Pose scoring by NMR

Recently, we have developed a fast approach to calculate NMR chemical shifts using the divide and conquer method at the semiempirical level. To demonstrate the utility of this approach for characterizing protein-ligand interactions, we used the deviation of calculated chemical shift perturbations from experiment to determine the orientation of a ligand (GPI-1046) in the binding pocket of the FK506 binding protein (FKBP12). Moreover, we were able to select the native state of the ligand from a collection of decoy poses. A key hydrogen bond between O1 and HN in Ile56 was also identified. Our results suggest that ligand-induced chemical shift perturbations can be used to refine protein/ligand structures.     

Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction

Pairwise decomposition of the interaction energy between molecules is shown to be a powerful tool that can increase our understanding of macromolecular recognition processes. Herein we calculate the pairwise decomposition of the interaction energy between the protein human carbonic anhydrase II (HCAII) and the fluorine-substituted ligand N-(4-sulfamylbenzoyl)benzylamine (SBB) using semiempirical quantum mechanics based methods. We dissect the interaction between the ligand and the protein by dividing the ligand and the protein into subsystems to understand the structure-activity relationships as a result of fluorine substitution. In particular, the off-diagonal elements of the Fock matrix that is composed of the interaction between the ionic core and the valence electrons and the exchange energy between the subsystems or atoms of interest is examined in detail. Our analysis reveals that the fluorine-substituted benzylamine group of SBB does not directly affect the binding energy. Rather, we find that the strength of the interaction between Thr199 of HCAII and the sulfamylbenzoyl group of SBB affects the binding affinity between the protein and the ligand. These observations underline the importance of the sulfonamide group in binding affinity as shown by previous experiments (Maren, T. H.; Wiley: C. E. J. Med. Chem. 1968, 11, 228-232). Moreover, our calculations qualitatively agree with the structural aspects of these protein-ligand complexes as determined by X-ray crystallography.     

Mutagenesis Mediated by Triple Helix–Forming Oligonucleotides Conjugated to Psoralen: Effects of Linker Arm Length and Sequence Context

Targeted mutagenesis and gene knock-out can be mediated by triple helix-forming oligonucleotides (TFO) linked to mutagenic agents, such as psoralen. However, this strategy is limited by the availability of homopurine/ homopyrimidine stretches at or near the target site because such sequences are required for high-affinity triplex formation. To overcome this limitation, we have tested TFO conjugated to psoralen via linker arms of lengths varying from 2 to 86 bonds, thereby designed to deliver the psoralen at varying distances from the third strand binding site present at the 3'end of the supFG1 mutation reporter gene. Following triplex formation and UVA irradiation, mutations were detected using an SV40-based shuttle vector assay in human cells. The frequency and distribution of mutations depended on the length of the linker arm. Precise targeting was observed only for linker arms of length 2 and 6, which also yielded the highest mutation frequencies (3 and 14%, respectively). Psoralen–TFO with longer tethers yielded mutations at multiple sites, with the maximum distance from the triplex site limited by the linker length but with the distribution within that range influenced by the propensity for psoralen intercalation at A:T base-pair-rich sites. Thus, gene modification can be extended beyond the site of third strand binding but with a decrease in the precision of the targeting.     

Direct selective detection of genomic DNA from coliform using a fiber optic biosensor

Fiber optic biosensors operated in a total internal reflection format were prepared based on covalent immobilization of 25mer lacZ single-stranded nucleic acid probe. Genomic DNA from Escherichia coli was extracted and then sheared by sonication to prepare fragments of approximately 300mer length. Other targets included a 25mer fully complementary lacZ sequence, 100mer polymerase chain reaction (PCR) products containing the lacZ sequence at various locations, and non-complementary DNA including genomic samples from salmon sperm. Non-selective adsorption of non-complementary oligonucleotides (ncDNA) was found to occur at a significantly faster rate than hybridization of complementary oligomers (cDNA) in all cases. The presence of ncDNA oligonucleotides did not inhibit selective interactions between immobilized DNA and cDNA in solution. The presence of high concentrations of non-complementary genomic DNA had little effect on extent or speed of hybridization of complementary oligonucleotides. Detection of genomic fragments containing the lacZ sequence was possible in as little as 20 s by observation of the steady-state fluorescence intensity increase or by time-dependent rate of fluorescence intensity changes.     

Studies on the thermal decomposition of N-2,4,6 tetranitro-N-methyl aniline

The kinetics of the initial stage of thermal decomposition of N-2,4,6 tetranitro-N-methyl aniline (tetryl) in condensed state has been investigated by high temperature infrared spectroscopy (IR) in conjunction with pyrolysis gas analysis and thermogravimetry (TG). The decomposition in KBr matrix in the temperature range of 131 to 145 °C shows rapid decrease in the N-NO₂ band intensity as compared to the C-NO₂ band. Decomposition products in the initial stage show mainly NO₂ gas and picric acid. The studies show that the initial stage of decomposition of tetryl occurs by the rupture of the N-NO₂ bond and the energy of activation for this process is 177 kJ/mol.

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Zusammenfassung Mittels Hochtemperatur-IR-Spektroskopie wurde in Verbindung mit Pyrolysengasanalyse und Thermogravimetrie (TG) die Kinetik des einleitenden Schrittes der thermischen Zersetzung von N-2,4,6-Tetranitro-N-Methylanilin (Tetryl) im kondensierten Zustand untersucht. Die Zersetzung in einer KBr-Matrix im Temperaturbereich von 131–145 °C äußert sich in einem schnellen Abnehmen der Intensität der N-NO₂ Bande bezogen auf die der C-NO₂ Bande. Zersetzungsprodukte des einleitenden Schrittes sind hauptsächlich NO₂ Gas und Pikrinsäure. Die Untersuchungen zeigten, daß der einleitende Schritt der Zersetzung von Tetryl die Spaltung der N-NO₂ Bindung ist. Die Aktivierungsenergie für diesen Prozess beträgt 177 kJ/mol.

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N-2,4,6-N- () , . 131–145 °C N-NO₂ C-NO₂. . , N-NO₂, 177 /.

     

An efficient ‘on-water’ synthesis of 1,4-dihydropyridines using Fe3O4@SiO2 nanoparticles as a reusable catalyst

An ‘on-water’, efficient, high yielding, expeditious method has been developed for the synthesis of 1,4-dihydropyridine (1,4-DHP) derivatives via an one-pot multi-component condensation of dimedone or 4-hydroxycoumarine, aldehydes, and ammonium acetate using Fe₃O₄@SiO₂ nanoparticles as a recyclable heterogeneous catalyst. This method takes advantage of the fact that water, a green solvent is used in combination with Fe₃O₄@SiO₂ nanoparticles as catalyst which can be easily recovered magnetically and reused for further runs.     

Surfactant mediated oxygen reuptake in water for green aerobic oxidation: mass-spectrometric determination of discrete intermediates to correlate oxygen uptake with oxidation efficiency

A novel strategy of catalytic green aerobic oxidation by surfactant-mediated oxygen reuptake in water offers a new dimension to the applications of surfactants to look beyond as solubility aids and a conceptual advancement in understanding the role of surfactants in aquatic organic reactions through mass spectrometry guided identification of discrete intermediates.     

Space- and time-like electromagnetic pion form factors in light-cone pQCD

We present a combined analysis of the space- and time-like electromagnetic pion form factors in light-cone perturbative QCD with transverse momentum dependence and Sudakov suppression. Including the genuine non-perturbative “soft” QCD and the power suppressed twist-3 corrections to the standard twist-2 perturbative QCD result, the experimental form factor data available at moderate energies/momentum transfers can be explained reasonably well. To this end, the bulk of the existing discrepancy between the space- and time-like experimental data is ostensibly reconciled.     

Isospin-breaking corrections in the pion–deuteron scattering length

It is shown that isospin-breaking corrections to the pion–deuteron scattering length can be very large, because of the vanishing of the isospin-symmetric contribution to this scattering length at leading order in chiral perturbation theory. We further demonstrate that these corrections can explain the bulk of the discrepancy between the recent experimental data on pionic hydrogen and pionic deuterium. We also give the first determination of the electromagnetic low-energy constant f₁$f_1$.