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.     

Anticancer SAR establishment and novel accruing signal transduction model of drug action using biscoumarin scaffold

In this paper, we have established methylenebis (4-hydroxy-2H-chromen-2-one) as a promising anticancer scaffold with kinesin spindle protein (KSP) inhibitory activity under malignant condition. A series of biscoumarin derivatives (MN1 to MN30) with different substituent were synthesized, and their anticancer activity was explored. Six biscoumarin derivatives that were found active were further selected to formulate organic nanoparticles (ONPs). Anticancer activity of both the forms (viz conventional and ONPs) was compared. MN30 was found most potent whereby MN10 showed good anticancer activity in both, i.e., conventional and ONP form; the structural activity relationship (SAR) study has been established. Computational investigation revealed biscoumarin scaffold as a suitable pharmacophore to bind against KSP protein. Molecular dynamics simulation studies revealed protein-ligand stability and dynamic behavior of biscoumarin-KSP complex. Finally, accruing signal transduction model was formulated to explain the observed MTT trend of conventional and ONP form. The model seems useful towards solving population specific varied results of chemotherapeutic agents. According to the model, MN10 and MN30 derivatives have good pharmacodynamics inertia and therefore, both the molecules were able to provide dose-dependent cytotoxic results.     

Characterization of new Pt(IV)–thiazole complexes: Analytical,spectral, molecular modeling and molecular docking studies and applications in two opposing pathways

New thiazole derivatives were synthesized and fully characterized, then coordinated with PtCl₄ salt. Also, the newly synthesized Pt(IV) complexes were investigated analytically (elemental and thermogravimetric analyses), spectrally (infrared, UV–visible, mass, ¹H NMR, ¹³C NMR, X‐ray diffraction) as well as theoretically (kinetics, modeling and docking). The data extracted led to the establishment of the best chemical and structural forms. Octahedral geometry was the only formula proposed for all complexes, which is favorable for d⁶ systems. The molecular ion peaks from mass spectral analysis coincide with all analytical data, confirming the molecular formula proposed. X‐ray diffraction (XRD) and scanning electron microscopy (SEM) allowed discrimination of features between crystalline particles and other amorphous morphology. By applying Gaussian09 as well as HyperChem 8.2 programs, the best structural forms were obtained, as well as computed significant parameters. Computed parameters such as softness, hardness, surface area and reactivity led us towards application in two opposing pathways: tumor inhibition and oxidation activation. The catalytic oxidation for CO was conducted over PtO₂, which was yielded from calcination of the most reactive complex. The success of catalytic role for synthesized PtO₂ was due to its particulate size and surface morphology, which were estimated from XRD patterns and SEM images, respectively. The antitumor activity was tested versus HCT‐116 and HepG‐2 cell lines. Mild toxicity was recorded for two of the derivatives and their corresponding complexes. This degree of toxicity is more favorable in most cases, due to exclusion of serious side effects, which is coherently attached with known antitumor drugs.     

o-Trityl phenoxy-imino vanadium (III) complexes: synthesis,characterization, and catalysis on ethylene (co)polymerization

Several phenoxy-imine ligands bearing o-trityl group in phenoxy moiety RN=CHArOH (Ar = C₆H₂(CPh₃)^tBu, R = 2,6-Me₂C₆H₃ ( L ₁ H ); 2,6-ⁱPr₂C₆H₃ ( L ₂ H ); 3,5-(CF₃)₂C₆H₃ ( L ₃ H ); 3,5-(OMe)₂C₆H₃ ( L ₄ H ); CHPh₂ ( L ₅ H ); CPh₃ ( L ₆ H )) were synthesized and characterized by¹H NMR and ¹³C NMR spectroscopy. The vanadium complexes based on these ligands LVCl₂(THF)₂ ( 1–6 ) were synthesized via conventional transmetalation reaction in moderate to high yields. Complexes 1–6 were fully characterized by FT-IR, elemental analyses and the molecular structures of 1 , 2 ·H₂O, (2 ·H₂O ) ₂ (μ-Cl) ₂ , 4 , and 5 were confirmed by X-ray crystallographic analysis in which the six-coordinated vanadium centers are in a typical octahedral geometry. Upon activation with Et₂AlCl in toluene, complexes 1–6 showed high activities in ethylene polymerization affording polymers with moderate molecular weight (5.9–11.8 × 10⁴ Da). Moreover, in hexane or CH₂Cl₂, 1–6 /Et₂AlCl exhibited enhanced activities. When activated with MAO or MMAO in toluene, these complexes showed relatively low activities but afforded polymers with ultra-high molecular weight (up to 3.30 × 10⁶ Da). 1–6 /Et₂AlCl also showed high activities in ethylene/1-hexene copolymerization at room temperature giving moderate molecular-weight polymers (6.5–11.4 × 10⁴ Da) with co-monomer incorporation being of 6.0 ~ 7.8%.     

New organoruthenium metallates containing ferrocenecarboxalidine thiosemicarbazones and their nucleic acid/albumin binding and in vitro cytotoxicity

A string of four new hetero binuclear Ru(III) complexes of ferrocenecarboxaldehyde-4(N)-substituted thiosemicarbazones were synthesized and characterized by various spectral (infrared, ultraviolet–visible, Electron Paramagnetic Resonance (EPR) and High Resolution Mass Spectrometry (HR-MS) techniques. The binding abilities of the ligands/complexes with nucleic acid (calf thymus DNA, CT-DNA) and bovine serum albumin (BSA) were analyzed by absorption and emission titration methods. The complexes exhibited better DNA binding affinity than their parent ligands. The interaction with CT-DNA was found to be intercalative and with BSA static quenching mechanism was observed. All the synthesized Ru(III) complexes were subjected to study their in vitro cytotoxicity against MCF-7 (human breast cancer) and HT-29 (human colon cancer) cell lines. Among the four complexes, complex 3 [RuCp (FF-etsc)PPh₃]Cl exhibited the highest cytotoxicity in MCF-7 cells and complex 4 [RuCp (FF-ptsc)PPh₃]Cl was the most active on HT-29 cells.     

Thermodynamic study of transthyretin association (wild‐type and senile forms) with heparan sulfate proteoglycan: pH effect and implication of the reactive histidine residue

The tetramer destabilization of transthyretin into monomers and its fibrillation are phenomena leading to amyloid deposition. Heparan sulfate proteoglycan (HSPG) has been found in all amyloid deposits. A chromatographic approach was developed to compare binding parameters between wild‐type transthyretin (wtTTR) and an amyloidogenic transthyretin (sTTR). Results showed a greater affinity of sTTR for HSPG at pH 7.4 compared with wtTTR owing to the monomeric form of sTTR. Analysis of the thermodynamic parameters showed that van der Waals interactions were involved at the complex interface for both transthyretin forms. For sTTR, results from the plot representing the number of protons exchanged vs pH showed that the binding mechanism was pH‐dependent with a critical value at a pH 6.5. This observation was due to the protonation of a histidine residue as an imidazolium cation, which was not accessible when TTR was in its tetrameric structure. At pH >6.5, dehydration at the binding interface and several contacts between nonpolar groups of sTTR and HSPG were also coupled to binding for an optimal hydrogen‐bond network. At pH <6.5, the protonation of the His residue from sTTR monomer when pH decreased broke the hydrogen‐bond network, leading to its destabilization and thus producing slight conformational changes in the sTTR monomer structure. Copyright © 2014 John Wiley & Sons, Ltd.     

Halomethanes in tri-n-octylamine and squalane mixtures at infinite dilution

The retention behavior of eight halomethanes and four saturated hydrocarbons was measured in gas chromatographic stationary phases consisting in tri-n-octylamine (TOA), squalane (SQ) and six TOA+SQ mixtures, at 55.0, 58.5, 62.5 and 65.0°C. Equlibrium constants for complex formation were extracted from experimental data by using a lattice model developed by Martire. The results may be interpreted in terms of the formation of weak hydrogen-bonded complexes, with sociation constants of about 0.13 L-mol^–1 for haloforms and 0.07 L-mol^–1 for dihalomethanes at 60°C.     

Studies of the compositions of Pd(II) hydrolysis products

The characterization of the clusters formed on alkaline hydrolysis of [PdCl₄]^2– was performed using¹⁷O,²³Na,³⁵Cl,¹³³Cs NMR and UV spectroscopy. The chemical composition of the clusters was found to be [Pd(OH)₂] _n ·nNaCl. No mononuclear oxo- or hydroxocomplexes were detected. The spatial structure of the clusters is stabilized by alkali metal cations.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 675–679, April, 1993.