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Journal articles on the topic 'Ligand Molecules'

Author: Grafiati

Published: 7 September 2023

Last updated: 31 July 2025

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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 (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 geometr

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2

Suwardi, Suwardi, Agus Salim, Joanda Ario Yudha Mahendra, et al. "Virtual Screening, Pharmacokinetic Prediction, Molecular Docking and Dynamics Approaches in the Search for Selective and Potent Natural Molecular Inhibitors of MAO-B for the Treatment of Neurodegenerative Diseases." Indonesian Journal of Chemistry and Environment 6, no. 2 (2023): 95–110. http://dx.doi.org/10.21831/ijoce.v6i2.68338.

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This research aims to find natural product compounds that have the potential to act as MAO-B inhibitors that are useful in the treatment of neurodegenerative diseases, through the stages: a) Virtual Screening, b) Molecule Docking, c) Pharmacokinetic and toxicity prediction, and d) Simulation approach Molecular dynamics.The research steps include the following steps: a) searching for molecules in the ZINC15 data base that are similar to the natural ligand molecule (safinamide) obtained from the protein data bank (PDB code: 2v5z) and the control ligand L-DOPA. A total of 481 molecules were downl

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3

Nagamalla, Lavanya, J. V. Shanmukha Kumar, Mohammed Rafi Shaik, et al. "Identification of Novel AXL Kinase Inhibitors Using Ligand-Based Pharmacophore Screening and Molecular Dynamics Simulations." Crystals 12, no. 8 (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 fr

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4

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 (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 b

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5

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 (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

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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 (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 net

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7

Yardan, Alper, and Cenk Paşa. "Spectroscopic, Crystallographic and Thermal Comparison of Two Asymmetric Tridentate Schiff Base Molecules." International Journal of Nature and Life Sciences 8, no. 2 (2024): 228–40. https://doi.org/10.47947/ijnls.1591265.

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Two similar asymmetric ONO type tridentate Schiff Base ligand molecules and their spectroscopic, crystallographic and thermal properties are comparised. Both of molecules obtained in the study were characterized by 1H-NMR, 13C-NMR, thermal analysis, IR spectroscopy and UV-Vis spectroscopy. However molecules were able to be obtained as single crystals and their structures were determined by single crystal X-ray technique. The space group of the geometric shape of the 2'-(2-hydroxy-anilidene)-4-hydroxy-pentane (L1) ligand is P212121. There are 4 molecules in the unit cell of the crystal system o

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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 (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 pro

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9

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 (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 le

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Salio, Mariolina, Wael Awad, Natacha Veerapen, et al. "Ligand-dependent downregulation of MR1 cell surface expression." Proceedings of the National Academy of Sciences 117, no. 19 (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 re

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11

Martín-Mora, David, Matilde Fernández, Félix Velando, et al. "Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges." International Journal of Molecular Sciences 19, no. 12 (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 ass

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12

Berezhnytska, Оleksandra, Artur Horbenko, Irina Savchenko, Oleksandr Rohovtsov, Nataliya Rusakova, and Оlena Trunova. "Investigation of Coordination Compounds of Gadolinium (III) With b-Diketones." Chemistry & Chemical Technology 17, no. 4 (2023): 748–57. http://dx.doi.org/10.23939/chcht17.04.748.

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New coordination compounds of gadolinium with -diketones containing unsaturated and aliphatic or aromatic substituents in the -positions of the chelate ring have been synthesized. The performed quantum-chemical calculations of ligand molecules indicate the best acceptor properties of ligands with aromatic substituents. An analysis of the IR spectra and quantum chemical calculations of the metal complexes indicates the bidentate-chelate coordination of the ligand molecules and their arrangement in different planes, regardless of the nature and geometric structure of the substituent in the β-d

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13

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 (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 anti

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14

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 (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-dimen

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15

Bharathwaj, J. Deepak Venkataraman N.* Charumathi P. Lakshminarasimman S. Purushothaman V. M. Sudharsan S. "An Overview of Basics, Types, Approaches, Applications, Advantages and Disadvantages of Docking." International Journal of Pharmaceutical Sciences 3, no. 3 (2025): 437–45. https://doi.org/10.5281/zenodo.14992121.

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Background-Molecular docking serves as an effective method for exploring the molecular targets of nutraceuticals in the treatment of diseases. Objectives-This review focuses on understanding the basics, types, approaches, applications, advantages and disadvantages of docking. Discussion-The basics of docking involve study of the ligands and proteins. The types of docking encompass Rigid Docking, Flexible-Rigid Docking and Flexible Docking. The approaches include determination of the energy profile for the docked conformer of the ligand target and determination of the complementarity of surface

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16

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 (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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Sher, Omer, Yuanyuan Han, Haoyuan Xu, et al. "Analysis of molecular ligand functionalization process in nano-molecular electronic devices containing densely packed nano-particle functionalization shells." Nanotechnology 33, no. 25 (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

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18

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 (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 interac

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Wan, Yichao, Chunxing Yan, Han Gao, and Tingting Liu. "Small-molecule PROTACs: novel agents for cancer therapy." Future Medicinal Chemistry 12, no. 10 (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 mechan

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Balius, Trent E., Marcus Fischer, Reed M. Stein, et al. "Testing inhomogeneous solvation theory in structure-based ligand discovery." Proceedings of the National Academy of Sciences 114, no. 33 (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 GIS

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Debreczeni, Judit É., and Paul Emsley. "Handling ligands with Coot." Acta Crystallographica Section D Biological Crystallography 68, no. 4 (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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Maneval, Daniel C., Cindy Yang, Cynthia Trevisiol, H. Michael Shepard, and Pei Jin. "Abstract 5975: Characterization and pharmacokinetics of ligand traps targeting the human epidermal growth factor receptor (HER) family." Cancer Research 84, no. 6_Supplement (2024): 5975. http://dx.doi.org/10.1158/1538-7445.am2024-5975.

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Abstract Antibodies targeting HER receptors have led to successful therapeutics for multiple human malignancies. Targeting the family of HER ligands provides an alternative strategy to inhibit signaling and subsequent proliferation of cancer cells. We have engineered ligand traps that bind the growth factors activating the HER family and have characterized a series of molecules (EN2000-Fc) using Surface Plasmon Resonance (SPR). Five distinct molecules were further evaluated for improved in vivo pharmacokinetics in mice that express human neonatal Fc receptor (FcRn). Mutations in the IgG Fc kno

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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 (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 coord

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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 p

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Wu, Jing, Shuang Li, Tete Li, et al. "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 pD

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Greaves, Paul, and John G. Gribben. "The role of B7 family molecules in hematologic malignancy." Blood 121, no. 5 (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 dem

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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 (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

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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 (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 i

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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 (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

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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 (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 molecul

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Jain, Shailesh V., Sanjaykumar B. Bari, and Rajnikant Namdeo. "In-silico Predicted New Lead Molecules for Type-2 Diabetes Mellitus Targeting Aldose Reductase." International Journal of Drug Design and Discovery 2, no. 3 (2024): 605–10. https://doi.org/10.37285/ijddd.2.3.10.

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n spite of insulin treatment, most diabetic patient eventually experience long term diabetic complication such as retinopathy, neuropathy, cataract and angiopathy. Aldose Reductase (AR) is widely expressed aldehyde-metabolizing enzyme which reduces glucose by the AR-catalyzed polyol pathway and linked to development of diabetic complication. The receptor protein structure of Aldose reductase was used and new ligand molecules were generated using structure based de novo approach. Here we report some potential lead molecules against the receptor binding site of aldose reductase based on the in s

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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 (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 identif

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33

Najar, Adel M., Ruwida M. K. Omar, Eman Bobtaina, et al. "Design, Synthesis, Pharmacological Evaluation and DFT Investigation of New Bioactive Unsymmetrical Bi-Functional Ligand." Journal of Drug Delivery and Therapeutics 12, no. 4 (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 al

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Modec, Barbara. "Polymorphism ofmer-μ-oxalato-bis[chloridotripyridinecobalt(II)] pyridine disolvate". Acta Crystallographica Section C Crystal Structure Communications 69, № 4 (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-bide

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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 (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 obs

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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 (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

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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 (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 mole

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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 (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 cy

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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 (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 molecu

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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 (2015): m242—m243. http://dx.doi.org/10.1107/s2056989015021829.

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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 cryst

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

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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 te

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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 (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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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 (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]nc

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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 (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 l

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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 (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

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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 (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 hydro

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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 (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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Singh, Dr Anamika, and Dr Rajeev Singh. "QSAR and its Role in Target-Ligand Interaction." Open Bioinformatics Journal 7, no. 1 (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 struc

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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 (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-H

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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 (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

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