Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Quadrupole interactions at 57Fe and 119Sn in 3d-metal antimonides

3d-metal antimonides: Fe_1+x Sb, N_+x Sb, Co_+x Sb and the (Ni_1?y Fe _y )Sb solid solution have been studied by the Mössbauer effect method at ⁵⁷Fe and ¹¹⁹Sn. It was found that the quadrupole interactions at the Fe and Sn nucleus in 3d-metal antimonides are very sensitive to the filling of different crystallographic sites with metal atoms. The metal atoms in trigonal-bipyramidal sites have a strong effect on the quadrupole splitting of ¹¹⁹Sn. They are nearest to anions (Sb or Sn) with the typical axial ratio of c/a = 1.25. The QS(x) dependence of ¹¹⁹ Sn in 3d-metal antimonides in the 0 ≤ x ≤ 0.1 concentration range can be used to determine x – the concentration of transition metal excess relative to the stoichiometric composition.     

Preparation and catalytic applications of partially fluorinated binaphthol ligands

New partially fluorinated binaphthols were obtained using a copper-catalyzed oxidative coupling. The corresponding enantiomerically pure compounds were prepared by fractional crystallization of the corresponding bis(menthyl)carbamates. Nucleophilic aromatic substitution using oxygen- and carbon-based nucleophiles resulted in functionalized derivatives without concomitant racemization. The titanium(IV) complexes of these ligands are catalytically active in the asymmetric oxidation of sulfides.     

Synthesis,characterization and properties of methylaminocellulose

Homogeneously prepared tosylcelluloses (TC) with degrees of substitution (DS) of DS_Tos 0.1–1.8 were used as intermediates for the synthesis of methylaminocelluloses (MAC) by nucleophilic substitution with methylamine. TC with DS_Tos up to 1.1 were shown to be valuable intermediates for selective synthesis of MAC with DS_MA varying from 0.1 to approximately 1. No nucleophilic substitution was observed at higher DS_Tos. At the chosen reaction conditions (60 °C, 48 h) residual tosyl moieties remained unchanged and little hydrolysis took place. The samples obtained were characterized by means of elemental analysis, FTIR and ¹³C CP/MAS NMR spectroscopy. ¹³C CP/MAS NMR spectroscopy was found to be an efficient tool for quantification of DS_MA. Furthermore, the swelling behaviour in water was investigated and preliminary tests concerning the bilirubin adsorption capacity of MAC were carried out.     

Fluorescence line narrowed spectra of Zn and metal-free cytochrome c

Fluorescence line narrowing (FLN) spectroscopy was used to study the role of the polypeptide chain in influencing the spectrum of Zn-substituted cytochrome c (Zn cyt c) and metal-free cyt c (porphyrin cyt c). For both derivatives the spectra show characteristics of relaxed fluorescence from an inhomogeneously broadened sample. Zero phonon lines and phonon wings can be clearly distinguished, and vibrational frequencies of the ground and excited states were identified. The inhomogeneous distribution width for porphyrin cyt c is slightly wider than that of Zn cyt c and a second population of molecules was apparent in the porphyrin cyt c. The phonon coupling was greater for Zn cyt c than for porphyrin cyt c, which may be due to the extra coupling to the polypeptide chain by metal ligation.This work has been done in partial fulfillment of the requirements for the Doctor of Philosophy degree.     

Toward phenanthridin-2-ylidene: electrophilicity versus acidity in planar-constrained C-aryl iminium salts

A phenanthridinium salt was prepared in four steps, including an intramolecular CH-arylation and a hydride abstraction reaction. Treatment with sterically demanding bases does not lead to the corresponding carbene, but rather to addition products: the planar-constrained geometry significantly enhances the electrophilicity over the acidity of C-aryl iminium salts.     

The synthesis of N-substituted ureas II: Nucleophilic substitution of ureas at the carbonyl group

Summary N-Arylsubstituted ureas undergo exchange of the N-residue upon reaction with amines. Using kinetic measurements, investigation of product distribution, regioselectivity, catalysis, and substrate influences, it was shown that this reaction proceeds via a second order nucleophilic substitution at the urea carbonyl center. By means of semiempirical calculations using the MNDO method the alternative mechanism of fragmentation was investigated.

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Zur Synthese N-substituierter Harnstoffe II: Nucleophile Substitution von Harnstoffen an der Carbonylgruppe

Zusammenfassung N-Arylsubstituierte Harnstoffe erleiden bei der Reaktion mit Aminen einen Austausch des N-Restes. Durch kinetische Messungen, Untersuchung der Produktverteilung, Regioselektivität, Katalyse und des Einflusses des Edukts konnte abgeleitet werden, daß es sich hiebei um eine nucleophile Substitution zweiter Ordnung am Carbonylzentrum des Harnstoffs handelt. Durch semiempirische Rechnungen mit Hilfe der MNDO Methode wurde der alternative Reaktionsmechanismus einer Fragmentierung untersucht.

     

Efficient synthesis of 2- and 3-substituted-2,3-dihydro [1,4]dioxino[2,3-b]pyridine derivatives

A versatile new approach for the synthesis in three steps of 2-substituted-2,3-dihydro[1,4]dioxino[2,3-b]pyridines B via a Smiles rearrangement using easily available reagents is described. A study illustrating the influence of experimental conditions on the progress of the reaction is reported.     

Quantum chemistry investigation on the active site of Mn-SOD

In this paper, we carried out a theoretical study on the active site structures of the Mn-SOD with ab initio Hartree–Fock SCF method, and analyzed the molecular orbital energies, charges and atomic orbital contribution to the frontier molecular orbital.