Ab Initio Design of Potent Anti-MRSA Peptides Based on Database Filtering Technology

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed. (1) This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when the most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g., amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database (2) by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 min. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. Our ab initio design combined with database screening (3) led to yet another peptide with enhanced potency. Because of the simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well.     

Synthesis and characterization of Ru(II)-DMSO-Cl-chalcone complexes: DNA binding, nuclease, and topoisomerase II inhibitory activity

The complexes of type cis-[Ru(S-DMSO)(3)(R-CO-CH═CH-R')Cl] (R = 2-hydroxyphenyl for all, R' = phenyl 1, naphthyl 2, anthracenyl 3, thiophene 4, 3-methyl thiophene 5) are synthesized and characterized using spectroscopic (IR, (1)H and (13)C NMR, and UV-vis) and single crystal X-ray diffraction techniques. Their crystal structures show the formation of both intermolecular and intramolecular H-bonding. The molecular assembly of complex 5 using secondary interactions provides a butterfly structure. The binding of complexes with calf thymus DNA is monitored using UV-vis spectral titrations. The binding interaction of complexes 1, 2, and 3 with DNA increases with increasing conjugation of aromatic rings. However, complexes 4 and 5 interact with DNA strongly. The emission from ethidium bromide (EB) bound DNA recorded in phosphate buffer solution (pH = 7.2) decreases by incremental addition of solution of the complexes. The complexes 4 and 5 (100 μM) bind with the minor groove of DNA and cleave double-stranded pBR322 DNA significantly even in the absence of an activator. In the presence of H(2)O(2), they cleave supercoiled DNA via oxidative pathway even at lower concentration (20 μM). Both complexes 4 and 5 inhibit topoisomerase II activity with IC(50) values of 18 and 13. These values suggest that 4 and 5 are potential topoisomerase II inhibitors as compared to some of known inhibitors like novobiocin and etoposide.     

Investigation of ethynylpyridines using the electron propagator theory

The optimized geometry, dipole moment, and HOMO–LUMO gap for three monoethynylpyridines and six diethynylpyridines have been computed using DFT/B3LYP/6‐311++g(3df,3p) level of theory, and the first 11 vertical ionization energies and electron affinity of these compounds have been calculated using various electron propagator decouplings. The outer valence Green's function approximant of the electron propagator theory offers closest agreement with experimental photoelectron spectrum, and the results for structural suitability, dipole moment, HOMO–LUMO gap, ionization energies, and electron affinity indicate that 2‐ethynylpyridine among monoethynylpyridines and 2,6‐diethynylpyridine among diethynylpyridines may be useful precursors for the preparation of conducting polymers. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 112:426–439, 2012     

2-(N-Allylaminomethyl)cinnamaldehydes as substrates for syntheses of aza-polycycles via intramolecular cycloaddition reactions

Syntheses of a variety of aza-polycycles employing 2-(N-allylaminomethyl)cinnamaldehydes derived from Morita–Baylis–Hillman adducts of acrylates via intramolecular 1,3-dipolar cycloaddition, or Aza-Diels–Alder or domino Knoevenagel/hetero Diels–Alder cycloaddition reactions are described. Whereas the Aza-Diels–Alder afforded a mixture of cis- and trans-isomers of substituted 1,2,3,4,4a,5,10,10a-octahydrobenzo[b][1,6]naphthyridines, the 1,3-dipolar cycloaddition and domino Knoevenagel/hetero Diels–Alder were diastereoselective to produce exclusively cis-derivatives of 1,2,3,4,4a,6,7,8,9,9a-decahydro-1H-pyrido[3,4-b]pyrrolizine-8a-carboxylates and 3,4,4a,5,7,8,9,10b-octahydro-1H-chromeno[3,4-c]pyridin-10(2H)-ones, respectively.     

Synthesis of sterically hindered ketones from aldehydes via O-silyl oximes

A mild and efficient method to synthesize sterically hindered ketones from aldehydes via O-silyl oximes was developed. Treatment of O-triphenylsilylated oximes with alkyl iodides in the presence of triethyl borane afforded the corresponding ketones.     

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

The linear interaction energy (LIE) method to compute binding free energies is applied to lectin‐monosaccharide complexes. Here, we calculate the binding free energies of monosaccharides to the Ralstonia solanacearum lectin (RSL) and the Pseudomonas aeruginosa lectin‐II (PA‐IIL). The standard LIE model performs very well for RSL, whereas the PA‐IIL system, where ligand binding involves two calcium ions, presents a major challenge. To overcome this, we explore a new variant of the LIE model, where ligand–metal ion interactions are scaled separately. This model also predicts the saccharide binding preference of PA‐IIL on mutation of the receptor, which may be useful for protein engineering of lectins. © 2012 Wiley Periodicals, Inc.     

Ordered self-assembled locked nucleic acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability

Locked nucleic acid (LNA) is a conformationally restricted nucleic acid analogue, which is potentially a better alternative than DNA for application in the nucleic acid based biosensor technologies, due to its efficient and sequence-specific DNA/RNA detection capability and lack of molecule-surface interaction on solid surfaces, compared to DNA. We report, for the first time, a straightforward way (based on simple immersion method) of generating an ordered self-assembled LNA monolayer, which is bioactive, onto a gold(111) surface. This layer is capable of giving rise to a stronger DNA recognition signal (4-4.5 times) than its DNA counterpart, and importantly, it can differentiate between a fully complementary DNA target and that having a single base mismatch, where the mismatch discrimination ratio is almost two times compared to the ratio relevant in case of DNA-based detection. We have presented high-resolution atomic force microscopy (AFM) topographs of the well-defined one-dimensional LNA molecular ordering (few hundred nanometers long) and of the two-dimensional ordered assembly formed over a large area (7 μm × 7 μm) due to parallel positioning of the one-dimensional ordered arrangements. The effects of different parameters such as LNA concentration and incubation time on LNA self-assembly have been investigated. Further, reflection absorption infrared (RAIR) spectroscopy has been applied to obtain information about the orientation of the surface-immobilized LNA molecules for the first time. It has been found that the LNA molecules undergo an orientational transition from the "lying down" to the "upright" configuration in a time scale of few hours.     

Physicochemical investigations of microemulsification of coconut oil and water using polyoxyethylene 2-cetyl ether (Brij 52) and isopropanol or ethanol

The microemulsification of coconut oil/polyoxyethylene 2-cetyl ether/2-propanol or ethanol/water was investigated. The phase behaviors of the mixed system were examined. The shear viscosity at different temperatures was measured to derive activation parameters for the viscous flow. The diffusion coefficient of the microemulsions at different compositions was determined by the DLS method. The energetics of solubilization of water into oil + Brij + alkanol as well as of oil into water + Brij + alkanol forming w/o and o/w microemulsions, respectively, were calorimetrically determined.     

Theoretical studies on atmospheric chemistry of HFE‐347mcc3: reactions with OH radicals and Cl atoms

Detailed theoretical investigation has been performed on the mechanism, kinetics and thermochemistry of the gas phase reactions of CF₃CF₂CF₂OCH₃ (HFE‐347mcc3) with OH radicals and Cl atoms using M06‐2X/6‐31 + G(d,p) level of theory. Reaction profiles are modeled including the formation of pre‐reactive and post‐reactive complexes at entrance and exit channels, respectively. Using group‐balanced isodesmic reactions, the standard enthalpies of formation for species are also reported. The calculated bond dissociation energy for C―H bond is in good agreement with previous data. The rate constants of the two reactions are determined for the first time in a wide temperature range of 250–1000 K. At 298 K, the calculated rate coefficients are in good agreement with the experimental results. The atmospheric life time of HFE‐347mcc3 is estimated to be 4.4 years. Copyright © 2014 John Wiley & Sons, Ltd.