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Biomedical subjects

A Leś

Publications and source records attributed to A Leś.

12 recordsLinked to original sources
PubMed1998

Crystal structures of 5-fluoro-dUrd and its 2 and/or 4-thio analogues: models of substituted dUMP pyrimidine ring interacting with thymidylate synthase.

In order to understand the influence on thymidylate synthase interactions with dUMP analogues of the pyrimidine ring 2- and/or 4-thio, and 5-fluoro substitutions, X-ray diffractions by crystals of 5-fluoro-dUrd and its 2- and 4-thio, and 2,4-dithio analogues were measured, the four structures solved and refined. The following conclusions were suggested by results of comparative analyses of structural parameters (bond lengths, valence angles), followed by theoretical considerations based on calculated resonance structure distributions and aromaticity indices of the uracil, thiouracil, fluorouracil and fluorothiouracil rings. The effect of 4-thio substitution of FdUMP, altering specificity of inactivation of thymidylate synthases from various sources, is probably due to weaker proton acceptor power of the 4-thio substituent and increasing acidity (enhanced proton-donor power) of the N(3)-H moiety, resulting in an impaired fitness into the network of hydrogen bonds in the enzyme active center cleft. 2,4-Dithio substitution results in (i) impaired pyrimidine ring recognition by the enzyme active center, due to the 4-thio substituent (ii) increased pyrimidine ring aromaticity in dUMP, leading to resistance of C(6) to nucleophilic attack by the enzyme active center cysteine and (iii) altered planarity of the pyrimidine ring and deflections, with respect to the ring plane, of substituents at C(2), C(4) and C(5). 5-Fluoro substitution apparently activates the pyrimidine ring towards the interaction with thymidylate synthase by producing local strain, which results in an increased reactivity as predicted by the Walsh-Bent rule.

Binding Sites↗
PubMed1998

DerivFit: a program for rate equation parameter fitting using derivatives.

A C program for fitting parameters in enzymatic rate equations is presented. The DerivFit program employs the reaction scheme in the form of ordinary differential equations (ODEs). The kinetic parameters are fitted to the experimental data by minimizing the sum of squared deviations of experimental points from theoretically predicted progress curves. In the minimization process we use the Gradient, Newton, and Marquardt algorithms. The gradients are calculated explicitly by solving a set of additional ODEs that are automatically attached by the program, taking advantage of a general formulation of the basic ODEs that determine the reaction's time course. The program is applied to simple enzymatic systems including slow tight-binding inhibition.

Algorithms↗
PubMed1998

13C CP (cross-polarization) MAS (magic angle spinning) NMR and GIAO-CHF calculations of buspirone analogues. Part 1. 3a,4,7,7a-Tetrahydro-2-[4-[4-(2-quinolinyl)-1-piperazinyl]butyl ]-4,7-ethane-1H-isoindole-1,3(2H)-dione hydrochloride and hydrobromide.

13C CP (cross-polarization) MAS (magic angle spinning) solid state NMR spectra of buspirone analogue 3a,4,7,7a-tetrahydro-2-[4-[4-(2-quinolinyl)-1-piperazinyl]butyl]-4,7-eth ane-1H-isoindole-1,3(2H)-dione were recorded. In the spectra of hydrochloride and hydrobromide, two sets of signals appeared, in agreement with single crystal X-ray diffraction data indicating that in each of the salts two independent cations were present in the crystal unit. The largest shielding differences of 3.2-4.6 ppm between two sets of signals were found for quinoline aromatic carbons C3 and C2. Ab initio calculations of the carbon and nitrogen shielding constants were performed with the use of the GIAO-CHF method for structural fragments: N-butylsuccinimide, quinoline-(N-methyl) piperazine hydrochloride and hydrobromide. Linear correlations between theoretical and solid state results were obtained, thus enabling a reasonable assignment of carbon resonances of the conformations present in the solid state. Due to the fast dynamics in solution, the carbon chemical shifts corresponded to the averaged values of the forms present in the solid state.

Anti-Anxiety Agents↗
PubMed1998

Modeling of reaction steps relevant to deoxyuridylate (dUMP) enzymatic methylation and thymidylate synthase mechanism-based inhibition.

Theoretical quantum mechanical ab initio Hartree-Fock calculations on molecular systems, modeling processes related to the specificity of thymidylate synthase inactivation are reported. We considered several steps of the methylation of the substrate dUMP and 4- or 5-mono- and 4,5-bisubstituted dUMP analogs, as well. The following reactions were modeled: the cysteine residue (Cys198 in the L.casei enzyme) nucleophilic attack on the substrate and the substrate C(5)-H proton abstraction. The substrate was modeled by the 1-methyluracil molecule and its structural analogs. The cysteine Cys198 residue was modeled by the methylmercaptane molecule. The substrate-enzyme binary complex was modeled by the 1-methyl-5,6-dihydro-6-thiomethyl-uracil (P1) molecule. The present theoretical calculations suggest that the cysteine nucleophilic attack on the substrate may result in the SH-group addition to the pyrimidine C(5)=C(6) bond in the course of a weakly exothermic reaction. The formerly presumed enolate carbanion appeared to be weakly stable or unstable and it can readily split into the thiol and pyrimidine residues. The s2-thio- (P2) and s2,4-dithio- (P3) substrate analogs should form stable thiolate anions after cysteine residue attachment to the C(6) position of the pyrimidine ring. Studies of the deformed P1 molecule interacting with a water molecule bound to the pyrimidine C(4)=O carbonyl residue allow a suggestion that this water molecule may be directly involved in the C(5)-H proton abstraction and may serve as a proton transmitter between the substrate and the proton acceptor residue, possibly located on the cofactor N10-nitrogen. Interaction of the pyrimidine C(4)=O group, or its modification, with the N5,10-methylenetetrahydrofolate N(10) nitrogen atom is suggested as an additional factor influencing the inhibition process.

Algorithms↗
PubMed1996

Molecular mechanism of thymidylate synthase-catalyzed reaction and interaction of the enzyme with 2- and/or 4-substituted analogues of dUMP and 5-fluoro-dUMP.

Thymidylate synthase is a target enzyme in anticancer, antiviral, antifungal and antiprotozoan chemotherapy. With two dUMP analogues, 5-fluoro-dUMP (FdUMP) and 5-(trifluoromethyl)-dUMP (CF3dUMP), strong thymidylate synthase inhibitors and active forms of drugs, the inhibition mechanism is based on the reaction mechanism. Recent comparative studies of new dUMP analogues, containing more than one substituent in the pyrimidine ring, showed that substitution of the pyrimidine ring C(4) = O group in FdUMP by either C(4) = N-OH group (in N4-hydroxy-FdCMP) or C(4) = S group (in 4-thio-FdUMP) preserves high inhibitory potency of the drug but may alter its specificity for thymidylate synthases from various sources, which differ in sensitivity to slow-binding inhibition by FdUMP. Informations suggesting mechanisms responsible for the foregoing have been reviewed, including results of molecular modeling studies suggesting interaction of the pyrimidine C(4) = O group, or its modification, with the N5,10-methylene.(ABSTRACT TRUNCATED)

Animals↗
PubMed1995

Buspirone analogues as ligands of the 5-HT1A receptor. 1. The molecular structure of buspirone and its two analogues.

An interdisciplinary (X-ray, 1H and 13C NMR, IR, and theoretical quantum mechanical) study on the potent 5-HT1A receptor ligand buspirone (1) and its two structural analogues, mesmar (4,4-dimethyl-1-[4-[4-(2-quinolinyl)-1-piperazinyl]butyl]-2,6- piperidinedione) (2) and kaspar (8-[4-[4-(2-quinolinyl)-1-piperazinyl]butyl]-8-azaspiro[4.5]decane - 7,9-dione) (3), has been reported. The results have shown that buspirone-like molecules should appear in an extended rod-shape form, possessing several potential interaction sites with the receptor.

Buspirone↗
PubMed1994

The role of hydration in the hydrolysis of pyrophosphate. A Monte Carlo simulation with polarizable-type interaction potentials.

The exchange of energy in biochemical reactions involves, in a majority of cases, the hydrolysis of phosphoanhydrides (P-O-P). This discovery has lead to a long discussion about the origin of the high energy of such bonds, and to a proposal that hydration plays a major role in the energetics of the hydrolysis. This idea was supported by recent ab initio quantum mechanical calculations (Saint-Martin et al. (1991) Biochim. Biophys. Acta 1080, 205-214) that predicted the hydrolysis of pyrophosphate is exothermic in the gas phase. This exothermicity can account for only a half of the total energy release that one measures in aqueous solutions. Here we address the problem of hydration of the reactants and products of the pyrophosphate hydrolysis by means of Monte Carlo simulations, employing polarizable potentials whose parameters are fitted to energy surfaces computed at the SCF/6-31G** level of the theory. The present results show that the hydration enthalpies of the reactants and products contribute significantly to the total energy output of the pyrophosphate hydrolysis. The study predicts that both, the orthophosphate and the pyrophosphate, have hydration spheres with the water molecules acting as proton acceptors in the P-OH ... O(water) hydrogen bonds. These water molecules weakly repel the water molecules in the further hydration spheres. The perturbation of the structure of the solvent caused by the presence of the solute molecules is short ranged: after ca. 5 A from the P atoms, the energy and the structure of water correspond to bulk water. Due mainly to nonadditive effects, the molecular structure of the hydrated pyrophosphate is quite different from two fused structures of the hydrated orthophosphates. The hydration sphere of pyrophosphate is very loose and has a limited effect on the water network, whereas for orthophosphate it has a well developed shell structure. Hence, upon hydration there will be both a gain in hydration enthalpy and a gain in entropy because of distortion of the water molecular network.

Action Potentials↗
PubMed1993

Structure and conformation of N4-hydroxycytosine and N4-hydroxy-5-fluorocytosine. A theoretical ab initio study.

Optimal molecular geometries and molecular energies were obtained for N4-hydroxycytosine and its 5-fluoro congener with the use of the theoretical ab initio quantum mechanical calculations within the Self Consistent Field method corrected for the electron correlation effects by the second-order Many Body Perturbation Theory (SCF + MBPT(2)). The 6-31G Gaussian basis set was employed. Several tautomeric and rotameric forms were considered. For N4-hydroxycytosine and N4-hydroxy-5-fluorocytosine the imino tautomer (in the conformation syn relatively to the N3-nitrogen atom) appeared to be the most stable form. The imino tautomer of N4-hydroxy-cytosine in the anti rotameric form is by 12.8 kJ mol-1 less stable than the imino-syn form. The 5-fluoro substituent raises the energy difference between the syn and anti rotamers up to 38.5 kJ mol-1. The potential energy barrier for the syn-anti rotation in the imino form of N4-hydroxycytosine is estimated to be about 180 kJ/mol. The results presented in this paper suggest that the syn-imino and anti-imino forms can be treated as two structural isomers that do not interconvert at temperatures relevant to biochemical conditions. The theoretical results also show that the amino tautomeric forms do not compete with the imino forms in the gas-phase and in non-polar and weakly-polar environment. In a polar environment (e.g., in aqueous solutions), however, one may expect an increased population of the amino forms. Qualitatively, the results of the present study agree well with the available experimental and theoretical data for N4-hydroxycytosine and some of its derivatives. The implications of the present study are discussed in relation to the molecular mechanisms of mutagenesis caused by NH2OH and of enzyme (thymidylate synthase) inhibition by N4-hydroxydeoxycytidine monophosphate.

Cytosine↗
PubMed1993

Theoretical and matrix-isolation experimental studies on 2-thiocytosine and 5-fluoro-2-thiocytosine.

2-Thiocytosine (s2Cyt) and 5-fluoro-2-thiocytosine (f5s2Cyt) were studied by means of IR spectroscopy under different environmental conditions: isolated in low-temperature inert gas matrices, associated in thin amorphous and polycrystalline films. The compounds isolated in matrices were only very slightly influenced by the environment. From the analysis of the IR spectra of both compounds it appears that they exist in inert gas matrices only in the amino-thiol tautomeric form. Strong environmental effects were observed for s2Cyt and f5s2Cyt deposited in the form of thin polycrystalline films. Contrary to matrices, in polycrystalline films the amino-thione form dominates for both s2Cyt and f5s2Cyt. The experimental findings are in agreement with the ab initio quantum mechanical calculations of the relative total energies of the tautomeric forms. Those energies were calculated using the Self Consistent Field method corrected for electron correlation effects with the use of the second-order many-body perturbation theory (SCF+MBPT(2)). The theoretical calculations show that the amino-thiol tautomeric form is more stable than the amino-thione form by 38 kJ mol-1 and 48 kJ mol-1 for s2Cyt and f5s2Cyt, respectively. Both molecules, s2Cyt and f5s2Cyt, may also appear in the uracil-like imino-thione tautomeric form, which is predicted to be only 8 kJ mol-1 less stable than the amino-thione form. A new method of the preparation of f5s2Cyt is reported.

Crystallization↗
PubMed1991

Ab initio calculations of the pyrophosphate hydrolysis reaction.

Ab initio quantum mechanical calculations were used to study the hydrolysis reaction H4P2O7 + H2O in equilibrium with 2H3PO4, as well as some molecular properties of the reactants and products. SCF calculations with several basis sets ranging from minimal to extended with polarization functions were used to look at the basis dependency of the reaction enthalpies and optimized geometries. Although the minimal basis sets yield erratic predictions of the enthalpy, when a more extended basis (3-21G*) was used for the geometry optimization, and the total energies of the reactants and products were computed with this and larger basis sets, we obtained more consistent predictions of the structural properties of the P-O-P bridge and of the heat of the hydrolysis reaction (delta E = -7.39 kcal/mol at the SCF/6-31G** level). A comparison is made with previous estimates performed with smaller basis sets and without taking into account the electron correlation effects, which are calculated in the present work. The inclusion of the zero point energy calculated using the harmonic approximation, and of the electronic correlation energy determined at the MBPT(2) level, raised the computed heat of the reaction to -3.83 kcal/mol, and when an estimate for the thermal energy was added, the value obtained was of -3.38 kcal/mol. In conclusion, we found that the hydrolysis of pyrophosphate should be exothermic in the gas phase. The implications of this result in relation to some recent theories about enzyme catalysis are discussed.

Diphosphates↗
PubMed1983

The interaction of gamma-aminobutiric acid with hydrated Ca2+ and Mg2+. A pseudopotential ab initio study.

As a continuation of a previous work we consider the interaction of Mg2+ and Ca2+ with a neurotransmitter, gamma-aminobutiric acid (GABA). The purpose is twofold, to determine if there is a direct interaction of Ca2+ with the amino acid, which could have some biological relevance, and to find out if such a hypothesis can account for the different role of Ca2+ and Mg2+ on the amino acid's release. We performed ab initio pseudopotential studies of the GABA-ion complex in the presence of the first hydration shell around the interaction's region. We calculated the interaction energy of the hydrated complex by means of a many-body expansion up to three-body terms. We found out that the three-body terms in systems involving the divalent ion have a considerable value and seems to be of a different character for Mg2+ and Ca2+. We found out that the three-body terms are responsible for the observed difference between the coordination properties of Mg2+ and Ca2+ and can lead to a difference in the aminoacid interaction with each ion. The hypothesis of a gamma-aminobutiric acid-Ca2+ complex, that facilitates the aminoacid release has been substantiated. The reasons for the different effect of Ca2+ and Mg2+ has been envisaged but not clearly established.

Calcium↗