Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

Monte carlo calculations of the conformal charge

The conformal charge is an important quantity which characterizes the nature of the two-dimensional phase transition. We report a first attempt to use a new numerical method to calculate the conformal charge. In this paper, we apply our method to the 2-dimensional, ⁴, continuous-spin Ising model. By varying the parameters in the Hamiltonian, one can change continuously from the known Gaussian limit to the Ising limit. It is well known that the critical points for these two systems are not in the same universality class. We study this behavior for the Gaussian model, the single-well ⁴ model, the border model, and the double-well ⁴ model for a large lattice. Our results, while giving a good general picture, are not so far sufficient to differentiate whether the non-Gaussian cases studied belong to the Ising model universality class or not. Further studies of other lattice sizes should serve to improve greatly our conclusions.     

Structural analysis of metal interactions with the dinucleotide duplex, dCG x dCG, using ion mobility mass spectrometry

The metal binding properties of the dinucleotide duplex, dCG x dCG, were analyzed in the gas phase with ion mobility mass spectrometry. Both MALDI and ESI were used to generate [M(dCG x dCG)]+ complexes. The collision cross section of each complex was measured in helium using ion mobility based methods and compared to calculated cross sections of theoretical structures. When metal cations classified as hard acids were combined with dCG x dCG, the [M(dCG x dCG)]+ complex organized into a globular structure. However, when soft acid metal cations were examined, a structure was observed where the two C-G base pairs were Watson-Crick bound.     

Facile Phenylphosphinidene Transfer Reactions from Carbene–Phosphinidene Zinc Complexes

Phosphinidenes [R-P] are convenient P₁ building blocks for the synthesis of a plethora of organophosphorus compounds. Thus far, transition-metal-complexed phosphinidenes have been used for their singlet ground-state reactivity to promote selective addition and insertion reactions. One disadvantage of this approach is that after transfer of the P₁ moiety to the substrate, a challenging demetallation step is required to provide the free phosphine. We report a simple method that enables the Lewis acid promoted transfer of phenylphosphinidene, [PhP], from NHC=PPh adducts (NHC=N-heterocyclic carbene) to various substrates to produce directly uncoordinated phosphorus heterocycles that are difficult to obtain otherwise.     

Nitrilotriacetamide: Synthesis in Concentrated Sulfuric Acid and Stability in Water

Acid hydrolysis of N(CH₂CN)₃ leads either nitrilotriacetamide, 1, and/or 3,5-dioxopiperazineacetamide, 4, in quantitative yield. 1 slowly and cleanly converts to 3,5-dioxopiperazineacetic acid, 5, in water, although ammonium salts prevent this reaction.     

One-pot synthesis of 3-arylaminomaleimides from terminal alkynes and isocyanates

The reaction of aryl acetylide anions with phenyl isocyanate and subsequent addition of a protonating agent such as ethanol affords good yields of 3-aminomaleimides, formed by the cyclization of one molecule of alkyne with two isocyanates. When the reaction is quenched with water instead, cyclopentadienone imines are formed as the major products.