Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution

Study of the interaction of Huperzia saururus Lycopodium alkaloids with the Acetylcholinesterase enzyme

In the present study, we describe and compare the binding modes of three Lycopodium alkaloids (sauroine, 6-hydroxylycopodine and sauroxine; isolated from Huperzia saururus) and huperzine A with the enzyme acetylcholinesterase. Refinement and rescoring of the docking poses (obtained with different programs) with an all atom force field helped to improve the quality of the protein?ligand complexes. Molecular dynamics simulations were performed to investigate the complexes and the alkaloid´s binding modes. The combination of the latter two methodologies indicated that binding in the active site is favored for the active compounds. On the other hand, similar binding energies in both the active and the peripheral sites were obtained for sauroine, thus explaining its experimentally determined lack of activity. MM-GBSA predicted the order of binding energies in agreement with the experimental IC50 valuesFil: Puiatti, Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones En Fisico- Química de Córdoba. Universidad Nacional de Córdoba. Facultad de Cs.químicas. Instituto de Investigaciones En Fisico- Química de Córdoba; ArgentinaFil: Borioni, José Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones En Fisico- Química de Córdoba. Universidad Nacional de Córdoba. Facultad de Cs.químicas. Instituto de Investigaciones En Fisico- Química de Córdoba; ArgentinaFil: Vallejo, Mariana Guadalupe. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Cabrera, Jose Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Agnese, Mariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Ortega, María Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Pierini, Adriana Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones En Fisico- Química de Córdoba. Universidad Nacional de Córdoba. Facultad de Cs.químicas. Instituto de Investigaciones En Fisico- Química de Córdoba; Argentin

Modelización en diseño de fármacos: Exploración conformacional de ligandos y diseño de inhibidores multipotentes

[spa] La presente Tesis Doctoral, presentada como compendio de publicaciones, tiene como objetivo general la aplicación de diversas técnicas computacionales al estudio de los determinantes moleculares que subyacen en la interacción ligando-receptor. Para ello, se han definido dos líneas de investigación, una de desarrollo metodológico y otra de aplicación. En el capítulo metodológico se incluye un único manuscrito (Juárez-Jiménez et. al., J. Phys. Chem. B, 2014) en el que extiende la metodología Multinivel desarrollada por Forti et. al. (J. Chem. Theory Comput. 2012) al uso de campos de fuerza de mecánica clásica. Dicho estudio es relevante de cara a optimizar la exploración de las preferencias conformacionales de fármacos y otras pequeñas moléculas orgánicas. En concreto, se evalúa el uso de campos de fuerza clásicos para llevar a cabo un muestreo a bajo nivel de teoría de las preferencias conformacionales de moléculas tipo feniletilamina y se comprueba que los resultados obtenidos son consistentes con los datos experimentales descritos en la bibliografia y con los resultados obtenidos con la implementación original del método, donde se empleaba el hamiltoniano semiempírico RM1. En segundo lugar, la nueva implementación del método se utiliza para predecir las preferencias conformacionales del antibiótico estreptomicina, obteniéndose resultados similares a los obtenidos experimentalmente por resonancia magnética nuclear, si bien sugerentes de posibles mejoras en la metodología. El capítulo de aplicación incluye tres publicaciones (Bolea et. al. J. Med. Chem. 2011; Juárez Jiménez et. al. BBA Proteins and Proteomics, 2014 y Viayna et. al. J. Med. Chem. 2014), obtenidas a partir de una colaboración multidisciplinar entre diversos grupos de diseño, síntesis y evaluación farmacológica de compuestos de potencial interés en la enfermedad de Alzheimer. Concretamente, se describe el desarrollo de dos familias de fármacos multipotentes: compuestos iMAO-iAChE y compuestos iBACE-1-iAChE, centrándose la discusión en la elucidación de los modos de unión y las relaciones estructura-actividad de dos series de compuestos multipotentes a sus principales dianas terapéuticas mediante la combinación de técnicas de modelización molecular, tales como el docking y la dinámica molecular. En el primer caso, se describen modelos de unión a AChE y MAO de compuestos híbridos donepezilo-PFN9601, abordándose en detalle los determinantes moleculares de las relaciones estructura-actividad y proponiéndose las causas estructurales del diferente comportamiento cinético observado para el mismo inhibidor en MAO A y en MAO B. Con el fin de mejorar el perfil farmacológico de los inhibidores, también se describe, mediante el empleo de compuestos selectivos MAO A, los determinantes moleculares de la selectividad entre las isoformas A y B que muestran algunos inhibidores de MAO. En el segundo caso, la modelización molecular ha permitido proponer un modo de unión a BACE-1 de compuestos híbridos huprina Y-rheína. Dicho modo de unión, sitúa la unidad de huprina Y en el sitio catalítico, mientras que sugiere que la unidad de rheína quedaría acomodada en un sitio de unión diferente al sitio catalítico, que hasta la fecha no ha sido explorado mediante técnicas de diseño racional de fármacos. Ello abre la puerta al desarrollo de nuevos compuestos que interaccionen con BACE aprovechando dicho centro de unión.[eng] The aim of this doctoral thesis is to use computational techniques to explore the molecular determinants that underlie the ligand-receptor interaction. To this end, it has been elaborated as a compendium of publications following two main research lines. First, the expansion of the Multilevel strategy previously developed in the research group (Forti et. al. J. Chem. Theo. Comput. 2012) to explore the conformational preferences of drug-like molecules. Second, the development of new multitarget directed ligands (MTDL) of potential therapeutic interest against Alzheimer’s disease. The extension of the Multilevel strategy is mainly focused in assessing the suitability of classical force fields as an alternative to the originally implemented RM1 semiempirical Hamiltonian and to investigate the performance of the technique for charged molecules. To this end, the conformational preferences of a set of phenylethyl amines are evaluated with both approximations and the results are compared with experimental data obtained by means of nuclear magnetic resonance techniques, reaching similar conclusions in both cases. Streptomycin is also used as a test case to further test the new implementation of the technique. The results are also consistent with experimental results, but also highlight some aspects that could be improved in future revisions of the methodology. The development of MTDL against Alzheimer’s disease is a multidisciplinary effort in the framework of collaborations with experimental research groups (Bolea et. al. J. Med. Chem. 2011; Juárez Jiménez et. al. BBA Proteins and Proteomics, 2014 y Viayna et. al. J. Med. Chem. 2014). Using several molecular modelling techniques, we disclose putative binding modes to their main therapeutic targets for two families of MTDL: iAChE-iMAO and iAChE-BACE-1. The discussion of structure-activity relationships allows us to rationalize the molecular determinants that justify the isoform selectivity between isoforms A and B of MAO. Furthermore, they also allow us to disclose how compounds bind to BACE-1 taking advantage of an exosite previously unexploited in rational drug design, which pave the way for the development of novel drug candidates

Exploring heterocyclic scaffolds in the development of multi-target anti-Alzheimer and multi-trypanosomatid compounds

[eng] The aim of this PhD thesis consists of the synergistic combination of both highly efficient synthetic approaches and molecular modelling tools for the structure-based drug design and synthesis of novel bioactive heterocyclic compounds. The work carried out has followed two main research lines, namely the development of novel disease-modifying anti-Alzheimer agents and still unexplored chemical entities for the treatment of Neglected Tropical Diseases (NTDs). The results obtained have been presented as a compendium of publications and draft manuscripts. In the framework of the anti-Alzheimer research line, first the hit-to-lead optimization of a practically inactive propidium-related compound easily accessed via a Povarov multicomponent reaction (MCR) approach (Di Pietro O. et al. Eur. J. Med. Chem., 2014, 73, 141), and the subsequent molecular hybridization with a 6-chlorotacrine unit through a molecular dynamics-driven tether length optimization, overall led to one of the most potent non-covalent dual binding site acetylcholinesterase inhibitor (AChEI) ever described in the literature (Di Pietro O. et al. Eur. J. Med. Chem., 2014, 84, 107). Second, the combined recourse to the highly versatile click-chemistry strategy, through the well-known Cu-catalyzed azide-alkyne cycloaddition reaction, and convenient computational chemistry tools, allowed the rational design and synthesis of a novel series of 1,4-disubstituted triazole-based propargylamines as irreversible MAO-B inhibitors (draft manuscript) with the perspective to be further linked to a second pharmacophoric moiety to derive novel MTDLs as potential anti-Alzheimer drug candidates. Furthermore, an extensive computation of the BACE-1 apo conformational ensemble by means of combined molecular dynamics technique and Principal Component Analysis (PCA) method, allowed to carry out an exhaustive study of a secondary transient druggable pocket (draft manuscript) and a virtual screening of 500,000 commercially available fragments for further drug discovery purposes. Finally, in the framework of the NTDs research line, 2−4-step sequences involving as the key step an initial Povarov MCR gave easy access to a small library of quinolones and tricyclic heterofused quinolines, which were subjected to phenotypic whole-cell screenings, leading to the individuation of several low micromolar multi-trypanosomatid hit compounds (Di Pietro et al. Eur. J. Med. Chem. 2015, accepted with minor revision)