Journal articles: 'NMR ligand-receptor interaction studies'

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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 (May 1, 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.

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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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Braitsch, Michaela, Hanspeter Kählig, Georg Kontaxis, Michael Fischer, Toshinari Kawada, Robert Konrat, and Walther Schmid. "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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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 (October 3, 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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Morales, Paula, Marta Bruix, and M. Angeles Jiménez. "Structural Insights into β-arrestin/CB1 Receptor Interaction: NMR and CD Studies on Model Peptides." International Journal of Molecular Sciences 21, no. 21 (October 30, 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 (May 15, 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, and Xu Wang. "The Q163C/Q309C mutant of αMI-domain is an active variant suitable for NMR characterization." PLOS ONE 18, no. 1 (January 25, 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 (May 15, 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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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 (April 1, 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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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 (May 20, 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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Mittag, Tanja, Stephen Orlicky, Wing-Yiu Choy, Xiaojing Tang, Hong Lin, Frank Sicheri, Lewis E. Kay, Mike Tyers, and Julie D. Forman-Kay. "Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor." Proceedings of the National Academy of Sciences 105, no. 46 (November 13, 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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Beglova, Natalia, and Chang-Jin Lee. "Mapping Interactions Between B2GPI and the Lipoprotein Receptors by Solution NMR Spectroscopy." Blood 112, no. 11 (November 16, 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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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 (May 1, 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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Kumar, Manish, Poonam Jangra Darolia, Nidhi Antil, Mahak Dalal, Jitender Narwal, K. K. Verma, and Sapana Garg. "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 (December 4, 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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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 (January 19, 2011): 210–13. http://dx.doi.org/10.1021/ja108383x.

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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 (January 28, 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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Bernini, Andrea, Arianna Ciutti, Ottavia Spiga, Maria Scarselli, Samuel Klein, Stefano Vannetti, Luisa Bracci, et al. "NMR and MD Studies on the Interaction Between Ligand Peptides and α-Bungarotoxin." Journal of Molecular Biology 339, no. 5 (June 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 (July 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 (December 16, 2022): 16018. http://dx.doi.org/10.3390/ijms232416018.

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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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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.

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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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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 (August 29, 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, Thahira B. S. A. Ravoof, Alister J. Page, Abhi Veerakumarasivam, Thiruventhan Karunakaran, and Mohd Rizal Razali. "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.

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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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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.

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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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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 (September 1, 2003): 417–23. http://dx.doi.org/10.1007/s00011-003-1195-3.

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Li, Yan, Shuang Liu, Elizabeth Yihui Ng, Rong Li, Anders Poulsen, Jeffrey Hill, Ajaybabu V. Pobbati, et al. "Structural and ligand-binding analysis of the YAP-binding domain of transcription factor TEAD4." Biochemical Journal 475, no. 12 (June 26, 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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Khalaf, Mai M., Hany M. Abd El-Lateef, Abdulrahman Alhadhrami, Fatma N. Sayed, Gehad G. Mohamed, Mohamed Gouda, Saad Shaaban, and Ahmed M. Abu-Dief. "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 (May 20, 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 (April 4, 2014): 2502–11. http://dx.doi.org/10.24297/jac.v10i3.2292.

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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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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 (October 26, 2020): 1254–64. http://dx.doi.org/10.3906/kim-2004-68.

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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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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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., 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 (October 25, 2022): 11–27. http://dx.doi.org/10.25303/2611rjce011027.

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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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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.

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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, Milita Kocharovskaya, Yury Chesnokov, Anton Chugunov, Mikhail Kirpichnikov, and Zakhar Shenkarev. "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 (June 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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Rajesh, Sundaresan, Pooja Sridhar, Birke Andrea Tews, Lucie Fénéant, Laurence Cocquerel, Douglas G. Ward, Fedor Berditchevski, and Michael Overduin. "Structural Basis of Ligand Interactions of the Large Extracellular Domain of Tetraspanin CD81." Journal of Virology 86, no. 18 (June 27, 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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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 (June 27, 2003): 649–50. http://dx.doi.org/10.1002/cbic.200300597.

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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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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 (April 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 (August 10, 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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Sahu, Gurunath, Edward R. T. Tiekink, and Rupam Dinda. "Study of DNA Interaction and Cytotoxicity Activity of Oxidovanadium(V) Complexes with ONO Donor Schiff Base Ligands." Inorganics 9, no. 9 (August 27, 2021): 66. http://dx.doi.org/10.3390/inorganics9090066.

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Two new oxidovanadium(V) complexes, (HNEt3)[VVO2L] (1) and [(VVOL)2μ-O] (2), have been synthesized using a tridentate Schiff base ligand H2L [where H2L = 4-((E)-(2-hydroxy-5-nitrophenylimino)methyl)benzene-1,3-diol] and VO(acac)2 as starting metal precursor. The ligand and corresponding metal complexes are characterized by physicochemical (elemental analysis), spectroscopic (FT-IR, UV–Vis, and NMR), and spectrometric (ESI–MS) methods. X-ray crystallographic analysis indicates the anion in salt 1 features a distorted square-pyramidal geometry for the vanadium(V) center defined by imine-N, two phenoxide-O, and two oxido-O atoms. The interaction of the compounds with CT–DNA was studied through UV–Vis absorption titration and circular dichroism methods. The results indicated that complexes showed enhanced binding affinity towards DNA compared to the ligand molecule. Finally, the in vitro cytotoxicity studies of H2L, 1, and 2 were evaluated against colon cancer (HT-29) and mouse embryonic fibroblast (NIH-3T3) cell lines by MTT assay. The results demonstrated that the compounds manifested a cytotoxic potential comparable with clinically referred drugs and caused cell death by apoptosis.

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Selvaratnam, Rajeevan, Madoka Akimoto, Bryan VanSchouwen, and Giuseppe Melacini. "cAMP-dependent allostery and dynamics in Epac: an NMR view." Biochemical Society Transactions 40, no. 1 (January 19, 2012): 219–23. http://dx.doi.org/10.1042/bst20110628.

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Epac (exchange protein directly activated by cAMP) is a critical cAMP receptor, which senses cAMP and couples the cAMP signal to the catalysis of guanine exchange in the Rap substrate. In the present paper, we review the NMR studies that we have undertaken on the CBD (cyclic-nucleotide-binding domain) of Epac1. Our NMR investigations have shown that cAMP controls distal autoinhibitory interactions through long-range modulations in dynamics. Such dynamically mediated allosteric effects contribute not only to the cAMP-dependent activation of Epac, but also to the selectivity of Epac for cAMP in contrast with cGMP. In addition, we have mapped the interaction networks that couple the cAMP-binding site to the sites involved in the autoinhibitory interactions, using a method based on the covariance analysis of NMR chemical shifts. We anticipate that this approach is generally applicable to dissect allosteric networks in signalling domains.

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Polo-Cerón, Dorian. "Cu(II) and Ni(II) Complexes with New Tridentate NNS Thiosemicarbazones: Synthesis, Characterisation, DNA Interaction, and Antibacterial Activity." Bioinorganic Chemistry and Applications 2019 (July 1, 2019): 1–14. http://dx.doi.org/10.1155/2019/3520837.

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This paper reports the synthesis and detailed characterisation of copper(II) and nickel(II) complexes with tridentate thiosemicarbazone ligands H2L1 and H2L2 derived from 2-acetylpyrazine. The ligands and their metal complexes were characterised by different physicochemical techniques, including elemental and thermogravimetric analysis; UV-Vis, IR, 1H-NMR, and 13C-NMR spectroscopy; molar conductance measurements; and mass spectrometry. The crystal structure of the H2L1 ligand was determined by single crystal X-ray diffraction studies. The spectral data showed that the thiosemicarbazone behaves as an NNS tridentate ligand through the nitrogen atoms of the azomethine group and pyrazine ring and the sulphur atom of the thioamide group. Elemental and thermal analyses indicated that the obtained metal complexes had a 1 : 1 stoichiometry (metal-ligand). The interactions between these complexes and calf thymus DNA (CT-DNA) were studied by electronic absorption and viscosity measurements. The activities of these compounds against oxidative DNA cleavage were examined by agarose gel electrophoresis. Cu(II) and Ni(II) complexes can wind DNA strands through groove interactions and promote strand breakage of the plasmid pmCherry under oxidative stress conditions. Moreover, all the complexes could interact more strongly with DNA than could with the free ligands. Finally, the antibacterial activities of the ligands and their complexes were determined by in vitro tests against Gram-positive bacterial strains (S. aureus ATCC 25923, L. monocytogenes ATCC 19115, and B. cereus ATCC 10876) and Gram-negative bacterial strains (E. coli ATCC 25922, S. typhimurium ATCC 14028, and K. pneumoniae ATCC BAA-2146) using the broth microdilution method. The metal complexes showed greater antimicrobial activities than the precursor ligands against some of the microorganisms.

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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 (April 14, 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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LeVatte, Marcia, Matthias Lipfert, Dipankar Roy, Andriy Kovalenko, and David Scott Wishart. "Cloning and high-level expression of monomeric human superoxide dismutase 1 (SOD1) and its interaction with pyrimidine analogs." PLOS ONE 16, no. 2 (February 26, 2021): e0247684. http://dx.doi.org/10.1371/journal.pone.0247684.

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Superoxide dismutase 1 (SOD1) is known to be involved in the pathogenesis of Amyotrophic Lateral Sclerosis (ALS) and is therefore considered to be an important ALS drug target. Identifying potential drug leads that bind to SOD1 and characterizing their interactions by nuclear magnetic resonance (NMR) spectroscopy is complicated by the fact that SOD1 is a homodimer. Creating a monomeric version of SOD1 could alleviate these issues. A specially designed monomeric form of human superoxide dismutase (T2M4SOD1) was cloned into E. coli and its expression significantly enhanced using a number of novel DNA sequence, leader peptide and growth condition optimizations. Uniformly 15N-labeled T2M4SOD1 was prepared from minimal media using 15NH4Cl as the 15N source. The T2M4SOD1 monomer (both 15N labeled and unlabeled) was correctly folded as confirmed by 1H-NMR spectroscopy and active as confirmed by an in-gel enzymatic assay. To demonstrate the utility of this new SOD1 expression system for NMR-based drug screening, eight pyrimidine compounds were tested for binding to T2M4SOD1 by monitoring changes in their 1H NMR and/or 19F-NMR spectra. Weak binding to 5-fluorouridine (FUrd) was observed via line broadening, but very minimal spectral changes were seen with uridine, 5-bromouridine or trifluridine. On the other hand, 1H-NMR spectra of T2M4SOD1 with uracil or three halogenated derivatives of uracil changed dramatically suggesting that the pyrimidine moiety is the crucial binding component of FUrd. Interestingly, no change in tryptophan 32 (Trp32), the putative receptor for FUrd, was detected in the 15N-NMR spectra of 15N-T2M4SOD1 when mixed with these uracil analogs. Molecular docking and molecular dynamic (MD) studies indicate that interaction with Trp32 of SOD1 is predicted to be weak and that there was hydrogen bonding with the nearby aspartate (Asp96), potentiating the Trp32-uracil interaction. These studies demonstrate that monomeric T2M4SOD1 can be readily used to explore small molecule interactions via NMR.

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Wong, Kok Tong, Hasnah Osman, Thaigarajan Parumasivam, Unang Supratman, Mohammad Tasyriq Che Omar, and Mohamad Nurul Azmi. "Synthesis, Characterization and Biological Evaluation of New 3,5-Disubstituted-Pyrazoline Derivatives as Potential Anti-Mycobacterium tuberculosis H37Ra Compounds." Molecules 26, no. 7 (April 5, 2021): 2081. http://dx.doi.org/10.3390/molecules26072081.

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A total of fourteen pyrazoline derivatives were synthesized through cyclo-condensation reactions by chalcone derivatives with different types of semicarbazide. These compounds were characterized by IR, 1D-NMR (1H, 13C and Distortionless Enhancement by Polarization Transfer - DEPT-135) and 2D-NMR (COSY, HSQC and HMBC) as well as mass spectroscopy analysis (HRMS). The synthesized compounds were tested for their antituberculosis activity against Mycobacterium tuberculosis H37Ra in vitro. Based on this activity, compound 4a showed the most potent inhibitory activity, with a minimum inhibitory concentration (MIC) value of 17 μM. In addition, six other synthesized compounds, 5a and 5c–5g, exhibited moderate activity, with MIC ranges between 60 μM to 140 μM. Compound 4a showed good bactericidal activity with a minimum bactericidal concentration (MBC) value of 34 μM against Mycobacterium tuberculosis H37Ra. Molecular docking studies for compound 4a on alpha-sterol demethylase was done to understand and explore ligand–receptor interactions, and to hypothesize potential refinements for the compound.

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Covaci, Ancuța, Cristian Silvestru, and Anca Silvestru. "Coordination behavior of PPh₂{C₆H₄[CH₂N(CH₂CH₂)₂O]-2}: Case study CdCl₂[PPh₂{C₆H₄[CH₂N(CH₂CH₂)₂O]-2}]." Main Group Metal Chemistry 44, no. 1 (January 1, 2021): 261–66. http://dx.doi.org/10.1515/mgmc-2021-0029.

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Abstract The reaction between CdCl2 and PPh2{C6H4 [CH2N(CH2CH2)2O]-2} (1) in a 1:1 molar ratio resulted in the cadmium(II) complex CdCl2[PPh2{C6H4[CH2N(CH2CH2)2O]-2}] (2). The complex 2 was characterized in solution by NMR spectroscopy (1H, 13C, and 31P). Single-crystal X-ray diffraction studies revealed no intramolecular N→P interaction in 1. The phosphane ligand behaves as a P,N chelating moiety in the cadmium complex 2, thus resulting in a species containing distorted tetrahedral environments around cadmium and phosphorus. Short intermolecular interactions CH‧‧‧π aryl and CH‧‧‧O in 1 and CH‧‧‧π aryl and CH‧‧‧Cl in 2 resulted in supramolecular networks.

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Andavar, Sasikumar, Mohanasrinivasan Vaithilingam, Divakar Selvaraj, Ajeeshkumar A. Kumaran, and Krishnaswamy Devanathan. "Design, Synthesis and Evaluation of Novel Substituted (5-methyl-1H-pyrazol-3-yl)- 1,3,4-oxadiazole as Potent Androgen Receptor Antagonist." Anti-Cancer Agents in Medicinal Chemistry 20, no. 1 (April 10, 2020): 84–93. http://dx.doi.org/10.2174/1871520619666191121095720.

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Background: Androgen Receptor (AR) is one of the highly explored targets for the treatment of prostate cancer. The emergence of point mutation in the Ligand Binding Domain (LBD) of AR has resulted in the development of resistance against AR antagonist. The point mutation T877A, W741L and F876L confer resistance to flutamide, bicalutamide and enzalutamide respectively. There is no AR antagonist in the present clinical set up without resistance. Hence, our aim in this study is to design a novel molecule to overcome the resistance caused by point mutation. Methods: Here, we developed novel AR antagonist bearing (5-methyl-1H-pyrazol-3-yl)-1, 3,4-oxadiazole core by rational drug design. The test molecules 8a-h were synthesized from the corresponding dihydrazide compounds 7a-h on treatment with phosphorous oxychloride on reflux conditions. The structure of the molecules was confirmed from spectral data such as IR, 1H-NMR, HRMS and 13C-NMR. The synthesized compounds were screened for cytotoxicity in prostate cancer cell lines LNCaP-FGC and PC3. The confirmation of AR mediated activity of the test compounds was confirmed by gene expression study. The interaction of the best active ligands with mutant AR was predicted and drug design was rationalized through docking studies. Results: The test compounds 8a-h were synthesized and the structures were conformed using suitable techniques like IR, 1H-NMR, HRMS and 13C-NMR. Among the tested compounds, 8b and 8d showed potent antiproliferative activity against mutant AR cell lines. Further, these compounds significantly decreased the gene expression of prostate cancer biomarkers. Conclusion: In this study, we have identified a potential hit molecule for AR antagonism that could be further developed to obtain a potent clinical candidate.

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Ahmad, Fawad, Muneera D. F. Alkahtani, Muhammad Babar Taj, Afnan M. Alnajeebi, Seraj Omar Alzahrani, Nouf Abubakr Babteen, Walla Alelwani, et al. "Synthesis of New Naphthyl Aceto Hydrazone-Based Metal Complexes: Micellar Interactions, DNA Binding, Antimicrobial, and Cancer Inhibition Studies." Molecules 26, no. 4 (February 17, 2021): 1044. http://dx.doi.org/10.3390/molecules26041044.

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In the present study, naphthyl acetohydrazide (HL) ligand was prepared and used for the synthesis of new six amorphous transition metal (Co(II), Ni(II), Cu(II), Zn(II), Pb(II), Cd(II)) complexes. All the compounds were characterized by elemental analysis, UV-vis, FT-IR, 1H- and 13C-NMR, and Matrix-Assisted Laser Desorption Ionization (MALDI). The solubilization study was carried out by estimating the interaction between the metal complexes with surfactants viz. sodium stearate (SS) and Cetyltrimethylammonium bromide (CTAB). UV-Visible spectroscopy was employed to determine partitioning and binding parameters, whereas electrical conductivity measurements were employed to estimate critical micellar concentration (CMC), the extent of dissociation, and free energy of micellization. The CT-DNA interaction of synthesized compounds with DNA represents the major groove binding. The synthesized ligand and metal complexes were also tested against bacterial and fungal strains and it has been observed that Cu(II) complex is active against all the strains except Candida albicans, while Cd(II) complex is active against all bacterial and fungal strains except Pseudomonas. Among all compounds, only the Pd(II) complex shows reasonable activity against cervical cancer HeLa cell lines, representing 97% inhibition.

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Sabbah, Dima A., Ameerah H. Ibrahim, Wamidh H. Talib, Khalid M. Alqaisi, Kamal Sweidan, Sanaa K. Bardaweel, Ghassan A. Sheikha, et al. "Ligand-Based Drug Design: Synthesis and Biological Evaluation of Substituted Benzoin Derivatives as Potential Antitumor Agents." Medicinal Chemistry 15, no. 4 (May 20, 2019): 417–29. http://dx.doi.org/10.2174/1573406414666180912111846.

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Background: Phosphoinositide 3-kinase α (PI3Kα) has emerged as a promising target for anticancer drug design. Objectives: Target compounds were designed to investigate the effect of the p-OCH3 motifs on ligand/PI3Kα complex interaction and antiproliferative activity. Methods: Synthesis of the proposed compounds, biological examination tests against human colon adenocarcinoma (HCT-116), breast adenocarcinoma (MCF-7), and breast carcinoma (T47D) cell lines, along with Glide docking studies. Results: A series of 1,2-bis(4-methoxyphenyl)-2-oxoethyl benzoates was synthesized and characterized by means of FT-IR, 1H and 13C NMR, and by elemental analysis. Biological investigation demonstrated that the newly synthesized compounds exhibit antiproliferative activity in human colon adenocarcinoma (HCT-116), breast adenocarcinoma (MCF-7), and breast carcinoma (T47D) cell lines possibly via inhibition of PI3Kα and estrogen receptor alpha (ERα). Additionally, results revealed that these compounds exert selective inhibitory activity, induce apoptosis, and suppress VEGF production. Compound 3c exhibited promising antiproliferative activity in HCT-116 interrogating that hydrogen bond-acceptor mediates ligand/PI3Kα complex formation on m- position. Compounds 3e and 3i displayed high inhibitory activity in MCF-7 and T47D implying a wide cleft discloses the o-attachment. Furthermore, compound 3g exerted selective inhibitory activity against T47D. Glide docking studies against PI3Kα and ERα demonstrated that the series accommodate binding to PI3Kα and/or ERα. Conclusion: The series exhibited a potential antitumor activity in human carcinoma cell lines encoding PI3Kα and/or ERα.

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Weeks, Amy M., Ningkun Wang, Jeffrey G. Pelton, and Michelle C. Y. Chang. "Entropy drives selective fluorine recognition in the fluoroacetyl–CoA thioesterase from Streptomyces cattleya." Proceedings of the National Academy of Sciences 115, no. 10 (February 16, 2018): E2193—E2201. http://dx.doi.org/10.1073/pnas.1717077115.

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Fluorinated small molecules play an important role in the design of bioactive compounds for a broad range of applications. As such, there is strong interest in developing a deeper understanding of how fluorine affects the interaction of these ligands with their targets. Given the small number of fluorinated metabolites identified to date, insights into fluorine recognition have been provided almost entirely by synthetic systems. The fluoroacetyl–CoA thioesterase (FlK) from Streptomyces cattleya thus provides a unique opportunity to study an enzyme–ligand pair that has been evolutionarily optimized for a surprisingly high 106 selectivity for a single fluorine substituent. In these studies, we synthesize a series of analogs of fluoroacetyl–CoA and acetyl–CoA to generate nonhydrolyzable ester, amide, and ketone congeners of the thioester substrate to isolate the role of fluorine molecular recognition in FlK selectivity. Using a combination of thermodynamic, kinetic, and protein NMR experiments, we show that fluorine recognition is entropically driven by the interaction of the fluorine substituent with a key residue, Phe-36, on the lid structure that covers the active site, resulting in an ∼5- to 20-fold difference in binding (KD). Although the magnitude of discrimination is similar to that found in designed synthetic ligand–protein complexes where dipolar interactions control fluorine recognition, these studies show that hydrophobic and solvation effects serve as the major determinant of naturally evolved fluorine selectivity.

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Struhatska, M., I. Olyshevets, V. Dyakonenko, V. Ovchynnikov, S. Shishkina, and V. Amirkhanov. "STRUCTURAL AND SPECTRAL STUDIES OF THE MIXED-LIGAND CATION COMPLEX OF LANTHANUM [Lа(L)2bipy2]BPh4 WITH CARBACYLAMIDOPHOSPHATE (CAPH) TYPE LIGAND AND 2,2'-BIPYRIDINE." Bulletin of Taras Shevchenko National University of Kyiv. Chemistry, no. 1 (57) (2020): 15–19. http://dx.doi.org/10.17721/1728-2209.2020.1(57).4.

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A new cationic mixed-ligand complex [Lа(L)2bipy2]BPh4 (where L-= bis(N,N'-diethylamide)(N'-trichloroacetyl)-triamidophosphate anion, bipy = 2,2'-bipyridine) has been synthesized and studied by the means of IR, 1H NMR spectroscopy, thermogravimetric and X-ray structural analyses. Low-frequency shifts of the absorption bands of the carbonyl and phosphoryl groups of phosphorylated ligand in the IR spectra of the complex compared with similar absorption bands in the spectrum of "free" CAPh ligand are Δν(C = O) = 117 cm–1 and Δν(P = O) = 137 cm–1. The analysis of integral signal intensity in the investigated NMR spectra of coordination compounds [Lа(L)2bipy2]BPh4 indicates the molar ratio of ligand : bipyridine : tetraphenylborate anion as a 2:2:1, which corresponds to the proposed structure of the complexes. The compound has been obtained in monocrystalline form. The structure of the complex has been determined by X-ray structural analysis, its ionic structure was proved, and the coordination of two CAPh ligands through the oxygen atoms of the carbonyl and phosphoryl groups was confirmed. Based on the structural data, it was determined that the La3+ ion is octocoordinated (surrounded by four oxygen atoms from two chelated phosphoryl ligands and four nitrogen atoms from two 2,2'-bipyridine molecules). The coordination polyhedron of central ion is interpreted as a square antiprism. Complex cations and tetraphenylborate anions are connected both by electrostatic interaction and by weak intermolecular C – H ∙∙∙ π-contacts between phenyl substituents of BPh4- and molecules of 2,2'-bipyridine. It was established by thermogravimetric analysis that the complex [Lа(L)2bipy2]BPh4 obtained is thermally stable up to a temperature of 150 °C. Significant decomposition of the complex begins at a temperature of 150 °C, occurs in one stage and most intensively continues up to 300 °C. The total weight loss is 78 %.

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Journal articles on the topic 'NMR ligand-receptor interaction studies'

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