Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein–ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate binders from nonbinders in virtual screening and to more accurately predict the ligand binding modes prior to the more computationally expensive FEP calculations of binding affinity.     

Synthesis of 2-(2,3,4-trimethoxyphenyl)-1-(substituted-phenyl)acrylonitriles: in vitro anticancer activity against MCF-7, PC-3 and A2780 cancer cell lines

A series of 2-(2,3,4-trimethoxyphenyl)-1-(substituted-phenyl)acrylonitrile (2–9) were designed and synthesized to develop new cancer drugs. The structures of synthesized compounds 2–9 were described by using melting point, mass (MALDI-TOF-MS), FT-IR, elemental analysis, ¹H, ¹³C, ¹³C-APT and 2D NMR spectroscopy. The in vitro anticancer activities of 2–9 against human breast cancer (MCF-7), human prostate cancer (PC-3) and human ovarian cancer cells (A2780) were investigated by [3-(4,5-dimethylthiazol)-2-yl]-2,5-diphenyl-2H-tetrazolium bromide] (MTT) assay method. Additionally, the LogIC₅₀ values of these compounds on A2780, MCF-7 and PC-3 cell lines were calculated by using inhibition % values by the GraphPad Prism 6 program on a computer. The results indicated that these compounds have high anticancer activity against MCF-7, PC-3 and A2780 cell lines (especially A2780 cell lines, p < 0.05).     

Identification of radical structures on 1‐pentamethylbenzyl‐3‐ethylimidazoliumsilver(I)bromide and 1,3‐bis(pentamethylbenzyl)‐4,5‐dimethylbenzimidazoliumsilver(I)bromide exposed to gamma rays: an EPR study

1‐Pentamethylbenzyl‐3‐ethylimidazoliumsilver(I)bromide and 1,3‐bis(pentamethylbenzyl)‐4,5dimethylbenzimidazoliumsilver(I)bromide and their Ag⁺ complexes were synthesized and their polycrystal forms were produced by recrystallization in dichloromethane/Et₂O solvent system. Structural determinations were carried out by ¹H NMR and ¹³C NMR with a Varian 400 NMR system using tetramethylsilane as internal standard and CDCl₃ as solvent. The disappearance of acidic N‐heterocyclic carbene proton showed the formation of Ag(I) complexes. Also, elemental analyses were carried out. Electron paramagnetic resonance (EPR) measurements were performed to determine the formed radical structure on the samples irradiated at the room temperature for 72 h by using ⁶⁰Co‐source with dose rate of 0.680 kGy. The EPR measurements were carried out in the temperature range of 200 K–450 K. Identical radicals were determined on the irradiated compounds. It was observed that the shapes of the spectra of the samples were independent of the temperature but, the resonance line intensities changed linearly with the temperature. Also, it was detected that the free radical on the 1‐pentamethylbenzyl‐3‐ethylimidazoliumsilver(I)bromide is not stable compared to that on the 1,3‐bis(pentamethylbenzyl)‐4,5dimethylbenzimidazoliumsilver(I)bromide. Copyright © 2016 John Wiley & Sons, Ltd.     

New Copper（Ⅱ） and Nickel（Ⅱ） Complexes of 4-Morpholinoacetophenone Thiosemicarbazone： Structural, Electrochemical and Antimicrobial Studies

4-Morpholinoacetophenone thiosemicarbazone, MAPT, and its nickel（Ⅱ） and copper（Ⅱ） complexes have been prepared and characterized by elemental analysis, magnetic susceptibility, spectral methods （FT-IR, ^1H NMR） and cyclic voltammetry. Electrochemical behaviors of the complexes have been studied by cyclic voltammetry in DMF media showing metal centered reduction processes for both of them. The redox properties, nature of the electrode processes and the stability of the complexes were discussed. [Cu（MAPT）2]Cl2 complex shows Cu（Ⅱ）/Cu（Ⅰ） couple and quasi-reversible wave associated with the Cu（Ⅲ）/Cu（Ⅱ） process. The reduction/oxidation potential values depend on the structures of complexes. Also, the antimicrobial activities of these complexes were determined against S. aureus, E. coli and B. subtilis.     

Determination of in vitro antioxidant and radical scavenging activities of propofol

Propofol (2,6-diisopropylphenol) is a hypnotic intravenous agent with in vivo antioxidant properties. This study was undertaken to examine the in vitro antioxidant activity of propofol using different antioxidant tests including by 1,1-diphenyl-2-picryl-hydrazil (DPPH.) radical scavenging, metal chelating, hydrogen peroxide scavenging, superoxide anion radical scavenging, reducing power and total antioxidant activities. At the concentrations of 25, 50, and 75 microg/ml, propofol exhibited 97.7, 98.6 and 100% inhibition on peroxidation of linoleic acid emulsion, respectively. On the other hand, at the 75 microg/ml concentration of standard antioxidants such as butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT) and alpha-tocopherol exhibited 88.7, 94.5, and 70.4% inhibition on peroxidation of linoleic acid emulsion, respectively. In addition, at same concentrations, propofol was shown that it had effective reducing power, DPPH. free radical scavenging, superoxide anion radical scavenging, hydrogen peroxide scavenging and metal chelating activities. These various antioxidant activities were compared to standard antioxidants such as BHA, BHT and alpha-tocopherol. These results indicate that propofol prevents lipid peroxidation and radicalic chain reactions. At the same time, propofol revealed more effective antioxidant capacity than BHA, BHT and alpha-tocopherol.     

Catalytic air oxidation of manganese in synthetic waters

An attempt was made to study the oxidation of manganese by air in synthetic waters. A series of batch experments were performed at differnet values of concentration, temperature and pH. Unoxidized manganese in the solution was determined by formaldoxime spectrometric method. Results of these studies indicated that the air oxidation of manganese soluble in water can be effectively performed in basic media and that oxidation yield increasedwith an increase in pH and concentration. The yield was very high in the presence of manganese dioxide, sepiolite or clinoptilolite in solution and, the oxidation was almost completed especially at high values of pH and concentration. The reaction was found to be first order with respect to Mn²⁺ with a very low activation energy. A yield of 62% was obtained for the air oxidation of wastewater taken from the treatment plant of Corum Municipality.     

Bis­(acesulfamato)­tetra­aqua­cobalt(II)

The crystal structure of the first acesulfame–metal complex, namely tetra­aqua­bis­[6‐methyl‐1,2,3‐oxa­thia­zin‐4(3H)‐onato 2,2‐dioxide‐κN]­cobalt(II), [Co(C₄H₄NO₄S)₂(H₂O)₄], is re­ported. The Co^II ion resides on a twofold axis and is coordinated by four aqua ligands defining the basal plane and by two monodentate acesulfamate ligands, via their ring N atoms, in the axial positions. Two intra‐ and three intermolecular hydrogen‐bonding interactions stabilize the crystal structure and form an infinite three‐dimensional lattice.     

Novel phthalocyanines with naphthalenic substituents

Phthalocyanines with four naphthyl-malonic ester groups on the periphery were synthesized by cyclotetramerization of 4-(1,1-dicarbethoxy-2-(1-naphthyl)-ethyl)-phthalonitrile. The new compounds were characterized by spectroscopic methods. The electronic spectra exhibit intense π–π* transitions from the naphthyl moiety together with the characteristic Q and B bands of the phthalocyanine core. The electrochemical properties of the 2,9,17,23-tetra-(1,1-(dicarbethoxy)-2-(1-naphthyl)-ethyl) phthalocyaninato copper(II) complex were studied by cyclic voltammetry.