Relevant bibliographies by topics / Small Molecular Organic Ligands

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Academic literature on the topic 'Small Molecular Organic Ligands'

Author: Grafiati
Published: 7 September 2023

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Journal articles on the topic "Small Molecular Organic Ligands"

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Nilsson, K. Peter R. "Small organic probes as amyloid specific ligands - Past and recent molecular scaffolds." FEBS Letters 583, no. 16 (April 17, 2009): 2593–99. http://dx.doi.org/10.1016/j.febslet.2009.04.016.

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Polowin, Joel, Robert Poe, and Michael C. Baird. "Extensions of the applicability of the MMX molecular modelling system to determination of barriers to rotation of π-bonded ligands." Canadian Journal of Chemistry 73, no. 7 (July 1, 1995): 1078–83. http://dx.doi.org/10.1139/v95-133.

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The commercially available molecular mechanics package PCMODEL, which has been shown to be very useful for determining conformational energy profiles for rotation of σ-bonded ligands, cannot be utilized to determine barriers to rotation of π-bonded ligands because of limitations in the way the π-bonding interactions are defined. This paper describes a partially successful modification of the dihedral driver of PCMODEL that makes possible reasonable calculations of the conformational energy profiles for rotation of the π-bonded arene ligands in the compounds (η6-arene)Cr(CO)2(PPh3) (arene = C6H6, C6Me6) and of the π-bonded ethylene ligands in [PtCl3(η2-CH2=CH2)]− and [(η5-C5H5)Re(NO)(PPh3)(η2-CH2=CH2)]+. The steric barriers to ethylene rotation in the latter two complexes were found to be small relative to the electronic barriers to ligand rotation. Keywords: molecular mechanics, olefin rotation, conformational energy profile.
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Milanesi, Eva, Paola Costantini, Alberto Gambalunga, Raffaele Colonna, Valeria Petronilli, Anna Cabrelle, Gianpietro Semenzato, Andrea M. Cesura, Emmanuel Pinard, and Paolo Bernardi. "The Mitochondrial Effects of Small Organic Ligands of BCL-2." Journal of Biological Chemistry 281, no. 15 (February 14, 2006): 10066–72. http://dx.doi.org/10.1074/jbc.m513708200.

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Norel, R., H. J. Wolfson, and R. Nussinov. "Small Molecule Recognition: Solid Angles Surface Representation and Molecular Shape Complementarity." Combinatorial Chemistry & High Throughput Screening 2, no. 4 (August 1999): 223–36. http://dx.doi.org/10.2174/1386207302666220204193837.

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Abstract: Here we examine the recognition of small molecules by their protein and DNA receptors. We focus on two questions: First, how well does the solid angle molecular surface representation perform in fitting together the surfaces of small ligands, such as drugs and cofactors to their corresponding receptors; And second, in particular, to what extent does the shape complementarity play a role in the matching (recognition) process of such small molecules. Both questions have been investigated in protein-protein binding: "Critical Points" based on solid angle calculations have been shown to perform well in the matching of large protein molecules. They are robust, may be few in numbers, and capture satisfactorily the molecular shape. Shape complementarity has been shown to be a critical factor in protein­ protein recognition, but has not been examined in drug-receptor recognition. To probe these questions, here we dock 185 receptor-small ligand molecule pairs. We find that such a representation performs adequately for the smaller ligands too, and that shape complementarity is also observed. These issues are important, given the large databases of drugs that routinely have to be scanned to find candidate, lead compounds. We have been able to carry out such large scale docking experiments owing to our efficient, computer-vision based docking algorithms. Its fast CPU matching times, on the order of minutes on a PC, allows such large scale docking experiments.
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Peterson, Leif. "Small Molecule Docking of DNA Repair Proteins Associated with Cancer Survival Following PCNA Metagene Adjustment: A Potential Novel Class of Repair Inhibitors." Molecules 24, no. 3 (February 12, 2019): 645. http://dx.doi.org/10.3390/molecules24030645.

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Natural and synthetic small molecules from the NCI Developmental Therapeutics Program (DTP) were employed in molecular dynamics-based docking with DNA repair proteins whose RNA-Seq based expression was associated with overall cancer survival (OS) after adjustment for the PCNA metagene. The compounds employed were required to elicit a sensitive response (vs. resistance) in more than half of the cell lines tested for each cancer. Methodological approaches included peptide sequence alignments and homology modeling for 3D protein structure determination, ligand preparation, docking, toxicity and ADME prediction. Docking was performed for unique lists of DNA repair proteins which predict OS for AML, cancers of the breast, lung, colon, and ovaries, GBM, melanoma, and renal papillary cancer. Results indicate hundreds of drug-like and lead-like ligands with best-pose binding energies less than −6 kcal/mol. Ligand solubility for the top 20 drug-like hits approached lower bounds, while lipophilicity was acceptable. Most ligands were also blood-brain barrier permeable with high intestinal absorption rates. While the majority of ligands lacked positive prediction for HERG channel blockage and Ames carcinogenicity, there was a considerable variation for predicted fathead minnow, honey bee, and Tetrahymena pyriformis toxicity. The computational results suggest the potential for new targets and mechanisms of repair inhibition and can be directly employed for in vitro and in vivo confirmatory laboratory experiments to identify new targets of therapy for cancer survival.
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Schwarz, Benjamin, and Carsten Streb. "Architectural control of urea in supramolecular 1D strontium vanadium oxide chains." Dalton Transactions 44, no. 9 (2015): 4195–99. http://dx.doi.org/10.1039/c4dt03691c.

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Tatikonda, Rajendhraprasad, Evgeny Bulatov, Zülal Özdemir, Nonappa Nonappa, and Matti Haukka. "Infinite coordination polymer networks: metallogelation of aminopyridine conjugates and in situ silver nanoparticle formation." Soft Matter 15, no. 3 (2019): 442–51. http://dx.doi.org/10.1039/c8sm02006j.

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Self-assembly of silver(i) and low molecular weight organic ligands derived from aminopyridine conjugates led to in situ generation of an infinite coordination polymer network and ultra small nanoparticles.
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Cho, Yeon-Jin, Sun-Hye Choi, Rami Lee, Hongik Hwang, Hyewhon Rhim, Ik-Hyun Cho, Hyoung-Chun Kim, Jeong-Ik Lee, Sung-Hee Hwang, and Seung-Yeol Nah. "Ginseng Gintonin Contains Ligands for GPR40 and GPR55." Molecules 25, no. 5 (March 2, 2020): 1102. http://dx.doi.org/10.3390/molecules25051102.

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Gintonin, a novel ginseng-derived glycolipoprotein complex, has an exogenous ligand for lysophosphatidic acid (LPA) receptors. However, recent lipid analysis of gintonin has shown that gintonin also contains other bioactive lipids besides LPAs, including linoleic acid and lysophosphatidylinositol (LPI). Linoleic acid, a free fatty acid, and LPI are known as ligands for the G-protein coupled receptors (GPCR), GPR40, and GPR55, respectively. We, herein, investigated whether gintonin could serve as a ligand for GPR40 and GPR55, using the insulin-secreting beta cell-derived cell line INS-1 and the human prostate cancer cell line PC-3, respectively. Gintonin dose-dependently enhanced insulin secretion from INS-1 cells. Gintonin-stimulated insulin secretion was partially inhibited by a GPR40 receptor antagonist but not an LPA1/3 receptor antagonist and was down-regulated by small interfering RNA (siRNA) against GPR40. Gintonin dose-dependently induced [Ca2+]i transients and Ca2+-dependent cell migration in PC-3 cells. Gintonin actions in PC-3 cells were attenuated by pretreatment with a GPR55 antagonist and an LPA1/3 receptor antagonist or by down-regulating GPR55 with siRNA. Taken together, these results demonstrated that gintonin-mediated insulin secretion by INS-1 cells and PC-3 cell migration were regulated by the respective activation of GPR40 and GPR55 receptors. These findings indicated that gintonin could function as a ligand for both receptors. Finally, we demonstrated that gintonin contained two more GPCR ligands, in addition to that for LPA receptors. Gintonin, with its multiple GPCR ligands, might provide the molecular basis for the multiple pharmacological actions of ginseng.
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Comess, Kenneth M., Mark E. Schurdak, Martin J. Voorbach, Michael Coen, Jonathan D. Trumbull, Houjun Yang, Lan Gao, et al. "An Ultraefficient Affinity-Based High-Throughout Screening Process: Application to Bacterial Cell Wall Biosynthesis Enzyme MurF." Journal of Biomolecular Screening 11, no. 7 (September 14, 2006): 743–54. http://dx.doi.org/10.1177/1087057106289971.

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The authors describe the discovery of a new class of inhibitors to an essential Streptococcus pneumoniae cell wall biosyn-thesis enzyme, MurF, by a novel affinity screening method. The strategy involved screening very large mixtures of diverse small organic molecules against the protein target on the basis of equilibrium binding, followed by iterative ultrafiltration steps and ligand identification by mass spectrometry. Hits from any affinity-based screening method often can be relatively nonselective ligands, sometimes referred to as “nuisance” or “promiscuous” compounds. Ligands selective in their binding affinity for the MurF target were readily identified through electronic subtraction of an empirically determined subset of promiscuous compounds in the library without subsequent selectivity panels. The complete strategy for discovery and identification of novel specific ligands can be applied to all soluble protein targets and a wide variety of ligand libraries.
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Shahroz, Mir Mohammad, Hemant Kumar Sharma, Abdulmalik S. A. Altamimi, Mubarak A. Alamri, Abuzer Ali, Amena Ali, Safar Alqahtani, et al. "Novel and Potential Small Molecule Scaffolds as DYRK1A Inhibitors by Integrated Molecular Docking-Based Virtual Screening and Dynamics Simulation Study." Molecules 27, no. 4 (February 9, 2022): 1159. http://dx.doi.org/10.3390/molecules27041159.

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The dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a novel, promising and emerging biological target for therapeutic intervention in neurodegenerative diseases, especially in Alzheimer’s disease (AD). The molMall database, comprising rare, diverse and unique compounds, was explored for molecular docking-based virtual screening against the DYRK1A protein, in order to find out potential inhibitors. Ligands exhibiting hydrogen bond interactions with key amino acid residues such as Ile165, Lys188 (catalytic), Glu239 (gk+1), Leu241 (gk+3), Ser242, Asn244, and Asp307, of the target protein, were considered potential ligands. Hydrogen bond interactions with Leu241 (gk+3) were considered key determinants for the selection. High scoring structures were also docked by Glide XP docking in the active sites of twelve DYRK1A related protein kinases, viz. DYRK1B, DYRK2, CDK5/p25, CK1, CLK1, CLK3, GSK3β, MAPK2, MAPK10, PIM1, PKA, and PKCα, in order to find selective DYRK1A inhibitors. MM/GBSA binding free energies of selected ligand–protein complexes were also calculated in order to remove false positive hits. Physicochemical and pharmacokinetic properties of the selected six hit ligands were also computed and related with the proposed limits for orally active CNS drugs. The computational toxicity webserver ProTox-II was used to predict the toxicity profile of selected six hits (molmall IDs 9539, 11352, 15938, 19037, 21830 and 21878). The selected six docked ligand–protein systems were exposed to 100 ns molecular dynamics (MD) simulations to validate their mechanism of interactions and stability in the ATP pocket of human DYRK1A kinase. All six ligands were found to be stable in the ATP binding pocket of DYRK1A kinase.
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Dissertations / Theses on the topic "Small Molecular Organic Ligands"

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Charmant, Jonathan Paul Henry. "Reactivity of the #mu#3-benzyne ligand towards small organic molecules." Thesis, University of Bristol, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.238905.

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Soules, Régis. "Proprietes cooperatives de complexes polymetalliques des ligands squarate et thiosquarate." Toulouse 3, 1987. http://www.theses.fr/1987TOU30178.

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Etude de l'emploi d'un coordinat assembleur qui puisse par coordination avec le centre metallique utilise (metaux de transition du groupe viii) aboutir a un agencement a une dimension des motifs moleculaires par empilement d'entites monomeres ou par formation de chaines. Par utilisation du coordinat squarate sous ses formes oxygenees et soufrees, obtention d'un certain nombre de complexes de pt, pd, ni et cu repondant aux criteres fixes. Etude des structures de ces composes, de leurs proprietes physiques et de la relation structure-propriete. La nature du coordinat comme le caractere specifique de l'arrangement structural ont ete discutes pour une approche de la comprehension de la nature de ces proprietes physiques
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Ashoka, Sahadevan Suchithra. "Anilate-based molecular building blocks for metal-organic frameworks and molecular conductors Conducting Anilate-Based Mixed-Valence Fe(II)Fe(III) Coordination Polymer: Small-Polaron Hopping Model for Oxalate-Type Fe(II)Fe(III) 2D Networks Nanosheets of Two-Dimensional Neutral Coordination Polymers Based on Near-Infrared-Emitting Lanthanides and a Chlorocyananilate Ligand." Thesis, Angers, 2019. http://bu.univ-angers.fr/Contact.

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Ce travail porte sur la synthèse et la caractérisation de matériaux moléculaires fonctionnels basés sur la molécule anilate et présentant des propriétés de conductivité, de magnétisme et de luminescence. Les anilates sont des dérivés de la 2,5-dihydroxy-1,4-benzoquinone substitués en positions 3 et 6 par une variété d’éléments (H, F, Cl, Br, I, CN, etc). Parmi eux, le seul composé hétérosubstitué ClCNAn2- a été choisi pour préparer une nouvelle famille de polymères de coordination bidimensionnels (PC 2D) avec des métaux de transition ou des ions lanthanides : i) un PC à valence mixte FeIIFeIII, de formule [TAG][FeIIFeIII(ClCNAn)3], contient pour la première fois le cation triaminoguanidinium dans un réseau de coordination.ii) Des PC basés sur le ligand ClCNAn2- et des ions lanthanides émettant dans le proche infrarouge (YbIII, NdIII, ErIII). Ces composés ont été exfoliés en monocouches, et des études de photoluminescence ont été menées à la fois sur les cristaux et les monocouches. iii) Une famille de PC hétéroleptiques basés sur des ions lanthanides et sur deux types de ligands pontants, le ligand ClCNAn2- et des ligands de type carboxylates (DOBDC et F4-BDC). iv) Une famille de PC basés sur des ions DyIII ont été préparés afin d’étudier leur propriétés magnétiques. v) Finalement, la capacité des ligands anilates à se combiner à des conducteurs moléculaires basés sur le BEDT-TTF a été démontrée à travers la synthèse et l’électrocristallisation de semiconducteurs organiques et de conducteurs magnétiques hybrides avec l’anion [Fe(ClCNAn)3]3-
This work reports on the design, synthesis and characterization of novel anilate-based functional molecular materials showing luminescent, magnetic and/or conducting properties. The family of anilate ligands comprises several derivatives obtained by introducing various substituents (H, F, Cl, Br, I, CN, etc.) at the 3 and 6 positions of the common 2,5-dihydroxy-1,4-benzoquinone framework. Among the anilate ligands, the only known heterosubstituted anilate with Cl/CN substituents at the 3,6 positions, ClCNAn2-, have been selected for preparing a novel family of 2D layered coordination polymers (2D CP) with both 3d metal ions and 4f lanthanide ions, through a general and straightforward synthetic strategy. i) Mixed-valence FeIIFeIII 2D CP, formulated as [TAG][FeIIFeIII(ClCNAn)3], containing, the tris(amino)-guanidinium (TAG) cation for the first time in such 2D networks has been synthesized and thoroughly characterized. ii) 2D CPs based on NIR-emitting lanthanides (YbIII, NdIII, ErIII) and the ClCNAn2- ligand, have been prepared and characterized. These layered compounds were exfoliated to nanosheets, by sonication-assisted solution synthesis. Time-resolved photoluminescence studies performed on both the bulk and nanosheets are also highlighted. iii) Novel family of heteroleptic 2D CPs based on NIR-emitting lanthanides and mixed ligands (ClCNAn2- and carboxylate ligands (DOBDC and F4-BDC)), were prepared and characterized. vi) Novel family of 2D CPs based on DyIII and ClCNAn2- were prepared in order to investigate their magnetic properties. v) Furthermore, the ability of anilate ligands to work as components of BEDT-TTF- based molecular conductors have been demonstrated through the synthesis, via electrocrystallization technique. vi) П-d hybrid multifunctional paramagnetic molecular conductors BEDT-TTF and [Fe(ClCNAn)3]3-) were also studied
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Hui, Yu 1977. "Heterjunctions of small molecular weight organic semiconductors." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=81540.

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Photodiodes made of small molecular weight organic semiconductors have been fabricated. The organic materials under investigation are p-type Copper phthalocyanine (CuPc) and n-type 3,4,9,10-perylenetetracarboxylic bisbenzimidazole (PTCBI). Current-voltage and capacitance-voltage measurements have been performed to evaluate the electrical properties of the organic photodiodes. Optical measurements including responsivity and temporal response have also been carried out. It has been found that device efficiency of the photodiodes is influenced by the thickness of organic layers as well as the device structures. It is believed that organic layer thickness is a strong function of materials' exciton diffusion lengths. The thickness of the organic layer employed in the fabricated photodiode is 100 A or less. However, the fabricated devices with thin organic layer showed poor performance in terms of saturation current and breakdown voltage. As a result, new device structures have been proposed to overcome the problems. Stacking structure double heterojunction (SDH) and novel comb-like structure single heterojunction (CSH) device configurations have shown a substantial improvement in both electrical and optical parameters. There is at least 3 times enhancement in photocurrent and 10 times increase in external quantum efficiency for photodiodes employing CSH device structure and 100 A organic layer. Improvements in saturation current and breakdown voltage have also been observed. In addition, responsivity measurements in CSH devices have yielded a 7 times improvement. Furthermore, the carrier lifetime of the photodiode is estimated to be around 1 microsecond from the temporal response measurements. The combined effect of thin organic layers and new device structures leads to an overall improvement in device performance.
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CIARAMELLI, CARLOTTA. "Synthesis and characterization of new small-molecule ligands of LPS binding proteins." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2015. http://hdl.handle.net/10281/77016.

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Lo scopo del presente lavoro è la progettazione, la sintesi e la caratterizzazione di nuove small molecules, attive come ligandi di LPS (lipopolisaccaridi)-binding proteins. Gli LPS, o endotossine batteriche, sono macromolecole anfifiliche ubiquitarie sulla membrana esterna dei batteri Gram-negativi. Le proteine che legano gli LPS studiate nel corso di questo progetto di tesi di dottorato appartengono a due categorie: le proteine batteriche di trasporto Lpt e il sistema recettoriale TLR4, che comprende anche i co-recettori LBP, CD14, MD2. Le proteine Lpt, e in particolare la proteina LptC, sono responsabili del meccanismo di esportazione del LPS alla superficie cellulare, che è uno step fondamentale della via biosintetica dell’LPS. Pertanto, la biogenesi dell’LPS rappresenta un target ideale per lo sviluppo di nuovi antibiotici contro i batteri Gram-negativi. Inoltre, le strutture delle proteine Lpt sono state risolte, ma il meccanismo di trasporto è ancora da elucidare. Nel presente lavoro di tesi sono stati utilizzate diverse tecniche per studiare l'interazione tra LPS e LptC, con particolare attenzione agli studi di interazione via NMR. Inoltre, un nuovo LPS fluorescente è stato prodotto ed è stato utilizzato come tool per studi di interazione LPS-LptC con tecniche di fluorescenza. Sono state anche sviluppate alcune nuove molecole sintetiche. Questi glicolipidi sono stati progettati e sintetizzati per ottenere ligandi di LptC e, in prospettiva, potenziali antibiotici contro i batteri Gram-negativi. Il Toll-like receptor 4 (TLR4), il recettore dell'immunità innata, riconosce l’LPS aiutato da altre proteine (LBP, CD14 e MD-2) ed è responsabile dell'induzione della risposta infiammatoria. Molecole sintetiche in grado di modulare l'attività dei recettori dell’immunità innata sono un potente mezzo per studiare il sistema recettoriale TLR4 e hanno grande interesse farmacologico come adiuvanti vaccinali (agonisti), agenti antisepsi e anti-infiammatori (antagonisti). L’attività biologica di glicolipidi con una funzione amminica (IAXO-102) come antagonisti del TLR4 è stata chiaramente dimostrata dal nostro gruppo di ricerca. La sintesi di molecole derivate da IAXO-102, che mantengano l'attività biologica del precursore, è stato un obiettivo di questo lavoro. In particolare, sono state portate a termine le sintesi di sonde fluorescenti, utilizzate per studi di interazione, derivati zwitterionici e molecole dimeriche. Nei nostri laboratori sono stati ottenuti anche antagonisti anionici del TLR4 con una struttura chimica più simile a Lipide A. Lo scopo di questo lavoro è stato valutare, tramite esperimenti NMR, la loro capacità di legare co-recettore dell'immunità innata MD-2. Il carattere anfifilico degli analoghi sintetici del lipide A sintetizzati finora è spesso associato ad una bassa solubilità in acqua e a scarsa biodisponibilità. Invece, i composti attivi sul TLR4 di origine naturale hanno una migliore solubilità e biodisponibilità. La modifica chimica di queste strutture è molto utile per modulare l'attività biologica e per migliorare la specificità nei confronti del target. Di conseguenza, in una fase successiva di questo lavoro di tesi, è stata intrapresa la sintesi di nuove molecole con strutture chimiche ispirate ai modulatori naturali del TLR4. Recentemente è stato dimostrato che alcuni composti fenolici estratti da olio di oliva hanno una buona attività come antagonisti del TLR4. Pertanto, la sintesi di alcuni analoghi di queste molecole è stata eseguita per ottenere nuovi potenziali antagonisti del TLR4, con una migliore solubilità in acqua e una ridotta tossicità.
The purpose of this work is the design, synthesis and characterization of new small molecules, active as ligands of two different lipopolysaccharide (LPS)-binding proteins. LPS, or bacterial endotoxin, is an amphiphilic macromolecule ubiquitous on the outer membrane of Gram-negative bacteria. The LPS binding proteins studied during this thesis project belong to two classes: the bacterial proteins of the Lpt transport machinery and the mammalian TLR4 receptor system, including the co-receptors LBP, CD14, MD-2. Lpt proteins, and in particular the protein LptC, are responsible for the export mechanism of LPS to the cell surface of Gram negative bacteria, which is a fundamental step of the LPS biosynthetic pathway. Therefore, the LPS biogenesis represents an ideal target for development of novel antibiotics against Gram-negative bacteria. Moreover, the structures of Lpt proteins have been elucidated, but very little is known about the mechanism of LPS transport. In this thesis work different techniques were used to study the interaction between LPS and LptC, particularly NMR binding studies. Moreover, a new fluorescent LPS was produced and it was used as a tool to perform LPS-LptC interaction studies with fluorescence techniques. Some new synthetic molecules were also developed during this thesis. Glycolipidic small molecules were designed and synthesized in order to obtain LptC ligands and, in perspective, potential antibiotics against Gram-negative bacteria. Toll-like receptor 4 (TLR4), the innate immunity receptor, recognizes LPS, helped by other proteins (LBP, CD14 and MD-2), and it is responsible for the induction of inflammatory responses. Synthetic small molecules able to modulate innate immunity receptors activity are a powerful mean to study the TLR4 receptor system and have great pharmacological interest as vaccine adjuvants (agonists), antisepsis and anti-inflammatory agents (antagonists). Antagonist activity on TLR4 receptor system of amino glycolipids (IAXO-102) was clearly demonstrated by our research group. The synthesis of molecules derived from IAXO-102 which retain the biological activity of the precursor was a target of this work. In particular, the synthesis of fluorescent probes, used for binding studies, zwitterionic derivatives and dimeric molecules were performed. Anionic TLR4 antagonists with a chemical structure more similar to Lipid A were also obtained in our labs. The aim of this work was the evaluation via NMR binding experiments of their ability to bind the innate immunity co-receptor MD-2. The amphiphilic character of the synthetic lipid A analogues synthesized so far is often associated with low water solubility and poor bioavailability. In this respect, the natural TLR4-active compounds have better solubility and bioavailability. The chemical modification of these structures is very helpful to modulate their biological activity and to enhance target specificity. Consequently, in a later stage of this work, the synthesis of new small molecules with chemical structures inspired to natural TLR4 modulators was pursued. Very recently it was found that some phenolic compounds from olive oil extracts presented a good activity as TLR4 antagonists. The synthesis of some analogues of these molecules was performed to obtain new potential TLR4 antagonists with better water solubility and reduced toxicity.
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Rooney, Timothy Patrick Christopher. "Development of small molecule inhibitors of the bromodomain-histone interaction." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:dfe22076-befc-4881-8433-b563a9329478.

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Bromodomains bind to acetylated lysine residues 1 to mediate a wide range of biological processes, including the assembly of transcriptional machinery at modified histones. This thesis describes the design of small molecule inhibitors of bromodomains, with particular focus on the bromodomain of CREBBP. A fragment based approach was employed to investigate bicyclic amides as acetyl lysine mimics. Initially the benzoxazinone scaffold (BNZ) 2 was shown to be a novel, ligand efficient bromodomain inhibitor. Structure based elaboration of the BNZ scaffold was employed to direct substitutions towards the region of CREBBP with greatest variability compared to other bromodomains. Ultimately, the compounds in this series were limited to micromolar affinity for CREBBP, but provided useful structure activity relationships. Subsequently the dihydroquinoxalinone scaffold (DHQN) 3 was also shown to be a novel acetyl lysine mimic. Attachment of the optimum side group identified in the BNZ series led to the discovery of the first sub micromolar inhibitor of CREBBP. A co crystal structure with CREBBP revealed that the side group of this compound bound in a newly identified induced fit pocket, mediated by a cation π interaction. A combination of structural, functional and computational studies confirmed that the cation π interaction contributed significantly towards the binding affinity of these ligands. Further work to elaborate the DHQN core, or develop an alternative acetyl lysine mimic into a CREBBP inhibitor, did not lead to an improvement. However, the optimum compound 4 was shown to displace CREBBP from chromatin in a cell based assay. Overall, cyclic amide based fragments were developed as CREBBP inhibitors, providing some of the first bromodomain ligands with nanomolar affinity outside of the BET family. In the process, key structural information about binding of ligands to CREBBP was revealed. Compound 4 provides a tool with which to study the biological implications of aberrant CREBBP activity and to investigate the therapeutic potential of bromodomain inhibition.
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Kueh, Alona Swee Hua. "Molecular imprinting of small, poorly functionalised organic compounds." The University of Waikato, 2008. http://hdl.handle.net/10289/2264.

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Molecularly imprinted polymers (MIPs) have been compared to natural antibodies in that they can specifically bind target compounds in a similar way that antibodies specifically bind to an antigen. The attraction of the MIPs technology is the ease of creating binding elements which are relatively cheap compared with the process of isolating natural antibodies. In this research monoterpenes, such as α-terpineol, were chosen to be the model compounds for investigating the molecular imprinting of small, poorly functionalised organic compounds. The conventional non-covalent approach was mainly used to synthesise these MIPs, but the sacrificial-spacer semi-covalent approach was also investigated. A less widely used method, porogen-imprinting - a variant of non-covalent imprinting - was adapted for α-terpineol. The latter novel terpene MIP appeared to specifically bind α-terpineol, by hydrogen bonding, so the polymer was characterised in detail. The main parameters which were altered for preparing non-covalent MIPs included the template (α-terpineol, (-)-menthol or trans-terpin); the functional monomer (methacrylic acid, 2-hydroxyethyl methacrylate, bilirubin and phenol [for the semi-covalent MIP]); the cross-linking monomer (ethylene glycol dimethacrylate, divinylbenzene and trimethylolpropane trimethacrylate); and also the polymerisation method (block or precipitation polymerisation). The binding specificity and cross-reactivity for all the polymers were tested using a liquid batch-binding setup. The batch-binding setup required the detection of analyte that was not bound in order to calculate by difference the fraction of analyte bound to the polymer. Initially the terpenes were to be detected by a colorimetric method; however attempts to make the method sensitive and reliable were not successful. In comparison, gas chromatography was more reliable for the detection of terpenes and was used for the experiments presented in this thesis. 1H-NMR studies of the interaction between α-terpineol and acetic acid (as a non-polymerisable analogue of methacrylic acid) were investigated as a basis for understanding the binding to the carboxyl functional group moiety employed in many of the non-covalent MIPs that were made. The interaction between (-)-menthol and phenol was also investigated because the phenol moiety was employed in the semi-covalent MIP. Only selected MIPs, which appeared to specifically bind the template, were physically characterised. This included optimising the batch-binding parameters, scanning electron microscopy imaging, surface area and pore radius analysis and in some cases Fourier transform-infrared spectroscopy of the polymers.
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Camuñas, i. Soler Joan. "Force-spectroscopy of small ligands binding to nucleic acids." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/286597.

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Single-molecule techniques allow to following biomolecular reactions with unprecedented resolution. Particularly, optical tweezers can be used to manipulate and apply forces to individual molecules tethered between plastic beads that are optically-trapped. Optical trapping is achieved by using highly focused laser beams that exert a gradient force onto the micrometer-sized dielectric particles that become confined close to the focal position of the laser. By specifically attaching the ends of the molecule under study to two optically-trapped beads, it is possible to manipulate and apply forces to an individual molecule. Typical experiments with optical tweezers consist in manipulating nucleic acids (DNA, RNA) or proteins one at a time. For instance DNA molecules can be stretched to measure its elastic properties, or unzipped to measure their base-pairing energies. Many small anticancer drugs target nucleic acids to exert their cytotoxic activity against cancer cells. To understand their mechanism of action it is important to know in which positions, how strong, and how fast do they bind to different specific sites in DNA. Single-molecule optical tweezers experiments can be used to unravel the binding thermodynamics and kinetics of many of these ligands, especially those difficult to characterize with bulk techniques. Thiocoraline is one of such drugs, and binds DNA through bis-intercalation. Experiments with optical tweezers show that the kinetics of intercalation are very slow (hours) and strongly force-dependent: force facilitates binding but slows down unbinding. Experiments performed in different conditions also reveal that the binding pathway proceeds through a mono-intercalated intermediate that causes the observed slow kinetics. In this sense, we present a three-state model that offers a theoretical framework from which the kinetic rates of the reaction can be extracted, and that could be useful to characterize other bis-intercalators. We also show that DNA unzipping experiments can be used to determine the preferred binding sequences of Thiocoraline, finding that it preferentially clamps CpG steps. This methodology is potentially very useful as it provides direct access to the preferred binding sites of small ligands due to its thermodynamic stability with one base pair resolution and without the requirement of restriction enzymes or radioactive labeling. This single-molecule footprinting technique is also adapted to a magnetic tweezers instrument in order to perform parallelized measurements. The fact that bis-intercalation does not modify the persistence length of dsDNA is also found in the pulling experiments. From the elasticity measurements, we also extract equilibrium quantitates of the interaction by using classic statistical models. This combination of DNA stretching and unzipping assays can also be used to follow how the anticancer agent Kahalalide F self-assembles and compacts DNA. Kahalalide F forms nanometric particles that are positively charged able to bind and condense DNA. The binding reaction shows to phases: an initial compaction of electrostatic origin, and its subsequent stiffening due to the hydrophobic collapse of the complex. The combination of quantitative force-spectroscopy measurements with AFM images of the complexes and other bulk tech- niques (DLS, EM) provides a consistent picture of the compaction and aggregation process. Modeling of the experiments provides the thermodynamic parameters of the interaction that are complemented with kinetic measurements. A simple technique to study ssDNA with optical tweezers is also presented and used to study how the stiffness of the polyanion affects the compaction process. We exploit this methodology to understand how the stiffness of the polyanion affects the compaction kinetics, and later on, we also show its utility to study the elasticity of ssDNA under varying ionic conditions. Finally, the utility of this methodology to study self-assembly and aggregation is explored with amyloidogenic peptides involved in neurodegenerative disorders.
Les tècniques de molècula individual permeten seguir les reaccions biomoleculars amb una resolució sense precedents, proveint als científics d’una sèrie d’instruments per a mesurar magnituds físiques i investigar sistemes experimentals difícilment accessibles amb les tradi­cionals mesures en volum (és a dir a on les mesures es realitzen amb mols de reactiu). Particularment, les pinces òptiques permeten manipular i aplicar forces a molècules individuals i determinar-ne així les seves propietats elàstiques i termodinàmiques. L’atrapament òptic es basa en l’ús d’un feix làser focalitzat per exercir una força òptica a les microesferes (diàmetre ~ 3 µm), que queden confinades a prop del punt focal a causa de la conservació del moment lineal. Els experiments de micromanipulació es realitzen unint els extrems de la molècula que es vol estudiar a la superfícies de dues microesferes diferents, podent així aplicar forces a la molècula quan desplacem una microesfera respecte de l’altra. Per ancorar les molècules a la superfície de les microesferes s’utilitzen unions moleculars que tenen una alta a.nitat (p.ex. enllaç biotina-estreptavidina). Típicament els experiments amb pinces òptiques consisteixen en la micromanipulació d’àcids nucleics (ADN, ARN) o proteïnes de forma individual. Per exemple, una molècula d’ADN pot ésser estirada per a estudiar-ne les propietats elàstiques, o oberta mecànicament (separant les dues cadenes que formen la doble hèlix) per a mesurar les energies lliures d’aparellament entre bases. Un gran nombre d’agents anticancerígens tenen com a diana els àcids nucleics, a on s’hi uneixen afi i efecte de dur a terme la seva acció citotòxica (p. ex. interferint amb processos cel·lulars essencials com són la replicació, la transcripció o els mecanismes de reparació). Per entendre el seu mecanisme d’acció és important conéixer en quines posicions, amb quina a.nitat, i amb quina cinètica s’uneixen a diferents seqüències d’ADN. Els experiments de molècula individual amb pinces òptiques permeten determinar la termodinàmica i cinètica d’unió de molts d’aquests lligands, especialment aquells difícils de caracteritzar mitjançant mesures en volum. És per això que un dels objectius principals d’aquesta tesi ha estat aprofitar les potencialitats de les mesures de molècula individual per a caracteritzar pèptids anti­cancerígens poc solubles i difícils d’estudiar amb tècniques alternatives: des de la cinètica i termodinàmica d’unió, a l’especi.citat en seqüència i la cinètica d’autoacoblament.
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Savard, Didier. "The Versatile Chemistry of Aryl Substituted 1,2,4-triazole Ligands in Molecular Magnetism." Thesis, University of Ottawa (Canada), 2010. http://hdl.handle.net/10393/28677.

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The work presented in this thesis focuses on exploring the versatile chemistry of 4-aryl substituted 1,2,4-triazole derivatives. The ligands 4-(4'-nitrophenyl)-1,2,4-triazole (npt) and 4-(4'-carboxyphenyl)-1,2,4-triazole (Hcpt) were prepared following a modified known synthetic strategy. Reaction of either of these ligands with transition metal or lanthanide precursor salts resulted in two novel complexes, namely [FeII3(npt) 6(EtOH)4(H2O)2](ptol)6·4(EtOH) (1) and [DyIII4(mu3-OH) 2(mu3-O)2(cpt)6(MeOH)6(H 2O)]2·15,(MeOH) (5), and of five analogous compounds. In the case of 1, the structural analyses and the magnetic properties indicated that the complex consisted of a linear trinuclear Spin Crossover FeII compound with a T1/2 of 148 K. For this complex, the SC-XRD analyses were performed at 100 and 181 K in order to characterize the structural changes occurring during the spin transition. For 5, the magnetic and structural data indicated that the complex was a dumbbell-shaped cubane dimer {DyIII 4}2 for which each cubane unit is a Single-Molecule Magnet with a small effective energy barrier.
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10

Hassan, Mohammad Rokib, and University of Lethbridge Faculty of Arts and Science. "Self-assembled molecular rods and squares with chalcogenadiazole framework ligands." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Chemistry and Biochemistry, c2010, 2010. http://hdl.handle.net/10133/2639.

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During the attempts to carry out Suzuki coupling reactions, the σ-bonded Pd−Caryl benzochalcogenadiazolyl complexes trans-[ClPd(PPh3)2(C6H2BrN2E)] (E = S, Se) were isolated. The corresponding bromo derivatives were also synthesized on purpose to investigate their activity in Stille coupling reactions. A head-to-tail dimer trans- [{ClPd(PPh3)(μ-C6H2BrN2Se)}2] was synthesized from the thermolysis of trans- [ClPd(PPh3)2(C6H2BrN2Se)] in the presence of SeO2. The reduction potentials of the mononuclear and dinuclear complexes were measured by cyclic voltammetry (CV) and square wave voltammetry (SWV). 4,7-bis(2/4-pyridyl)benzochalcogenadiazole ligands were synthesized by Stille coupling reactions and the 1,5-bis(4-pyridyl)naphthalene ligand was prepared by a Suzuki coupling reaction. Reactions of the labile complex [BrRe(CO)4(NCMe)] with 4,7-bis(4- pyridyl)benzochalcogenadiazole ligands in a 2:1 ratio afforded self-assembled molecular rods [{ReBr(CO)4}2(μ-4,7-bis(4-pyridyl)benzochalcogenadiazoles)]. Palladium directed molecular squares [(enPd)(μ-4,7-bis(4-pyridyl)benzochalcogenadiazole)]4[PF6]8 were prepared by reactions of enPd(PF6)2 and 4,7-bis(4-pyridyl)benzochalco-genadiazoles in a 1:1 ratio. The optoelectronic properties of the ligands and the molecular rods were investigated by CV and SWV, and by luminescence spectroscopy. The optical properties of the square complexes were also studied by luminescence spectroscopy.
xvii, 152 leaves : ill. (some col.) ; 29 cm
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Books on the topic "Small Molecular Organic Ligands"

1

Keiller, B. T. The vibrational spectra of metal cluster compounds containing small organic ligands. Norwich: University of East Anglia, 1988.

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Julius, Rebek. Hydrogen-bonded capsules: Molecular behavior in small spaces. Hackensack, NJ: World Scientific, 2015.

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M, Villalgordo José, ed. Solid-supported combinatorial and parallel synthesis of small-molecular-weight compound libraries. [New York]: Pergamon, 1998.

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Nino, Russo, Salahub Dennis R. 1946-, Witko Malgorzata, and North Atlantic Treaty Organization. Scientific Affairs Division., eds. Metal-ligand interactions: Molecular-, nano-, micro-, and macro-systems in complex environments. Dordrecht: Kluwer Academic Publishers, 2003.

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Jr, Rebek Julius. Hydrogen-Bonded Capsules: Molecular Behavior in Small Spaces. World Scientific Publishing Co Pte Ltd, 2015.

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Obrecht, D., and J. M. Villalgordo. Solid-Supported Combinatorial and Parallel Synthesis of Small-Molecular-Weight Compound Libraries. Elsevier Science & Technology Books, 1998.

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Obrecht, D., and J. M. Villalgordo. Solid-Supported Combinatorial and Parallel Synthesis of Small-Molecular-Weight Compound Libraries. Elsevier Science & Technology Books, 1998.

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Tavassoli, Ali. Inhibitors of Protein-Protein Interactions: Small Molecules, Cyclic Peptides, Macrocycles and Antibodies. Royal Society of Chemistry, The, 2020.

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Tavassoli, Ali. Inhibitors of Protein-Protein Interactions: Small Molecules, Cyclic Peptides, Macrocycles and Antibodies. Royal Society of Chemistry, The, 2020.

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(Editor), N. Russo, Dennis R. Salahub (Editor), and Malgorzata Witko (Editor), eds. Metal-Ligand Interactions Molecular-, Nano-, Micro-systems in Complex Environments (NATO Science Series II: Mathematics, Physics and Chemistry). Springer, 2003.

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Book chapters on the topic "Small Molecular Organic Ligands"

1

Rehder, Dieter. "Polyoxovanadates with Organic Ligands." In Topics in Molecular Organization and Engineering, 157–66. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0920-8_11.

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Dickinson, Helena, Melanie Lukasser, Günter Mayer, and Alexander Hüttenhofer. "Cell-SELEX: In Vitro Selection of Synthetic Small Specific Ligands." In Methods in Molecular Biology, 213–24. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2547-6_20.

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Chhajed, Santosh S., Sandeep S. Sonanwane, Harshala Chaudhari, and Aarti Sonar. "Drug Interactions: Highlights of Adverse Effects of Low Molecular Weight Ligands." In Biologically Active Small Molecules, 333–48. New York: Apple Academic Press, 2022. http://dx.doi.org/10.1201/9781003283119-18.

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Puschnig, Peter, Georg Koller, Claudia Draxl, and Michael G. Ramsey. "The Structure of Molecular Orbitals Investigated by Angle-Resolved Photoemission." In Small Organic Molecules on Surfaces, 3–23. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-33848-9_1.

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Pozharski, Edwin, Marc C. Deller, and Bernhard Rupp. "Validation of Protein–Ligand Crystal Structure Models: Small Molecule and Peptide Ligands." In Methods in Molecular Biology, 611–25. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7000-1_25.

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Chhajed, Santosh S., and Parag A. Pathade. "High-Throughput Screening Technique: Role in the Drug Discovery of Low Molecular Weight Ligands." In Biologically Active Small Molecules, 259–71. New York: Apple Academic Press, 2022. http://dx.doi.org/10.1201/9781003283119-14.

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Lathan, W. A., L. A. Curtiss, W. J. Hehre, J. B. Lisle, and J. A. Pople. "Molecular Orbital Structures for Small Organic Molecules and Cations." In Progress in Physical Organic Chemistry, 175–261. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2007. http://dx.doi.org/10.1002/9780470171905.ch3.

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Day, Christopher J., and Victoria Korolik. "Identification of Specific Ligands for Sensory Receptors by Small-Molecule Ligand Arrays and Surface Plasmon Resonance." In Methods in Molecular Biology, 303–17. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7577-8_24.

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Tayeb-Fligelman, Einav, and Meytal Landau. "X-Ray Structural Study of Amyloid-Like Fibrils of Tau Peptides Bound to Small-Molecule Ligands." In Methods in Molecular Biology, 89–100. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6598-4_5.

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Hoffer, Laurent, Philippe Roche, and Xavier Morelli. "Rational Design of PDZ Domain Inhibitors: Discovery of Small Organic Compounds Targeting PDZ Domains." In Methods in Molecular Biology, 277–89. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1166-1_16.

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Conference papers on the topic "Small Molecular Organic Ligands"

1

Nicolau, Ioana, Alexandra Bumbacaru, Codruta Badescu Singureanu, Niculina Hadade, and Mihaela Matache. "Design and synthesis of multidentate organic ligands for protein-based supra molecular constructs." In RAD Conference. RAD Centre, 2023. http://dx.doi.org/10.21175/rad.abstr.book.2023.2.7.

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Borota, Ana, Simona Funar-Timofei, and Luminita Crisan. "MOLECULAR DOCKING STUDY OF THE INTERACTIONS OF PROSTANOID EP4 RECEPTOR WITH POTENT LIGANDS." In The 21st International Electronic Conference on Synthetic Organic Chemistry. Basel, Switzerland: MDPI, 2017. http://dx.doi.org/10.3390/ecsoc-21-04747.

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Lee, Yi-Ting, Yung-Ting Chang, Chin-Ti Chen, and Chao-Tsen Chen. "Solution processable small molecular host materials for blue and white phosphorescence OLEDs." In SPIE Organic Photonics + Electronics, edited by Franky So and Chihaya Adachi. SPIE, 2013. http://dx.doi.org/10.1117/12.2021451.

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Fleetham, Tyler, Barry O'Brien, John P. Mudrick, Jiangeng Xue, and Jian Li. "Efficiency enhancement in small molecular organic photovoltaic devices employing dual anode interfacial layers." In SPIE Organic Photonics + Electronics, edited by Zakya H. Kafafi and Paul A. Lane. SPIE, 2013. http://dx.doi.org/10.1117/12.2023679.

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Islam, Mohammad K., David E. Thurston, and Khondaker M. Rahman. "Abstract B204: Targeting key DNA/RNA heteroduplex of telomerase by small-molecule ligands." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Oct 19-23, 2013; Boston, MA. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1535-7163.targ-13-b204.

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Savvate'ev, Vadim, J. H. Friedl, L. Zou, K. Christensen, W. Oldham, Lewis J. Rothberg, Zoe Chen-Esterlit, Raoul Kopelman, and Joseph Shinar. "Transient electroluminescence from multilayer small organic molecular light-emitting devices." In International Symposium on Optical Science and Technology, edited by Zakya H. Kafafi. SPIE, 2001. http://dx.doi.org/10.1117/12.416898.

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Zhang, Xuan, Wenge Guo, Ming Li, Wentao Ma, and Sen Meng. "Advances in simulation study on organic small molecular solar cells." In The International Conference on Photonics and Optical Engineering and the Annual West China Photonics Conference (icPOE 2014), edited by Ailing Tian, Anand Asundi, Weiguo Liu, and Chunmin Zhang. SPIE, 2015. http://dx.doi.org/10.1117/12.2075692.

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Shim, Hyun-Sub, Hyo Jung Kim, Ji Whan Kim, Sei-Yong Kim, Won-Ik Jeong, Tae-Min Kim, and Jang-Joo Kim. "Enhanced sensitivity to near-infrared with high fill factor in small molecular organic solar cells." In SPIE Organic Photonics + Electronics, edited by Zakya H. Kafafi, Christoph J. Brabec, and Paul A. Lane. SPIE, 2012. http://dx.doi.org/10.1117/12.930244.

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Tsang, Sai Wing. "Exciton binding energy and dielectric effect in small molecular and polymeric photovoltaic materials (Conference Presentation)." In Organic, Hybrid, and Perovskite Photovoltaics XX, edited by Kwanghee Lee, Zakya H. Kafafi, Paul A. Lane, and Ana Flávia Nogueira. SPIE, 2019. http://dx.doi.org/10.1117/12.2528570.

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Datta, Supriyo, Weidong Tian, and Clifford P. Kubiak. "”Resistance” of a molecular wire." In Chemistry and Physics of Small-Scale Structures. Washington, D.C.: Optica Publishing Group, 1997. http://dx.doi.org/10.1364/cps.1997.ctub.2.

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A number of groups have recently reported experimental studies of the electronic conduction through a monolayer of organic molecules self-assembled between two large metallic contacts [1-5]. Measured resistances to date are at least several megohms per molecule and has to be lowered by a few orders of magnitude before such wires can be considered seriously for interconnect applications. In this paper we present a simple model that lends insight into the factors affecting the molecular resistance and suggests possible schemes for designing molecular wires with lower resistance that can be truly said to 'conduct'.
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Reports on the topic "Small Molecular Organic Ligands"

1

Cheon, Kwang-Ohk. The Electric and Optical Properties of Doped Small Molecular Organic Light-Emitting Devices. Office of Scientific and Technical Information (OSTI), January 2003. http://dx.doi.org/10.2172/816444.

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2

Banin, Amos, Joseph Stucki, and Joel Kostka. Redox Processes in Soils Irrigated with Reclaimed Sewage Effluents: Field Cycles and Basic Mechanism. United States Department of Agriculture, July 2004. http://dx.doi.org/10.32747/2004.7695870.bard.

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The overall objectives of the project were: (a) To measure and study in situ the effect of irrigation with reclaimed sewage effluents on redox processes and related chemical dynamics in soil profiles of agricultural fields. (b) To study under controlled conditions the kinetics and equilibrium states of selected processes that affect redox conditions in field soils or that are effected by them. Specifically, these include the effects on heavy metals sorption and desorption, and the effect on pesticide degradation. On the basis of the initial results from the field study, increased effort was devoted to clarifying and quantifying the effects of plants and water regime on the soil's redox potential while the study of heavy metals sorption was limited. The use of reclaimed sewage effluents as agricultural irrigation water is increasing at a significant rate. The relatively high levels of suspended and, especially, dissolved organic matter and nitrogen in effluents may affect the redox regime in field soils irrigated with them. In turn, the changes in redox regime may affect, among other parameters, the organic matter and nitrogen dynamics of the root zone and trace organic decomposition processes. Detailed data of the redox potential regime in field plots is lacking, and the detailed mechanisms of its control are obscure and not quantified. The study established the feasibility of long-term, non-disturbing monitoring of redox potential regime in field soils. This may enable to manage soil redox under conditions of continued inputs of wastewater. The importance of controlling the degree of wastewater treatment, particularly of adding ultrafiltration steps and/or tertiary treatment, may be assessed based on these and similar results. Low redox potential was measured in a field site (Site A, KibutzGivat Brenner), that has been irrigated with effluents for 30 years and was used for 15 years for continuous commercial sod production. A permanently reduced horizon (Time weighted averaged pe= 0.33±3.0) was found in this site at the 15 cm depth throughout the measurement period of 10 months. A drastic cultivation intervention, involving prolonged drying and deep plowing operations may be required to reclaim such soils. Site B, characterized by a loamy texture, irrigated with tap water for about 20 years was oxidized (Time weighted average pe=8.1±1.0) throughout the measurement period. Iron in the solid phases of the Givat Brenner soils is chemically-reduced by irrigation. Reduced Fe in these soils causes a change in reactivity toward the pesticide oxamyl, which has been determined to be both cytotoxic and genotoxic to mammalian cells. Reaction of oxamyl with reduced-Fe clay minerals dramatically decreases its cytotoxicity and genotoxicity to mammalian cells. Some other pesticides are affected in the same manner, whereas others are affected in the opposite direction (become more cyto- and genotoxic). Iron-reducing bacteria (FeRB) are abundant in the Givat Brenner soils. FeRB are capable of coupling the oxidation of small molecular weight carbon compounds (fermentation products) to the respiration of iron under anoxic conditions, such as those that occur under flooded soil conditions. FeRB from these soils utilize a variety of Fe forms, including Fe-containing clay minerals, as the sole electron acceptor. Daily cycles of the soil redox potential were discovered and documented in controlled-conditions lysimeter experiments. In the oxic range (pe=12-8) soil redox potential cycling is attributed to the effect of the daily temperature cycle on the equilibrium constant of the oxygenation reaction of H⁺ to form H₂O, and is observed under both effluent and freshwater irrigation. The presence of plants affects considerably the redox potential regime of soils. Redox potential cycling coupled to the irrigation cycles is observed when the soil becomes anoxic and the redox potential is controlled by the Fe(III)/Fe(II) redox couple. This is particularly seen when plants are grown. Re-oxidation of the soil after soil drying at the end of an irrigation cycle is affected to some degree by the water quality. Surprisingly, the results suggest that under certain conditions recovery is less pronounced in the freshwater irrigated soils.
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3

Altstein, Miriam, and Ronald J. Nachman. Rational Design of Insect Control Agent Prototypes Based on Pyrokinin/PBAN Neuropeptide Antagonists. United States Department of Agriculture, August 2013. http://dx.doi.org/10.32747/2013.7593398.bard.

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The general objective of this study was to develop rationally designed mimetic antagonists (and agonists) of the PK/PBAN Np class with enhanced bio-stability and bioavailability as prototypes for effective and environmentally friendly pest insect management agents. The PK/PBAN family is a multifunctional group of Nps that mediates key functions in insects (sex pheromone biosynthesis, cuticular melanization, myotropic activity, diapause and pupal development) and is, therefore, of high scientific and applied interest. The objectives of the current study were: (i) to identify an antagonist biophores (ii) to develop an arsenal of amphiphilic topically active PK/PBAN antagonists with an array of different time-release profiles based on the previously developed prototype analog; (iii) to develop rationally designed non-peptide SMLs based on the antagonist biophore determined in (i) and evaluate them in cloned receptor microplate binding assays and by pheromonotropic, melanotropic and pupariation in vivo assays. (iv) to clone PK/PBAN receptors (PK/PBAN-Rs) for further understanding of receptor-ligand interactions; (v) to develop microplate binding assays for screening the above SMLs. In the course of the granting period A series of amphiphilic PK/PBAN analogs based on a linear lead antagonist from the previous BARD grant was synthesized that incorporated a diverse array of hydrophobic groups (HR-Suc-A[dF]PRLa). Others were synthesized via the attachment of polyethylene glycol (PEG) polymers. A hydrophobic, biostablePK/PBAN/DH analog DH-2Abf-K prevented the onset of the protective state of diapause in H. zea pupae [EC50=7 pmol/larva] following injection into the preceding larval stage. It effectively induces the crop pest to commit a form of ‘ecological suicide’. Evaluation of a set of amphiphilic PK analogs with a diverse array of hydrophobic groups of the formula HR-Suc-FTPRLa led to the identification of analog T-63 (HR=Decyl) that increased the extent of diapause termination by a factor of 70% when applied topically to newly emerged pupae. Another biostablePK analog PK-Oic-1 featured anti-feedant and aphicidal properties that matched the potency of some commercial aphicides. Native PK showed no significant activity. The aphicidal effects were blocked by a new PEGylated PK antagonist analog PK-dF-PEG4, suggesting that the activity is mediated by a PK/PBAN receptor and therefore indicative of a novel and selective mode-of-action. Using a novel transPro mimetic motif (dihydroimidazole; ‘Jones’) developed in previous BARD-sponsored work, the first antagonist for the diapause hormone (DH), DH-Jo, was developed and shown to block over 50% of H. zea pupal diapause termination activity of native DH. This novel antagonist development strategy may be applicable to other invertebrate and vertebrate hormones that feature a transPro in the active core. The research identifies a critical component of the antagonist biophore for this PK/PBAN receptor subtype, i.e. a trans-oriented Pro. Additional work led to the molecular cloning and functional characterization of the DH receptor from H. zea, allowing for the discovery of three other DH antagonist analogs: Drosophila ETH, a β-AA analog, and a dF analog. The receptor experiments identified an agonist (DH-2Abf-dA) with a maximal response greater than native DH. ‘Deconvolution’ of a rationally-designed nonpeptide heterocyclic combinatorial library with a cyclic bis-guanidino (BG) scaffold led to discovery of several members that elicited activity in a pupariation acceleration assay, and one that also showed activity in an H. zea diapause termination assay, eliciting a maximal response of 90%. Molecular cloning and functional characterization of a CAP2b antidiuretic receptor from the kissing bug (R. prolixus) as well as the first CAP2b and PK receptors from a tick was also achieved. Notably, the PK/PBAN-like receptor from the cattle fever tick is unique among known PK/PBAN and CAP2b receptors in that it can interact with both ligand types, providing further evidence for an evolutionary relationship between these two NP families. In the course of the granting period we also managed to clone the PK/PBAN-R of H. peltigera, to express it and the S. littoralis-R Sf-9 cells and to evaluate their interaction with a variety of PK/PBAN ligands. In addition, three functional microplate assays in a HTS format have been developed: a cell-membrane competitive ligand binding assay; a Ca flux assay and a whole cell cAMP ELISA. The Ca flux assay has been used for receptor characterization due to its extremely high sensitivity. Computer homology studies were carried out to predict both receptor’s SAR and based on this analysis 8 mutants have been generated. The bioavailability of small linear antagonistic peptides has been evaluated and was found to be highly effective as sex pheromone biosynthesis inhibitors. The activity of 11 new amphiphilic analogs has also been evaluated. Unfortunately, due to a problem with the Heliothis moth colony we were unable to select those with pheromonotropic antagonistic activity and further check their bioavailability. Six peptides exhibited some melanotropic antagonistic activity but due to the low inhibitory effect the peptides were not further tested for bioavailability in S. littoralis larvae. Despite the fact that no new antagonistic peptides were discovered in the course of this granting period the results contribute to a better understanding of the interaction of the PK/PBAN family of Nps with their receptors, provided several HT assays for screening of libraries of various origin for presence of PK/PBAN-Ragonists and antagonists and provided important practical information for the further design of new, peptide-based insecticide prototypes aimed at the disruption of key neuroendocrine physiological functions in pest insects.
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