Статті в журналах: "Ligand Molecules"

1

Zhou, Mengbo, Li Song, Feng Niu, Kangying Shu та Wenxiang Chai. "A square-pyramidal copper(II) complex with strong intramolecular hydrogen bonds: diaqua(N,N′-dimethylformamide-κO)bis[2-(diphenylphosphoryl)benzoato-κO]copper(II)". Acta Crystallographica Section C Crystal Structure Communications 69, № 5 (9 квітня 2013): 463–66. http://dx.doi.org/10.1107/s0108270113008317.

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In the title CuIIcomplex, [Cu(C19H14O3P)2(C3H7NO)(H2O)2], the molecule is bisected by a twofold axis relating the two 2-(diphenylphosphoryl)benzoate (ODPPB) ligands. The asymmetric unit consists of a CuIImetal centre on the symmetry axis, an ODPPB ligand, one water ligand and one dimethylformamide (DMF) ligand (disordered around the twofold axis). The CuIIion has fivefold coordination provided by two carboxylate O atoms from two ODPPB ligands, two O atoms from two coordinated water molecules and another O atom from a (disordered) DMF molecule, giving a CuO5square-pyramidal coordination geometry. The ODPPB ligand adopts a terminal monocoordinated mode with two free O atoms forming two strong intramolecular hydrogen bonds with the coordinated water molecules, which may play a key role in the stability of the molecular structure, as shown by the higher release temperature for the coordinated water molecules than for the coordinated DMF molecule. The optical absorption properties of powder samples of the title compound have also been studied.

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2

Nagamalla, Lavanya, J. V. Shanmukha Kumar, Mohammed Rafi Shaik, Chintakindi Sanjay, Ali M. Alsamhan, Mohsin Ahmed Kasim, and Abdulrahman Alwarthan. "Identification of Novel AXL Kinase Inhibitors Using Ligand-Based Pharmacophore Screening and Molecular Dynamics Simulations." Crystals 12, no. 8 (August 17, 2022): 1158. http://dx.doi.org/10.3390/cryst12081158.

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AXL kinase is a promising target in novel drug discovery for cancer. A ligand-based pharmacophore model was generated with the Pharmit web server. Its inbuilt PubChem molecule database was screened and led to 408 candidate molecules. Docking of the AXL kinase active sites with the identified list of candidate molecules was carried out with Autodock Vina docking software. This resulted in four compounds selected for further investigation. Molecular dynamics simulation of two ligands (PubChem-122421875 and PubChem-78160848) showed considerable binding with AXL kinase. From the MM-PBSA binding free energies investigation, the PubChem-122421875 (G = −179.3 kJ/mol) and PubChem-78160848 (G = −208.3 kJ/mol) ligands had favorable protein-ligand complex stability and binding free energy. Hence, PubChem-122421875 and PubChem-78160848 molecules identified in this work could be a potent starting point for developing novel AXL kinase inhibitor molecules.

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3

Kim, Yun Young, та Joseph M. Tanski. "Crystal structure of a rare trigonal bipyramidal titanium(IV) coordination complex: trichlorido(3,3′-di-tert-butyl-2′-hydroxy-5,5′,6,6′-tetramethyl-1,1′-biphenyl-2-olato-κO2)(tetrahydrofuran-κO)titanium(IV)". Acta Crystallographica Section E Crystallographic Communications 73, № 1 (1 січня 2017): 88–91. http://dx.doi.org/10.1107/s2056989016020156.

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The title compound, [Ti(C24H33O2)Cl3(C4H8O)], is a rare example of a trigonal–bipyramidal titanium coordination complex with three chloride and two oxygen donor ligands. The asymmetric unit contains two independent molecules having essentially the same conformation. The molecules feature the titanium(IV) metal cation complexed with three chloride ligands, a tetrahydrofuran molecule, and one oxygen atom from the resolved ligand precursor (R)-(+)-5,5′,6,6′-tetramethyl-3,3′-di-t-butyl-1,1′-biphenyl-2,2′-diol, where the remaining phenolic hydrogen atom engages in intermolecular O—H...Cl hydrogen bonding. In one molecule, the THF ligand is disordered over two orientations with refined site occupancies of 0.50 (3).

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4

Lie, W. R., N. B. Myers, J. M. Connolly, J. Gorka, D. R. Lee, and T. H. Hansen. "The specific binding of peptide ligand to Ld class I major histocompatibility complex molecules determines their antigenic structure." Journal of Experimental Medicine 173, no. 2 (February 1, 1991): 449–59. http://dx.doi.org/10.1084/jem.173.2.449.

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To better understand the biological implications of the association of ligand with major histocompatibility complex class I molecules, we have studied the Ld molecule of the mouse. The culturing of various nonselected cell lines with three different known Ld peptide ligands resulted in a two- to fourfold specific increase in surface Ld expression as detected by 10 of 11 different monoclonal antibodies (mAbs) recognizing Ld epitopes. These findings suggest that Ld molecules are not saturated with endogenous peptide ligands and thus have accessible binding sites. Exploiting this feature of Ld we demonstrate that the physical association of Ld with ligand is exquisitely specific, indicating that they function in determinant selection. In addition, a non-peptide-bound antigenic variant of Ld was specifically detected with an exceptional mAb designated 64-3-7. In comparison with other Ld molecules, 64-3-7+ Ld molecules are not peptide ligand inducible, are more susceptible to proteolysis, lack beta 2 microglobulin association, and display a slower rate of oligosaccharide maturation. In spite of their deficiencies, the non-ligand-associated 64-3-7 Ld molecules were detected on the surface of all cell types tested; however, they appear not to be recognized by alloreactive cytotoxic T lymphocytes.

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5

Baisya, Siddhartha S., та Parag S. Roy. "(2-Amino-7-methyl-4-oxidopteridine-6-carboxylato-κ3O4,N5,O6)aqua(ethane-1,2-diamine-κ2N,N′)nickel(II) dihydrate". Acta Crystallographica Section E Structure Reports Online 69, № 2 (12 січня 2013): m99—m100. http://dx.doi.org/10.1107/s160053681300069x.

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The NiIIatom in the title complex, [Ni(C8H5N5O3)(C2H8N2)(H2O)]·2H2O, is six-coordinated in a distorted octahedral geometry by a tridentate 2-amino-7-methyl-4-oxidopteridine-6-carboxylate (pterin) ligand, a bidentate ancillary ethane-1,2-diamine (en) ligand and a water molecule. The pterin ligand forms two chelate rings. The en and pterin ligands are arranged nearly orthogonally [dihedral angle between the mean plane of the en molecule and the pterin ring = 77.1 (1)°]. N—H...O, O—H...N and O—H...O hydrogen bonds link the complex molecules and lattice water molecules into a three-dimensional network. π–π interactions are observed between the pyrazine and pyrimidine rings [centroid–centroid distance = 3.437 (2) Å].

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6

Gupta, Shivani. "Investigation of anti-microbial activity of imidazol [2, 1-B][1,3,4] thiadiazole by using molecular docking and ADMET studies." Indian Journal of Pharmacy and Pharmacology 9, no. 3 (August 15, 2022): 201–4. http://dx.doi.org/10.18231/j.ijpp.2022.036.

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This report consists of molecular docking based on series of imidazol [2,1-b], , thiadiazole-benzimidazole derivative. Molecular docking is software which gives information about molecular modeling in which molecule fits into target binding sites and predict structure of intermolecular complex. These molecules were investigated by protein ligand binding score, protein ligand interaction and ADME studies. All the target molecules were analyzed against which is a gram positive bacteria found on skin and upper respiratory tract. The protein molecule selected for the analysis was PDB code 4LAE protein ligand. Basically it is a oxidoreductase inhibitor and its structure is based on 7(benzimidazole-1-yl)-2, 4-diaminoquinazolines. Out of all twenty nine compounds five compounds (5B,5G,5H,5N and 5Q) were estimated as most potent molecules as antibacterial agent.

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7

Salio, Mariolina, Wael Awad, Natacha Veerapen, Claudia Gonzalez-Lopez, Corinna Kulicke, Dominic Waithe, Anne W. J. Martens, et al. "Ligand-dependent downregulation of MR1 cell surface expression." Proceedings of the National Academy of Sciences 117, no. 19 (April 27, 2020): 10465–75. http://dx.doi.org/10.1073/pnas.2003136117.

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The antigen-presenting molecule MR1 presents riboflavin-based metabolites to Mucosal-Associated Invariant T (MAIT) cells. While MR1 egress to the cell surface is ligand-dependent, the ability of small-molecule ligands to impact on MR1 cellular trafficking remains unknown. Arising from an in silico screen of the MR1 ligand-binding pocket, we identify one ligand, 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoic acid, DB28, as well as an analog, methyl 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoate, NV18.1, that down-regulate MR1 from the cell surface and retain MR1 molecules in the endoplasmic reticulum (ER) in an immature form. DB28 and NV18.1 compete with the known MR1 ligands, 5-OP-RU and acetyl-6-FP, for MR1 binding and inhibit MR1-dependent MAIT cell activation. Crystal structures of the MAIT T cell receptor (TCR) complexed with MR1-DB28 and MR1-NV18.1, show that these two ligands reside within the A′-pocket of MR1. Neither ligand forms a Schiff base with MR1 molecules; both are nevertheless sequestered by a network of hydrophobic and polar contacts. Accordingly, we define a class of compounds that inhibits MR1 cellular trafficking.

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8

Koehler, Melanie, Anny Fis, Hermann J. Gruber, and Peter Hinterdorfer. "AFM-Based Force Spectroscopy Guided by Recognition Imaging: A New Mode for Mapping and Studying Interaction Sites at Low Lateral Density." Methods and Protocols 2, no. 1 (January 8, 2019): 6. http://dx.doi.org/10.3390/mps2010006.

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Ligand binding to receptors is one of the most important regulatory elements in biology as it is the initiating step in signaling pathways and cascades. Thus, precisely localizing binding sites and measuring interaction forces between cognate receptor–ligand pairs leads to new insights into the molecular recognition involved in these processes. Here we present a detailed protocol about applying a technique, which combines atomic force microscopy (AFM)-based recognition imaging and force spectroscopy for studying the interaction between (membrane) receptors and ligands on the single molecule level. This method allows for the selection of a single receptor molecule reconstituted into a supported lipid membrane at low density, with the subsequent quantification of the receptor–ligand unbinding force. Based on AFM tapping mode, a cantilever tip carrying a ligand molecule is oscillated across a membrane. Topography and recognition images of reconstituted receptors are recorded simultaneously by analyzing the downward and upward parts of the oscillation, respectively. Functional receptor molecules are selected from the recognition image with nanometer resolution before the AFM is switched to the force spectroscopy mode, using positional feedback control. The combined mode allows for dynamic force probing on different pre-selected molecules. This strategy results in higher throughput when compared with force mapping. Applied to two different receptor–ligand pairs, we validated the presented new mode.

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9

Martín-Mora, David, Matilde Fernández, Félix Velando, Álvaro Ortega, José Gavira, Miguel Matilla, and Tino Krell. "Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges." International Journal of Molecular Sciences 19, no. 12 (November 26, 2018): 3755. http://dx.doi.org/10.3390/ijms19123755.

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Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.

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10

Nimthong-Roldán, Arunpatcha, Nichakan Promsuwhan, Walailak Puetpaiboon та Yupa Wattanakanjana. "Crystal structure of chlorido[1-(4-nitrophenyl)thiourea-κS]bis(triphenylphosphane-κP)copper(I)". Acta Crystallographica Section E Crystallographic Communications 73, № 1 (1 січня 2017): 41–44. http://dx.doi.org/10.1107/s2056989016019368.

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The mononuclear mixed-ligand title complex, [CuCl(C7H7N3O2S)(C18H15P)2], displays a distorted tetrahedral coordination sphere around the CuIatom, with two P atoms from two triphenylphosphane molecules, one terminal S atom from a 1-(4-nitrophenyl)thiourea molecule and a chloride ion as ligands. An intramolecular N—H...Cl hydrogen bond stabilizes the molecular conformation [graph-set motifR22(6)]. In the crystal, further N—H...Cl hydrogen bonds connect individual molecules into zigzag chains parallel to [001]. The chains are linked by weak C—H...O hydrogen-bonding interactions into a three-dimensional network.

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11

Li, Ming Xue, Jing Zhou, Chun Ling Chen, and Jing Ping Wang. "Synthesis, Crystal Structure and Antitumor Study of a Zinc Complex of the 2-Benzoylpyridine Thiosemicarbazone Ligand." Zeitschrift für Naturforschung B 63, no. 3 (March 1, 2008): 280–84. http://dx.doi.org/10.1515/znb-2008-0309.

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A zinc complex of the 2-benzoylpyridine thiosemicarbazone (Hbpt) ligand, Zn(bpt)2 · DMF, has been synthesized and characterized by elemental analysis, IR spectra and single crystal X-ray diffraction. The molecular structure has a Zn2+ cation bonded to two perpendicular bpt ligands in a distorted octahedral geometry through two sulfur and four nitrogen atoms. The crystal contains a disordered DMF solvate molecule. Adjacent molecules are interconnected by means of hydrogen bonding generating a 1-D chain structure. The cytotoxic activity measurement indicates that the complex exhibits higher antitumor activity against lung cancer A549 cell lines than the free ligand.

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12

Sher, Omer, Yuanyuan Han, Haoyuan Xu, Hu Li, Tianbo Daun, Sharath Kumar, Anton Grigoriev, et al. "Analysis of molecular ligand functionalization process in nano-molecular electronic devices containing densely packed nano-particle functionalization shells." Nanotechnology 33, no. 25 (April 1, 2022): 255706. http://dx.doi.org/10.1088/1361-6528/ac5cfc.

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Abstract Molecular electronic devices based on few and single-molecules have the advantage that the electronic signature of the device is directly dependent on the electronic structure of the molecules as well as of the electrode-molecule junction. In this work, we use a two-step approach to synthesise functionalized nanomolecular electronic devices (nanoMoED). In first step we apply an organic solvent-based gold nanoparticle (AuNP) synthesis method to form either a 1-dodecanethiol or a mixed 1-dodecanethiol/ω-tetraphenyl ether substituted 1-dodecanethiol ligand shell. The functionalization of these AuNPs is tuned in a second step by a ligand functionalization process where biphenyldithiol (BPDT) molecules are introduced as bridging ligands into the shell of the AuNPs. From subsequent structural analysis and electrical measurements, we could observe a successful molecular functionalization in nanoMoED devices as well as we could deduce that differences in electrical properties between two different device types are related to the differences in the molecular functionalization process for the two different AuNPs synthesized in first step. The same devices yielded successful NO2 gas sensing. This opens the pathway for a simplified synthesis/fabrication of molecular electronic devices with application potential.

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13

Fortuné, Rose-Verla, Emilie Verguet, Paul O. Oguadinma та Frank Schaper. "[N,N′-Bis(2,6-dimethylphenyl)pentane-2,4-diiminato-κ2 N,N′]trichlorido(tetrahydrofuran-κO)zirconium". Acta Crystallographica Section E Structure Reports Online 63, № 11 (26 жовтня 2007): m2822. http://dx.doi.org/10.1107/s160053680704322x.

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The nacnac (pentane-2,4-diiminato) ligand in the title compound, [Zr(C21H25N2)Cl3(C4H8O)], displays a κ2-coordination to the Zr center. Three chlorido ligands and a coordinated tetrahydrofuran (THF) molecule complete the octahedral environment of the metal. Despite the C 2 symmetry observed in the 1H NMR spectrum, the THF molecule is found trans to one of the N atoms of the nacnac ligand. The asymmetric unit contains two molecules. In one THF ligand one C atom and four H atoms are disordered over two sites in the ratio ca 0.58:0.42.

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14

Wan, Yichao, Chunxing Yan, Han Gao, and Tingting Liu. "Small-molecule PROTACs: novel agents for cancer therapy." Future Medicinal Chemistry 12, no. 10 (May 2020): 915–38. http://dx.doi.org/10.4155/fmc-2019-0340.

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Proteolysis-targeting chimera (PROTAC) is a new technology to selectively degrade target proteins via ubiquitin-proteasome system. PROTAC molecules (PROTACs) are a class of heterobifunctional molecules, which contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. They provide several advantages over traditional inhibitors in potency, selectivity and drug resistance. Thus, many promising PROTACs have been developed in the recent two decades, especially small-molecule PROTACs. In this review, we briefly introduce the mechanism of PROTACs and focus on the progress of small-molecule PROTACs based on different E3 ligases. In addition, we also introduce the opportunities and challenges of small-molecule PROTACs for cancer therapy.

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15

Klueg, K. M., and M. A. Muskavitch. "Ligand-receptor interactions and trans-endocytosis of Delta, Serrate and Notch: members of the Notch signalling pathway in Drosophila." Journal of Cell Science 112, no. 19 (October 1, 1999): 3289–97. http://dx.doi.org/10.1242/jcs.112.19.3289.

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Molecular evidence has established that direct heterotypic interactions occur between the Drosophila receptor Notch and the ligands Delta and Serrate, and that homotypic interactions occur between Delta molecules on opposing cell surfaces. Using an aggregation assay developed for Drosophila cultured cells, we have compared the affinities of these interactions. We find that the heterotypic interactions between Notch and the ligands Delta and Serrate have higher affinities than homotypic interactions between Delta molecules. Contrary to previous suggestions, our evidence implies that the interactions between Serrate and Notch are similar in affinity to those between Delta and Notch. We find that Fringe does not detectably affect the ligand-receptor interactions of the Notch pathway in cultured cells. Furthermore, we find that Serrate, like Delta, is a transmembrane ligand that can participate in reciprocal trans-endocytosis of ligand and receptor between expressing cells. Our findings imply that qualitative differences between Delta- and Serrate-mediated Notch signalling depend on characteristics other than intrinsic ligand-receptor affinities or the ability to participate in reciprocal ligand and receptor trans-endocytosis.

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16

Balius, Trent E., Marcus Fischer, Reed M. Stein, Thomas B. Adler, Crystal N. Nguyen, Anthony Cruz, Michael K. Gilson, Tom Kurtzman, and Brian K. Shoichet. "Testing inhomogeneous solvation theory in structure-based ligand discovery." Proceedings of the National Academy of Sciences 114, no. 33 (July 31, 2017): E6839—E6846. http://dx.doi.org/10.1073/pnas.1703287114.

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Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance. We thus turned to prospective docking of large libraries to investigate GIST’s impact on ligand discovery, geometry, and water structure in a model cavity site well-suited to exploring these terms. Although top-ranked docked molecules with and without the GIST term often overlapped, many ligands were meaningfully prioritized or deprioritized; some of these were selected for testing. Experimentally, 13/14 molecules prioritized by GIST did bind, whereas none of the molecules that it deprioritized were observed to bind. Nine crystal complexes were determined. In six, the ligand geometry corresponded to that predicted by GIST, for one of these the pose without the GIST term was wrong, and three crystallographic poses differed from both predictions. Notably, in one structure, an ordered water molecule with a high GIST displacement penalty was observed to stay in place. Inclusion of this water-displacement term can substantially improve the hit rates and ligand geometries from docking screens, although the magnitude of its effects can be small and its impact in drug binding sites merits further controlled studies.

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17

Debreczeni, Judit É., and Paul Emsley. "Handling ligands with Coot." Acta Crystallographica Section D Biological Crystallography 68, no. 4 (March 16, 2012): 425–30. http://dx.doi.org/10.1107/s0907444912000200.

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Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here.

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18

Wu, Jing, Shuang Li, Tete Li, Xinping Lv, Mingyou Zhang, Guoxia Zang, Chong Qi, Yong-Jun Liu, Liang Xu, and Jingtao Chen. "pDC Activation by TLR7/8 Ligand CL097 Compared to TLR7 Ligand IMQ or TLR9 Ligand CpG." Journal of Immunology Research 2019 (April 9, 2019): 1–10. http://dx.doi.org/10.1155/2019/1749803.

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Plasmacytoid dendritic cells (pDCs) express high levels of the toll-like receptors (TLRs) TLR7 and TLR9. In response to TLR7 and TLR9 ligands, pDCs are primary producers of type I interferons. Our previous study demonstrated that pDCs activated by the TLR7 ligand imiquimod (IMQ) and the TLR9 ligand CpG A can kill breast cancer cells in vitro and inhibit tumor growth in vivo. Moreover, we observed a distinctive morphological, phenotypic change in pDCs after activation by IMQ and CpG A. However, the effect of other TLR7 and TLR9 ligands on pDCs remains less understood. In this study, we treat pDCs with the TLR7 ligand IMQ, TLR7/8 ligands (CL097 and CL075), and three TLR9 ligands (different types of CpGs). The size of pDCs increased significantly after activation by TLR7, or TLR7/8 ligands. TLR7, TLR7/8, and TLR9 ligands similarly modulated cytokine release, as well as protein expression of pDC markers, costimulatory molecules, and cytotoxic molecules. Interestingly, TLR7/8 ligands, especially CL097, induced stronger responses. These results are relevant to the further study of the role and mechanism of pDC-induced antitumor effects and may aid in the development of a new strategy for future tumor immunotherapy.

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19

Aşkın, Gülçin Şefiye, Hacali Necefoğlu, Safiye Özkaya, Raziye Çatak Çelik та Tuncer Hökelek. "Crystal structure of diaquabis(4-tert-butylbenzoato-κO)bis(nicotinamide-κN1)cobalt(II) dihydrate". Acta Crystallographica Section E Crystallographic Communications 72, № 7 (3 червня 2016): 888–91. http://dx.doi.org/10.1107/s2056989016008689.

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The asymmetric unit of the mononuclear cobalt complex, [Co(C11H13O2)2(C6H6N2O)2(H2O)2]·2H2O, contains one half of the complex molecule, one coordinating and one non-coordinating water molecule, one 4-tert-butylbenzoate (TBB) ligand and one nicotinamide (NA) ligand; the Co atom lies on an inversion centre. All ligands coordinating to the Co atom are monodentate. The four nearest O atoms around the Co atom form a slightly distorted square-planar arrangement, with the distorted octahedral coordination completed by the two pyridine N atoms of the NA ligands at distances of 2.1638 (11) Å. The coordinating water molecules are hydrogen bonded to the carboxyl O atoms [O ... O = 2.6230 (17) Å], enclosing anS(6) hydrogen-bonding motif, while intermolecular O—H...O hydrogen bonds link two of the non-coordinating water molecules to the coordinating water molecules and NA anions. The dihedral angle between the planar carboxylate group and the adjacent benzene ring is 29.09 (10)°, while the benzene and pyridine rings are oriented at a dihedral angle of 88.53 (4)°. In the crystal, O—H...O and N—H...O hydrogen bonds link the molecules, enclosingR22(8),R22(10) andR44(12) ring motifs, forming layers parallel to (001). The C and H atoms of thetert-butyl group of the TBB ligand are disordered over two sets of sites with an occupancy ratio of 0.631 (5):0.369 (5).

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20

Greaves, Paul, and John G. Gribben. "The role of B7 family molecules in hematologic malignancy." Blood 121, no. 5 (January 31, 2013): 734–44. http://dx.doi.org/10.1182/blood-2012-10-385591.

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AbstractThe B7 family consists of structurally related, cell-surface proteins that regulate immune responses by delivering costimulatory or coinhibitory signals through their ligands. Eight family members have been identified to date including CD80 (B7-1), CD86 (B7-2), CD274 (programmed cell death-1 ligand [PD-L1]), CD273 (programmed cell death-2 ligand [PD-L2]), CD275 (inducible costimulator ligand [ICOS-L]), CD276 (B7-H3), B7-H4, and B7-H6. B7 ligands are expressed on both lymphoid and nonlymphoid tissues. The importance of the B7 family in regulating immune responses is clear from their demonstrated role in the development of immunodeficiency and autoimmune diseases. Manipulation of the signals delivered by B7 ligands shows great potential in the treatment of cancers including leukemias and lymphomas and in regulating allogeneic T-cell responses after stem cell transplantation.

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21

Albrecht, R. M., S. R. Simmons, S. J. Eppell, and R. E. Marchant. "Correlative microscopy of colloidal gold-labeled and unlabeled cell-surface-associated molecules: LV-SEM, SEM, and VLM." Proceedings, annual meeting, Electron Microscopy Society of America 52 (1994): 1016–17. http://dx.doi.org/10.1017/s0424820100172814.

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Video enhanced, interference based light microscopy (VLM) is sufficiently sensitive to permit observation, via the inflated diffraction image, of colloidal gold particles as small as 15nm. These particles can be directly coupled to ligands such that ligand binding, distribution, and ligand-receptor complex movement can be observed on living cells (Fig.1a-d) and correlated subsequently with HVEM and/or SEM images of the same cell (Fig. 1e). The size of the gold particles used in these studies is such that, other than for very large ligands, generally two or more ligand molecules are bound per particle. Thus questions regarding the role of the polyvalent “particle” (ligand-gold conjugate) vs. soluble ligand can arise. Observation of individual labeled or unlabeled ligand molecules can therefore become useful in resolving such questions when they occur.

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22

Idemudia, Omoruyi G., та Eric C. Hosten. "Bis(4-benzoyl-3-methyl-1-phenyl-1H-pyrazol-5-olato-κ2O,O′)bis(ethanol-κO)cobalt(II)". Acta Crystallographica Section E Structure Reports Online 68, № 8 (25 липня 2012): m1107—m1108. http://dx.doi.org/10.1107/s1600536812032837.

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The title compound, [Co(C17H13N2O2)2(C2H5OH)2], is a CoIIcomplex with two 4-benzoyl-3-methyl-1-phenyl-1H-pyrazol-5-olate (BMPP) ligands and two coordinating ethanol molecules. In the asymmetric unit, there are two half molecules, with the CoIIatoms located on inversion centres. The two cobalt complexes have slightly different geometries and in one, the ethyl group of the ethanol is disordered over two sets of sites [occupancy ratio 0.757 (7):0.243 (7)]. Each BMPP ligand is deprotonated with the negative charge delocalized. The hydroxy group of each ethanol molecule forms hydrogen bonds with a pyrazole N atom in an adjacent BMPP ligand. Weaker C—H...O and C—H...N interactions link the molecules into a three-dimensional structure.

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23

Jeffrey, Polly-Anne, Martín López-García, Mario Castro, Grant Lythe, and Carmen Molina-París. "On Exact and Approximate Approaches for Stochastic Receptor-Ligand Competition Dynamics—An Ecological Perspective." Mathematics 8, no. 6 (June 20, 2020): 1014. http://dx.doi.org/10.3390/math8061014.

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Cellular receptors on the cell membrane can bind ligand molecules in the extra-cellular medium to form ligand-bound monomers. These interactions ultimately determine the fate of a cell through the resulting intra-cellular signalling cascades. Often, several receptor types can bind a shared ligand leading to the formation of different monomeric complexes, and in turn to competition for the common ligand. Here, we describe competition between two receptors which bind a common ligand in terms of a bi-variate stochastic process. The stochastic description is important to account for fluctuations in the number of molecules. Our interest is in computing two summary statistics—the steady-state distribution of the number of bound monomers and the time to reach a threshold number of monomers of a given kind. The matrix-analytic approach developed in this manuscript is exact, but becomes impractical as the number of molecules in the system increases. Thus, we present novel approximations which can work under low-to-moderate competition scenarios. Our results apply to systems with a larger number of population species (i.e., receptors) competing for a common resource (i.e., ligands), and to competition systems outside the area of molecular dynamics, such as Mathematical Ecology.

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24

Geiger, David K., та Dylan E. Parsons. "Poly[[tris(μ2-acetato-κ2O:O′)(4-chlorobenzene-1,2-diamine-κN)(μ3-hydroxido)dizinc] ethanol monosolvate]". Acta Crystallographica Section E Structure Reports Online 70, № 7 (7 червня 2014): m247—m248. http://dx.doi.org/10.1107/s1600536814012641.

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The title compound, {[Zn2(CH3CO2)3(OH)(C6H7ClN2)]·C2H5OH}n, has alternating octahedrally and tetrahedrally coordinated Zn2+ions. The octahedral coordination sphere is composed of one N atom of the monodentate diaminochlorobenzene ligand, three acetate O atoms and two bridging hydroxide ligands. The tetrahedral coordination sphere consists of three acetate O atoms and the hydroxide ligand. The zinc ions are bridged by acetate and hydroxide ligands. The result is a laddered-chain structure parallel to [100] with ethanol solvent molecules occupying the space between the chains. The diamine ligand chlorine substitutent is disordered over two equally populated positions as a result of a crystallographically imposed inversion center between adjacent ligands. The ethanol solvent molecule exhibits disorder with the two components having refined occupancies of 0.696 (11) and 0.304 (11). O—H...O hydrogen bonds form between the hydroxide ligand and the ethanol solvent molecule. N—H...O and N—H...N hydrogen bonding between the uncoordinated amine group and the acetate ligands and the coordinated amine group are also observed.

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25

Lie, Mette A., René Thomsen, Christian N. S. Pedersen, Birgit Schiøtt, and Mikael H. Christensen. "Molecular Docking with Ligand Attached Water Molecules." Journal of Chemical Information and Modeling 51, no. 4 (March 31, 2011): 909–17. http://dx.doi.org/10.1021/ci100510m.

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26

Liu, Fang, Jing-Jing Zhang, Ming-Yuan Lei та Qing-Fu Zhang. "A two-dimensional cadmium(II) coordination polymer based on 5-(pyridin-4-yl)isophthalic acid: poly[[tetraaquabis[μ3-5-(pyridin-4-yl)isophthalato]dicadmium(II)] pentahydrate]". Acta Crystallographica Section C Structural Chemistry 71, № 9 (27 серпня 2015): 834–38. http://dx.doi.org/10.1107/s2053229615015612.

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The title CdIIcompound, {[Cd2(C13H7NO4)2(H2O)4]·5H2O}n, was synthesized by the hydrothermal reaction of Cd(NO3)2·4H2O and 5-(pyridin-4-yl)isophthalic acid (H2L). The asymmetric unit contains two crystallographically independent CdIIcations, two deprotonatedL2−ligands, four coordinated water molecules and five isolated water molecules. One of the CdIIcations adopts a six-coordinate octahedral coordination geometry involving three O atoms from one bidentate chelating and one monodentate carboxylate group of two differentL2−ligands, one N atom of anotherL2−ligand and two coordinated water molecules. The second CdIIcation adopts a seven-coordinate pentagonal–bipyramidal coordination geometry involving four O atoms from two bidentate chelating carboxylate groups of two differentL2−ligands, one N atom of anotherL2−ligand and two coordinated water molecules. EachL2−ligand bridges three CdIIcations and, likewise, each CdIIcation connects to threeL2−ligands, giving rise to a two-dimensional graphite-like 63layer structure. These two-dimensional layers are further linked by O—H...O hydrogen-bonding interactions to form a three-dimensional supramolecular architecture. The photoluminescence properties of the title compound were also investigated.

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27

Xiao, Wei, Disha Wang, Zihao Shen, Shiliang Li, and Honglin Li. "Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites." Molecules 23, no. 9 (September 11, 2018): 2321. http://dx.doi.org/10.3390/molecules23092321.

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Water molecules play an important role in modeling protein-ligand interactions. However, traditional molecular docking methods often ignore the impact of the water molecules by removing them without any analysis or keeping them as a static part of the proteins or the ligands. Hence, the accuracy of the docking simulations will inevitably be damaged. Here, we introduce a multi-body docking program which incorporates the fixed or the variable number of the key water molecules in protein-ligand docking simulations. The program employed NSGA II, a multi-objective optimization algorithm, to identify the binding poses of the ligand and the key water molecules for a protein. To this end, a force-field-based hydration-specific scoring function was designed to favor estimate the binding affinity considering the key water molecules. The program was evaluated in aspects of the docking accuracy, cross-docking accuracy, and screening efficiency. When the numbers of the key water molecules were treated as fixed-length optimization variables, the docking accuracy of the multi-body docking program achieved a success rate of 80.58% for the best RMSD values for the recruit of the ligands smaller than 2.0 Å. The cross-docking accuracy was investigated on the presence and absence of the key water molecules by four protein targets. The screening efficiency was assessed against those protein targets. Results indicated that the proposed multi-body docking program was with good performance compared with the other programs. On the other side, when the numbers of the key water molecules were treated as variable-length optimization variables, the program obtained comparative performance under the same three evaluation criterions. These results indicated that the multi-body docking with the variable numbers of the water molecules was also efficient. Above all, the multi-body docking program developed in this study was capable of dealing with the problem of the water molecules that explicitly participating in protein-ligand binding.

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28

Goodall, Katharine Jennifer, Angela Nguyen, Craig McKenzie, Sidonia Barbara Guiomar Eckle, Lucy Catherine Sullivan та Daniel Mark Andrews. "The murine CD94/NKG2 ligand, Qa-1b, is a high-affinity, functional ligand for the CD8αα homodimer". Journal of Biological Chemistry 295, № 10 (28 січня 2020): 3239–46. http://dx.doi.org/10.1074/jbc.ra119.010509.

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The immune co-receptor CD8 molecule (CD8) has two subunits, CD8α and CD8β, which can assemble into homo or heterodimers. Nonclassical (class-Ib) major histocompatibility complex (MHC) molecules (MHC-Ibs) have recently been identified as ligands for the CD8αα homodimer. This was demonstrated by the observation that histocompatibility 2, Q region locus 10 (H2-Q10) is a high-affinity ligand for CD8αα which also binds the MHC-Ib molecule H2-TL. This suggests that MHC-Ib proteins may be an extended source of CD8αα ligands. Expression of H2-T3/TL and H2-Q10 is restricted to the small intestine and liver, respectively, yet CD8αα-containing lymphocytes are present more broadly. Therefore, here we sought to determine whether murine CD8αα binds only to tissue-specific MHC-Ib molecules or also to ubiquitously expressed MHC-Ib molecules. Using recombinant proteins and surface plasmon resonance–based binding assays, we show that the MHC-Ib family furnishes multiple binding partners for murine CD8αα, including H2-T22 and the CD94/NKG2-A/B-activating NK receptor (NKG2) ligand Qa-1b. We also demonstrate a hierarchy among MHC-Ib proteins with respect to CD8αα binding, in which Qa-1b > H2-Q10 > TL. Finally, we provide evidence that Qa-1b is a functional ligand for CD8αα, distinguishing it from its human homologue MHC class I antigen E (HLA-E). These findings provide additional clues as to how CD8αα-expressing cells are controlled in different tissues. They also highlight an unexpected immunological divergence of Qa-1b/HLA-E function, indicating the need for more robust studies of murine MHC-Ib proteins as models for human disease.

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29

Najar, Adel M., Ruwida M. K. Omar, Eman Bobtaina, Salem Jabber, Najwa Mohamed, Tahani Aeyad, Salha M. Tawati, and Aliaa M. M. Khalifa. "Design, Synthesis, Pharmacological Evaluation and DFT Investigation of New Bioactive Unsymmetrical Bi-Functional Ligand." Journal of Drug Delivery and Therapeutics 12, no. 4 (July 15, 2022): 73–80. http://dx.doi.org/10.22270/jddt.v12i4.5429.

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Compounds with more than one bioactive motif become of great interest. In this regard, a new tridentate 1,2-unsymmetrical ligand consists of flexible and rigid bioactive arms spaced by benzene ring in an ortho position designed to form a bifunctional molecule. The 2-((3-(pyridin-2-yl)-1H-pyrazol-1-yl)methyl)benzonitrile (PPMB) synthesized under phase transfer reaction and characterized using 1H-NMR and mass spectroscopy and studied as potent kinase inhibitors. Theoretically, the molecule structure was investigated at the B3LYP/6-311++G(d,p) level of theory in the gas phase and revealed that all bond lengths and bond angles within the accepted limit. The frontier molecular orbitals (FMO) energies (HOMO and LUMO), energy gap, dipole moment, chemical softness and chemical hardness were calculated. Pharmacologically, the ligand activity was investigated in silico using SWISS ADME. Furthermore, the compound was docked into the transforming growth factor (TGF) beta type I receptor kinase active site to evaluate the ability of ligand as a kinase inhibitor. Keywords: DFT, pyrazolyl-pyridine, physiochemical, properties molecular docking, bioactive molecules, unsymmetrical ligands

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30

Tallquist, Michelle D., Arthur J. Weaver, and Larry R. Pease. "Degenerate Recognition of Alloantigenic Peptides on a Positive-Selecting Class I Molecule." Journal of Immunology 160, no. 2 (January 15, 1998): 802–9. http://dx.doi.org/10.4049/jimmunol.160.2.802.

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Abstract The well-defined 2C T cell was used to investigate alloreactive degeneracy. A panel of class I molecules that are known ligands for the 2C TCR were sensitized with three known peptide ligands, p2Ca (LSPFPFDL), dEV-8 (EQYKFYSV), and SIYR-8 (SIYRYYGL). The peptide p2Ca was originally identified as the allopeptide seen in the Ld class I molecule by 2C T cells, 2C recognizes the dEV-8 peptide as the ligand in the Kbm3 class I molecule, and SIYR-8 was recently identified as a peptide ligand for 2C in the context of the Kb class I molecule. Strong recognition of all three Ag-presenting molecules occurred in the context of their respective allopeptides, but 2C recognized all three peptides to a measurable extent in the context of Kb. Molecular modeling of these Kb/peptide complexes revealed a high degree of similarity between dEV-8 and SIYR-8, but very little conformational similarity of either of these peptides with p2Ca. Furthermore, the structural changes in the mutant Kbm3 binding site resulted in generalized changes in the conformation of each of five bound peptides compared with those of the same peptides bound to Kb. The finding that degenerate recognition occurs on Kb, the restriction element responsible for selecting 2C T cells, suggests a unique relationship between a TCR and the Ag-presenting molecule that mediates its positive selection.

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31

Singh, Dr Anamika, and Dr Rajeev Singh. "QSAR and its Role in Target-Ligand Interaction." Open Bioinformatics Journal 7, no. 1 (December 27, 2013): 63–67. http://dx.doi.org/10.2174/1875036201307010063.

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Each molecule has its own specialty, structure and function and when these molecules are combined together they form a compound. Structure and function of a molecule are related to each other and QSARs (Quantitative Structure– Activity relationships) are based on the criteria that the structure of a molecule must contain the features responsible for its physical, chemical, and biological properties, and on the ability to represent the chemical by one, or more, numerical descriptor(s). By QSAR models, the biological activity of a new or untested chemical can be inferred from the molecular structure of similar compounds whose activities have already been assessed. QSARs attempt to relate physical and chemical properties of molecules to their biological activities. For this there are so many descriptors (for example, molecular weight, number of rotatable bonds, Log P) and simple statistical methods such as Multiple Linear Regression (MLR) are used to predict a model. These models describe the activity of the data set and can predict activities for further sets of (untested) compounds. These types of descriptors are simple to calculate and allow for a relatively fast analysis. 3D-QSAR uses probe-based sampling within a molecular lattice to determine three-dimensional properties of molecules (particularly steric and electrostatic values) and can then correlate these 3D descriptors with biological activity. Physicochemical descriptors, include hydrophobicity, topology, electronic properties, and steric effects etc. These descriptors can be calculated empirically, statistically or through more recent computational methods. QSARs are currently being applied in many disciplines, with many pertaining to drug design and environmental risk assessment.

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32

Prytula-Kurkunova, Angelina Yu, Victor A. Trush, Viktoriya V. Dyakonenko, Tetyana Yu Sliva та Vladimir M. Amirkhanov. "Tris(N-{bis[methyl(phenyl)amino]phosphoryl}benzenesulfonamidato-κ2O,O′)(1,10-phenanthroline-κ2N,N′)lanthanum(III)". Acta Crystallographica Section E Crystallographic Communications 73, № 7 (27 червня 2017): 1076–81. http://dx.doi.org/10.1107/s2056989017008970.

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The asymmetric unit of [La(C20H21N3O3PS)3(C12H8N2)] is created by one LaIIIion, three deprotonatedN-{bis[methyl(phenyl)amino]phosphoryl}benzenesulfonamidate (L−) ligands and one 1,10-phenanthroline (Phen) molecule. Each LaIIIion is eight-coordinated (6O+2N) by three phosphoryl O atoms, three sulfonyl O atoms of threeL−ligands and two N atoms of the chelating Phen ligand, leading to the formation of six- and five-membered metallacycles, respectively. The lanthanum coordination polyhedron has a bicapped trigonal–prismatic geometry. `Sandwich-like' intramolecular π–π stacking interactions are observed between the 1,10-phenanthroline ligand and two benzene rings of two differentL−ligands. The phenyl rings ofL−that are not involved in the stacking interactions show minor positional disorder. Molecules form layers parallel to the (010) plane due to weak C—H...O intermolecular hydrogen bonds. Unidentified highly disordered solvate molecules that occupyca400 Å3large voids have been omitted from the refinement model.

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33

Anstey, Mitchell R., John L. Bost, Anna S. Grumman, Nicholas D. Kennedy та Matthew T. Whited. "Crystal structures of trans-acetyldicarbonyl(η5-cyclopentadienyl)(1,3,5-triaza-7-phosphaadamantane)molybdenum(II) and trans-acetyldicarbonyl(η5-cyclopentadienyl)(3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane)molybdenum(II)". Acta Crystallographica Section E Crystallographic Communications 76, № 4 (17 березня 2020): 547–51. http://dx.doi.org/10.1107/s2056989020003679.

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The title compounds, [Mo(C5H5)(COCH3)(C6H12N3P)(CO)2], (1), and [Mo(C5H5)(COCH3)(C9H16N3O2P)(C6H5)2))(CO)2], (2), have been prepared by phosphine-induced migratory insertion from [Mo(C5H5)(CO)3(CH3)]. The molecular structures of these complexes are quite similar, exhibiting a four-legged piano-stool geometry with trans-disposed carbonyl ligands. The extended structures of complexes (1) and (2) differ substantially. For complex (1), the molybdenum acetyl unit plays a dominant role in the organization of the extended structure, joining the molecules into centrosymmetrical dimers through C—H...O interactions with a cyclopentadienyl ligand of a neighboring molecule, and these dimers are linked into layers parallel to (100) by C—H...O interactions between the molybdenum acetyl and the cyclopentadienyl ligand of another neighbor. The extended structure of (2) is dominated by C—H...O interactions involving the carbonyl groups of the acetamide groups of the DAPTA ligand, which join the molecules into centrosymmetrical dimers and link them into chains along [010]. Additional C—H...O interactions between the molybdenum acetyl oxygen atom and an acetamide methyl group join the chains into layers parallel to (101).

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34

Modec, Barbara. "Polymorphism ofmer-μ-oxalato-bis[chloridotripyridinecobalt(II)] pyridine disolvate". Acta Crystallographica Section C Crystal Structure Communications 69, № 4 (6 березня 2013): 340–43. http://dx.doi.org/10.1107/s010827011300499x.

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Single crystals of a triclinic polymorphic form ofmer-μ-oxalato-bis[chloridotripyridinecobalt(II)] pyridine disolvate, [Co2(C2O4)Cl2(C5H5N)6]·2C5H5N, have been prepared by solvothermal methods. The structure and geometric parameters strongly resemble those of the previously reported monoclinic polymorph [Bolte (2006).Acta Cryst.E62, m597–m598]. In both polymorphic forms, the dinuclear complex molecules are located on a crystallographic centre of inversion, with the CoIIcations in a distorted octahedral environment consisting of a chloride ligand, three pyridine ligands and a chelating bis-bidentate oxalate ligand. This last serves as a bridging ligand between two CoIIcations. The polymorphs differ in the mutual orientation of their pyridine ligands in the dinuclear molecules and in their intermolecular connectivity. In the triclinic polymorph, C—H...O, C—H...Cl, C—H...π and π–π interactions link the dinuclear molecules into a three-dimensional structure. Pyridine solvent molecules are attached to this structureviaweak interactions.

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35

Stone, Geoffrey W., Suzanne Barzee, Victoria Snarsky, Celsa A. Spina, Jeffrey D. Lifson, Vinod Kumar Bhaskara Pillai, Rama Rao Amara, François Villinger, and Richard S. Kornbluth. "Macaque Multimeric Soluble CD40 Ligand and GITR Ligand Constructs Are Immunostimulatory Molecules In Vitro." Clinical and Vaccine Immunology 13, no. 11 (September 20, 2006): 1223–30. http://dx.doi.org/10.1128/cvi.00198-06.

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ABSTRACT CD40 ligand (CD40L) and GITR ligand (glucocorticoid-induced tumor necrosis factor receptor-related protein ligand [GITRL]) are tumor necrosis factor superfamily molecules that can be used as vaccine adjuvants. In a previous human immunodeficiency virus (HIV) DNA vaccine study in mice, we found that plasmids expressing multimeric soluble forms of trimeric CD40L (i.e., many trimers) were stronger activators of CD8+ T-cell responses than were single-trimer soluble forms or the natural membrane-bound molecule. This report describes similar multimeric soluble molecules that were constructed for studies in macaques. Both two-trimer and four-trimer forms of macaque CD40L were active in B-cell proliferation assays using macaque and human cells. With human cells, four-trimer macaque GITRL costimulated CD4+ T-cell proliferation and abrogated the immunosuppressive effects of CD4+ CD25+ regulatory T cells on a mixed leukocyte reaction. These molecular adjuvants provide new tools for vaccine development in the simian immunodeficiency virus system and other macaque models.

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36

Suckert, Stefan, Susanne Wöhlert, Inke Jess та Christian Näther. "Crystal structure of diaquabis(2,6-dimethylpyrazine-κN4)bis(thiocyanato-κN)cobalt(II) 2,5-dimethylpyrazine monosolvate". Acta Crystallographica Section E Crystallographic Communications 71, № 12 (1 грудня 2015): m242—m243. http://dx.doi.org/10.1107/s2056989015021829.

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Анотація:

In the crystal structure of the title compound, [Co(NCS)2(C6H8N2)2(H2O)2]·C6H8N2, the CoIIcation is coordinated by the N atoms of two terminal thiocyanate anions, the O atoms of two water molecules and two N atoms of two 2,6-dimethylpyrazine ligands. The coordination sphere of the resulting discrete complex is that of a slightly distorted octahedron. The asymmetric unit comprises a CoIIcation and half of a 2,5-dimethylpyrazine ligand, both of which are located on centres of inversion, and a water ligand, a 2,6-dimethylpyrazine ligand and one thiocyanate anion in general positions. In the crystal, the discrete complexes are arranged in such a way that cavities are formed in which the 2,5-dimethylpyrazine solvent molecules are located. The coordination of the 2,5-dimethylpyrazine molecules to the metal is apparently hindered due to the bulky methyl groups in vicinal positions to the N atoms, leading to a preferential coordination of the 2,6-dimethylpyrazine ligands. The discrete complexes are linked by O—H...N hydrogen bonds between one water H atom and the non-coordinating N atom of the 2,6-dimethylpyrazine ligands. The remaining water H atom is hydrogen bonded to one N atom of the 2,5-dimethylpyrazine solvent molecule. This arrangement leads to the formation of a two-dimensional network extending parallel to (010).

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37

Zheng, Fang, and Chang-Guo Zhan. "Computational Modeling of Solvent Effects on Protein-Ligand Interactions Using Fully Polarizable Continuum Model and Rational Drug Design." Communications in Computational Physics 13, no. 1 (January 2013): 31–60. http://dx.doi.org/10.4208/cicp.130911.121011s.

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AbstractThis is a brief review of the computational modeling of protein-ligand interactions using a recently developed fully polarizable continuum model (FPCM) and rational drug design. Computational modeling has become a powerful tool in understanding detailed protein-ligand interactions at molecular level and in rational drug design. To study the binding of a protein with multiple molecular species of a ligand, one must accurately determine both the relative free energies of all of the molecular species in solution and the corresponding microscopic binding free energies for all of the molecular species binding with the protein. In this paper, we aim to provide a brief overview of the recent development in computational modeling of the solvent effects on the detailed protein-ligand interactions involving multiple molecular species of a ligand related to rational drug design. In particular, we first briefly discuss the main challenges in computational modeling of the detailed protein-ligand interactions involving the multiple molecular species and then focus on the FPCM model and its applications. The FPCM method allows accurate determination of the solvent effects in the first-principles quantum mechanism (QM) calculations on molecules in solution. The combined use of the FPCM-based QM calculations and other computational modeling and simulations enables us to accurately account for a protein binding with multiple molecular species of a ligand in solution. Based on the computational modeling of the detailed protein-ligand interactions, possible new drugs may be designed rationally as either small-molecule ligands of the protein or engineered proteins that bind/metabolize the ligand. The computational drug design has successfully led to discovery and development of promising drugs.

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38

Mura, Ulrike, Matthias Pfeiffer, Rupert Handgretinger, and Peter J. Lang. "Expression of Activating Natural Killer Cell Receptor Ligands in Childhood Acute Lymphoblastic Leukemia." Blood 108, no. 11 (November 16, 2006): 4478. http://dx.doi.org/10.1182/blood.v108.11.4478.4478.

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Abstract Activating and inhibitory cell surface receptors regulate natural killer (NK) cell effector functions. The extent of expression of their activating ligands on target cells probably plays a critical role in tumor immune surveillance, but the data of this expression on blasts of leukemia patients are still poor. We examined blasts of children with ALL for the activating human NKG2D ligands MICA, MICB, ULBP1, ULBP2 and ULBP3, and for the ligands of the activating human natural cytotoxic receptors (NCRs) NKp30, NKp44 and NKp46. Using ligand specific mouse monoclonal antibodies and flow cytometry, we screened 24 children (23 common-ALL, one pre-T-ALL) for the expression of NKG2D ligands and 15 children (all common-ALL) for NCR ligands. In 13 patients (all common-ALL), also the density of the NKG2D ligands was determined by quantitative flow cytometry. Considering cells positive for a particular ligand in case of a two fold increase of median fluorescence above negative control, 38 percent of the patients were positive for one or more NKG2D ligands, while only 13 percent expressed one or more NCR ligands at significant levels. ULBP1 was most frequently expressed (29 percent of patients positive), while no patients were positive for ULBP2 and NKp44 ligands. ULBP3 was positive in 17 percent of the patients, NKp30 and NKp46 ligands in 13 percent, MICA and MICB in 4 percent. The patient with pre-T-ALL was positive only for ULBP1. So ULBP1 was expressed more frequently, while the other NKG2D ligands were expressed less frequently in children than reported for adult leukemia patients before (Salih et al. Blood.2003;102:1389–1396.). The density of detected NKG2D ligand molecules was always rather low. For MICA the maximum were 1700 molecules per cell in a single patient, for MICB 900, for ULBP1 1100, and for ULBP3 1000 molecules per cell. In summary, blasts of pediatric ALL patients displayed low or negative surface levels of ligands for the human activating NK cell receptors NKG2D, NKp30, NKp44 and NKp46. QUALITATIVE LIGAND EXPRESSION QUALITATIVE LIGAND EXPRESSION QUANTITATIVE LIGAND EXPRESSION QUANTITATIVE LIGAND EXPRESSION

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39

Neidle, Stephen. "Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids." Pharmaceuticals 15, no. 1 (December 22, 2021): 7. http://dx.doi.org/10.3390/ph15010007.

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Анотація:

The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.

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40

Ma, Fengji, Caixia Yu, Huijuan Wang та Feng Zhao. "The three-dimensional coordination polymer poly[[aqua[μ4-2,2′-(diazene-1,2-diyl)dibenzoato]lead(II)] 1,2-bis(pyridin-4-yl)ethylene hemisolvate]". Acta Crystallographica Section C Structural Chemistry 70, № 10 (4 вересня 2014): 934–36. http://dx.doi.org/10.1107/s2053229614017951.

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A novel three-dimensional coordination polymer, {[Pb(C14H8N2O4)(H2O)]·0.5C12H10N2}n, has been synthesized by hydrothermal reaction of Pb(OAc)2·3H2O (OAc is acetate), 2,2′-(diazene-1,2-diyl)dibenzoic acid (H2L) and 1,2-bis(pyridin-4-yl)ethylene (bpe). The asymmetric unit contains a crystallographically independent PbIIcation, oneL2−ligand, an aqua ligand and half a bpe molecule. Each PbIIcentre is seven-coordinated by six O atoms of bridging–chelating carboxylate groups fromL2−ligands and by one O atom from a coordinated water molecule. The PbIIcations are bridged byL2−ligands, forming [PbO2]nchains along theaaxis. These chains are further connected byL2−ligands along thebandcaxes to give a three-dimensional framework with a 41263topology. The channel voids are occupied by bpe molecules.

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41

Cancino, Patricio, Evgenia Spodine, Verónica Paredes-García, Diego Venegas-Yazigi та Andrés Vega. "The layered structure of poly[[hexaaqua(μ4-benzene-1,2,4,5-tetracarboxylato)dicopper(II)] tetrahydrate]". Acta Crystallographica Section C Crystal Structure Communications 69, № 11 (12 жовтня 2013): 1344–47. http://dx.doi.org/10.1107/s0108270113026620.

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In the structure of the title compound, {[Cu2(C10H2O8)(H2O)6]·4H2O}n, the benzene-1,2,4,5-tetracarboxylate ligand, (btec)4−, is located on a crystallographic inversion centre in a μ4-coordination mode. The coordination environment of each pentacoordinated CuIIcentre is square pyramidal (SBP), formed by three water molecules and two carboxylate O atoms from two different (btec)4−ligands. The completely deprotonated (btec)4−ligand coordinates in a monodentate mode to four CuIIatoms. The alternation of (btec)4−ligands and SBP CuIIcentres leads to the formation of a planar two-dimensional covalent network of parallelograms, parallel to theabplane. Hydrogen bonds between a basal water molecule and an apical one from an adjacent [Cu(btec)0.5(H2O)3] unit exist in the intralayer space. Hydrogen bonds are also present between the two-dimensional network and the water molecules filling the channels in the structure.

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42

Suckert, Stefan, Inke Jess та Christian Näther. "Crystal structure of bis(3,5-dimethylpyridine-κN)bis(methanol-κO)bis(thiocyanato-κN)cobalt(II)". Acta Crystallographica Section E Crystallographic Communications 72, № 12 (18 листопада 2016): 1824–26. http://dx.doi.org/10.1107/s2056989016018326.

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The asymmetric unit of the title complex, [Co(NCS)2(C7H9N)2(CH3OH)2], comprises of one CoIIcation located on a centre of inversion, one thiocyanate ligand, one methanol ligand and one 3,5-dimethylpyridine ligand. The CoIIcation is octahedrally coordinated by two terminal N-bonding thiocyanate anions, two methanol molecules and two 3,5-dimethylpyridine ligands into a discrete complex. The complex molecules are linked by intermolecular O—H...S hydrogen bonding into chains that elongate in the direction parallel to thebaxis.

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43

Qadir, Adnan M., Sevgi Kansiz, Necmi Dege, Georgina M. Rosair, and Igor O. Fritsky. "Crystal structure and DFT study of a zinc xanthate complex." Acta Crystallographica Section E Crystallographic Communications 75, no. 11 (October 3, 2019): 1582–85. http://dx.doi.org/10.1107/s2056989019013148.

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In the title compound, bis(2-methoxyethyl xanthato-κS)(N,N,N′,N′-tetramethylethylenediamine-κ2 N,N′)zinc(II) acetone hemisolvate, [Zn(C4H7O2S2)2(C6H16N2)]·0.5C3H6O, the ZnII ion is coordinated by two N atoms of the N,N,N′,N′-tetramethylethylenediamine ligand and two S atoms from two 2-methoxyethyl xanthate ligands. The amine ligand is disordered over two orientations and was modelled with refined occupancies of 0.538 (6) and 0.462 (6). The molecular structure features two C—H...O and two C—H...S intramolecular interactions. In the crystal, molecules are linked by weak C—H...O and C—H...S hydrogen bonds, forming a three-dimensional supramolecular architecture. The molecular structure was optimized using density functional theory (DFT) at the B3LYP/6–311 G(d,p) level. The smallest HOMO–LUMO energy gap (3.19 eV) indicates the suitability of this crystal for optoelectronic applications. The molecular electrostatic potential (MEP) further identifies the positive, negative and neutral electrostatic potential regions of the molecules. Half a molecule of disordered acetone was removed with the solvent-mask procedure in OLEX2 [Dolomanov et al. (2009). J. Appl. Cryst. 42, 339–341] and this contribition is included in the formula.

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44

Zhao, Qing-Lan, та Guo-Peng Li. "Dibromido(2,2′:6′,2′′-terpyridine-κ3N,N′,N′′)zinc(II)". Acta Crystallographica Section E Structure Reports Online 65, № 6 (29 травня 2009): m693. http://dx.doi.org/10.1107/s1600536809019266.

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In the title compound, [ZnBr2(C15H11N3)], the ZnIIion is five-coordinated by the three N atoms from a 2,2′:6′,2′′-terpyridine ligand (terpy) and two bromide anions in a distorted trigonal bipyramidal configuration. Each molecule is situated on a twofold rotational axis that passes through the ZnIIion and the central ring of the terpy ligand. In the crystal structure, aromatic π–π interactions between terpy ligands [centroid–centroid distances = 3.6265 (9) Å] link molecules into stacks propagated in the [001] direction.

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45

Drake, J. R., E. A. Repasky, and R. B. Bankert. "Endocytosis of antigen, anti-idiotype, and anti-immunoglobulin antibodies and receptor re-expression by murine B cells." Journal of Immunology 143, no. 6 (September 15, 1989): 1768–76. http://dx.doi.org/10.4049/jimmunol.143.6.1768.

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Abstract The endocytosis of Ag mediated by membrane-associated Ig (mIg) molecules has been spectrophotometrically monitored using a cell line (2C3) specific for the hapten phthalate (Xmp) and employing conjugates of Xmp and horseradish peroxidase (HRP) as the labeled ligand. Approximately 50% of both Xmp-HRP, or the larger ligand, Xmp-keyhole limpet hemocyanin-HRP, are internalized rapidly, reaching an initial plateau by 30 min. The rate of endocytosis of anti-idiotype-HRP is similar to the rates that were observed for the hapten-bearing ligands, while a slower rate of endocytosis of anti-Ig-HRP was observed. The percent of ligand bound that is internalized and the rate of endocytosis appear to be largely independent of the size and amount of ligand bound per cell. However, mIg-mediated endocytosis is markedly reduced when mIg-ligand complexes are more extensively cross-linked by the binding of a second antibody. In addition to the initial rapid phase of endocytosis, there is a prolonged phase during which more of the bound ligand is internalized, and up to 90% of the internalized ligand is degraded. Re-expression of Ag-binding receptors by the 2C3 cells is independent of new protein synthesis and is accomplished in part by the translocation of a presynthesized pool of mIg molecules from the cytoplasm to the plasma membrane of the cell. The kinetics of endocytosis of HRP-labeled anti-Ig antibodies by BALB/c splenic B-lymphocytes and other B-lymphocyte cell lines is very similar to the endocytosis of Ag and anti-idiotype observed with the 2C3 cell line. Light and electron microscopy are also performed to visually confirm that the HRP-labeled ligands are being internalized and to determine the percentage of cells involved in this process. Finally it was determined that the transmembrane and cytoplasmic domains of the mIg molecules are required for endocytosis since the secreted form of the molecule (which lacks these domains) fails to mediate the internalization of bound ligand.

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46

Neumann, Tristan, Inke Jess та Christian Näther. "Crystal structure ofcatena-poly[[[bis(pyridine-4-carbothioamide-κN1)cadmium]-di-μ-thiocyanato-κ2N:S;κ2S:N] methanol disolvate]". Acta Crystallographica Section E Crystallographic Communications 72, № 3 (20 лютого 2016): 370–73. http://dx.doi.org/10.1107/s2056989016002632.

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The asymmetric unit of the polymeric title compound, {[Cd(NCS)2(C6H6N2S)]·2CH3OH}n, consists of one cadmium(II) cation that is located on a centre of inversion as well as one thiocyanate anion, one pyridine-4-carbothioamide ligand and one methanol molecule in general positions. The CdIIcations are octahedrally coordinated by the pyridine N atom of two pyridine-4-carbothioamide ligands and by the S and N atoms of four thiocyanate anions and are linked into chains along [010] by pairs of anionic ligands. These chains are further linked into layers extending along (201) by intermolecular N—H...O and O—H...S hydrogen bonds. One of the amino H atoms of the pyridine-4-carbothioamide ligand is hydrogen-bonded to the O atom of a methanol molecule, and a symmetry-related methanol molecule is the donor group to the S atom of another pyridine-4-carbothioamide ligand whereby each of the pyridine-4-carbothioamide ligands forms two pairs of centrosymmetric N—H...S and O—H...S hydrogen bonds. The methanol molecules are equally disordered over two orientations.

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47

Al Balushi, Rayya A., Muhammad S. Khan, Md Serajul Haque Faizi, Ashanul Haque, Kieran Molloy та Paul R. Raithby. "Synthesis and structural characterization of hexa-μ2-chlorido-μ4-oxido-tetrakis{[4-(phenylethynyl)pyridine-κN]copper(II)} dichloromethane monosolvate". Acta Crystallographica Section E Crystallographic Communications 77, № 1 (1 січня 2021): 42–46. http://dx.doi.org/10.1107/s2056989020015935.

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In the crystal structure of the title compound, [Cu4Cl6O(C13H9N)4]·CH2Cl2, the core molecular structure consists of a Cu4 tetrahedron with a central interstitial O atom. Each edge of the Cu4 tetrahedron is bridged by a chlorido ligand. Each copper(II) cation is coordinated to the central O atom, two chlorido ligands and one N atom of the 4-phenylethynylpyridine ligand. In the crystal, the molecules are linked by intermolecular C—H...Cl interactions. Furthermore, C—H...π and π–π interactions also connect the molecules, forming a three-dimensional network. Hirshfeld surface analysis indicates that the most important contributions for the packing arrangement are from H...H and C...H/H...C interactions.

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48

Young, Michael C., Yi Sun, Claire H. Woodward, Julia N. Danon, Hau V. Truong, and Nikolaos G. Sgourakis. "Universal, open MHC-I for rapid ligand loading and enhanced complex stability across classical and non-classical allotypes." Journal of Immunology 210, no. 1_Supplement (May 1, 2023): 251.15. http://dx.doi.org/10.4049/jimmunol.210.supp.251.15.

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Abstract The instability of class I major histocompatibility complex (MHC-I) and MHC-like molecules loaded with suboptimal peptides, metabolites, or glycolipids presents an important biochemical challenge for identifying disease-relevant antigens and antigen-specific T cell receptors (TCRs) for autologous therapy development. Here, we leverage the coupled binding between ligand and the light chain (beta-2 microglobulin, β 2m) to the MHC-I heavy chain with the aim of developing conformationally stable molecules by engineering a disulfide bond to bridge the interface between the heavy and light chain. The resulting MHC-I molecules are stabilized in a ligand-receptive/open state, exhibit favorable ligand exchange properties, and are readily loaded with moderate affinity ligands to afford properly conformed protein complexes of enhanced stability compared to the wild type. We demonstrate the generality of the structural design using polymorphic HLA representatives covering multiple HLA-A and B supertypes, the nonclassical and oligomorphic HLA-Ib molecules, as well as MHC-like molecules, MR1 and CD1. Our platform allows spontaneous and rapid ligand exchange, which enables a range of approaches for ligand screening and the functional screening and characterization of polyclonal TCR repertoires. Supported by grants from NIH (R01AI143997, R35GM125034, U01DK112217).

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49

Halder, Gregory J., and Cameron J. Kepert. "Iron(II) Molecular Framework Materials with 4,4'-Azopyridine." Australian Journal of Chemistry 58, no. 5 (2005): 311. http://dx.doi.org/10.1071/ch04290.

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Three new iron(ii) molecular-framework materials incorporating the bridging ligand 4,4′-azopyridine (azpy) have been synthesized and structurally characterized: Fe2(azpy)4(NCS)4·(azpy) (A), Fe(azpy)(NCSe)2(EtOH)2·(azpy) (B), and Fe(azpy)2(NCSe)2·2(MeCN) (C). A and C consist of non-interpenetrating (4,4) grids of iron(ii) centres bridged by azpy ligands with non-coordinating azpy ligands or acetonitrile molecules occupying the spaces within and between the layers. For B, hydrogen-bonding interactions between coordinated ethanol molecules and non-coordinated azpy ligands link linear Fe–azpy chains to give a two-dimensional framework.

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50

Lense, Sheri, Ilia A. Guzei, Jessica Andersen, and Kong Choua Thao. "Crystal structures of a manganese(I) and a rhenium(I) complex of a bipyridine ligand with a non-coordinating benzoic acid moiety." Acta Crystallographica Section E Crystallographic Communications 74, no. 5 (April 27, 2018): 731–36. http://dx.doi.org/10.1107/s2056989018006047.

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The structures of two facially coordinated Group VII metal complexes are reported, namely: fac-bromido[2-(2,2′-bipyridin-6-yl)benzoic acid-κ2 N,N′]tricarbonylmanganese(I) tetrahydrofuran monosolvate, [MnBr(C17H12N2O2)(CO)3]·C4H8O, I, and fac-[2-(2,2′-bipyridin-6-yl)benzoic acid-κ2 N,N′]tricarbonylchloridorhenium(I) tetrahydrofuran monosolvate, [ReCl(C17H12N2O2)(CO)3]·C4H8O, II. In both complexes, the metal ion is coordinated by three carbonyl ligands, a halide ion, and a 2-(2,2′-bipyridin-6-yl)benzoic acid ligand, in a distorted octahedral geometry. In manganese complex I, the tetrahydrofuran (THF) solvent molecule could not be refined due to disorder. The benzoic acid fragment is also disordered over two positions, such that the carboxylic acid group is either positioned near to the bromide ligand or to the axial carbonyl ligand. In the crystal of I, the complex molecules are linked by a pair of C—H...Br hydrogen bonds, forming inversion dimers that stack up the a-axis direction. In the rhenium complex II, there is hydrogen bonding between the benzoic acid moiety and a disordered co-crystallized THF molecule. In the crystal, the molecules are linked by C—H...Cl hydrogen bonds, forming layers parallel to (100) separated by layers of THF solvent molecules.

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