An evolution of bioinorganic chemistry from molecular to geological level—Daryle H. Busch's contribution

The evolution of the discipline Bioinorganic Chemistry and how Daryle H. Busch contributed to it are reviewed from a personal perspective of this author. The initial motivation was intimated in a review article published in the third volume (1968) of this journal. Bioinorganic chemistry has been expanded from the molecular level to include the environmental and geological aspects.     

Molecular dynamics study on the ligand recognition by tandem SH3 domains of p47phox, regulating NADPH oxidase activity

The phagocyte NADPH oxidase complex plays a crucial role in host defense against microbial infection through the production of superoxides. Chronic granulomatous disease (CGD) is an inherited immune deficiency caused by the absence of certain components of the NADPH oxidase. Key to the activation of the NADPH oxidase is the cytoplasmic subunit p47phox, which includes the tandem SH3 domains (N-SH3 and C-SH3). In active phagocytes, p47phox forms a stable complex with the cytoplasmic region of membrane subunit p22phox that forms a left-handed polyproline type-II (PPII) helix conformation. In this report, we have analyzed the conformational changes of p47phox-p22phox complexes of wild-type and three mutants, which have been detected in CGD patients, using molecular dynamics simulations. We have found that in the wild-type, two basal planes of PPII prism in cytoplasmic region of p22phox interacted with N-SH3 and C-SH3. In contrast, in the modeled mutants, the residue at the ape of PPII helix, which interacts simultaneously with both of the tandem SH3 domains in the wild-type, moved toward C-SH3. Furthermore, interaction energies of the cytoplasmic region of p22phox with C-SH3 tend to decrease in these mutants. All these findings led us to conclude that interactions between N-SH3 of p47phox and PPII helix, which is formed by cytoplasmic region of p22phox, may play a significant role in the activation of the NADPH oxidase.     

Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes

Here, the comparisons of performance of nine consensus scoring strategies, in which multiple scoring functions were used simultaneously to evaluate candidate structures for a protein-ligand complex, in combination with nine scoring functions (FlexX score, GOLD score, PMF score, DOCK score, ChemScore, DrugScore, PLP, ScreenScore, and X-Score), were carried out. The systematic naming of consensus scoring strategies was also proposed. Our results demonstrate that choosing the most appropriate type of consensus score is essential for model selection in computational docking; although the vote-by-number strategy was an effective selection method, the number-by-number and rank-by-number strategies were more appropriate when computational tractability was taken into account. By incorporating these consensus scores into the FlexX program, reasonable complex models can be obtained more efficiently than those selected by independent FlexX scores. These strategies might also improve the scoring of other docking programs, and more-effective structure-based drug design should result from these improvements.     

Statistical nonstationarity of the composition of styrene with methyl methacrylate in the cooligomer

It was found that the composition of cooligomer produced in the styrene(A)–methyl methacrylate(B)–CCl₄(S) system deviates from the statistical steady-state composition predicted from the Mayo-Lewis equation on the low molecular weight side when the molar ratio of [A]/[B] is large. When the molar ratio of [A]/[B] is small, however, it is not obvious whether or not this phenomenon is observed, because the cooligomer of low molecular weight cannot be obtained easily since the chain transfer constant of the poly(methyl methacrylate) radical to CCl₄ is very small in comparison, with that of the polystyryl radical. This behavior is shown to be attributable mainly to the preferential consumption of styrene monomer in the initiation step, based on the structure of the cooligomer, as inferred from the mechanism of the initiation, transfer, and termination, and the stochastic approach in which the cooligomerization process is regarded as a Markov process.     

Multi-electron transfer processes for molecular conversions

Multi-electron transfer plays an important role in many chemical reactions. A collection of examples, both of metal complexes that exhibit one-step, multi-electron transfer process, and of chemical reactions based on a multi-electron transfer system, is presented. Emphasis is placed on the role of multi-electron transfer process in a sense that some molecular conversion systems such as reduction of O₂ and oxidation of H₂O become feasible through multi-electron transfer. As an important example of molecular conversion, oxidative polymerization of sulfur-containing compounds through two-electron transfer, is also reviewed.     

Synthesis of poly(sulfonium cation) as an alkylating reagent

Methyl 4-phenylthiophenyl sulfoxide is polymerized to poly(methyl-4-phenylthiophenylsulfonium) in poly(phosphoric acid) with a yield higher than 90%. The demethylation of poly(sufonium cation) is examined to control the composition ratio of the thiophenylene unit in the polycation. The polycation is soluble in common solvents due to the alternative structure of phenylene sufide and phenylenesulfonium cation and is easily converted to poly(phenylene sulfide) through the demethylation with a nucleophile. The poly(sulfonium cation) can be applicable as an alkylating agent for phenol, aniline and benzoic acid to the corresponding to anisole, N-methyl aniline, N,N-dimethyl aniline and benzoic methyl ester, respectively, with high conversion through the demethylation. These products can be isolated without a complicated purification because poly(phenylene sulfide) is precipitated in the mixture as the side product due to the poor solvent solubility.     

Role of polymer ligands in the oxygenation of metal chlorophyllins

In order to obtain information about the characteristics of polymer-(metal chlorophyllins), their redox and oxygenation reactions were studied. Complexes composed of metal chlorophyllins (MChn) and partially quaternized poly(4-vinylpyridine) (QPVP) exhibited an increased stability due to electrostatic interaction between polymer cation and carboxylate anions of side groups in the MChn. The reduction of these polymer complexes by S₂O₄^2- occurred easily with an decrease in their apparent reduction potentials. The resulting low-valence complexes had an ability to absorb molecular oxygen. The oxygenation of these polymer complexes was not completely reversible; however the rate of the irreversible reoxidation was less by a factor of 10¹⁰ for the polymeric complex than that for the monomeric MChn-pyridine complex. The stability of these oxygen complexes is discussed in relation to the hydrophobicity of QPVPs.