New insights into human farnesyl pyrophosphate synthase inhibition by second-generation bisphosphonate drugs.

Pamidronate, alendronate, APHBP and neridronate are a group of drugs, known as second-generation bisphosphonates (2G-BPs), commonly used in the treatment of bone-resorption disorders, and recently their use has been related to some collateral side effects. The therapeutic activity of 2G-BPs is related to the inhibition of the human Farnesyl Pyrophosphate Synthase (hFPPS). Available inhibitory activity values show that 2G-BPs act time-dependently, showing big differences in their initial inhibitory activities but similar final IC50 values. However, there is a lack of information explaining this similar final inhibitory potency. Although different residues have been identified in the stabilization of the R2 side chain of 2G-BPs into the active site, similar free binding energies were obtained that highlighted a similar stability of the ternary complexes, which in turns justified the similar IC50 values reported. Free binding energy calculations also demonstrated that the union of 2G-BPs to the active site were 38 to 54 kcal mol-1 energetically more favourable than the union of the natural substrate, which is the basis of the inhibition potency of the hFPPS activity.

Formation mechanism of glyoxal-DNA adduct, a DNA cross-link precursor.

DNA nucleobases undergo non-enzymatic glycation to nucleobase adducts which can play important roles in vivo. In this work, we conducted a comprehensive experimental and theoretical kinetic study of the mechanisms of formation of glyoxal-guanine adducts over a wide pH range in order to elucidate the molecular basis for the glycation process. Also, we performed molecular dynamics simulations to investigate how open or cyclic glyoxal-guanine adducts can cause structural changes in an oligonucleotide model. A thermodynamic study of other glycating agents including methylglyoxal, acrolein, crotonaldehyde, 4-hydroxynonenal and 3-deoxyglucosone revealed that, at neutral pH, cyclic adducts were more stable than open adducts; at basic pH, however, the open adducts of 3-deoxyglucosone, methylglyoxal and glyoxal were more stable than their cyclic counterparts. This result can be ascribed to the ability of the adducts to cross-link DNA. The new insights may contribute to improve our understanding of the connection between glycation and DNA cross-linking.

A DFT study of the carboxymethyl-phosphatidylethanolamine formation from glyoxal and phosphatidylethanolamine surface. Comparison with the formation of N(ε)-(carboxymethyl)lysine from glyoxal and L-lysine.

Mechanisms of the generation of carboxymethyl compounds Nε-(carboxymethyl)lysine (CML) and carboxymethyl-phosphatidylethanolamine (CM-PE) from the reactions between glyoxal and L-lysine, and glyoxal and phosphatidylethanolamine (PE) were studied using the DFT method at the PBE/DNP level of theory. In order to study the reaction with PE, a periodic model of the PE surface was built. The starting surface model includes two molecules of PE, a molecule of monohydrated form of glyoxal, and five water molecules as explicit solvent that form a hydrogen bond network, which are involved in the reactions by stabilizing reaction intermediates and transition states and as proton-transfer carriers, important in all steps of reactions. Both reactions take place in three steps, namely, (1) carbino-diol-amine formation; (2) dehydration; and (3) rearrangement into carboxymethyl final products. The rate-limiting step for the formation of CML/CM-PE was the dehydration stage. The comparison of both reactions in their equivalent stages showed a catalytic role of the PE surface; it is highlighted in the case of dehydration step where its relative free energy barrier had a value of 5.3 kcal mol(-1) lower than that obtained in the L-lysine-glyoxal system. This study gives insights into the active role of the phospholipid surface in some chemical reactions that occur above it. Our results also give support to consider the pathway of formation of CML and CM-PE from the reactions between glyoxal and L-lysine, and glyoxal and PE as an alternative pathway for generation of these advanced glycation end-products (AGEs).

Theoretical study on the influence of the Mg2+ and Al3+ octahedral cations on the vibrational spectra of the hydroxy groups of dioctahedral 2:1 phyllosilicate models.

The effect on the vibrational spectrum of the hydroxy groups in dioctahedral 2:1 phyllosilicates of the isomorphous cation substitution of Mg(2+) by Al(3+) in the octahedral sheet was investigated at the DFT level. Ortho, meta and para Mg(2+) configurational polymorphs were defined. The theoretical vibration frequencies of OH groups depend significantly on the nature of the cations they are joined with. Theoretical values are spread out over narrow ranges: 3,612-3,626 cm(-1) for ν(AlOHMg), 3,604-3,606 cm(-1) for ν(AlOHAl), and 3,657-3,660 cm(-1) for ν(MgOHMg); 803-830 cm(-1) for δ(AlOHMg), 877 cm(-1) for δ(AlOHAl), and 693-711 cm(-1) for δ(MgOHMg), in agreement with known experimental values. From the intensities of the XOHY bands, we observe that the vibrational adsorptivities of the ν(OH) vibrations are not the same for all XOHY groups, and that ν(MgOHMg) absorptivity is much lower than that of ν(AlOHAl). These theoretical results should be taken into account in quantitative analysis of experimental vibrational studies in clay minerals, introducing different molar extinction coefficients in the Lambert-Beer law to determine the relative concentrations of both cationic arrangements.

High- and low-spin Fe(III) complexes of various AGE inhibitors.

Density functional theory calculations [CPCM/UM06/6-31+G(d,p)] were used to elucidate the structures and relative stability of Fe(III) complexes with various ligands that inhibit the formation of advanced glycation end products (AGEs) or iron overloaded disease (viz. aminoguanidine, pyridoxamine, LR-74, Amadori compounds, and ascorbic acid). EDTA was used as the free energy reference ligand. The distorted neutral octahedral complex containing one iron atom and three molecules of pyridoxamine [Fe(PM)(3)] was found to be the most stable. The stability of the complexes decreases in the following chelate sequence: pyridoxamine, Amadori complex, aminoguanidine, LR inhibitor, and ascorbic acid.

Hydrolysis of a chlorambucil analogue. A DFT study.

We study by density functional theory the hydrolysis of a chlorambucil analogue. Three SN(1) and one SN(2) mechanisms have been compared. Results show that the most likely mechanism involves the formation of an aziridinium ion via a first-order reaction subject to an energy barrier of 24.8 kcal/mol. Additionally, a kinetic study, using the thermodynamic formulation of the Transition State Theory, has been carried out. Theoretical results coincide with experimental values obtained under similar conditions of pH, temperature and chloride concentration.

DFT studies on Schiff base formation of vitamin B6 analogues. Reaction between a pyridoxamine-analogue and carbonyl compounds.

A comprehensive theoretical study based on density functional theory calculations (B3LYP and M06-2X functionals) of the formation of Schiff bases of pyridoxamine analogues with two different aldehydes was conducted. The reaction mechanism was found to involve two steps, namely: (1) formation of a carbinolamine and (2) dehydration of the carbinolamine to give the final imine. Also, consistent with available experimental evidence, the carbinolamine dehydration was the rate-determining step of the process determined by means of M06-2X functional. Using an appropriate solvation method and reactant conformation ensures that all proton transfers involved will be intramolecular, which substantially reduces energy barriers and facilitates reaction in all cases. The formation of a Schiff base between pyridoxal 5-phosphate (PLP) and an amine or amino acid requires the contribution of an external water molecule in order to facilitate proton transfers. On the other hand, the formation of a Schiff base between pyridoxamine 5-phosphate (PMP) and a carbonyl compound requires no external aid since the spatial arrangement of the functional groups in PMP ensures that all proton transfers will be intramolecular.