The role of the Zn(II) binding domain in the mechanism of E. coli DNA topoisomerase I

Background  

Escherichia coli DNA topoisomerase I binds three Zn(II) with three tetracysteine motifs which, together with the 14 kDa C-terminal region, form a 30 kDa DNA binding domain (ZD domain). The 67 kDa N-terminal domain (Top67) has the active site tyrosine for DNA cleavage but cannot relax negatively supercoiled DNA. We analyzed the role of the ZD domain in the enzyme mechanism.     

Nonnatural amino acid incorporation into the methionine 214 position of the metzincin <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> alkaline protease

Background  

The alkaline protease from Pseudomonas aeruginosa(AprA) is a member of the metzincin superfamily of metalloendoproteases. A key feature of these proteases is a conserved methionine-containing 1,4-tight β turn at the base of the active site zinc binding region.     

Phage display-derived inhibitor of the essential cell wall biosynthesis enzyme MurF

Background  

To develop antibacterial agents having novel modes of action against bacterial cell wall biosynthesis, we targeted the essential MurF enzyme of the antibiotic resistant pathogen Pseudomonas aeruginosa. MurF catalyzes the formation of a peptide bond between D-Alanyl-D-Alanine (D-Ala-D-Ala) and the cell wall precursor uridine 5'-diphosphoryl N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-diaminopimelic acid (UDP-MurNAc-Ala-Glu-meso-A2pm) with the concomitant hydrolysis of ATP to ADP and inorganic phosphate, yielding UDP-N-acetylmuramyl-pentapeptide. As MurF acts on a dipeptide, we exploited a phage display approach to identify peptide ligands having high binding affinities for the enzyme.     

Design of new secreted phospholipase A<Subscript>2</Subscript> inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor

Docking calculations that allow the estimation of the binding energy of small ligands in the GIIA sPLA₂ active site were used in a structure-based design protocol. Four GIIA sPLA₂ inhibitors co-crystallised with the enzyme, were used for examining the enzyme active site and for testing the FlexX in SYBYL 6.8 molecular docking program to reproduce the crystallographic experimental data. The FPL67047XX inhibitor was chosen as a prototype structure for applying free energy perturbation (FEP) studies. Structural modifications of the initial structure of the FPL67047XX inhibitor (IC₅₀ 0.013 μM) were performed in an effort to optimise the interactions in the GIIA sPLA₂ active site. The structural modifications were based on: (1) the exploration of absolute configuration (i.e. comparison of the binding score of (R)- and (S)-enantiomers); (2) bioisosterism (i.e. replacement of the carboxylate group with the bioisosteric sulphonate and phosphonate groups); (3) insertion of substituents that fit better in the active site. The generated new structures exhibited higher binding energy. Such structures may spark off the interest of medicinal chemists for synthesizing potentially more active GIIA sPLA₂ inhibitors.     

PocketPicker: analysis of ligand binding-sites with shape descriptors

Background  

Identification and evaluation of surface binding-pockets and occluded cavities are initial steps in protein structure-based drug design. Characterizing the active site's shape as well as the distribution of surrounding residues plays an important role for a variety of applications such as automated ligand docking or in situ modeling. Comparing the shape similarity of binding site geometries of related proteins provides further insights into the mechanisms of ligand binding.     

Orthophosphate binding at the dimer interface of <Emphasis Type="Italic">Corynebacterium callunae</Emphasis> starch phosphorylase: mutational analysis of its role for activity and stability of the enzyme

Background  

Orthophosphate recognition at allosteric binding sites is a key feature for the regulation of enzyme activity in mammalian glycogen phosphorylases. Protein residues co-ordinating orthophosphate in three binding sites distributed across the dimer interface of a non-regulated bacterial starch phosphorylase (from Corynebacterium callunae) were individually replaced by Ala to interrogate their unknown function for activity and stability of this enzyme.     

Study of the conjugation reaction between bovine serum albumin and gentamicin with Ponceau S as fluorescence probe

Abstract  

Ponceau S (PS) can quench the fluorescence of bovine serum albumin (BSA) in aqueous solution of pH 7.40. The static fluorescence-quenching process between BSA and PS was confirmed and the binding constant, the number of binding sites, and thermodynamic data for the interaction between BSA and PS were obtained. The results showed that the number of binding sites was 1 and that electrostatic attraction was important in the binding of BSA to PS. On the basis of the theory of F?rster resonance energy transfer, the binding distance (r < 7 nm) between PS and BSA was obtained. Site marker competitive experiments indicated that binding of PS to BSA primarily occurred in sub-domain IIA (site I). There was no obvious fluorescence intensity change on combining BSA and gentamicin (GM), so the conjugation reaction between BSA and GM cannot be studied by spectroscopy. It was observed that when GM was added to the BSA–PS system, the relative fluorescence intensity of the system recovered gradually with increasing concentration of GM, which showed there was a conjugation reaction between GM and BSA and that binding of GM to BSA primarily occurred in sub-domain IIA (site I).     

Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model

Abstract  

A series of 27 benzamidine inhibitors covering a wide range of biological activity and chemical diversity was analysed to derive a Linear Interaction Energy in Continuum Electrostatics (LIECE) model for analysing the thrombin inhibitory activity. The main interactions occurring at the thrombin binding site and the preferred binding conformations of inhibitors were explicitly biased by including into the LIECE model 10 compounds extracted from X-ray solved thrombin-inhibitor complexes available from the Protein Data Bank (PDB). Supported by a robust statistics (r ² = 0.698; q ² = 0.662), the LIECE model was successful in predicting the inhibitory activity for about 76% of compounds (r _ext² ≥ 0.600) from a larger external test set encompassing 88 known thrombin inhibitors and, more importantly, in retrieving, at high sensitivity and with better performance than docking and shape-based methods, active compounds from a thrombin combinatorial library of 10240 mimetic chemical products. The herein proposed LIECE model has the potential for successfully driving the design of novel thrombin inhibitors with benzamidine and/or benzamidine-like chemical structure.     

Probing stereoselective inhibition of the acyl binding site of cholesterol esterase with four diastereomers of 2'-<Emphasis Type="Italic">N</Emphasis>-α-methylbenzylcarbamyl-1, 1'-bi-2-naphthol

Background  

Recently there has been increased interest in pancreatic cholesterol esterase due to correlation between enzymatic activity in vivo and absorption of dietary cholesterol. Cholesterol esterase plays a role in digestive lipid absorption in the upper intestinal tract, though its role in cholesterol absorption in particular is controversial. Serine lipases, acetylcholinesterase, butyrylcholinesterase, and cholesterol esterase belong to a large family of proteins called the α/β-hydrolase fold, and they share the same catalytic machinery as serine proteases in that they have an active site serine residue which, with a histidine and an aspartic or glutamic acid, forms a catalytic triad. The aim of this work is to study the stereoselectivity of the acyl chain binding site of the enzyme for four diastereomers of an inhibitor.     

Small-molecule and mutational analysis of allosteric Eg5 inhibition by monastrol

Background  

A recent crystal structure of monastrol in a ternary complex with the kinesin Eg5 motor domain highlights a novel, induced-fit drug binding site at atomic resolution. Mutational obliteration of the monastrol binding site results in a monastrol-resistant, but otherwise catalytically active Eg5 motor domain. However, considering the conformational changes at this site, it is unclear what specific interactions stabilize the interaction between monastrol and the Eg5 motor domain.     

Characterization of <Emphasis Type="Italic">Bacillus anthracis</Emphasis> arginase: effects of pH,temperature, and cell viability on metal preference

Background  

Arginase (RocF) hydrolyzes L-arginine to L-ornithine and urea. While previously characterized arginases have an alkaline pH optimum and require activation with manganese, arginase from Helicobacter pylori is optimally active with cobalt at pH 6. The arginase from Bacillus anthracis is not well characterized; therefore, this arginase was investigated by a variety of strategies and the enzyme was purified.     

Synthesis and binding properties of guanidinium biscarboxylates

Abstract  

The ammonium ion binding site of the enzyme glutaminase HisF inspired us to design guanidinium biscarboxylates as potential self-organized ionophores in molecular recognition. The syntheses of the title compounds based on aliphatic and aromatic building blocks, along with a general method for the preparation of δ-aminoethoxyacetic acids, are presented in this work. Investigation of the binding properties of the title compounds in dimethyl sulfoxide (DMSO) and methanol solution revealed no ammonium ion affinity, but interaction of the guanidinium moiety with acetate ions.     

An Approach for Visualization of the Active Site of Enzymes with Unknown Three-Dimensional Structures

Abstract

A new approach for virtual characterization of the active site structure of enzymes with unknown three-dimensional (3D) structure has been proposed. It includes analysis of data on enzyme interaction with reversible competitive inhibitors, their 3D structures and moulding of the substrate-binding region. The superposition of ligands in biologically active conformations allows to determine the shape and dimension of the active site cavity accommodating these compounds. Monoamine oxidase A (MAO-A), a “typical” enzyme with unknown spatial organisation, was used to test this method. The correctness of such approach was validated by the analysis of HIV protease interaction with its inhibitors using 3D structures of their complexes. Mould of the substrate/inhibitor binding site can be used for the visualization of this binding site and for searching new ligands in molecular databases.     

Kinetics, mechanism, and DFT calculations of thermal degradation of a Zn(II) complex with N-benzyloxycarbonylglycinato ligands

Abstract  

A Zn(II) complex with N-benzyloxycarbonylglycinato ligands was studied by non-isothermal methods, in particular Kissinger–Akahira–Sunose’s method, and further analysis of these results was performed by Vyazovkin’s algorithm and an artificial compensation effect. Density functional theory calculations of thermodynamic quantities were performed, and results obtained by both methods are consistent, thus clarifying the mechanism of this very interesting multi-step degradation.     

The mononuclear metal center of type-I dihydroorotase from aquifex aeolicus

Background

Dihydroorotase (DHO) is a zinc metalloenzyme, although the number of active site zinc ions has been controversial. E. coli DHO was initially thought to have a mononuclear metal center, but the subsequent X-ray structure clearly showed two zinc ions, α and β, at the catalytic site. Aquifex aeolicus DHO, is a dodecamer comprised of six DHO and six aspartate transcarbamoylase (ATC) subunits. The isolated DHO monomer, which lacks catalytic activity, has an intact α-site and conserved β-site ligands, but the geometry of the second metal binding site is completely disrupted. However, the putative β-site is restored when the complex with ATC is formed and DHO activity is regained. Nevertheless, the X-ray structure of the complex revealed a single zinc ion at the active site. The structure of DHO from the pathogenic organism, S. aureus showed that it also has a single active site metal ion.

Results

Zinc analysis showed that the enzyme has one zinc/DHO subunit and the addition of excess metal ion did not stimulate catalytic activity, nor alter the kinetic parameters. The metal free apoenzyme was inactive, but the full activity was restored upon the addition of one equivalent of Zn²⁺ or Co²⁺. Moreover, deletion of the β-site by replacing the His180 and His232 with alanine had no effect on catalysis in the presence or absence of excess zinc. The 2.2 Å structure of the double mutant confirmed that the β-site was eliminated but that the active site remained otherwise intact.

Conclusions

Thus, kinetically competent A. aeolicus DHO has a mononuclear metal center. In contrast, elimination of the putative second metal binding site in amidohydrolyases with a binuclear metal center, resulted in the abolition of catalytic activity. The number of active site metal ions may be a consideration in the design of inhibitors that selectively target either the mononuclear or binuclear enzymes.

     

Synthesis, Crystal Structure, Photophysical Properties, and DFT Calculations of a Bis(tetrathia-calix[4]arene) Tetracadmium Complex

Abstract  

Thiacalix[4]arenes are a unique family of polydentate ligands that offer a combination of four soft sulfur atoms together with four hard phenol oxygen atoms for binding to metal ions. In this study, the tetranuclear cadmium (II) complex Cd₄^II(tca)₂·1.5CH₂Cl₂ (tca⁴⁻ = tetra-anionic p-tert-butylthiacalix[4]arene) (1) was synthesized by reaction of a deprotonated p-tert-butylthiacalix[4]arene and various Cd^II salts. The structure of 1 was established by single crystal X-ray diffraction analysis. The neutral complex 1 contains a square arrangement of four cadmium (II) ions sandwiched between two tca⁴⁻ ligands that have a ‘cone’ conformation similar to that of the free ligand. The absorption and emission properties of the free ligand H₄tca and complex 1 have been recorded and explained by DFT calculations of the molecular orbitals and electronic transitions between them.     

Effects of synthetic food colorants on the interaction between norfloxacin and bovine serum albumin by fluorescence spectroscopy

Abstract  

The effects of synthetic food colorants like tartrazine, sunset yellow, and erythrosine on the binding reaction between norfloxacin and bovine serum albumin (BSA) were investigated by fluorescence spectroscopy. Results showed that food colorants bound to BSA by van der Waals force and hydrogen bonding formation and norfloxacin by electrostatic interaction. In addition, marker competitive experiments suggested that the primary binding site for both norfloxacin and food colorants was located at subdomain IIA of BSA (site I). The presence of food colorants could alter the binding constant and distance between BSA and norfloxacin. The effects of colorants were dependent on their concentrations and binding affinity to BSA. The interaction could result in the change of the free, biologically active fraction of norfloxacin in blood.     

Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificity

Background  

Escherichia coli MutY (EcMutY) reduces mutagenesis by removing adenines paired with guanines or 7,8-dihydro-8-oxo-guanines (8-oxoG). V45 and Q182 of EcMutY are considered to be the key determinants of adenine specificity. Both residues are spatially close to each other in the active site and are conserved in MutY family proteins but not in Methanobacterium thermoautotrophicum Mig.MthI T/G mismatch DNA glycosylase (A50 and L187 at the corresponding respective positions).     

Molecular insights into the binding affinity and specificity of the hemagglutinin cleavage loop from four highly pathogenic H5N1 isolates towards the proprotein convertase furin

Abstract  

The furin (FR) complex with each of four different sequences of hemagglutinin from the highly pathogenic H5N1 strains (HPH5), which were identified during the 2004–2010 influenza outbreaks in Thailand, were evaluated by molecular dynamics simulations, so as to compare the specificity and recognition of the enzyme–substrate binding. Relative to the conventional HPH5 inserted (H5Sq1, RERRRKKR), the S5-R or S6-R arginine residue is replaced by the smaller lysine in the H5Sq2 (RERKRKKR) and H5Sq3 (REKRRKKR) strains, respectively, whereas the S3-K lysine residue is deleted in H5Sq4 (RERRR_KR). The molecular dynamics results of the intermolecular interactions, in terms of hydrogen bonds and per-residue decomposition energy, between the substrate and furin revealed that the deletion of the positively charged amino acid at the S3 position in H5Sq4 leads to a notably weaker binding and specificity with the furin active site compared with that of FR–H5Sq1. A slight change in the substrate binding was found in the FR–H5Sq2 and FR–H5Sq3 complexes as a result of the replacement of the arginine with the shorter side-chained lysine (same positive charge). Altogether, the predicted binding free energy of the enzyme–substrate complexes was found to be in the following order: FR–H5Sq1 < FR–H5Sq2 ~ FR–H5Sq3 ≪ FR–H5Sq4.