acid, was synthesized and its coordination behavior with first row transition metal(II) ions was investigated by isolating and elucidating the structure of the complexes using elemental analysis, conductivity and magnetic susceptibility measurements, as well as IR, 1H-NMR, electronic and EPR spectral techniques. The ligand forms mononuclear metal(II) complexes of the type [CoLH(H 2O)2], [NiLH(H 2O)2], [CuLH] and [ZnLH]. The ligand field parameters, Dq, B and ? values, in the case of the cobalt and nickel complexes support not only the octahedral geometry around the metal ion, but also imply the covalent nature of the bonding in the complexes. The EPR study revealed the presence of a spin exchange interaction in the solid copper complex and the covalent nature of the bonding. The 1H-NMR study of the zinc(II) complex indicated the non-involvement of the COOH group in the coordination. The physico-chemical study supports for the presence of octahedral geometry around cobalt(II), nickel(II) and tetrahedral geometry around copper(II) and zinc(II) ions. .
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Velkov, Tony. "Interactions between Human Liver Fatty Acid Binding Protein and Peroxisome Proliferator Activated Receptor Selective Drugs." PPAR Research 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/938401.
Texte intégralRésumé :
Fatty acid binding proteins (FABPs) act as intracellular shuttles for fatty acids as well as lipophilic xenobiotics to the nucleus, where these ligands are released to a group of nuclear receptors called the peroxisome proliferator activated receptors (PPARs). PPAR mediated gene activation is ultimately involved in maintenance of cellular homeostasis through the transcriptional regulation of metabolic enzymes and transporters that target the activating ligand. Here we show that liver- (L-) FABP displays a high binding affinity for PPAR subtype selective drugs. NMR chemical shift perturbation mapping and proteolytic protection experiments show that the binding of the PPAR subtype selective drugs produces conformational changes that stabilize the portal region of L-FABP. NMR chemical shift perturbation studies also revealed that L-FABP can form a complex with the PPAR ligand binding domain (LBD) of PPARα. This protein-protein interaction may represent a mechanism for facilitating the activation of PPAR transcriptional activity via the direct channeling of ligands between the binding pocket of L-FABP and the PPARαLBD. The role of L-FABP in the delivery of ligands directly to PPARαvia this channeling mechanism has important implications for regulatory pathways that mediate xenobiotic responses and host protection in tissues such as the small intestine and the liver where L-FABP is highly expressed.
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Lyukmanova, Ekaterina, Maxim Zaigraev, Dmitrii Kulbatskii та ін. "Abstract OR-3: Integrative Structural Study of the Complex of Snake Toxin WTX with α7-type Nicotinic Acetylcholine Receptor". International Journal of Biomedicine 11, Suppl_1 (2021): S7—S8. http://dx.doi.org/10.21103/ijbm.11.suppl_1.or3.
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Background: Nicotinic acetylcholine receptors are ligand-gated ion channels present in the nervous system, epithelium, and the immune system. The α7-type nicotinic receptor (α7-nAChR) is a homopentameric membrane protein containing five ligand binding sites located at the interface between subunits in the extracellular domain of the receptor. α7-nAChR is considered a promising target for the treatment of cancer and cognitive dysfunction in Alzheimer's disease, schizophrenia, and depression. WTX is a non-conventional three-finger neurotoxin from the Naja kaouthia venom inhibiting α7-nAChR. WTX structure consists of three loops protruding from the “head” (core) stabilized by a system of disulfide bonds. Methods: The complex of the α7-nAChR extracellular domain with a recombinant analogue of WTX was studied by cryo-electron microscopy. The structure of the complex of full-length α7-nAChR with the toxin in the membrane environment was reconstructed by in silico molecular modeling. Interaction of WTX with the lipid membrane was confirmed by NMR-spectroscopy. Results: Analysis of electronic images confirmed the homopentameric organization of the extracellular domain with a diameter of ~ 9 nm and a height of ~ 7 nm. On the electron density map, additional regions corresponding to five WTX molecules located at the intersubunit interfaces of the domain were observed. Fitting the known spatial structures of the extracellular domain and the WTX toxin into the obtained electron density made it possible to reconstruct the structure of the complex (although with a low resolution of ~ 8 Ǻ due to the predominant orientation of particles in the ice) and to determine the topology of the toxin-receptor interaction. It was revealed that WTX interacts with the extracellular domain of α7-nAChR by the loop II, while the loop I and the toxin’s head seem to interact with the surface of the lipid membrane surrounding the receptor. Model of the complex of the full-length α7-nAChR receptor with WTX in the membrane environment corresponding to the neuronal membrane was constructed using computer simulation methods. Molecular dynamics for >1500 ns confirmed the stability of the complex. The predicted membrane-active site of the WTX molecule includes residues Lys13 and Arg18. The study of WTX and its mutants Lys13Ala and Arg18Ala by NMR-spectroscopy confirmed the importance of these residues for interaction with lipid membrane. Conclusion: Interaction mode of non-conventional neurotoxins with nAChR has been determined for the first time.
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Ramgeetha, L., and K. Arunsunai Kumar. "Exploring the DNA Interaction and Antimicrobial Screening of Mixed Ligand Transition Metal(II) Complexes containing Isoniazid-Lawsone Schiff Base: Synthesis, Structural Elucidation and Molecular Docking." Asian Journal of Chemistry 37, no. 6 (2025): 1271–81. https://doi.org/10.14233/ajchem.2025.33699.
Texte intégralRésumé :
Designing of novel metal-based molecular drugs is an effective approach to fight against the ongoing threat of antimicrobial, anticancer and antioxidant resistance. With this objective, in current work, novel mixed ligand Cu(II), Co(II), Ni(II) and Zn(II) complexes have been designed and prepared by coordinating isoniazid Schiff base as main ligand and lawsone as co-ligand. Moreover, the synthesis of these complexes have been explored with the purpose of creating stable and planar co-ligand (lawsone), thereby investigating their DNA interaction ability and other biological applications. The geometrical characteristics of these synthesized complexes were examined by elemental analysis, UV-Vis, FT-IR, NMR, Mass and EPR spectral analyses and conductivity measurements. The observed spectral data support an octahedral geometry of the complexes. The low molar conductance value specifies the non-electrolytic nature of the synthesized complexes. Their magnetic susceptibility and EPR spectral data confirm the monomeric nature of all the metal(II) complexes. The interaction between the complexes and ct-DNA is evaluated using electronic absorption titration and viscosity measurements, cyclic voltammetry and molecular modelling studies. DNA study reveals that the complexes have intercalation type of binding. The MIC values of the synthesized complexes expose their better antimicrobial inhibiting features than the ligand. DFT studies were also carried out using Gaussian 09 software 6-31G/B3LYP set. Moreover, the molecular docking interaction was done in order to support the in vitro DNA interaction experiments. The conclusions of all the studies reveal that Cu(II) complex exhibits good biological characteristics than the free ligand and other metal(II) complexes.
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Bednarek, Elżbieta, Wojciech Bocian, Jerzy Sitkowski, Magdalena Urbanowicz, and Lech Kozerski. "New 5-Substituted SN38 Derivatives: A Stability Study and Interaction with Model Nicked DNA by NMR and Molecular Modeling Methods." International Journal of Molecular Sciences 24, no. 24 (2023): 17445. http://dx.doi.org/10.3390/ijms242417445.
Texte intégralRésumé :
The new 5-substituted SN-38 derivatives, 5(R)-(N-pyrrolidinyl)methyl-7-ethyl-10-hydroxycamptothecin (1) and its diastereomer 5(S) (2), were investigated using a combination of nuclear magnetic resonance (NMR) spectroscopy and molecular modeling methods. The chemical stability, configuration stability, and propensity to aggregate as a function of concentration were determined using 1H NMR. The calculated self-association constants (Ka) were found to be 6.4 mM−1 and 2.9 mM−1 for 1 and 2, respectively. The NMR experiments were performed to elucidate the interaction of each diastereomer with a nicked decamer duplex, referred to as 3. The calculated binding constants were determined to be 76 mM−1 and 150 mM−1 for the 1–3 and 2–3 complexes, respectively. NMR studies revealed that the interaction between 1 or 2 and the nicked decamer duplex occurred at the site of the DNA strand break. To complement these findings, molecular modeling methods and calculation protocols were employed to establish the interaction mode and binding constants and to generate molecular models of the DNA/ligand complexes.
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Rajesh, Sundaresan, Pooja Sridhar, Birke Andrea Tews, et al. "Structural Basis of Ligand Interactions of the Large Extracellular Domain of Tetraspanin CD81." Journal of Virology 86, no. 18 (2012): 9606–16. http://dx.doi.org/10.1128/jvi.00559-12.
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Hepatitis C virus (HCV) causes chronic liver disease, cirrhosis, and primary liver cancer. Despite 130 million people being at risk worldwide, no vaccine exists, and effective therapy is limited by drug resistance, toxicity, and high costs. The tetraspanin CD81 is an essential entry-level receptor required for HCV infection of hepatocytes and represents a critical target for intervention. In this study, we report the first structural characterization of the large extracellular loop of CD81, expressed in mammalian cells and studied in physiological solutions. The HCV E2 glycoprotein recognizes CD81 through a dynamic loop on the helical bundle, which was shown by nuclear magnetic resonance (NMR) spectroscopy to adopt a conformation distinct from that seen in crystals. A novel membrane binding interface was revealed adjacent to the exposed HCV interaction site in the extracellular loop of CD81. The binding pockets for two proposed inhibitors of the CD81-HCV interaction, namely, benzyl salicylate and fexofenadine, were shown to overlap the HCV and membrane interaction sites. Although the dynamic loop region targeted by these compounds presents challenges for structure-based design, the NMR assignments enable realistic screening and validation of ligands. Together, these data provide an improved avenue for developing potent agents that specifically block CD81-HCV interaction and also pave a way for elucidating the recognition mechanisms of diverse tetraspanins.
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Eno, Ededet A., Emmanuel E. D. Okon, Hitler Louis, et al. "Synthesis, spectral characterization, DFT studies, and computational screening of 4‐amino‐3‐mercapto‐5‐methyl‐1,2,4‐triazole and its cadmium(II) mixed ligands complexes as potential antimalaria drug." Vietnam Journal of Chemistry 61, no. 2 (2023): 187–203. http://dx.doi.org/10.1002/vjch.202200110.
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AbstractIn this research paper we report the detailed synthesis, spectral (1H‐NMR, FT‐IR, and UV‐Vis), crystal structure determination, DFT studies, and molecular modeling of 4‐amino‐3‐mercapto‐5‐methyl‐1,2,4‐triazole (L2) Schiff base ligand and its complexes of cadmium as suitable bioactive agents for the treatment of malaria. From the spectroscopic results, the synthesized Schiff base has potentialtridentate coordination with themetal ion via hydroxy naphthalinic‐O, azomethine‐N and sulphur atom of the thione group. First principle theoretical calculations within the framework of density functional theory (DFT) were conducted to scrutinize the stability, reactivity, energetics, and the nature of bonding interactions in the studied Schiff base and its complexes. In‐silico molecular simulation was also executed to comprehend the conformation of interaction of the studied compounds against malaria (1LS5) protein for possible treatment of the disease. The observed binding affinity for the ligand (L2), its mono‐ligand complex [CdL2Cl], mixed ligands complex [CdL2TH]Cl and the standard drug are ‐7.23, ‐7.63, ‐7.3, and ‐7.60 kcal/mol, respectively, indicating that the Schiff base and is Cd2+ complexes have the potential to be developed into therapeutic drug for the treatment of malaria.
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Jeslin Kanaga Inba, P., B. Annaraj, S. Thalamuthu, and M. A. Neelakantan. "Cu(II), Ni(II), and Zn(II) Complexes of Salan-Type Ligand Containing Ester Groups: Synthesis, Characterization, Electrochemical Properties, andIn VitroBiological Activities." Bioinorganic Chemistry and Applications 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/439848.
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A salen ligand on reduction and N-alkylation affords a novel [N2O2] chelating ligand containing ester groups [L = diethyl-2,2′-(propane-1,3-diylbis((2-hydroxy-3-methoxy benzyl)azanediyl))diacetate]. The purity of the ligand was confirmed by NMR and HPLC chromatograms. Its Cu(II), Ni(II), and Zn(II) complexes were synthesized and characterized by a combination of elemental analysis, IR, NMR, UV-Vis, and mass spectral data, and thermogravimetric analysis (TG/DTA). The magnetic moments, UV-Vis, and EPR spectral studies support square planar geometry around the Cu(II) and Ni(II) ions. A tetrahedral geometry is observed in four-coordinate zinc with bulky N-alkylated salan ligand. The redox properties of the copper complex were examined in DMSO by cyclic voltammetry. The voltammograms show quasireversible process. The interaction of metal complexes with CT DNA was investigated by UV-Vis absorption titration, ethidium bromide displacement assay, cyclic voltammetry methods, and agarose gel electrophoresis. The apparent binding constant values suggest moderate intercalative binding modes between the complexes and DNA. Thein vitroantioxidant and antimicrobial potentials of the synthesized compounds were also determined.
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Sujatha, G., T. Pazhanisamy, M. Suresh, and P. Ramanathan. "Synthesis and docking studies of some novel heterocyclic moieties acting as superior inhibitors." Research Journal of Chemistry and Environment 28, no. 8 (2024): 16–22. http://dx.doi.org/10.25303/288rjce016022.
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We created new xanthene derivatives in this study for the traditional approach and the derivatives validity is supported by mass spectral, NMR and infrared imaging methods. In the current situation, the virus has been affecting a large number of people worldwide for the last two years. Docking studies were conducted to explore the potential binding mechanism of the target compounds and xanthene derivatives were used in the prediction of molecular docking for novel compounds. The lowest binding energies, which were verified by protein binding to the compounds, were -5.43, -5.57, -6.25, -5.99 and -5.47 kcal/mol, appropriate binding confirmation for the docking validates the hydrogen bonding interactions. Compound 3 molecular researches revealed that the three main interactions involving this ligands attachment to the SARS-CoV-2 acceptor are the presence of hydrogen bonds, hydrophobic contacts and moderate polar interactions. The docked compound 3 two-dimensional interaction diagram showed that hydrophobic residues like CYSA:42 and HISA:101 surround the ligand. This observation led to the conclusion that the binding process involves both de-solvation effects and hydrophobic contacts. Moreover, the target ligand 3 surface is surrounded by hydrophilic residues such as THRA:41, GLYA:40, PROA:10, ASPA:39, SERA:8 and LEUA:37. Compound 3 (para-methoxy substituted) among the synthesised compounds 1-6 exhibited a good docking score of -6.25 and binding energy of -4.60 kcal/mol. Compound 3 appears to have superior ligand-protein interactions while the remaining moieties show only moderate activity in docking tests.
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YAO, Letitia J., and Kevin H. MAYO. "Interactions of integrin GPIIb/IIIa-derived peptides with fibrinogen investigated by NMR spectroscopy." Biochemical Journal 315, no. 1 (1996): 161–70. http://dx.doi.org/10.1042/bj3150161.
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Three peptides derived from platelet integrin receptor glycoprotein αIIbβ3 (GPIIb/IIIa) have been identified recently as fibrinogen-binding sequences: GPIIb 300–314 and 656–667 and GPIIIa 211–223. NMR spectroscopy has been used here to investigate the interactions of these peptides with parent fibrinogen. Based on resonance broadening and chemical-shift changes of peptides in the presence and absence of fibrinogen, interactions in the fast ligand-exchange regime are apparent and interfacial residues can be proposed. Positively charged arginines and histidines, along with several hydrophobic residues, are implicated as being crucial to the binding process. Transferred nuclear Overhauser effects and distance geometry calculations allow discussion of probable conformations in peptide-‘bound’ states. These identifications are consistent with other biological/ chemical data and provide the basis for further studies aimed at understanding fibrinogen-mediated platelet aggregation on the molecular level.
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Sahoo, Amita R., and Matthias Buck. "Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors." International Journal of Molecular Sciences 22, no. 16 (2021): 8593. http://dx.doi.org/10.3390/ijms22168593.
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Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.
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Haugaard-Jönsson, Linda M., Mohammed Akhter Hossain, Norelle L. Daly, David J. Craik, John D. Wade, and K. Johan Rosengren. "Structure of human insulin-like peptide 5 and characterization of conserved hydrogen bonds and electrostatic interactions within the relaxin framework." Biochemical Journal 419, no. 3 (2009): 619–27. http://dx.doi.org/10.1042/bj20082353.
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INSL5 (insulin-like peptide 5) is a two-chain peptide hormone related to insulin and relaxin. It was recently discovered through searches of expressed sequence tag databases and, although the full biological significance of INSL5 is still being elucidated, high expression in peripheral tissues such as the colon, as well as in the brain and hypothalamus, suggests roles in gut contractility and neuroendocrine signalling. INSL5 activates the relaxin family peptide receptor 4 with high potency and appears to be the endogenous ligand for this receptor, on the basis of overlapping expression profiles and their apparent co-evolution. In the present study, we have used solution-state NMR to characterize the three-dimensional structure of synthetic human INSL5. The structure reveals an insulin/relaxin-like fold with three helical segments that are braced by three disulfide bonds and enclose a hydrophobic core. Furthermore, we characterized in detail the hydrogen-bond network and electrostatic interactions between charged groups in INSL5 by NMR-monitored temperature and pH titrations and undertook a comprehensive structural comparison with other members of the relaxin family, thus identifying the conserved structural features of the relaxin fold. The B-chain helix, which is the primary receptor-binding site of the relaxins, is longer in INSL5 than in its close relative relaxin-3. As this feature results in a different positioning of the receptor-activation domain ArgB23 and TrpB24, it may be an important contributor to the difference in biological activity observed for these two peptides. Overall, the structural studies provide mechanistic insights into the receptor selectivity of this important family of hormones.
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Leone, Marilisa, Ricard A. Rodriguez-Mias, and Maurizio Pellecchia. "Selective Incorporation of 19F-Labeled Trp Side Chains for NMR-Spectroscopy-Based Ligand-Protein Interaction Studies." ChemBioChem 4, no. 7 (2003): 649–50. http://dx.doi.org/10.1002/cbic.200300597.
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