- Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies
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Hematopoietic prostaglandin D synthase (H-PGDS) is one of the two enzymes that catalyze prostaglandin D2 synthesis and a potential therapeutic target of allergic and inflammatory responses. To reveal key molecular interactions between a high-affinity ligand and H-PGDS, we designed and synthesized a potent new inhibitor (KD: 0.14 nM), determined the crystal structure in complex with human H-PGDS, and quantitatively analyzed the ligand–protein interactions by the fragment molecular orbital calculation method. In the cavity, 10 water molecules were identified, and the interaction energy calculation indicated their stable binding to the surface amino acids in the cavity. Among them, 6 water molecules locating from the deep inner cavity to the peripheral part of the cavity contributed directly to the ligand binding by forming hydrogen bonding interactions. Arg12, Gly13, Gln36, Asp96, Trp104, Lys112 and an essential co-factor glutathione also had strong interactions with the ligand. A strong repulsive interaction between Leu199 and the ligand was canceled out by forming a hydrogen bonding network with the adjacent conserved water molecule. Our quantitative studies including crystal water molecules explained that compounds with an elongated backbone structure to fit from the deep inner cavity to the peripheral part of the cavity would have strong affinity to human H-PGDS.
- Takaya, Daisuke,Inaka, Koji,Omura, Akifumi,Takenuki, Kenji,Kawanishi, Masashi,Yabuki, Yukako,Nakagawa, Yukari,Tsuganezawa, Keiko,Ogawa, Naoko,Watanabe, Chiduru,Honma, Teruki,Aritake, Kosuke,Urade, Yoshihiro,Shirouzu, Mikako,Tanaka, Akiko
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- UREA DERIVATIVE MODULATORS OF TRYPTOPHAN CATABOLISM
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There are described compounds of formula (I): (I) and their use as a medicament in the treatment of diseases associated with the abnormal or elevated catabolism of tryptophan, such as, cancer, immunosuppression, viral infection, depression, a neurodegener
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Page/Page column 120-121
(2019/12/25)
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- Copper-Catalyzed Coupling Reaction of (Hetero)Aryl Chlorides and Amides
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Cu2O/N,N′-bis(thiophen-2-ylmethyl)oxalamide is established to be an effective catalyst system for Goldberg amidation with inferior reactive (hetero)aryl chlorides, which have not been efficiently documented by Cu-catalysis to date. The reaction is well liberalized toward a variety of functionalized (hetero)aryl chlorides and a wide range of aromatic and aliphatic primary amides in good to excellent yields. Furthermore, the arylation of lactams and oxazolidinones is achieved. The present catalytic system also accomplished an intramolecular cross-coupling product.
- De, Subhadip,Yin, Junli,Ma, Dawei
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supporting information
p. 4864 - 4867
(2017/09/23)
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- Phenyl Esters Are Potent Inhibitors of Caseinolytic Protease P and Reveal a Stereogenic Switch for Deoligomerization
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Caseinolytic protease P (ClpP) represents a central bacterial degradation machinery that is involved in cell homeostasis and pathogenicity. The functional role of ClpP has been studied by genetic knockouts and through the use of beta-lactones, which remain the only specific inhibitors of ClpP discovered to date. Beta-lactones have served as chemical tools to manipulate ClpP in several organisms; however, their potency, selectivity and stability is limited. Despite detailed structural insights into the composition and conformational flexibility of the ClpP active site, no rational efforts to design specific non-beta-lactone inhibitors have been reported to date. In this work, an unbiased screen of more than 137000 compounds was used to identify five phenyl ester compounds as highly potent ClpP inhibitors that were selective for bacterial, but not human ClpP. The potency of phenyl esters largely exceeded that of beta-lactones in ClpP peptidase and protease inhibition assays and displayed unique target selectivity in living S. aureus cells. Analytical studies revealed that while phenyl esters are cleaved like native peptide substrates, they remain covalently trapped as acyl-enzyme intermediates in the active site. The synthesis of 36 derivatives and subsequent structure-activity relationship (SAR) studies provided insights into conserved structural elements that are important for inhibition potency and acylation reactivity. Moreover, the stereochemistry of a methyl-substituent at the alpha position to the ester, resembling amino acid side chains in peptide substrates, impacted ClpP complex stability, causing either dissociation into heptamers or retention of the tetradecameric state. Mechanistic insights into this intriguing stereo switch and the phenyl ester binding mode were obtained by molecular docking experiments.
- Hackl, Mathias W.,Lakemeyer, Markus,Dahmen, Maria,Glaser, Manuel,Pahl, Axel,Lorenz-Baath, Katrin,Menzel, Thomas,Sievers, Sonja,B?ttcher, Thomas,Antes, Iris,Waldmann, Herbert,Sieber, Stephan A.
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supporting information
p. 8475 - 8483
(2015/07/15)
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- Heterogeneous CuII-catalysed solvent-controlled selective N-arylation of cyclic amides and amines with bromo-iodoarenes
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A selective N-arylation of cyclic amides and amines in DMF and water, respectively, catalysed by CuII/Al2O3 has been achieved. This protocol has been employed for the synthesis of a library of arenes bearing a cyclic amide and an amine moiety at two ends, including a few scaffolds of therapeutic importance. The mechanism has been established based on detailed electron paramagnetic resonance (EPR) spectroscopy, X-ray photoelectron spectroscopy (XPS), UV diffuse reflectance spectroscopy (DRS) and inductively coupled plasma-mass spectrometry (ICP-MS) studies of the catalyst at different stages of the reaction. The CuII/Al2O 3 catalyst was recovered and recycled for subsequent reactions. One over the other: A selective N-arylation of cyclic amides and amines in DMF and water, respectively, catalyzed by CuII/Al2O3 has been achieved (see scheme). This protocol has been employed for the synthesis of a library of arenes bearing cyclic amide and amine moieties at two ends including a few scaffolds of therapeutic importance. The mechanism has been established based on detailed spectroscopic studies (FG=functional group). Copyright
- Kundu, Debasish,Bhadra, Sukalyan,Mukherjee, Nirmalya,Sreedhar, Bojja,Ranu, Brindaban C.
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p. 15759 - 15768
(2013/11/19)
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- Highly selective reduction of nitroarenes by iron(0) nanoparticles in water
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Highly selective reduction of nitroarenes has been achieved using iron metal nanoparticles in water at room temperature. A wide spectrum of reducible functionalities remained inert under the reaction conditions. During the reaction a change in shape of Fe nanoparticles was observed.
- Dey, Raju,Mukherjee, Nirmalya,Ahammed, Sabir,Ranu, Brindaban C.
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supporting information; experimental part
p. 7982 - 7984
(2012/09/08)
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- Hydrogenation of azides over copper nanoparticle surface using ammonium formate in water
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Aryl azides undergo clean reduction by copper nanoparticles and ammonium formate in water. The surface hydrogen on copper nanoparticles is considered to be the active reducing species. A variety of functionalized aryl azides and aryl sulfonyl azides are reduced by this procedure to the corresponding amines with excellent chemoselectivity in high yields.
- Ahammed, Sabir,Saha, Amit,Ranu, Brindaban C.
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experimental part
p. 7235 - 7239
(2011/10/18)
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- Copper-catalyzed C-N coupling of amides and nitrogen-containing heterocycles in the presence of cesium fluoride
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The copper-catalyzed C-N coupling of amides to aryl halides usually requires the use of strong alkali metal bases, such as K2CO3, K3PO4, and Cs2CO3, at high temperature. We discovered that
- Phillips, Dean P.,Zhu, Xue-Feng,Lau, Thomas L.,He, Xiaohui,Yang, Kunyong,Liu, Hong
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supporting information; experimental part
p. 7293 - 7296
(2010/03/03)
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- CYSTEINE PROTEASE INHIBITORS
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To provide a compound having an excellent cysteine protease inhibitory effect, and to provide a drug for treatment or prevention of the disease selected from the group consisting of osteoporosis, osteoarthritis, chronic rheumatoid arthritis, Paget's disea
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Page/Page column 56-57
(2009/12/05)
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- PYRAZINE DICARBOXAMIDES AND THE USE THEREOF
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The invention relates to novel pyrazine dicarboxamides, methods for the use thereof, their use for treating and/or preventing diseases as well as to their use for producing medicaments for treating and/or preventing diseases, particularly thromboembolic disorders.
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Page/Page column 23
(2010/11/08)
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- IMIDAZOQUINOLINES AS LIPID KINASE INHIBITORS
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The invention relates to novel organic compounds of formula (I) processes for the preparation thereof, the application thereof in a process for the treatment of the human or animal body, the use thereof - alone or in combination with one or more other pharmaceutically active compounds - for the treatment of an inflammatory or obstructive airway disease, such as asthma, disorders commonly occurring in connection with transplantation, or a proliferative disease, such as a tumor disease.
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Page/Page column 54
(2008/06/13)
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- 1H-IMIDAZO[4,5-C]QUINOLINE DERIVATIVES IN THE TREATMENT OF PROTEIN KINASE DEPENDENT DISEASES
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The invention relates to the use of imidazoquinolines and salts thereof in the treatment of protein kinase diseases and for the manufacture of pharmaceutical preparations for the treatment of said diseases, imidazoquinolines for use in the treatment of protein kinase dependent diseases, a method of treatment against said diseases, comprising administering the imidazoquinolines to a warm-blooded animal, especially a human, pharmaceutical preparations comprising an imidazoquinoline, especially for the treatment of a protein kinase dependent disease, novel imidazoquinolines, and a process for the preparation of the novel imidazoquinolines.
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Page/Page column 103
(2010/02/12)
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- Indazole-derivatives as factor Xa inhibitors
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The present invention relates to compounds of the formulae I and Ib wherein R0 ; R1 ; R2 ;Q; V, G and M have the meanings indicated in the claims. The compounds of the formula I are valuable pharmacologically active compounds. They exhibit a strong antithrombotic effect and are suitable, for example, for the therapy and prophylaxis of cardiovascular disorders like thromboembolic diseases or restenoses. They are reversible inhibitors of the blood clotting enzymes factor Xa (FXa) and/or factor VIIa (FVIIa), and can in general be applied in conditions in which an undesired activity of factor Xa and/or factor VIIa is present or for the cure or prevention of which an inhibition of factor Xa and/or factor VIIa is intended. The invention furthermore relates to processes for the preparation of compounds of the formulae I and Ib, their use, in particular as active ingredients in pharmaceuticals, and pharmaceutical preparations comprising them.
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