Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK

We have used virtual screening to develop models for the binding of aryl substituted heterocycles to p38α MAPK. Virtual screening was conducted on a number of p38α MAPK crystal structures using a library of 46 known p38α MAPK inhibitors containing a heterocyclic core substituted by pyridine and fluorophenyl rings (structurally related to SB203580) and a set of decoy compounds. Multiple protonation states and tautomers of active and decoy compounds were considered. Each docking model was evaluated using receiver operating characteristic (ROC) curves and enrichment factors. The two best performing single crystal structures were found to be 1BL7 and 2EWA, with enrichment factors of 14.1 and 13.0 at 2 % of the virtual screen respectively. Ensembles of up to four receptors of similar conformations were generated, generally giving good or very good performances with high ROC AUCs and good enrichment. The 1BL7-2EWA ensemble was able to outperform each of its constituent receptors and gave high enrichment factors of 17.3, 12.0, 8.0 at 2, 5 and 10 % respectively, of the virtual screen. A ROC AUC of 0.94 was obtained for this ensemble. This method may be applied to other proteins where there are a large number of inhibitor classes with different binding site conformations.     

Investigation of antibacterial phytochemicals in the bark and leaves of Ficus coronata by high-performance liquid chromatography-electrospray ionization-ion trap mass spectrometry (HPLC-ESI-MS(n) ) and ESI-MS(n)

The ethyl acetate extracts of the bark and leaves of Ficus coronata were separated by column chromatography and the resulting fractions tested for their bioactivity toward methicillin-resistant-Staphylococcus aureus (MRSA) and M. luteus. The bioactive column chromatography fractions were further separated by preparative thin layer chromatography (TLC) and the resulting bands investigated by high-performance liquid chromatography-electrospray ionization-ion trap mass spectrometry (HPLC-ESI-MS(n) ) and ESI-MS(n) . The resulting retention times, molecular masses, their fragmentation patterns, and the chemnet database (www.chemnetbase.com) were then used in the dereplication process by structural elucidation of some of the compounds when compared with known structures of natural origin. Some molecular masses and the corresponding fragmentations were found that did not correlate with any known compounds thus revealing potentially novel natural products that could be investigated on a larger scale and could ultimately find application as new drugs against MRSA and other multidrug-resistant microorganisms. Structures are also proposed for known compounds that have not been previously reported for F. coronata.     

New Cu-based catalysts supported on TiO2 films for Ullmann S(N)Ar-type C-O coupling reactions

New routes for the preparation of highly active TiO(2)-supported Cu and CuZn catalysts have been developed for C-O coupling reactions. Slurries of a titania precursor were dip-coated onto glass beads to obtain either structured mesoporous or non-porous titania thin films. The Cu and CuZn nanoparticles, synthesized using a reduction by solvent method, were deposited onto calcined films to obtain a Cu loading of 2 wt%. The catalysts were characterized by inductively coupled plasma (ICP) spectroscopy, temperature-programmed oxidation/reduction (TPO/TPR) techniques, (63)Cu nuclear magnetic resonance (NMR) spectroscopy, X-ray diffraction (XRD), scanning and transmission electron microscopy (S/TEM-EDX) and X-ray photo-electron spectroscopy (XPS). The activity and stability of the catalysts obtained have been studied in the C-O Ullmann coupling of 4-chloropyridine and potassium phenolate. The titania-supported nanoparticles retained catalyst activity for up to 12 h. However, catalyst deactivation was observed for longer operation times due to oxidation of the Cu nanoparticles. The oxidation rate could be significantly reduced over the CuZn/TiO(2) catalytic films due to the presence of Zn. The 4-phenoxypyridine yield was 64% on the Cu/nonporous TiO(2) at 120 °C. The highest product yield of 84% was obtained on the Cu/mesoporous TiO(2) at 140 °C, corresponding to an initial reaction rate of 104 mmol g(cat) (-1) s(-1). The activation energy on the Cu/mesoporous TiO(2) catalyst was found to be (144±5) kJ mol(-1), which is close to the value obtained for the reaction over unsupported CuZn nanoparticles (123±3 kJ mol(-1)) and almost twice the value observed over the catalysts deposited onto the non-porous TiO(2) support (75±2 kJ mol(-1)).     

Selective response of mesoporous silicon to adsorbants with nitro groups

We demonstrate that the electronic structure of mesoporous silicon is affected by adsorption of nitro-based explosive molecules in a compound-selective manner. This selective response is demonstrated by probing the adsorption of two nitro-based molecular explosives (trinitrotoluene and cyclotrimethylenetrinitramine) and a nonexplosive nitro-based aromatic molecule (nitrotoluene) on mesoporous silicon using soft X-ray spectroscopy. The Si atoms strongly interact with adsorbed molecules to form Si-O and Si-N bonds, as evident from the large shifts in emission energy present in the Si L(2,3) X-ray emission spectroscopy (XES) measurements. Furthermore, we find that the energy gap (band gap) of mesoporous silicon changes depending on the adsorbant, as estimated from the Si L(2,3) XES and 2p X-ray absorption spectroscopy (XAS) measurements. Our ab initio molecular dynamics calculations of model compounds suggest that these changes are due to spontaneous breaking of the nitro groups upon contacting surface Si atoms. This compound-selective change in electronic structure may provide a powerful tool for the detection and identification of trace quantities of airborne explosive molecules.     

Serum albumin targeted, pH-dependent magnetic resonance relaxation agents

The objective of this work was the synthesis of serum albumin targeted, Gd(III)-based magnetic resonance imaging (MRI) contrast agents exhibiting a strong pH-dependent relaxivity. Two new complexes (Gd-glu and Gd-bbu) were synthesized based on the DO3A macrocycle modified with three carboxyalkyl substituents?α to the three ring nitrogen atoms, and a biphenylsulfonamide arm. The sulfonamide nitrogen coordinates the Gd in a pH-dependent fashion, resulting in a decrease in the hydration state, q, as pH is increased and a resultant decrease in relaxivity (r(1)). In the absence of human serum albumin (HSA), r(1) increases from 2.0 to 6.0?mM(-1) s(-1) for Gd-glu and from 2.4 to 9.0?mM(-1) s(-1) for Gd-bbu from pH?5 to 8.5 at 37?°C, 0.47?T, respectively. These complexes (0.2?mM) are bound (>98.9?%) to HSA (0.69?mM) over the pH range 5-8.5. Binding to albumin increases the rotational correlation time and results in higher relaxivity. The r(1) increased 120?% (pH?5) and 550?% (pH?8.5) for Gd-glu and 42?% (pH?5) and 260?% (pH?8.5) for Gd-bbu. The increases in r(1) at pH?5 were unexpectedly low for a putative slow tumbling q=2 complex. The Gd-bbu system was investigated further. At pH?5, it binds in a stepwise fashion to HSA with dissociation constants K(d1)=0.65, K(d2)=18, K(d3)=1360?μM. The relaxivity at each binding site was constant. Luminescence lifetime titration experiments with the Eu(III) analogue revealed that the inner-sphere water ligands are displaced when the complex binds to HSA resulting in lower than expected r(1) at pH?5. Variable pH and temperature nuclear magnetic relaxation dispersion (NMRD) studies showed that the increased r(1) of the albumin-bound q=0 complexes is due to the presence of a nearby water molecule with a long residency time (1-2?ns). The distance between this water molecule and the Gd ion changes with pH resulting in albumin-bound pH-dependent relaxivity.     

Spectroscopic evidence for the unusual stereochemical configuration of an endosome-specific lipid

At a glance: The stereochemical configuration of the diglycerophosphate backbone of the endosome-specific lipid bis(monoacylglycero)phosphate (BMP, see picture) was determined by (1)H?NMR spectroscopy. Enantiomeric discrimination was facilitated by introduction of D-camphor ketals as chiral shift reagents, and enantiopure synthetic BMP analogues were prepared as reference materials. Natural BMP exhibited the unusual sn-1,1' diglycerophosphate backbone.     

Progress in adsorption-based CO2 capture by metal-organic frameworks

Metal-organic frameworks (MOFs) have recently attracted intense research interest because of their permanent porous structures, large surface areas, and potential applications as novel adsorbents. The recent progress in adsorption-based CO(2) capture by MOFs is reviewed and summarized in this critical review. CO(2) adsorption in MOFs has been divided into two sections, adsorption at high pressures and selective adsorption at approximate atmospheric pressures. Keys to CO(2) adsorption in MOFs at high pressures and low pressures are summarized to be pore volumes of MOFs, and heats of adsorption, respectively. Many MOFs have high CO(2) selectivities over N(2) and CH(4). Water effects on CO(2) adsorption in MOFs are presented and compared with benchmark zeolites. In addition, strategies appeared in the literature to enhance CO(2) adsorption capacities and/or selectivities in MOFs have been summarized into three main categories, catenation and interpenetration, chemical bonding enhancement, and electrostatic force involvement. Besides the advantages, two main challenges of using MOFs in CO(2) capture, the cost of synthesis and the stability toward water vapor, have been analyzed and possible solutions and path forward have been proposed to address the two challenges as well (150 references).     

Structure of the stapled p53 peptide bound to Mdm2

Mdm2 is a major negative regulator of the tumor suppressor p53 protein, a protein that plays a crucial role in maintaining genome integrity. Inactivation of p53 is the most prevalent defect in human cancers. Inhibitors of the Mdm2-p53 interaction that restore the functional p53 constitute potential nongenotoxic anticancer agents with a novel mode of action. We present here a 2.0 ? resolution structure of the Mdm2 protein with a bound stapled p53 peptide. Such peptides, which are conformationally and proteolytically stabilized with all-hydrocarbon staples, are an emerging class of biologics that are capable of disrupting protein-protein interactions and thus have broad therapeutic potential. The structure represents the first crystal structure of an i, i + 7 stapled peptide bound to its target and reveals that rather than acting solely as a passive conformational brace, a staple can intimately interact with the surface of a protein and augment the binding interface.