Blind prediction of HIV integrase binding from the SAMPL4 challenge

Here, we give an overview of the protein-ligand binding portion of the Statistical Assessment of Modeling of Proteins and Ligands 4 (SAMPL4) challenge, which focused on predicting binding of HIV integrase inhibitors in the catalytic core domain. The challenge encompassed three components—a small “virtual screening” challenge, a binding mode prediction component, and a small affinity prediction component. Here, we give summary results and statistics concerning the performance of all submissions at each of these challenges. Virtual screening was particularly challenging here in part because, in contrast to more typical virtual screening test sets, the inactive compounds were tested because they were thought to be likely binders, so only the very top predictions performed significantly better than random. Pose prediction was also quite challenging, in part because inhibitors in the set bind to three different sites, so even identifying the correct binding site was challenging. Still, the best methods managed low root mean squared deviation predictions in many cases. Here, we give an overview of results, highlight some features of methods which worked particularly well, and refer the interested reader to papers in this issue which describe specific submissions for additional details.     

Enantioselective Synthesis of Functionalized Arenes by Nickel-Catalyzed Site-Selective Hydroarylation of 1,3-Dienes with Aryl Boronates

A catalytic method for the site-selective and enantioselective synthesis of functionalized arenes by the intermolecular hydroarylation of terminal and internal 1,3-dienes with aryl pinacolato boronates is reported. The reactions are promoted by 5.0 mol % of a readily available monodentate phosphoramidite-Ni complex in ethanol, affording a variety of enantioenriched products in up to 96 % yield and 99:1 er. Mechanistic studies indicate that Ni–allyl formation is irreversible and related to the nature of the arylboronate.     

A Gas Chromatography-Molecular Rotational Resonance Spectroscopy Based System of Singular Specificity

We designed and demonstrated the unique abilities of the first gas chromatography–molecular rotational resonance spectrometer (GC-MRR). While broadly and routinely applicable, its capabilities can exceed those of high-resolution MS and NMR spectroscopy in terms of selectivity, resolution, and compound identification. A series of 24 isotopologues and isotopomers of five organic compounds are separated, identified, and quantified in a single run. Natural isotopic abundances of mixtures of compounds containing chlorine, bromine, and sulfur heteroatoms are easily determined. MRR detection provides the added high specificity for these selective gas-phase separations. GC-MRR is shown to be ideal for compound-specific isotope analysis (CSIA). Different bacterial cultures and groundwater were shown to have contrasting isotopic selectivities for common organic compounds. The ease of such GC-MRR measurements may initiate a new era in biosynthetic/degradation and geochemical isotopic compound studies.     

Sensitivity‐Enhanced 13C‐NMR Spectroscopy for Monitoring Multisite Phosphorylation at Physiological Temperature and pH

Abundant phosphorylation events control the activity of nuclear proteins involved in gene regulation and DNA repair. These occur mostly on disordered regions of proteins, which often contain multiple phosphosites. Comprehensive and quantitative monitoring of phosphorylation reactions is theoretically achievable at a residue‐specific level using ¹H‐¹⁵N NMR spectroscopy, but is often limited by low signal‐to‐noise at pH>7 and T>293 K. We have developed an improved ¹³Cα‐¹³CO correlation NMR experiment that works equally at any pH or temperature, that is, also under conditions at which kinases are active. This allows us to obtain atomic‐resolution information in physiological conditions down to 25 μm . We demonstrate the potential of this approach by monitoring phosphorylation reactions, in the presence of purified kinases or in cell extracts, on a range of previously problematic targets, namely Mdm2, BRCA2, and Oct4.     

Oriented O(3P2), Ne(3P2), and He(3S1) atoms emerging from a bent magnetic guide

We describe our observation of strongly oriented total electronic angular momentum J in O(³P₂), Ne(³P₂), and He(³S₁) atoms emerging from a bent magnetic multipole guide, as measured by resonant multiphoton ionisation. This was contrary to our expectation because no additional (uniform) magnetic fields were applied to orient the atoms behind the exit of the guide. Two- and three-photon ionisation techniques were employed to determine the degree of J polarisation, from which we infer that atoms become oriented as a result of a combination of weak fringe fields, possible stray fields, and the fact that molecular beam packets do not oscillate around the geometric center of the bent multipole guide. We conclude that similar effects may exist in other, related experiments and that a detailed characterisation of the degree of orientation is required prior to any study of chemical dynamics or spectroscopy. This paper should serve as a warning for anybody using similar devices not to assume isotropic angular momentum distributions of atoms and molecules emerging from a magnetic guide or a decelerator, particularly when it is bent; whenever possible, the possibility for a J anisotropy should be experimentally checked.