Sets and indices in linear programming modelling and their integration with relational data models

LP models are usually constructed using index sets and data tables which are closely related to the attributes and relations of relational database (RDB) systems. We extend the syntax of MPL, an existing LP modelling language, in order to connect it to a given RDB system. This approach reuses existing modelling and database software, provides a rich modelling environment and achieves model and data independence. This integrated software enables Mathematical Programming to be widely used as a decision support tool by unlocking the data residing in corporate databases.     

Synthesis and Intracellular Redox Cycling of Natural Quinones and Their Analogues and Identification of Indoleamine‐2,3‐dioxygenase (IDO) as Potential Target for Anticancer Activity

Natural quinones, often linked with cellular oxidation processes, exhibit pronounced biological activity. In particular, the structurally unique isothiazolonaphthoquinone aulosirazole, isolated from blue‐green alga, possesses selective antitumor cytotoxicity, although its mechanism of action is unknown. The first synthesis of aulosirazole uses a route centered upon a late‐stage regioselective Diels–Alder reaction. The structurally related natural product pronqodine A, an inhibitor of prostaglandin release, and analogues thereof, were also prepared for comparison. Biological evaluation of the compounds identified one potential target as the immunoregulatory enzyme indoleamine‐2,3‐dioxygenase (IDO). The isothiazoloquinones are also efficient substrates for the human quinone reductase NQO1, and undergo intracellular NQO1‐dependent redox cycling resulting in the generation of reactive oxygen species, and at lower doses have the potential to alter the ratio of intracellular oxidized to reduced pyridine nucleotides.     

Competitive and noncompetitive phage immunoassays for the determination of benzothiostrobin

Twenty-three phage-displayed peptides that specifically bind to an anti-benzothiostrobin monoclonal antibody (mAb) in the absence or presence of benzothiostrobin were isolated from a cyclic 8-residue peptide phage library. Competitive and noncompetitive phage enzyme linked immunosorbent assays (ELISAs) for benzothiostrobin were developed by using a clone C3-3 specific to the benzothiostrobin-free mAb and a clone N6-18 specific to the benzothiostrobin immunocomplex, respectively. Under the optimal conditions, the half maximal inhibition concentration (IC₅₀) of the competitive phage ELISA and the concentration of analyte producing 50% saturation of the signal (SC₅₀) of the noncompetitive phage ELISA for benzothiostrobin were 0.94 and 2.27 ng mL⁻¹, respectively. The noncompetitive phage ELISA showed higher selectivity compared to the competitive. Recoveries of the competitive and the noncompetitive phage ELISAs for benzothiostrobin in cucumber, tomato, pear and rice samples were 67.6–119.6% and 70.4–125.0%, respectively. The amounts of benzothiostrobin in the containing incurred residues samples detected by the two types of phage ELISAs were significantly correlated with that detected by high-performance liquid chromatography (HPLC).     

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

\(\alpha\)-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.     

Modal testing of an avlb bridge

Experimental Techniques -     

Naturally-occurring nitro compounds

Naturally-occurring nitro compounds display great structural diversity, and a wide range of biological activities. This review summarizes current information on the structures of naturally-occurring nitro compounds and on the biosynthesis of the nitro group.     

Regioselectivity of the Claisen rearrangement in meta-allyloxy aryl ketones: an experimental and computational study, and application in the synthesis of (R)-(-)-pestalotheol D

A study of the regioselectivity of the Claisen rearrangement of meta-allyloxy aryl ketones showed that the electron-withdrawing carbonyl group has a major influence and strongly directs rearrangement to the more hindered ortho position. However, when the ketone is part of a ring structure, its electronic effect can be negated by conversion into its triisopropylsilyl enol ether, which dramatically reverses the regiochemistry of the Claisen rearrangement. DFT calculations suggest that the effect is electronic although there is also a steric effect of the bulky silyl group. This strategy for influencing the regiochemical outcome of the Claisen rearrangement was then employed in a short synthesis of the furo[2,3-g]chromene, (-)-pestalotheol D, that confirms the absolute stereochemistry of the natural product.     

Telomestatin: formal total synthesis and cation-mediated interaction of its seco-derivatives with G-quadruplexes

The structurally unique natural product telomestatin incorporates seven oxazole rings and one sulfur-containing thiazoline in a macrocyclic arrangement. The compound is a potent inhibitor of the enzyme telomerase and therefore provides a structural framework for developing new potential therapeutic agents for cancer. An efficient formal total synthesis of telomestatin is reported in which the key steps are the use of dirhodium(II)-catalyzed reactions of diazocarbonyl compounds to generate six oxazole rings, demonstrating the power of rhodium carbene methodology in organic chemical synthesis. CD spectroscopy establishes that seco-derivatives of telomestatin are potent stabilizers of G-quadruplex structures derived from the human telomeric repeat sequence. Mass spectrometry studies, confirmed by molecular dynamics simulations, provide the first evidence that high affinity binding to terminal G-tetrads in both 1:1 and 2:1 ligand complexes is mediated through the macrocycle coordinating a monovalent cation, with selectivity for the antiparallel structure.     

Synthesis of amino-1,4-benzoquinones and their use in Diels-Alder approaches to the aminonaphthoquinone antibiotics

A new protocol for the synthesis of protected amino-1,4-benzoquinones by oxidation of the corresponding 2,5-dimethoxyaniline derivatives using PhI(OAc)(2) or PhI(OCOCF(3))(2) in water containing 2.5% methanol is reported. The process represents an improvement over previously reported methods, both in terms of yield and number of steps, and in the range of nitrogen protecting groups that it tolerates. A number of novel aminobenzoquinones were prepared and subsequently used as dienophiles in Diels-Alder reactions to form building blocks for the synthesis of the aminonaphthoquinone antibiotics such as salinisporamycin.     

New nuclides: Neptunium-243 and neptunium-244

We have observedγ-rays following the β^?-decay of²⁴³Np and²⁴⁴Np after chemical isolation of neptunium isotopes from the products of the reaction of 835 MeV¹³⁶Xe with²⁴⁴Pu. The ground-state of 1.85-min²⁴³Np hasJ=5/2. The decay of 2.29-min²⁴⁴Np (probableJ ^π=7^?) populates high-spin members of the ground state rotational band in²⁴⁴Pu.