Ricaurte Rodríguez

Molecular modeling study of dihydrofolate reductase inhibitors. Molecular dynamics simulations, quantum mechanical calculations, and experimental corroboration.

A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC₅₀ values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper.

Hydrogen-bonded sheets of R2(2)(10) and R4(4)(24) rings in 1-deoxy-1-morpholino-D-fructopyranose.

In the title compound, C(10)H(19)NO(6), both rings adopt almost perfect chair conformations and their mutual orientation is influenced by an intramolecular O-H...N hydrogen bond. The molecules are linked by three independent O-H...O hydrogen bonds into sheets containing equal numbers of R2(2)(10) and R4(4)(24) rings.

Synthesis of 1-Benzyl-6-(4-chlorophenyl)-2-(4-R-phenyl)-4-(4-Rstyryl)-2,3-dihydropyrazolo[3,4-b][1,4]diazepines

The reaction of 4-amino-5-benzylamino-3-(4-chlorophenyl)-1H-pyrazole (1) with substituted diarylidenketones (2) constitutes a convenient synthetic route to the hitherto unknown 1-benzyl-6-(4-chlorophenyl)-2-(4-R-phenyl)-4-(4-R-styryl)-2,3-dihydropyrazolo-[3,4-b][1,4]diazepines (3). Structures of all products were consistent with their IR, 1H-NMR, 13C-NMR and MS spectral data. X-ray crystallography data confirm the assigned structures.

New substituted aminopyrimidine derivatives as BACE1 inhibitors: in silico design, synthesis and biological assays

We report in this work new substituted aminopyrimidine derivatives acting as inhibitors of the catalytic site of BACE1. These compounds were obtained from a molecular modeling study. The theoretical and experimental study reported here was carried out in several steps: docking analysis, Molecular Dynamics (MD) simulations, Quantum Theory Atom in Molecules (QTAIM) calculations, synthesis and bioassays and has allowed us to propose some compounds of this series as new inhibitors of the catalytic site of BACE1. The QTAIM study has allowed us to obtain an excellent correlation between the electronic densities and the experimental data of IC50. Also, using combined techniques (MD simulations and QTAIM calculations) enabled us to describe in detail the molecular interactions that stabilize the different L-R complexes. In addition, our results allowed us to determine what portion of these compounds should be changed in order to increase their affinity with the BACE1. Another interesting result is that a sort of synergism was observed when the effects of these new catalytic site inhibitors were combined with Ac-Tyr5-Pro6-Tyr7-Asp8-Ile9-Pro10-Leu11-NH2, which we have recently reported as a modulator of BACE1 acting on its exosite.

Different hydrogen-bonded structures in the isomeric solvates 2-amino-6-anilino-4-methoxy-5-[(E)-4-nitrobenzylideneamino]pyrimidine dimethyl sulfoxide solvate and 2-amino-6-[methyl(phenyl)amino]-5-[(E)-4-nitrobenzylideneamino]pyrimidin-4(3H)-one dimethyl sulfoxide solvate.

The title solvates, (I) and (II), both C(18)H(16)N(6)O(3).C(2)H(6)OS, are isomeric. The conformations adopted by the 6-substituent are significantly different, with the 6-aminophenyl unit remote from the nitrophenyl ring in methoxypyrimidine (I) but adjacent to it in pyrimidinone (II). Pairs of pyrimidine molecules in (I) are linked by N-H...N hydrogen bonds to form cyclic centrosymmetric dimers from which the dimethyl sulfoxide molecules are pendent, while in (II) a combination of three independent N-H...O hydrogen bonds links the components into a chain containing both R(2)(2)(8) and R(4)(2)(8) rings, in which the dimethyl sulfoxide component acts as a double acceptor of hydrogen bonds. The significance of this study lies in its observation of different conformations for the pyrimidine components in (I) and (II), and different hydrogen-bonded structures, apparently dominated by the different roles adopted by the dimethyl sulfoxide components.

Hydrogen-bonded dimers in 3-amino-4-anilino-1H-isochromen-1-one and a hydrogen-bonded sheet in 3-amino-4-[methyl(phenyl)amino]-1H-isochromen-1-one.

The molecules of 3-amino-4-anilino-1H-isochromen-1-one, C15H12N2O2, (I), and 3-amino-4-[methyl(phenyl)amino]-1H-isochromen-1-one, C16H14N2O2, (II), adopt very similar conformations, with the substituted amino group PhNR, where R = H in (I) and R = Me in (II), almost orthogonal to the adjacent heterocyclic ring. The molecules of (I) are linked into cyclic centrosymmetric dimers by pairs of N-H···O hydrogen bonds, while those of (II) are linked into complex sheets by a combination of one three-centre N-H···(O)2 hydrogen bond, one two-centre C-H···O hydrogen bond and two C-H···π(arene) hydrogen bonds.

A three-dimensional hydrogen-bonded framework in 2-amino-6-(N-methylanilino)pyrimidin-4(3H)-one and a ribbon of fused hydrogen-bonded rings in 2-amino-6-(N-methylanilino)-5-nitropyrimidin-4(3H)-one.

The molecular dimensions of both 2-amino-6-(N-methylanilino)pyrimidin-4(3H)-one, C11H12N4O, (I), and 2-amino-6-(N-methylanilino)-5-nitropyrimidin-4(3H)-one, C11H11N5O3, (II), are consistent with considerable polarization of the molecular-electronic structures. The molecules of (I) are linked into a three-dimensional framework by a combination of one N-H...N hydrogen bond, two independent N-H...O hydrogen bonds and one C-H...pi(arene) hydrogen bond. The molecules of (II) are linked into ribbons containing three types of edge-fused ring by the combination of two independent three-centre N-H...(O)2 hydrogen bonds.