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Journal articles on the topic 'Ligands'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Oszwałdowski, Sławomir, Katarzyna Zawistowska-Gibuła, and Kenneth Roberts. "Characterization of CdSe quantum dots with bidentate ligands by capillary electrophoresis." Open Chemistry 9, no. 4 (2011): 572–84. http://dx.doi.org/10.2478/s11532-011-0037-3.

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AbstractThe CdSe quantum dots (QDs) with bidentate ligands: a-diimine (NN) and dihydrolipoic acid (DHLA) were synthesized and characterized by UV-Vis, particle size and capillary electrophoretic techniques. Two systems were analyzed: CdSe with one ligand (CdSe/ligand) and CdSe with two different ligands (CdSe//ligand1/ligand2), where ligand = α-diimine or DHLA. Hydrodynamic features of functionalized QDs were characterized by zone capillary electrophoretic (CZE), and particle size techniques and these methods were consistent. It was established that CZE, micellar (MEKC) and microemulsion (MEEK

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Bakhtiari, Atefeh, and Javad Safaei-Ghomi. "Effects of Chiral Ligands on the Asymmetric Carbonyl-Ene Reaction." Synlett 30, no. 15 (2019): 1738–64. http://dx.doi.org/10.1055/s-0037-1611875.

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The carbonyl-ene reaction is one of the most well-known reactions for C–C bond formation. Based on frontier molecular orbitals (FMO), carbonyl-ene reactions occur between the highest occupied molecular orbital (HOMO) of the ene compound bearing an active hydrogen atom at the allylic center and the lowest unoccupied molecular orbital (LUMO) of the electron-deficient enophile, which is a carbonyl compound. A high activation barrier enforces the concerted ene reaction rather than a Diels–Alder reaction at high temperature. Employing a catalytic system can eliminate defects in the ene reaction, an

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Murphy, Patrick B., Feng Liu, Stephen C. Cook, et al. "Structural control of Au and Au–Pd nanoparticles by selecting capping ligands with varied electronic and steric effects." Canadian Journal of Chemistry 87, no. 11 (2009): 1641–49. http://dx.doi.org/10.1139/v09-127.

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Weakly interacting ligands including three Gemini surfactants, didodecyldimethylammonium bromide (DDAB), and amines (RNH2, R2NH, and R3N) were used to prepare Au nanoparticles (NPs). Aqueous Au NPs capped with DDAB and Gemini surfactants showed similar sizes (3–4 nm), whereas toluene-based NPs stabilized with DDAB, amines, and their mixtures range from 2.5 to 9.3 nm. Ligand effect on Au–Pd NP structure was also studied with EXAFS. These findings were consistently accounted for by considering the ligand’s electronic/steric effects and mixed ligands coadsorption, and suggest useful ways to contr

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Guseva, Polina B., Alexander R. Badikov, Oleg S. Butorlin, et al. "Complexation of Lanthanides(III) Ions with Terephthalic Acid in Aqueous Solutions by Potentiometric Titration Combined with Photoluminescence Spectroscopy." Chemistry 7, no. 2 (2025): 57. https://doi.org/10.3390/chemistry7020057.

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The complexation behavior of lanthanide(III) ions with terephthalic acid (1,4-benzene-dicarboxylic acid) in 0.01 M KNO3 aqueous solutions was studied across a broad pH range and at two metal-to-ligand ratios using potentiometric titration combined with photoluminescence spectroscopy. Chemometric analysis of titration curves enabled the determination of relative molar fractions, stability constants, and probable stoichiometry of the formed complexes. In solutions with a 1:2 metal-to-ligand ratio, bis-complexes (two terephthalate ligands per lanthanide ion) predominated, while ligand-rich condit

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Finkina, Ekaterina I., Daria N. Melnikova, Ivan V. Bogdanov, et al. "Impact of Different Lipid Ligands on the Stability and IgE-Binding Capacity of the Lentil Allergen Len c 3." Biomolecules 10, no. 12 (2020): 1668. http://dx.doi.org/10.3390/biom10121668.

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Previously, we isolated the lentil allergen Len c 3, belonging to the class of lipid transfer proteins, cross-reacting with the major peach allergen Pru p 3 and binding lipid ligands. In this work, the allergenic capacity of Len c 3 and effects of different lipid ligands on the protein stability and IgE-binding capacity were investigated. Impacts of pH and heat treating on ligand binding with Len c 3 were also studied. It was shown that the recombinant Len c 3 (rLen c 3) IgE-binding capacity is sensitive to heating and simulating of gastroduodenal digestion. While being heated or digested, the

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Moreno, Maria João, Luís M. S. Loura, Jorge Martins, Armindo Salvador, and Adrian Velazquez-Campoy. "Analysis of the Equilibrium Distribution of Ligands in Heterogeneous Media–Approaches and Pitfalls." International Journal of Molecular Sciences 23, no. 17 (2022): 9757. http://dx.doi.org/10.3390/ijms23179757.

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The equilibrium distribution of small molecules (ligands) between binding agents in heterogeneous media is an important property that determines their activity. Heterogeneous systems containing proteins and lipid membranes are particularly relevant due to their prevalence in biological systems, and their importance to ligand distribution, which, in turn, is crucial to ligand’s availability and biological activity. In this work, we review several approaches and formalisms for the analysis of the equilibrium distribution of ligands in the presence of proteins, lipid membranes, or both. Special a

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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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Fan, Qikui, Hao Yang, Juan Ge, et al. "Customizable Ligand Exchange for Tailored Surface Property of Noble Metal Nanocrystals." Research 2020 (January 21, 2020): 1–12. http://dx.doi.org/10.34133/2020/2131806.

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It is highly desirable, while still challenging, to obtain noble metal nanocrystals with custom capping ligands, because their colloidal synthesis relies on specific capping ligands for the shape control while conventional ligand exchange processes suffer from “the strong replaces the weak” limitation, which greatly hinders their applications. Herein, we report a general and effective ligand exchange approach that can replace the native capping ligands of noble metal nanocrystals with virtually any type of ligands, producing flexibly tailored surface properties. The key is to use diethylamine

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Miller, Shannon M., Van Cybulski, Lois Walsh, et al. "Investigation of novel TLR7/8 ligands in combination with TLR4 ligands as adjuvants to drive cell mediated anti-influenza immunity." Journal of Immunology 200, no. 1_Supplement (2018): 125.16. http://dx.doi.org/10.4049/jimmunol.200.supp.125.16.

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Abstract Influenza is a highly communicative viral pathogen that infects 9–35 million individuals and results in 12,000–56,000 deaths in the US annually. For the most commonly used seasonal influenza vaccine, historical efficacy rates range from 10–60% thus improvements to the current vaccine are needed. We identified a novel series of synthetic TLR7/8 ligands that improve influenza vaccine efficacy when used alone or in combination with our synthetic TLR4 ligand. In human PBMCs, TLR7/8 ligands elicited secretion of the inflammatory cytokines TNFα, IL-6, and IL-1β as well as the Th1-polarizing

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Sim, Jaeung, Taemin Kim та Jin Kuk Yang. "Poly[(μ6-benzene-1,3,5-tricarboxylato-κ6O1:O1′:O3:O3′:O5:O5′)tris(N,N-dimethylformamide-κO)tris(μ3-formato-κ3O:O:O′)trizinc(II)]". Acta Crystallographica Section E Structure Reports Online 69, № 11 (2013): m619. http://dx.doi.org/10.1107/s1600536813028687.

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The asymmetric unit of the title compound, [Zn3(HCO2)3(C9H3O6)(C3H7NO)3]n, contains one Zn ion, one formate ligand, oneN,N-dimethylformamide (DMF) ligand and one-third of a benzene-1,3,5-tricarboxylate (btc) ligand situated on a crystallographic 3 axis. Each ZnIIatom is coordinated by one O atom from a DMF ligand, two O atoms from two btc ligands and three O atoms from three formate ligands in a distorted octahedral geometry. The ZnIIatoms are connected by the formate and btc ligands, forming hexanuclear cores, which are linked by btc ligands, constructing a two-dimensional layered network alo

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Chen, Yujie, Matthew Tom Anderson, Nathaniel Payne, Fabio R. Santori, and Natalia B. Ivanova. "Nuclear Receptors and the Hidden Language of the Metabolome." Cells 13, no. 15 (2024): 1284. http://dx.doi.org/10.3390/cells13151284.

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Nuclear hormone receptors (NHRs) are a family of ligand-regulated transcription factors that control key aspects of development and physiology. The regulation of NHRs by ligands derived from metabolism or diet makes them excellent pharmacological targets, and the mechanistic understanding of how NHRs interact with their ligands to regulate downstream gene networks, along with the identification of ligands for orphan NHRs, could enable innovative approaches for cellular engineering, disease modeling and regenerative medicine. We review recent discoveries in the identification of physiologic lig

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Crawford, Sarah M., Craig A. Wheaton, Vinayak Mishra, and Mark Stradiotto. "Probing the effect of donor-fragment substitution in Mor-DalPhos on palladium-catalyzed C–N and C–C cross-coupling reactivity." Canadian Journal of Chemistry 96, no. 6 (2018): 578–86. http://dx.doi.org/10.1139/cjc-2017-0749.

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The competitive catalytic screening of 18 known and newly prepared Mor-DalPhos ligand variants in the palladium-catalyzed cross-coupling of chlorobenzene with aniline, octylamine, morpholine, indole, ammonia, or acetone is presented, including ligands derived from the new secondary phosphine HP(Me2Ad)2 (Me2Ad = 3,5-dimethyladamantyl). Although triarylphosphine ancillary ligand variants performed poorly in these test reactions, ligands featuring either PAd2 or P(Me2Ad)2 donors (Ad = 1-adamantyl) gave rise to superior catalytic performance. Multiple Mor-DalPhos variants proved effective in cross

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Sarie, Aldila Divana, and Marsah Rahmawati Utami. "Bioactivity Analysis of Chalcone-Derived Compounds Based on In-Silico Molecular Docking Study." Jurnal Pijar Mipa 20, no. 2 (2025): 251–59. https://doi.org/10.29303/jpm.v20i2.8550.

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Chalcone compounds are aromatic ketones and enones that have been found to have several activities, such as antimalarial, antioxidant, anti-inflammatory, anticancer, antiviral, anti-HIV, antifungal, antihyperglycemic, and carboxygenase inhibitors. A ligand's bioactivity can be predicted through in-silico tests using molecular docking. Molecular docking studies are conducted to study the interaction between ligand and receptor and identify the receptor's active site that matches the ligand when the ligand and receptor bind in a stable complex. This study can be a preliminary test before conduct

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Karasev, Dmitry, Boris Sobolev, Alexey Lagunin, Dmitry Filimonov, and Vladimir Poroikov. "Prediction of Protein–ligand Interaction Based on Sequence Similarity and Ligand Structural Features." International Journal of Molecular Sciences 21, no. 21 (2020): 8152. http://dx.doi.org/10.3390/ijms21218152.

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Computationally predicting the interaction of proteins and ligands presents three main directions: the search of new target proteins for ligands, the search of new ligands for targets, and predicting the interaction of new proteins and new ligands. We proposed an approach providing the fuzzy classification of protein sequences based on the ligand structural features to analyze the latter most complicated case. We tested our approach on five protein groups, which represented promised targets for drug-like ligands and differed in functional peculiarities. The training sets were built with the or

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Mamasakhlisov, A. Ye, and Ye Sh Mamasakhlisov. "THE CONDUCTIVITY OF THE MONOLAYER OF COMPLEXES OF DNA WITH QUANTUM DOTS IN THE PRESENCE OF INTERCALATING LIGANDS." Proceedings of the YSU A: Physical and Mathematical Sciences 53, no. 3 (250) (2019): 203–7. http://dx.doi.org/10.46991/pysu:a/2019.53.3.203.

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The noncompetitive DNA hybridization and conductivity in the presence of non-charged ligands have been investigated and the comparison is made with the ligand-free case. It has been shown that the intercalating ligands enhance the sensitivity of the DNA chips as compared with the ligand-free case at the high enough concentration of ligands.

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Ali M., Feryal, та Alyaa S.M.O. Al-barwari. "Divalent transition metal complexes with mixed of β-enaminone and N,O-donor ligands: synthesis, characterization and biological assessment". Bulletin of the Chemical Society of Ethiopia 39, № 1 (2024): 65–78. http://dx.doi.org/10.4314/bcse.v39i1.5.

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This study extensively describes the synthesizing and characterizing of new β-enaminone complexes derived from dimedone and amines coordinated with transition metals Fe(II), Co(II), Ni(II), and Cu(II), also two ligand's metformin (Met) and 8-hydroxyquinoline (8-hq). These were determined via FT-IR, 1H-NMR, electron and mass spectroscopy, molar electrical conductivity, thermal analysis (TGA, DTA and DSC) and characterized by metal content determination (%), magnetic susceptibility and elemental analysis (C.H.N.) and SEM technique. The measurements indicate that the complexes have six coordinati

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Southern, Craig, Jennifer M. Cook, Zaynab Neetoo-Isseljee та ін. "Screening β-Arrestin Recruitment for the Identification of Natural Ligands for Orphan G-Protein–Coupled Receptors". Journal of Biomolecular Screening 18, № 5 (2013): 599–609. http://dx.doi.org/10.1177/1087057113475480.

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A variety of G-protein–coupled receptor (GPCR) screening technologies have successfully partnered a number of GPCRs with their cognate ligands. GPCR-mediated β-arrestin recruitment is now recognized as a distinct intracellular signaling pathway, and ligand-receptor interactions may show a bias toward β-arrestin over classical GPCR signaling pathways. We hypothesized that the failure to identify native ligands for the remaining orphan GPCRs may be a consequence of biased β-arrestin signaling. To investigate this, we assembled 10 500 candidate ligands and screened 82 GPCRs using PathHunter β-arr

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Minucci, S., M. Leid, R. Toyama, et al. "Retinoid X receptor (RXR) within the RXR-retinoic acid receptor heterodimer binds its ligand and enhances retinoid-dependent gene expression." Molecular and Cellular Biology 17, no. 2 (1997): 644–55. http://dx.doi.org/10.1128/mcb.17.2.644.

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Retinoic acid receptor (RAR) and retinoid X receptor (RXR) form heterodimers and regulate retinoid-mediated gene expression. We studied binding of RXR- and RAR-selective ligands to the RXR-RAR heterodimer and subsequent transcription. In limited proteolysis analyses, both RXR and RAR in the heterodimer bound their respective ligands and underwent a conformational change in the presence of a retinoic acid-responsive element. In reporter analyses, the RAR ligand (but not the RXR ligand), when added singly, activated transcription, but coaddition of the two ligands led to synergistic activation o

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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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Lee, Jaeseok, Youngjun Lee, Young Mee Jung, Ju Hyun Park, Hyuk Sang Yoo, and Jongmin Park. "Discovery of E3 Ligase Ligands for Target Protein Degradation." Molecules 27, no. 19 (2022): 6515. http://dx.doi.org/10.3390/molecules27196515.

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Target protein degradation has emerged as a promising strategy for the discovery of novel therapeutics during the last decade. Proteolysis-targeting chimera (PROTAC) harnesses a cellular ubiquitin-dependent proteolysis system for the efficient degradation of a protein of interest. PROTAC consists of a target protein ligand and an E3 ligase ligand so that it enables the target protein degradation owing to the induced proximity with ubiquitin ligases. Although a great number of PROTACs has been developed so far using previously reported ligands of proteins for their degradation, E3 ligase ligand

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Itoh, Yasushi, Bernhard Hemmer, Roland Martin, and Ronald N. Germain. "Serial TCR Engagement and Down-Modulation by Peptide:MHC Molecule Ligands: Relationship to the Quality of Individual TCR Signaling Events." Journal of Immunology 162, no. 4 (1999): 2073–80. http://dx.doi.org/10.4049/jimmunol.162.4.2073.

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Abstract In the present study, we examined the relationships among quantitative aspects of TCR engagement as measured by receptor down-modulation, functional responses, and biochemical signaling events using both mouse and human T cell clones. For T cells from both species, ligands that are more potent in inducing functional responses promote TCR down-modulation more efficiently than weaker ligands. At low ligand density, the number of down-modulated TCR exceeds the number of available ligands by as much as 80–100:1 in the optimal human case, confirming the previous description of serial ligan

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Shen, Lu, Yu-Yang Wang, Teng-Fei He, Lu-Yi Zou, Jing-Fu Guo, and Ai-Min Ren. "A Theoretical Investigation into the Homo- and Hetero-leptic Cu(I) Phosphorescent Complexes Bearing 2,9-dimethyl-1, 10-phenanthroline and bis [2-(diphenylphosphino)phenyl]ether Ligand." Materials 15, no. 20 (2022): 7253. http://dx.doi.org/10.3390/ma15207253.

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Cu(I) complexes have received widespread attention as a promising alternative to traditional noble-metal complexes. Herein, we systematically study the properties of Cu(I) complexes from homo- to hetero-ligands, and found the following: (1) hetero-ligands are beneficial to regulate phosphorescent efficiency; (2) when the hetero-ligands in a tetracoordinated Cu(I) complex are 1:1, the ligands coordinate along the dx2-y2 direction of Cu(I) ion, which can observably suppress structural deformation; (3) unlike the P^P ligand, the N^N ligand can enhance the participation of Cu(I) during the transit

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Wen, Yan-Mei, Tian-Jun Feng та Li-Xin He. "Poly[[aquabis(μ3-isonicotinato-κ3O:O′:N)tris(μ2-isonicotinato-κ3O,O′:N)(nitrato-κO)bis(μ4-oxalato-κ6O1,O2:O2:O1′,O2′:O1′)dierbium(III)tetrasilver(I)] tetrahydrate]". Acta Crystallographica Section E Structure Reports Online 65, № 6 (2009): m676—m677. http://dx.doi.org/10.1107/s160053680901842x.

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In the title coordination polymer, {[Ag4Er2(C6H4NO2)5(C2O4)2(NO3)(H2O)]·4H2O}n, each ErIIIatom is coordinated in a bicapped trigonal–prismatic coordination geometry by three O atoms from two isonicotinate (IN) ligands, four O atoms from two oxalate ligands and one O atom from either a nitrate ion or a water molecule, both of which are half-occupied over the same site. One AgIatom has a Y-shaped geometry defined by one N atom from one IN ligand, one O atom from another IN ligand and one O atom from an oxalate ligand. The other AgIatom is coordinated by two IN ligands and one O atom from an oxal

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Murata, Shogo, Toshiki Mushino, Hiroki Hosoi, et al. "Soluble NKG2D Ligands Are Potential Biomarkers and Sentinels of Immune-Mediated Bone Marrow Injury in Bone Marrow Failure Syndromes." Acta Haematologica 143, no. 1 (2019): 33–39. http://dx.doi.org/10.1159/000500657.

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Immune-mediated processes are considered important in the pathogenesis of bone marrow failure syndromes (BFS). We previously reported that natural killer group 2D (NKG2D) ligands were expressed on pathological blood cells of patients with BFS and that NKG2D immunity may be involved in bone marrow failure. In addition to membranous NKG2D ligands on the cell surface, soluble NKG2D ligands can exist in plasma. We therefore examined the relationship between soluble NKG2D ligands and blood cell counts in 86 patients with BFS, including aplastic anemia, myelodysplastic syndrome with single lineage d

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Vaishnav, Brijesh Kumar, and S. K. Verma. "Development of Nickel(II) Thiosemicarbazone Complexes as Potential Antibacterial Agents: Microwave Assisted Synthesis, Spectral Characterization and Antibacterial Studies." Oriental Journal Of Chemistry 41, no. 1 (2025): 193–200. https://doi.org/10.13005/ojc/410123.

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Some novel Nickel(II) aryl thiosemicarbazone complexes with the formula [Ni(LIGAND-1)2(NO3)2], [Ni(LIGAND-2)2(NO3)2], [Ni(LIGAND-3)2(NO3)2], and [Ni(LIGAND-4) 2(NO3)2] have been successfully synthesized. LIGAND-1 corresponds to 4-Phenyl-3-buten-2-one thiosemicarbazone (PBTSC), LIGAND-2 is 4-Hydroxy-3-methylbenzaldehyde thiosemicarbazone (HMBTSC), LIGAND-3 refers to 4-Methoxybenzaldehyde thiosemicarbazone (MBTSC), and LIGAND-4 represents Propiophenone thiosemicarbazone (PTSC). The Ligands were synthesized by reacting thiosemicarbazide with substituted aromatic aldehydes and ketones using microw

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Pratama, Mohammad Rizki Fadhil, Hadi Poerwono, and Siswandono Siswodihardjo. "Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions." Indonesian Journal of Biotechnology 26, no. 1 (2021): 54. http://dx.doi.org/10.22146/ijbiotech.62194.

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Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained be

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Chakraborty, Biswarup, Ivy Ghosh, Rahul Dev Jana, and Tapan Kanti Paine. "Oxidative C–N bond cleavage of (2-pyridylmethyl)amine-based tetradentate supporting ligands in ternary cobalt(ii)–carboxylate complexes." Dalton Transactions 49, no. 11 (2020): 3463–72. http://dx.doi.org/10.1039/c9dt04438h.

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Co(ii)–carboxylate complexes of N4 ligands containing (2-pyridylmethyl)amine backbone activate O<sub>2</sub> and exhibit oxidative C–N bond cleavage of the ligands. The coordination of carboxylate co-ligand plays important role to affect the ligand oxidation.

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Xu, Xianjin, and Xiaoqin Zou. "Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies." International Journal of Molecular Sciences 22, no. 22 (2021): 12320. http://dx.doi.org/10.3390/ijms222212320.

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The molecular similarity principle has achieved great successes in the field of drug design/discovery. Existing studies have focused on similar ligands, while the behaviors of dissimilar ligands remain unknown. In this study, we developed an intercomparison strategy in order to compare the binding modes of ligands with different molecular structures. A systematic analysis of a newly constructed protein–ligand complex structure dataset showed that ligands with similar structures tended to share a similar binding mode, which is consistent with the Molecular Similarity Principle. More importantly

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Kuldeep Patel, Richa Dubey, Shaifali Soni, Jagdish Chandra Rathi, and Neerupma Dhiman. "Molecular Docking and ADME Study of Quinoline and Chalcone based Derivatives for Anti-Cancer Activity." International Journal of Research in Pharmaceutical Sciences 12, no. 3 (2021): 2252–64. http://dx.doi.org/10.26452/ijrps.v12i3.4849.

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Cancer is a big issue that affects people all over the world. It develops as a result of uncontrolled cell growth. The interaction between developed ligands and thymine phosphorylation was investigated in this study, which was computationally optimized. The aim of this study was to examine the anticancerous activity of designed ligands in thymine phosphorylation (PDB ID: 1UOU) in order to minimize the cost and time required to develop a novel anticancer drug with minimal side effects. All the designed ligands showed mild to excellent binding with proteins. Most of the ligands exhibited better

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Micovic, Vuk, Milovan Ivanovic та Ljiljana Dosen-Micovic. "Structural requirements for ligands of the δ-opioid receptor". Journal of the Serbian Chemical Society 74, № 11 (2009): 1207–17. http://dx.doi.org/10.2298/jsc0911207m.

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The ?-opioid receptor is sensitive to ligand geometry. In order to assist the synthesis of new ?-selective opioid ligands, the structure elements of ?-selective opioid ligands necessary for their effective binding were investigated. The automated docking procedure with a flexible ligand was used to simulate the binding of 17 ?-selective ligands to the ?-receptor. It was found that voluminous N-alkyl groups reduce the binding potency of naltrindole derivatives by preventing the ligands from adopting the preferred conformation in the receptor. This was confirmed by enantiospecific binding of chi

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Ferreira-Faria, Diogo, and M. Ângela Taipa. "Thermal Stabilization of Lipases Bound to Solid-Phase Triazine-Scaffolded Biomimetic Ligands: A Preliminary Assessment." Processes 12, no. 2 (2024): 371. http://dx.doi.org/10.3390/pr12020371.

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Biomimetic ligands are synthetic compounds that mimic the structure and binding properties of natural biological ligands. The first uses of textile dyes as pseudo-affinity ligands paved the way for the rational design and de novo synthesis of low-cost, non-toxic and highly stable triazine-scaffolded affinity ligands. A novel method to assess and enhance protein stability, employing triazine-based biomimetic ligands and using cutinase from Fusarium solani pisi as a protein model, has been previously reported. This innovative approach combined the concepts of molecular modeling and solid-phase c

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Gerringa, Loes J. A., Micha J. A. Rijkenberg, Charles-Edouard Thuróczy, and Leo R. M. Maas. "A critical look at the calculation of the binding characteristics and concentration of iron complexing ligands in seawater with suggested improvements." Environmental Chemistry 11, no. 2 (2014): 114. http://dx.doi.org/10.1071/en13072.

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Environmental context The low concentration of iron in the oceans limits growth of phytoplankton. Dissolved organic molecules, called ligands, naturally present in seawater, bind iron thereby increasing its solubility and, consequently, its availability for biological uptake by phytoplankton. The characteristics of these ligands are determined indirectly with various mathematical solutions; we critically evaluate the underlying method and calculations used in these determinations. Abstract The determination of the thermodynamic characteristics of organic Fe binding ligands, total ligand concen

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Blasco, Salvador, Begoña Verdejo, María Paz Clares, and Enrique García-España. "Transition Metals Meet Scorpiand-like Ligands." Crystals 13, no. 9 (2023): 1338. http://dx.doi.org/10.3390/cryst13091338.

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Scorpiand-like ligands combine the preorganization of the donor atoms of macrocycles and the degrees of freedom of the linear ligands. We prepared the complexes of several of these ligands with transition metal ions and made a crystallographic and water solution speciation studies. The analysis of the resulting crystal structures show that the ligands have the ability to accommodate several metal ions and that the coordination geometry is mostly determined by the ligand. Ligand 6-[3,7-diazaheptyl]-3,6,9–triaza-1-(2,6)-pyridinacyclodecaphane (L3) is an hexadentate ligand that affords a family o

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Korbecki, Jan, Mateusz Bosiacki, Dariusz Chlubek, and Irena Baranowska-Bosiacka. "Bioinformatic Analysis of the CXCR2 Ligands in Cancer Processes." International Journal of Molecular Sciences 24, no. 17 (2023): 13287. http://dx.doi.org/10.3390/ijms241713287.

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Human CXCR2 has seven ligands, i.e., CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, CXCL7, and CXCL8/IL-8—chemokines with nearly identical properties. However, no available study has compared the contribution of all CXCR2 ligands to cancer progression. That is why, in this study, we conducted a bioinformatic analysis using the GEPIA, UALCAN, and TIMER2.0 databases to investigate the role of CXCR2 ligands in 31 different types of cancer, including glioblastoma, melanoma, and colon, esophageal, gastric, kidney, liver, lung, ovarian, pancreatic, and prostate cancer. We focused on the differences in the regul

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James, Marisa, Madelyn R. Shevlin, Thomas B. Green, Megan M. Smart, Colin D. McMillen, and Jared A. Pienkos. "Crystal Structures of DNA Intercalating Agents Dipyrido[3,2-f:2′,3′-h]quinoxaline (dpq), (Benzo[i]dipyrido[3,2-a:2′,3′c]phenazine (dppn), and [Ir(ppy)2(dppn)][PF6] (Where Hppy = 2-Phenylpyridine)." Inorganics 11, no. 9 (2023): 353. http://dx.doi.org/10.3390/inorganics11090353.

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Pyrazino-phenanthroline ligands are commonly used with transition metals as DNA intercalation agents. Herein, we report the characterization of two commonly utilized pyrazino-phenanthroline ligands, dipyrido[3,2-f:2′,3′-h]quinoxaline (dpq) and (benzo[i]dipyrido[3,2-a:2′,3′c]phenazine (dppn), by single-crystal X-ray diffraction. Additionally, the characterization of [Ir(ppy)2(dppn)][PF6], where Hppy = 2-phenylpyridine, by single-crystal X-ray diffraction is described. Both the dpq and dppn ligands crystallize as chloroform solvates where the chloroform molecule occupies the equivalent binding p

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Ben-Shlomo, Izhar, Rami Rauch, Orna Avsian-Kretchmer, and Aaron J. W. Hsueh. "Matching Receptome Genes with Their Ligands for Surveying Paracrine/Autocrine Signaling Systems." Molecular Endocrinology 21, no. 8 (2007): 2009–14. http://dx.doi.org/10.1210/me.2007-0087.

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Abstract Sequencing of genomes from diverse organisms facilitates studies on the repertoire of genes involved in intercellular signaling. Extending previous efforts to annotate most human plasma membrane receptors in the Human Plasma Membrane Receptome database, we matched cognate ligands with individual receptors by surveying the published literature. In the updated online database we called “liganded receptome,” users can search for individual ligands or receptors to reveal their pairing partners and browse through receptor or ligand families to identify relationships between ligands and rec

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Mehta, Simpi, and Seema R. Pathak. "INSILICO DRUG DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL COUMARIN DERIVATIVES AS ANTI-CANCER AGENTS." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (2017): 335. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.16826.

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Objective: Cancer is the major worldwide problem. It arises due to uncontrolled growth of cells. In the present study a series of novel coumarin derivatives were designed and computationallyoptimized to investigate the interaction between designed ligands and 10 pdb files of five selected proteins. The objective here was to analyse in silico anticancerous activity of designed ligands to reduce cost and time for getting novel anticancerous drug with minimum side effects.Methods: Docking studies were performed to find outmaximum interaction between designed ligands and selected five proteins usi

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Park, Jumi, Taehee Kim, and Dongho Kim. "Charge Injection and Energy Transfer of Surface-Engineered InP/ZnSe/ZnS Quantum Dots." Nanomaterials 13, no. 7 (2023): 1159. http://dx.doi.org/10.3390/nano13071159.

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Surface passivation is a critical aspect of preventing surface oxidation and improving the emission properties of nanocrystal quantum dots (QDs). Recent studies have demonstrated the critical role of surface ligands in determining the performance of QD-based light-emitting diodes (QD-LEDs). Herein, the underlying mechanism by which the capping ligands of InP/ZnSe/ZnS QDs influence the brightness and lifetime of the QD-LEDs is investigated. The electrochemical results demonstrate that highly luminescent InP/ZnSe/ZnS QDs exhibit modulated charge injection depending on the length of the surface l

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Galstyan, Anzhela, Wei-Zheng Shen, and Bernhard Lippert. "AquaGroupAcidity in Complexes of theType trans-[Pt(NH3 )2(L)(H2O)]2+ (with L = Substituted Pyridines). Linear, yetWeak Dependence of pKa of the Aqua Ligand from L Basicity." Zeitschrift für Naturforschung B 64, no. 11-12 (2009): 1653–61. http://dx.doi.org/10.1515/znb-2009-11-1252.

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The pKa of the aqua ligand in complexes of the type trans-[Pt(NH3)2(L)(H2O)]n+ depends on the nature of the ligand trans to H2O, as expected. With L = NH3 or NH2R and n = 2, the pKa is around 6.0 - 6.4.With L = N-heterocyclic ligands generally higher acidities of the aqua ligands are observed, with pKa values being in the range of 4.7 - 5.4. These values are between those for L = H2O, n = 2 (4.4) and L = Cl−, n = 1 (5.7). For differently substituted pyridine ligands L a linear relationship exists between the pKa of the H2O ligand and the basicity of the heterocyclic ligand L, which is relative

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Ardiningsih, Indah, Kyyas Seyitmuhammedov, Sylvia G. Sander, et al. "Fe-binding organic ligands in coastal and frontal regions of the western Antarctic Peninsula." Biogeosciences 18, no. 15 (2021): 4587–601. http://dx.doi.org/10.5194/bg-18-4587-2021.

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Abstract. Organic ligands are a key factor determining the availability of dissolved iron (DFe) in the high-nutrient low-chlorophyll (HNLC) areas of the Southern Ocean. In this study, organic speciation of Fe is investigated along a natural gradient of the western Antarctic Peninsula, from an ice-covered shelf to the open ocean. An electrochemical approach, competitive ligand exchange – adsorptive cathodic stripping voltammetry (CLE-AdCSV), was applied. Our results indicated that organic ligands in the surface water on the shelf are associated with ice-algal exudates, possibly combined with me

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Jones, W. M., G. M. Watts, M. K. Robinson, D. Vestweber, and M. A. Jutila. "Comparison of E-selectin-binding glycoprotein ligands on human lymphocytes, neutrophils, and bovine gamma delta T cells." Journal of Immunology 159, no. 7 (1997): 3574–83. http://dx.doi.org/10.4049/jimmunol.159.7.3574.

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Abstract We compared E-selectin-binding cell surface ligands on bovine gamma delta T cells and human leukocytes using an E-selectin/Ig chimera. The chimera worked well in flow cytometric studies and showed that bovine gamma delta T cells were the only lymphocyte population in newborn animals that bound E-selectin chimera. Furthermore, the chimera blocked gamma delta T cell rolling on E-selectin. Chimera reacted with four potential glycoprotein ligands of 180, 200, 250, and 300 kDa in Western blot analysis of gamma delta T cell detergent lysates, and it specifically precipitated at least two of

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Leng, Qixin, Martin C. Woodle, and A. James Mixson. "Targeted Delivery of siRNA Therapeutics to Malignant Tumors." Journal of Drug Delivery 2017 (November 9, 2017): 1–22. http://dx.doi.org/10.1155/2017/6971297.

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Over the past 20 years, a diverse group of ligands targeting surface biomarkers or receptors has been identified with several investigated to target siRNA to tumors. Many approaches to developing tumor-homing peptides, RNA and DNA aptamers, and single-chain variable fragment antibodies by using phage display, in vitro evolution, and recombinant antibody methods could not have been imagined by researchers in the 1980s. Despite these many scientific advances, there is no reason to expect that the ligand field will not continue to evolve. From development of ligands based on novel or existing bio

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43

Balakrishnan, M., P. Supriya, S. K. Soam, Rao CH Srinivasa, and K. Sumalatha. "Comparative Molecular docking analysis of Target fruit ripening enzyme Tomato Beta galactosidase (TBG-4)." Research Journal of Biotechnology 17, no. 1 (2021): 29–39. http://dx.doi.org/10.25303/1701rjbt2939.

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Tomatoes comprise a high level of TBG4 (Tomato Beta galactosidase-4) enzyme activity that plays a key role in fruit softening by significant changes in the galactosyl content in the pericarp cell wall. In the present work, in silico docking studies of beta galactosidase with specific elucidated ligands were carried out. For the better understanding of protein ligand interactions, a set of 16 ligands were used for docking studies. In the present study, two different comparative docking softwares, Autodock4.0 and iGEMDOCK were used to study the protein–ligand interactions and performed to get th

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Ben-Shlomo, Izhar, and Aaron J. W. Hsueh. "Three’s Company: Two or More Unrelated Receptors Pair with the Same Ligand." Molecular Endocrinology 19, no. 5 (2005): 1097–109. http://dx.doi.org/10.1210/me.2004-0451.

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Abstract Intercellular communication relies on signal transduction mediated by extracellular ligands and their receptors. Although the ligand-receptor interaction is usually a two-player event, there are selective examples of one polypeptide ligand interacting with more than one phylogenetically unrelated receptor. Likewise, a few receptors interact with more than one polypeptide ligand, and sometimes with more than one coreceptor, likely through an interlocking of unique protein domains. Phylogenetic analyses suggest that for certain triumvirates, the matching events could have taken place at

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Horiuchi, Keisuke, Sylvain Le Gall, Marc Schulte, et al. "Substrate Selectivity of Epidermal Growth Factor-Receptor Ligand Sheddases and their Regulation by Phorbol Esters and Calcium Influx." Molecular Biology of the Cell 18, no. 1 (2007): 176–88. http://dx.doi.org/10.1091/mbc.e06-01-0014.

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Signaling via the epidermal growth factor receptor (EGFR), which has critical roles in development and diseases such as cancer, is regulated by proteolytic shedding of its membrane-tethered ligands. Sheddases for EGFR-ligands are therefore key signaling switches in the EGFR pathway. Here, we determined which ADAMs (a disintegrin and metalloprotease) can shed various EGFR-ligands, and we analyzed the regulation of EGFR-ligand shedding by two commonly used stimuli, phorbol esters and calcium influx. Phorbol esters predominantly activate ADAM17, thereby triggering a burst of shedding of EGFR-liga

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Ciccarelli, Emma Jo, Zachary Wing, Moshe Bendelstein та ін. "TGF-β ligand cross-subfamily interactions in the response of Caenorhabditis elegans to a bacterial pathogen". PLOS Genetics 20, № 6 (2024): e1011324. http://dx.doi.org/10.1371/journal.pgen.1011324.

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The Transforming Growth Factor beta (TGF-β) family consists of numerous secreted peptide growth factors that play significant roles in cell function, tissue patterning, and organismal homeostasis, including wound repair and immunity. Typically studied as homodimers, these ligands have the potential to diversify their functions through ligand interactions that may enhance, repress, or generate novel functions. In the nematode Caenorhabditis elegans, there are only five TGF-β ligands, providing an opportunity to dissect ligand interactions in fewer combinations than in vertebrates. As in vertebr

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47

Urien, S., F. Brée, B. Testa та J. P. Tillement. "pH-dependency of basic ligand binding to α1-acid glycoprotein (orosomucoid)". Biochemical Journal 280, № 1 (1991): 277–80. http://dx.doi.org/10.1042/bj2800277.

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The binding interactions of a series of basic ligands with alpha 1-acid glycoprotein (AAG) were examined as a function of pH. The binding to AAG increased with increasing pH, and the binding data were satisfactorily fitted to a model that incorporates the effect of pH and discriminates the association constants of neutral (non-protonated) and protonated forms of ligands. It was shown that ligands in the neutral form have a markedly higher affinity for AAG than the protonated forms, resulting in a concomitant decrease in the pKa of bound ligands. The u.v.-visible difference spectra generated up

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Solo, Peter, Sangdintuile Zeliang, Muluvelu Lohe, Avünü Neikha, and Akumsunep Jamir. "Structure-based Drug Design, ADME and Molecular Docking analyses of anti-viral agents against SARS-CoV-2 virus, Zika virus and Hepatitis C virus." Journal of Drug Delivery and Therapeutics 13, no. 7 (2023): 65–74. http://dx.doi.org/10.22270/jddt.v13i7.5909.

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Computer-aided drug design has been taking an increasing role in the field of modern drug discovery. These in silico computational methods are cost-effective, reduce the use of animal models in pharmacological research, and can be used to study pathogenic organisms without the need for any facilities. Based on the structure of known anti-viral agents, a total of 812 ligands have been designed. All ligands were screened for drug-likeness based on Lipinski rule of five. A database of ligands was constructed and in silico docking analyses were performed using MOE 2015.10 program against three sel

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Stefansson, S., M. Z. Kounnas, J. Henkin, et al. "gp330 on type II pneumocytes mediates endocytosis leading to degradation of pro-urokinase, plasminogen activator inhibitor-1 and urokinase-plasminogen activator inhibitor-1 complex." Journal of Cell Science 108, no. 6 (1995): 2361–68. http://dx.doi.org/10.1242/jcs.108.6.2361.

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Glycoprotein 330 (gp330) is a member of a family of receptors related to the low density lipoprotein receptor (LDLR). Although several ligands have been shown to bind gp330 in solid-phase assays, the ability of gp330 to mediate ligand endocytosis has not been demonstrated. To develop a cellular model for gp330 function we screened a variety of cultured cell lines and identified several that expressed this protein, including immortalized rat type II pneumocytes and a human and two rodent tumor cell lines. Using type II pneumocytes, endocytosis of a previously described gp330 ligand, urokinase (

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Ruff, Kiersten M., Furqan Dar, and Rohit V. Pappu. "Ligand effects on phase separation of multivalent macromolecules." Proceedings of the National Academy of Sciences 118, no. 10 (2021): e2017184118. http://dx.doi.org/10.1073/pnas.2017184118.

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Biomolecular condensates enable spatial and temporal control over cellular processes by concentrating biomolecules into nonstoichiometric assemblies. Many condensates form via reversible phase transitions of condensate-specific multivalent macromolecules known as scaffolds. Phase transitions of scaffolds can be regulated by changing the concentrations of ligands, which are defined as nonscaffold molecules that bind to specific sites on scaffolds. Here, we use theory and computation to uncover rules that underlie ligand-mediated control over scaffold phase behavior. We use the stickers-and-spac

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