The role of radicals in enzymatic processes

Research on the mechanism of action of coenzyme B12, adenosylcobalamin, as a graduate student introduced the author to the field of organic free radicals in enzymology. Twenty years later, related work on S-adenosylmethionine (SAM) as a "poor man's coenzyme B12" was initiated in a detailed analysis of the mechanism of action of lysine 2,3-aminomutase (LAM). The interconversion of L-lysine and L-beta-lysine is catalyzed by LAM, which requires SAM, pyridoxal-5'-phosphate (PLP), and a [4Fe-4S] cluster as coenzymes. The mechanism of this reaction has been delineated as a radical isomerization, in which radical formation is initiated by the [4Fe-4S]-dependent cleavage of the SAM into methionine and the 5'-deoxyadenosyl radical. The mechanism of this process is discussed, together with the role of this radical in hydrogen abstraction from lysine to initiate the substrate radical isomerization. The chemistry underlying the functions of SAM, PLP, and [4Fe-4S] in the action of LAM is novel in all respects, except for the formation of a lysine-PLP aldimine at the active site. Of the four free radicals in the mechanism, three have been characterized by EPR spectroscopy. In the suicide inactivation of adenosylcobalamin-dependent dioldehydrase (DDH) by glycolaldehyde, the formation of cob(II)alamin and 5'-deoxyadenosine is accompanied by the conversion of glycolaldehyde to cis-ethanesemidione radical at the active site. The cis-ethanesemidione radical has been characterized by EPR spectroscopy. Its exceptional stability at the active site is the basis for the inactivation of DDH by glycolaldehyde.     

A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum

Pyridoxal 5′-phosphate (PLP) is the active form of vitamin B6, but it is highly reactive and poisonous in its free form. YggS is a PLP-binding protein found in bacteria and humans that mediates PLP homeostasis by delivering PLP to target enzymes or by performing a protective function. Several biochemical and structural studies of YggS have been reported, but the mechanism by which YggS recognizes PLP has not been fully elucidated. Here, we report a functional and structural analysis of YggS from Fusobacterium nucleatum (FnYggS). The PLP molecule could bind to native FnYggS, but no PLP binding was observed for selenomethionine (SeMet)-derivatized FnYggS. The crystal structure of FnYggS showed a type III TIM barrel fold, exhibiting structural homology with several other PLP-dependent enzymes. Although FnYggS exhibited low (<35%) amino acid sequence similarity with previously studied YggS proteins, its overall structure and PLP-binding site were highly conserved. In the PLP-binding site of FnYggS, the sulfate ion was coordinated by the conserved residues Ser201, Gly218, and Thr219, which were positioned to provide the binding moiety for the phosphate group of PLP. The mutagenesis study showed that the conserved Ser201 residue in FnYggS was the key residue for PLP binding. These results will expand the knowledge of the molecular properties and function of the YggS family.     

Anticancer activity of novel 3-azaxanthenes

Novel 3-azaxanthenes have been synthesized via acid-catalyzed one-pot Friedel–Crafts reaction of pyridoxal/pyridoxal-5'-phosphate with naphthols followed by dehydration of the intermediate bis(2-hydroxyaryl)-(pyridin-4-yl)methane derivatives. The cytotoxicity of the obtained 3-azaxanthenes against M-HeLa and HuTu-80 tumor cell lines is comparable to that of tamoxifen, whereas the cytotoxicity against normal cell line is absent in the tested concentrations range, which makes this class of compounds interesting for further studies.     

Phosphorylation of pyridoxal azomethines. Synthesis of phosphorus containing azomethines and furopyridines

New O-phosphorylated pyridoxal derivatives have been synthesized through the reaction of azomethines with Р^V acid chlorides. 2-Chloro-2-thioxo-5,5-dimethyl-1,3,2-dioxaphosphinanes and diethylchlorothiophosphate have been employed as phosphorylating agents. Regardless of the nature of the phosphorylating agent, the reaction is regioselective at phenolic hydroxyl group. The structure of final products is determined by the nature of the substituent at the nitrogen atom. If R is alkyl or cycloalkyl group, the products of the reaction represent phosphorylated pyridoxal imines, whereas phosphorylated furopyridines are formed in the case R is aryl substituent.     

Bioactive Penta-Coordinated Diorganotin(Iv) Complexes of Pyridoxalimine Schiff Bases

Abstract

Diorganotin(IV) complexes of an extended system derived from the condensation of pyridoxal hydrochloride with 2-amino phenol (H₂L¹), 2-amino-4-methyl phenol (H₂L²), 2-amino-4-chloro phenol (H₂L³), 2-amino-4-nitro phenol (H₂L⁴), 1-amino-2-naphthol hydrochloride (H₂L⁵) have been synthesized by the reaction of dichlorodiorganotin(IV) in a 1:1 molar ratio with these ligands. Spectral studies (IR, ¹H, ¹³C, ¹¹⁹Sn NMR) along with physical data evidenced the formation of penta-coordinated species with the ligands acting as tridentate (ONO) with oxygen occupying the axial positions, and nitrogen at one of the equatorial positions. The ligands and their organotin complexes have been evaluated for antimicrobial activity against phytopathogenic fungi Candida albicans and Aspergillus niger at 25 ± 1 °C and bacteria Bacillus subtilis, Escherichia coli, and Staphylococcus aureus at 37 ± 1 °C. The activities of the ligands have been enhanced on complexation and the results indicate that they exhibit significant antimicrobial properties.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.     

Thermodynamic and kinetic effects of Lewis acid complexation on a Schiff base present in two tautomeric forms

The effect of complexation with Lewis acids on the tautomeric equilibrium of a derivative of pyridoxal has been explored using density functional theory. Three complexation sites (pyridine nitrogen, aromatic ring, and carbonyl group) have been considered. The tautomeric equilibrium can be modulated with the formation of complexes at the different sites. The changes observed in the geometric, energetic and electronic properties of the tautomers and transition states have been analyzed. Relationships have been found between those parameters, including a relationship between energetic and geometric parameters in agreement with the Hammond postulate. Copyright © 2010 John Wiley & Sons, Ltd.     

Interactions of native and modified cyclodextrins with some B-vitamins

Interactions of native and modified α- and β-cyclodextrins with nicotinic acid, pyridoxine and pyridoxal were studied by isothermal titration calorimetry, solution calorimetry, and ¹H NMR spectroscopy at 298.15 K and pH 6.8. Weak 1:1 complex formation was found only between α-cyclodextrin and nicotinic acid. The stability constant and corresponding thermodynamic parameters of complex formation (Δ_c G, Δ_c H and Δ_c S) were calculated using the calorimetric data. The ¹H NMR data indicate the shallow insertion of the carboxylic group of the nicotinic acid molecule into α-CD cavity. For all other compounds the weak interactions, not accompanied by complex formation, were characterized by the enthalpic virial coefficients calculated on the basis of McMillan-Mayer approach. The obtained thermodynamic parameters were analyzed in the terms of influence of the solutes’ structure on the selectivity of intermolecular host-guest interactions.     

Complexation between nickel(II), cobalt(III) and hydrazones derived from pyridoxal 5′-phosphate and hydrazides of 2-,3-,4-pyridinecarboxylic acids in aqueous solution

abstract

The present work reports on stoichiometry, apparent stability constants of biologically relevant complexes of nickel(II), cobalt(III) with hydrazones derived from pyridoxal 5′-phosphate and hydrazides of 2-,3-,4-pyridinecarboxylic acids at pH 7.4, T?=?25.0?°C, I?=?0.25 determined using UV-Vis spectroscopy. The thermodynamic constants of some complexes formation (NiL, NiL₂, NiL₂H) were estimated. Cobalt(II) ion was found to be oxidized to cobalt(III). Co(II) and Co(III) form low-spin state complexes. Hydrazones binding ability (pL_0.5) in the medium mimicking biological ones towards Ni(II) and Co(III) was estimated.