Efficient calculation of SAMPL4 hydration free energies using OMEGA,SZYBKI, QUACPAC,and Zap TK

Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson–Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5–2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors.     

Label-free cell-based assays for GPCR screening

G protein-coupled receptors (GPCRs) have been proven to be the largest family of druggable targets in the human genome. Given the importance of GPCRs as drug targets and the de-orphanization of novel targets, GPCRs are likely to remain the frequent targets of many drug discovery programs. With recent advances in instrumentation and understanding of cellular mechanisms for the signals measured, biosensor-centered label-free cell assay technologies become a very active area for GPCR screening. This article reviews the principles and potential of current label-free cell assay technologies in GPCR drug discovery.     

Insight into the hard-soft acid-base properties of differently substituted phenylhydrazines in reactions with dimethyl carbonate

Following the preliminary studies on the reactivity of the ambident nucleophile phenylhydrazine with dimethyl carbonate, investigations involving para-substituted phenylhydrazines were carried out in order to probe differences in the reactivity within this class of nucleophile. Phenylhydrazines substituted by electron withdrawing or donating substituents showed an increase in reactivity of the phenylhydrazine toward dimethyl carbonate. Under the basic conditions used, all phenylhydrazines displayed hard nucleophilicity, signifying that para-substitution on the phenyl ring has little effect on the hard-soft behavior of this class of nucleophile. This conclusion fits well within the results previously obtained using other para-substituted nucleophiles, i.e., phenols.     

Synthesis, crystal structure, studies in solution and cytotoxicity of two new fluorescent platinum(II) compounds containing anthracene derivatives as a carrier ligand

Two new cytotoxic fluorescent platinum(II) compounds, cis-[Pt(A9opy)Cl2] (1) and cis-[Pt(A9pyp)(DMSO)Cl2] (2),have been designed, synthesized, and characterized by IR, 1H NMR, and 195Pt NMR spectroscopy; electrospray ionization mass spectrometry (ESI-MS); and single-crystal X-ray diffraction. The carrier ligands selected for thesynthesis of these fluorescent platinum(II) compounds are E-2-[1-(9-anthryl)-3-oxo-3-prop-2-enylpyridine] (abbreviatedas A9opy) and E-1-(9-anthryl)-3-(2-pyridyl)-2-propenone (abbreviated as A9pyp). The compound cis-[Pt(A9opy)Cl2](1) comprises a peculiar cis-platinum(II) organometallic compound, in which the platinum(II) ion is bound to the photoisomerizable carbon-carbon double bond of the carrier ligand. The effects of the metal-ion coordination on the photoisomerization of the carbon-carbon double bond of the ligand have been studied. In contrast, the carrier ligand A9pyp used for the synthesis of the cis-[Pt(A9pyp)(DMSO)Cl2] compound (2) does not undergo such anisomerization process and remains in the E conformation, while coordinated to the platinum(II) ion through the nitrogen of the pyridine ring. In addition to the synthesis and characterization, solution studies of both compounds have also been performed in detail, including NMR and ESI-MS spectroscopy. Moreover, a high degree of cytotoxicactivity of compound 1 was found, as compared to cisplatin and its corresponding platinum-free molecule, in a series of human tumor cell lines. Compound 2 was also found to be highly active against these cell lines but appeared less active compared to the platinum-free molecule.     

Inorganic asymmetric synthesis: diastereoselective syntheses of mono- and dinuclear complexes containing octahedral, two-bladed propeller, bis(pyridine-2-aldehyde 2'-pyridylhydrazone)iron(II) stereocenters

A C2 hexadentate diester derived from (5-hydroxymethyl)pyridine-2-aldehyde 2'-pyridylhydrazone (5-HOCH2PAPHY) and an enantiomerically pure (aS)-spirane dicarboxylic acid diastereoselectively reacts with iron(II) benzenesulfonate in methanol to furnish a 20% diastereomeric excess (de) of a two-bladed propeller, octahedral iron complex in which the P configuration of the newly created (+/-)-[Fe(PAPHY)2](2+) stereocenter predominates; when the reaction mixture is heated under reflux for 12 h, however, the excess of the diastereomer having the P configuration at iron increases to 80%, as determined by (1)H NMR spectroscopy. The configuration at iron in the major diastereomer of the complex was determined by comparison of the circular dichroism spectrum of the deprotonated complex with that of a related complex of known configuration. Repositioning of the hydroxymethyl group of the pyridine-2-aldehyde from the 5- to the 6-position produced a C2-spirane ligand that generates a double-stranded diiron(II) helicate in >99% de. Single crystal X-ray structure determinations of the racemates of the protonated and deprotonated helicates revealed that the complexes crystallize diastereoselectively, that is, two ligand strands of a S configuration generate two octahedral iron(II) stereocenters of P configuration to give a dinuclear metal helicate of P configuration and vice versa for the ligand of a R configuration.     

Sterically Congested Phosphite Ligands: Synthesis,crystallographic characterization,and observation of unprecedented eight-Bond 31P,31P coupling in the 31P-NMR spectra

The synthesis and characterization of 2-{1-{3,5-bis(1,1-dimethylethyl)-2-{[2,4,8,10-tetrakis(1,1-dimethylethyl)dibenzo[d,f][1,3,2]dioxaphosphepin-6-yl]oxy}phenyl}ethyl}-4,6-bis(1,1-dimethylethyl)phenyl diphenyl phosphite ( 6 ) is described. In the ³¹P-NMR spectrum (¹H-decoupled) of 6 , an unprecedented eight-bond P,P coupling of J = 72.8 Hz is observed. In the X-ray crystal structure of 6 , an intramolecular P–P distance of 3.67 Å is found, which is within the sum of the van-der-Waals radii of the P-atoms. The observed intramolecular P–P distance suggests that a through-space coupling mechanism is operative. The solid-state conformation of 6 is compared to the conformation obtained by semi-empirical MO geometry optimizations (PM3 method). The calculated geometry suggests that the solid-state structure is near a true energy minimum, but that crystal-packing forces decrease the intramolecular P–P distance in the solid state. In the absence of crystal-packing forces, however, the collisional and vibrational energy available in solution may lead to the population of states with a shortened intramolecular P–P distance in 6 . The proximity of the P-atoms in 6 is due to restricted conformational freedom resulting from steric congestion within the molecule. The free energy of activation (ΔG* = 10.2 and 10.8 kcal/mol for unequal populations of exchanging conformers) for ring inversion of the dibenzo[d,f][1,3,2]dioxaphosphepin ring in 6 is determined by variable-temperature ³¹P-NMR spectroscopy. Semi-empirical MO calculation on model compounds suggest that the structure of the transition state for ring inversion has the two aryl rings and O-atoms in a common plane, with the P-atom lying above this plane.     

Synthesis and spectral studies on some tetrahydrobenzoxanthen-11-ones: crystal and molecular structure of 9,9-dimethyl-12-(2-nitrophenyl)-8,9,10,12-tetrahydrobenzo[<Emphasis Type="Italic">a</Emphasis>]xanthen-11-one

A series of 12-aryl-8,9,10,12-tetrahydrobenzo[a]xanthen-11-ones have been synthesized by the multicomponent reaction (MCR) of β-naphthol, aryl aldehydes, and dimedone by using BF₃:OEt₂ as a catalyst. The derived compounds have been analyzed by IR, NMR (1D and 2D), and mass spectra. The single crystal X-ray structural analysis of 9,9-dimethyl-12-(2-nitrophenyl)-8,9,10,12-tetrahydrobenzo[a]-xanthen-11-one evidences the envelope conformation of the cyclohexane ring and the pyran ring tends to adopt flattened-boat conformation.     

Protecting group free syntheses of (±)-columbianetin and (±)-angelmarin

A five-step and protecting group free synthesis of (±)-columbianetin from cyclohexane-1,3-dione is reported. The former compound was converted into its p-hydroxycinnamate derivative, (±)-angelmarin, using Coster’s esterification procedure. Efforts to modify the synthesis so as to prepare angelmarin and columbianetin in an enantioselective manner are described.