Albert Rimola

Design, selection, and characterization of thioflavin-based intercalation compounds with metal chelating properties for application in Alzheimer's disease.

Metal chelation is considered a rational therapeutic approach for interdicting Alzheimers amyloid pathogenesis. At present, enhancing the targeting and efficacy of metal-ion chelating agents through ligand design is a main strategy in the development of the next generation of metal chelators. Inspired by the traditional dye Thioflavin-T, we have designed new multifunctional molecules that contain both amyloid binding and metal chelating properties. In silico techniques have enabled us to identify commercial compounds that enclose the designed molecular framework (M1), include potential antioxidant properties, facilitate the formation of iodine-labeled derivatives, and can be permeable through the blood-brain barrier. Iodination reactions of the selected compounds, 2-(2-hydroxyphenyl)benzoxazole (HBX), 2-(2-hydroxyphenyl)benzothiazole (HBT), and 2-(2-aminophenyl)-1H-benzimidazole (BM), have led to the corresponding iodinated derivatives HBXI, HBTI, and BMI, which have been characterized by X-ray diffraction. The chelating properties of the latter compounds toward Cu(II) and Zn(II) have been examined in the solid phase and in solution. The acidity constants of HBXI, HBTI, and BMI and the formation constants of the corresponding ML and ML2 complexes [M = Cu(II), Zn(II)] have been determined by UV-vis pH titrations. The calculated values for the overall formation constants for the ML2 complexes indicate the suitability of the HBXI, HBTI, and BMI ligands for sequestering Cu(II) and Zn(II) metal ions present in freshly prepared solutions of beta-amyloid (Abeta) peptide. This was confirmed by Abeta aggregation studies showing that these compounds are able to arrest the metal-promoted increase in amyloid fibril buildup. The fluorescence features of HBX, HBT, BM, and the corresponding iodinated derivatives, together with fluorescence microscopy studies on two types of pregrown fibrils, have shown that HBX and HBT compounds could behave as potential markers for the presence of amyloid fibrils, whereas HBXI and HBTI may be especially suitable for radioisotopic detection of Abeta deposits. Taken together, the results reported in this work show the potential of new multifunctional thioflavin-based chelating agents as Alzheimers disease therapeutics.

Ab Initio Modeling of Protein/Biomaterial Interactions : Glycine Adsorption at Hydroxyapatite Surfaces

How does glycine adsorb at hydroxyapatite surfaces? Ab initio simulations based on periodic B3LYP GTO calculations reveal the detailed mechanism of binding to the (001) and (010) surfaces by shedding light on how acid and basic amino acid residues of proteins interact with hydroxyapatite based biomaterials.

Deep-space glycine formation via Strecker-type reactions activated by ice water dust mantles. A computational approach

A Strecker-type synthesis of glycine by reacting NH(3), H(2)C=O and HCN in presence of ice water (H(2)O-ice) as a catalyst has been theoretically studied at B3LYP/6-31+G(d,p) level within a cluster approach in order to mimic reactions occurring in the interstellar and circumstellar medium (ICM). Results indicate that, despite the exoergonic character of the considered reactions occurring at the H(2)O-ice surface, the kinetics are slow due to relatively high electronic energy barriers (ΔU(0)(≠)=15-45 kcal mol(-1)). Reactions occurring within H(2)O-ice cavities, in which ice bulk effects have been modeled by assuming a dielectric continuum (ε=78), show energy barriers low enough to allow NH(2)CH(2)OH formation but not NH=CH2 (ΔU(0)(≠)= 2 and 21 kcal mol(-1), respectively) thus hindering the NH(2)CH(2)CN formation, i.e. the precursor of glycine, through Strecker channels. Moreover, hydrolysis of NH(2)CH(2)CN to give glycine is characterized by high electronic energy barriers (ΔU(0)(≠)=27-34 kcal mol(-1)) and cannot readily occur at cryogenic temperatures. Nevertheless, the facts that NH=CH(2) formation can readily be achieved through the radical-radical HCN+2H - NH−−>CH2 reaction [D. E. Woon, Astrophys. J., 2002, 571, L177-L180], and that present results indicate that the Strecker step of NH=CH(2)+HCN−−>NH(2)CH(2)CN exhibits a relative low energy barrier (ΔU(0)(≠)=8–9 kcal mol(-1)), suggest that a combination of these two mechanisms allows for the formation of NH(2)CH(2)CN in the ICM. These results strengthen the thesis that NH(2)CH(2)CN could have been formed and protected by icy dust particles, and then delivered through micro-bombardments onto the early Earth, leading to glycine formation upon contact with the primordial ocean.

Crystal structure of thioflavin-T and its binding to amyloid fibrils: insights at the molecular level

Combining X-ray data on thioflavin-T and theoretical calculations on its binding to a peptide model for Abeta(1-42) fibrils gives evidence of main stabilizing interactions, which influence the dihedral angle between the two moieties of thioflavin-T and thereby its fluorescence properties; these results shed new light on possible strategies for the design of dyes to bind amyloid fibrils more specifically.

Neutral vs zwitterionic glycine forms at the water/silica interface: structure, energies, and vibrational features from B3LYP periodic simulations.

B3LYP periodic calculations with a triple-xi-polarized Gaussian basis set have been used to study adsorption of glycine on a hydroxylated silica surface (2.2 OH/nm2) model derived from the (001) surface of edingtonite. The simulation envisages glycine adsorbed either as a gas-phase molecule or when microsolvated by up to five H20 molecules. Both neutral and zwitterionic forms of glycine have been considered and their structural, energetic, and spectroscopic vibrational features compared internally and with experiments. As a gas phase glycine sticks in its neutral form at the silica surface, the zwitterion being highly unstable and with transition-state character. When glycine is microsolvated at the silica interface, two H20 molecules render the zwitterion population comparable to that of the neutral form whereas with four H2O molecules the neutral glycine population is wiped out in favor of the zwitterion. With four H20 molecules the most stable structure shows no direct contact between glycine and the silica surface, H20 acting as a mediator via H-bond interactions. The B3LYP energies and structural data were also supported by comparing the scaled harmonic vibrational features with literature FTIR data of glycine adsorbed on an amorphous silica surface either from the gas phase or in water solution.

Ab initio modeling of protein/biomaterial interactions: competitive adsorption between glycine and water onto hydroxyapatite surfaces

Both glycine and water exhibit a high affinity towards the hydroxyapatite HA surfaces. What happens when they are co-adsorbed at the HA (001) surface? B3LYP periodic calculations reveal that glycine displaces the pre-adsorbed water interacting directly with the HA surface.

Combined quantum chemical and modeling study of CO hydrogenation on water ice

Context. Successive hydrogenation reactions of CO on interstellar icy grain surfaces are considered one of the most e cient mechanisms in interstellar environments for the formation of H2CO and CH3OH, two of the simplest organic molecules detected in space. In the past years, several experimental and theoretical works have been focused on these reactions, providing relevant information both at the macroscopic and atomic scale. However, several questions still remain open, such as the exact role played by water in these processes, a crucial aspect because water is the dominant constituent of the ice mantles around dust grain cores. Aims. We here present a quantum chemical description of the successive H additions to CO both in the gas phase and on the surfaces of several water clusters. Methods. The hydrogenation steps were calculated by means of accurate quantum chemical methods and structural cluster models consisting of 3, 18, and 32 water molecules. Results. Our main result is that the interaction of CO and H2CO with the water cluster surfaces through H-bonds with the O atoms increases the C O polarization, thus weakening the C O bond. Consequently, the C atoms are more prone to receiving H atoms, which in turn lowers the energy barriers for the H additions compared to the gas-phase processes. The calculated energy barriers and transition frequencies associated with the reaction coordinate were adopted as input parameters in our numerical model of the surface chemistry (GRAINOBLE) to simulate the distribution of the H2CO and CH3OH ice abundances (with respect to water). Our GRAINOBLE results based on the energy barriers and transition frequencies for the reactions on the 32 water molecule cluster compare well with the observed abundances in low-mass protostars and dark cores.

Ab initio modelling of protein-biomaterial interactions: influence of amino acid polar side chains on adsorption at hydroxyapatite surfaces

The adsorption from the gas phase of five different amino acids (AAs), namely Gly, Ser, Lys, Gln and Glu, on three surface models of hexagonal hydroxyapatite (HA) has been studied at B3LYP level with Gaussian type basis set within a periodic approach. The AA adsorption was simulated on the (001) and (010) stoichiometric surfaces, the latter both in its pristine and water-reacted form. Low/high AA coverage has been studied by doubling the HA unit cell size. The AAs have been docked to the HA surfaces following the electrostatic complementarity between the electrostatic potentials of AA and the bare HA. Gly adsorbs as a zwitterion at the (001) surface, whereas at the (010) ones, the proton of the COOH group is transferred to the surface resulting in an HA+/Gly− ion pair. For the other AAs, the common COOH−CH−NH2 moiety behaves like in Gly, while the specific side-chain functionalities adsorb at the HA surfaces by maximizing electrostatic and H-bond interactions. The interactions between the side chains and the HA surface impart a higher stability compared with the Gly case, with Glu being the strongest adsorbate owing to its high Ca affinity and H-bond donor propensity. For AAs of large size, the adsorption is more favourable in conditions of low coverage as repulsion between adjacent AAs is avoided. For all considered AAs, the strongest interaction is always established on the (010) faces rather than on the (001) one, therefore suggesting an easier growth along the c-direction of HA crystals from AA solutions.

The role of defective silica surfaces in exogenous delivery of prebiotic compounds: clues from first principles calculations

The reaction of glycine (Gly) with a strained (SiO)(2) four-membered ring defect (D2) at the surface of an interstellar silica grain dust has been studied at ONIOM2[B3LYP/6-31+G(d,p):MNDO] level within a cluster approach in the context of hypothetical reactions occurring in the interstellar medium. The D2 opens up exothermically for reaction with Gly (Delta(r)U(0)=-26.3 kcal mol(-1)) to give a surface mixed anhydride S(surf)-O-C([double bond, length as m-dash]O)-CH(2)NH(2) as a product. The reaction barriers, DeltaU( not equal)(0), are 0.1 and 10.4 kcal mol(-1) for reactive channels involving COOH and NH(2) as attacking groups, respectively. Calculations show the surface mixed anhydride to be rather stable under the action of interstellar processes, such as reactions with isolated H(2)O and NH(3) molecules or the exposure to cosmic rays and UV radiation. The hydrolysis of the surface mixed anhydride to release again Gly was modelled by microsolvation (from 1 to 4 H(2)O molecules) mimicking what could have happened to the interstellar dust after seeding the primordial ocean in the early Earth. Results for these calculations show that the reaction is exergonic and activated, the Delta(r)G(298) becoming more negative and the DeltaG( not equal)(298) being dramatically reduced as a function of increasing number of H(2)O molecules. The present results are relevant because they show that defects present at interstellar dust surfaces could have played a significant role in capturing, protecting and delivering essential prebiotic compounds on the early Earth.

Coordination properties of glycylglycine to Cu+, Ni+ and Co+. Influence of metal cation electronic configuration

The structure, vibrational frequencies and binding energies of the complexes formed by the interaction of Cu+(d10, 1S), Ni+(d9, 2D) and Co+(d8, 3F and 1G) with glycylglycine have been theoretically determined. The most stable structure of Cu+–glycylglycine is bicoordinated with the Cu+ cation interacting with the terminal carbonyl oxygen and the amino group. However, for Ni+–glycylglycine and Co+–glycylglycine the lowest energy structures are tricoordinated, the interaction of the metal cation given by the same groups of Cu+-glycylglycine plus the nitrogen or oxygen atoms of the peptide bond. As for glycine, De values follow the order Ni+ > Co+ (triplet) ∼ Cu+, but the interaction energies are about 11–13 kcal mol−1 larger. Differences on the coordination properties of the metal cations are discussed and interpreted according to their electronic structure.