Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase

The interactions between biologically important enzymes and drugs are of great interest. In order to address some aspects of these interactions we have initiated a program to investigate enzymedrug interactions. Specifically, the interactions between one of the isozymes of carbonic anhydrase and a family of drugs known as sulfonamides have been studied using computational methods. In particular the electrostatic free energy of binding of carbonic anhydrase II with acetazolamide, methazolamide,p-chlorobenzenesulfonamide,p-aminobenzenesulfonamide and three new compounds (MK1, MK2, and MK3) has been computed using finite-difference Poisson-Boltzmann (FDPB) [1] method and the semimacroscopic version [2, 3] of the protein dipole Langevin dipole (PDLD) method [4]. Both methods, FDPB and PDLD, give similar results for the electrostatic free energy of binding even though different charges and different treatments were used for the protein. The calculated electrostatic binding free energies are in reasonable agreement with the experimental data. The potential and the limitation of electrostatic models for studies of binding energies are discussed.     

Mass spectrometric behaviour of carboxylated polyethylene glycols and carboxylated octylphenol ethoxylates

Mass spectrometric behaviour of mono- and di-carboxylated polyethylene glycols (PEGCs and CPEGCs) and carboxylated octylphenol ethoxylates (OPECs) are discussed. The tendency for ionisation (deprotonation, protonation and cationisation by alkali metal cations) of carboxylated PEGs was compared with that of non-carboxylated correspondents by using both secondary ion mass spectrometry (SIMS) and electrospray ionisation (ESI). The fragmentation of the PEGCs and CPEGCs is discussed and also compared with their neutral correspondents, PEGs. The B/E mass spectra were recorded, using secondary ion mass spectrometry as a method for generation, for deprotonated and protonated molecules and molecules cationised by alkali metal cations. The fragmentation behaviour of PEGs is found to be different from that of CPEGCs, The presence of carboxylic groups may be confirmed not only by the determination of molecular weights of the ethoxylates studied, but also on the basis of the fragment ions formed. The metastable decomposition of the [OPEC-H](-) ions proceed through the cleavage of the bond between the octylphenol moiety and the ethoxylene chain leading to the octylphenoxy anions. It permits determination of the mass of the hydrophobic moiety of the studied carboxylated alkylphenol ethoxylate. ESI mass spectra recorded in the negative ion mode were found to be more suitable for the determination of the average molecular weight of carboxylated ethoxylates than SI mass spectra.     

Orthorhombic polymorphs of two trans‐4‐aminoazoxybenzenes

The two isomeric compounds 4‐amino‐ONN‐azoxy­benzene [or 1‐(4‐amino­phenyl)‐2‐phenyl­diazene 2‐oxide], i.e. the α isomer, and 4‐amino‐NNO‐azoxy­benzene [or 2‐(4‐amino­phenyl)‐1‐phenyl­diazene 2‐oxide], i.e. the β isomer, both C₁₂H₁₁N₃O, crystallized from a polar solvent in orthorhombic space groups, and their crystal and molecular structures have been determined using X‐ray diffraction. There are no significant differences in the bond lengths and valence angles in the two isomers, in comparison with their monoclinic polymorphs. However, the conformations of the mol­ecules are different due to rotation along the Ar—N bonds. In the α isomer, the benzene rings are twisted by 31.5 (2) and 14.4 (2)° towards the plane of the azoxy group; the torsion angles along the Ar—N bond in the β isomer are 24.3 (3) and 23.5 (3)°. Quantum‐mechanical calculations indicate that planar conformations are energetically favourable for both isomers. The N—H?O hydrogen bonds observed in both networks may be responsible for the deformation of these flexible mol­ecules.     

Origins of the activity of PAL and LAP enzyme inhibitors: toward ab initio binding affinity prediction

Interaction energies of phenylalanine ammonia-lyase (PAL) active site residues with a series of PAL inhibitors have been partitioned into electrostatic, exchange, delocalization, and correlation components and compared with analogous results obtained previously for leucine aminopeptidase (LAP). In the latter metalloenzyme, either of the two charged residues controls entirely relative inhibitor binding energies, while at least four residues are required to determine ligand relative stabilization in neutral PAL. Significant correlation with experimental inhibitory activity was found between the stabilization energy at gradually decreasing levels of theory (MP2, SCF) down to the first-order Heitler-London term. Contrary to the LAP case, where the electrostatic term was sufficient to reproduce experimentally observed trends, in the case of PAL, exchange repulsion effects also have to be considered. Computational protocol presented herein constitutes a promising way to incorporate the first principle calculation's accuracy into the process of rational binding affinity prediction, revealing the physical nature of the interactions, where successive approximations can be introduced in a systematic and justifiable manner.     

Can triorganoboroxins exist in a “monomeric” R---B=O form? MNDO calculations and ebulliometric molecular weight determination

MNDO calculations were made for triethylboroxin (EtBO)₃ and triphenylboroxin (PhBO)₃ using both X-ray determined and optimized geometry of these molecules. The results were compared with hypothetical “monomeric” molecules R---B=O. Calculated energies of trimerization are about −200 kJ mol⁻¹ for both compounds and confirm the much higher stability of the “trimer”. Ebulliometric determination of molecular weight of triphenylboroxin in 2-pentanone confirms its trimeric character.     

Dispersive solid-phase extraction for the determination of sulfonamides in chicken muscle by liquid chromatography

A new, fast and low-cost sample preparation for the determination of sulfonamide (SA) residues in chicken muscle by LC technique has been developed. The procedure involves single extraction of sample with acetonitrile, followed by a rapid clean-up and was called "dispersive solid-phase extraction" (dispersive SPE). Using dispersive SPE 25 mg of octadecyl sorbent was added to 1 ml of acetonitrile extract, mixed and centrifuged. The acetonitrile layer was evaporated and residue was dissolved in acetate buffer (pH 3.5). Analysed compounds were detected by fluorescence detector after pre-column derivatization with fluorescamine. The separation of analytes was performed with gradient elution with mobile phase methanol: 2% acetic acid and RP-LC analytical column. The whole procedure was evaluated for six sulfonamides (sulfadiazine, sulfamerazine, sulfamethazine, sulfametoxypirydazine, sulfametoxazole and sulfadimetoxine) according to the European Commission Decision 2002/657/EC. Specificity, decision limit (CCalpha), detection capacity (CCbeta), trueness and precision were determined during validation process. The dispersive SPE with octadecyl sorbent was found suitable for sample preparation before sulfonamide determination in chicken muscle. As it was found the most of endogenous matrix components were removed and the analytes were isolated from spiked samples with recoveries above 90%. The used analytical conditions allow to successively separate all the tested sulfonamides with the limit of detection at the level of 1-5 microg/kg. The method is simple, rapid and more effective than conventional methods.     

Discrete dynamical equations in Minkowski space

Discrete difference equations in Minkowski space are obtained and the discrete Minkowski force is shown to be a four-vector. A transformation from a discrete dynamical equation in Minkowski space to a Lorentz-invariant difference equation in one-dimensional space is given.     

Time-dependent quantum wave-packet description of the 1pi sigma* photochemistry of phenol

The photoinduced hydrogen elimination reaction in phenol via the conical intersections of the dissociative 1pi sigma* state with the 1pi pi* state and the electronic ground state has been investigated by time-dependent quantum wave-packet calculations. A model including three intersecting electronic potential-energy surfaces (S0, 1pi sigma*, and 1pi pi*) and two nuclear degrees of freedom (OH stretching and OH torsion) has been constructed on the basis of accurate ab initio multireference electronic-structure data. The electronic population transfer processes at the conical intersections, the branching ratio between the two dissociation channels, and their dependence on the initial vibrational levels have been investigated by photoexciting phenol from different vibrational levels of its ground electronic state. The nonadiabatic transitions between the excited states and the ground state occur on a time scale of a few tens of femtoseconds if the 1pi pi*-1pi sigma* conical intersection is directly accessible, which requires the excitation of at least one quantum of the OH stretching mode in the 1pi pi* state. It is shown that the node structure, which is imposed on the nuclear wave packet by the initial preparation as well as by the transition through the first conical intersection (1pi pi*-1pi sigma*), has a profound effect on the nonadiabatic dynamics at the second conical intersection (1pi sigma*-S0). These findings suggest that laser control of the photodissociation of phenol via IR mode-specific excitation of vibrational levels in the electronic ground state should be possible.     

Novel C60 Fullerenol-Gentamicin Conjugate–Physicochemical Characterization and Evaluation of Antibacterial and Cytotoxic Properties

This study aimed to develop, characterize, and evaluate antibacterial and cytotoxic properties of novel fullerene derivative composed of C₆₀ fullerenol and standard aminoglycoside antibiotic–gentamicin (C₆₀ fullerenol-gentamicin conjugate). The successful introduction of gentamicin to fullerenol was confirmed by X-ray photoelectron spectroscopy which together with thermogravimetric and spectroscopic analysis revealing the formula of the composition as C₆₀(OH)₁₂(GLYMO)₁₁(Gentamicin)_0.8. The dynamic light scattering (DLS) revealed that conjugate possessed ability to form agglomerates in water (size around 115 nm), while Zeta potential measurements demonstrated that such agglomerates possessed neutral character. In vitro biological assays indicated that obtained C₆₀ fullerenol-gentamicin conjugate possessed the same antibacterial activity as standard gentamicin against Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, and Escherichia coli, which proves that combination of fullerenol with gentamicin does not cause the loss of antibacterial activity of antibiotic. Moreover, cytotoxicity assessment demonstrated that obtained fullerenol-gentamicin derivative did not decrease viability of normal human fibroblasts (model eukaryotic cells) compared to control fibroblasts. Thus, taking into account all of the results, it can be stated that this research presents effective method to fabricate C₆₀ fullerenol-gentamicin conjugate and proves that such derivative possesses desired antibacterial properties without unfavorable cytotoxic effects towards eukaryotic cells in vitro. These promising preliminary results indicate that obtained C₆₀ fullerenol-gentamicin conjugate could have biomedical potential. It may be presumed that obtained fullerenol may be used as an effective carrier for antibiotic, and developed fullerenol-gentamicin conjugate may be apply locally (i.e., at the wound site). Moreover, in future we will evaluate possibility of its applications in inter alia tissue engineering, namely as a component of wound dressings and implantable biomaterials.     

Comparison of Physical Adsorption and Covalent Coupling Methods for Surface Density-Dependent Orientation of Antibody on Silicon

The orientation of antibodies, employed as capture molecules on biosensors, determines biorecognition efficiency and bioassay performance. In a previous publication we demonstrated for antibodies attached covalently to silicon that an increase in their surface amount Γ, evaluated with ellipsometry, induces changes in their orientation, which is traced directly using Time-of-Flight Secondary Ion Mass Spectroscopy combined with Principal Component Analysis. Here, we extend the above studies to antibodies adsorbed physically on a 3-aminopropyltriethoxysilane (APTES) monolayer. Antibodies physisorbed on APTES (0 ≤ Γ ≤ 3.5 mg/m²) reveal the Γ ranges for flat-on, side-on, and vertical orientation consistent with random molecular packing. The relation between orientation and Γ is juxtaposed for silicon functionalized with APTES, APTES modified with glutaraldehyde (APTES/GA) and N-hydroxysuccinimide-silane (NHS-silane). Antibody reorientation occurs at lower Γ values when physisorption (APTES) is involved rather than chemisorption (APTES/GA, NHS-silane). At high Γ values, comparable proportions of molecules adapting head-on and tail-on vertical alignment are concluded for APTES and the NHS-silane monolayer, and they are related to intermolecular dipole–dipole interactions. Intermolecular forces seem to be less decisive than covalent binding for antibodies on the APTES/GA surface, with dominant head-on orientation. Independently, the impact of glutaraldehyde activation of APTES on vertical orientation is confirmed by separate TOF-SIMS measurements.