Study and applications of dynamic chemical networks of pseudopeptidic compounds

Abstract

The present research project can be included in the broad supramolecular chemistry field that was defined by Nobel laureate Jean Marie Lehn as the "chemistry beyond the molecule".1 It is based on processes of molecular assembly through intermolecular forces and it has allowed synthesizing fascinating architectures with very important applications in Biology, Material Science and Catalysis. Our project is specifically defined within the dynamic combinatorial chemistry that has emerged as an important methodology for the generation of new molecules formed by reversible reactions of simple "Building Blocks" (BB).2 This work is focused on the study of covalent dynamic libraries arising from the combination of BBs with different abilities to form reversible bonds3,4 in aqueous media through disulphide chemistry. Thus, by combining a series of BB with different valence, in principle a broad structural variety is expected. Nevertheless, it was observed that self-recognition events within the BBs during the equilibration process can lead the equilibrium to the formation of a discrete compound instead of a diverse library.5 This allowed us to evaluate the effect of the molecular topology/geometry in the dynamic systems. We found that with the appropriate cooperative supramolecular interactions between the BBs could result in the emergence of self-recognition processes and in the selective formation of a singular constitution even when it is statistically disfavored. We show the importance of the synergic action of subtle recognition events within the components of a DCL. Those findings made us envision that the generation of molecular diversity will open the possibility of creating highly complex and efficient molecular recognition systems, starting from structurally simple BBs. After the assumption that stabilizing intramolecular interactions are responsible for the selection of a single compound, we decided to study the adaptive behavior of these dynamic combinatorial libraries to support this premise.6 The systematic study of the intrinsic (chemical structure and valence of the BB) and extrinsic (pH, ionic strength and organic co-solvent) factors rendered important information about noncovalent intramolecular interactions.7 If we understand the behavior of the interactions that are responsible of the formation of different products and learn what factors are leading to their constitution, we will be able to decode the key to direct the thermodynamic equilibrium towards a desired assembly of products. Systematically planned variations of the BBs structures and of the experimental conditions can provide a basis for a better understanding of supramolecular associations in natural and synthetic systems and for the theoretical prediction of noncovalent interactions. This knowledge can result into an excellent tool to predict the emergence of new compounds and to contribute to the understanding of biologically important associations. With the knowledge acquired and the results obtained, we focused on the synthesis and study of selective chemical sensors of amino acids in aqueous media. We designed a dynamic molecular network able to selectively sense biologically relevant molecules with high sensitivity.8 Instead of a discrete fluorescent probe derived from one molecule, the sensor comprises an ensemble of species that work as a dynamic network that rearranges and releases a fluorescent component in response to the analyte.9 This system works in aqueous media to exclusively sense Cys in its reduced or oxidized form against other biothiols and, even more importantly, in human urine

which the consequent application for the diagnosis of cystinuria, a metabolic disease related to a deficient transport of this amino acid. Overall, the results comprehended in this thesis represent a contribution to expand the study of combinatorial dynamical libraries and in the subsequent utilization of these for practical purposes. The combination of pseudopeptidic BBs in DCvC processes allowed us to investigate a wide variety of structural diversity. The generation of this molecular diversity and the exhaustive study of its adaptive properties open the possibility of creating highly complex and efficient molecular recognition systems, from structurally simple BBs.

References: [1] J.-M. Lehn; Angew. Chem. Int. Ed. Engl.; 1988; 27, 89. [2] J.Li, P.Nowak, S.Otto. J. Am. Chem. Soc., 2013, 135, 9222-9239. [3] J. Atcher and I. Alfonso; RSC Advances; 2013; 3, 25605-25608. [4] K. R. West, K. D. Bake and S. Otto, Organic Letters; 2005; 7, 2615-2618. [5] J. Solà, M. Lafuente, J. Atcher and I. Alfonso; Chemical Communications; 2014; 50, 4564-4566. [6] M. Lafuente, J.Atcher, J. Solà and I. Alfonso; Chem. Eur. J.; 2015; 21, 17002. [7] J. Atcher, A. Moure and I. Alfonso; Chemical Communications; 2013; 49, 487-489. [8] M. Lafuente, J. Solà ans I. Alfonso; Angewandte Chemie, https://doi.org/10.1002/anie.201802189 [9] D. Zhang, Z . Yang, H. Li, Z. Pei, S. Sun and Y. Xu; Chem. Commun.; 2016, 52, 749.

El presente proyecto de investigación se puede incluir en el amplio campo de la química supramolecular que definió el Premio Nobel Jean Marie Lehn como la "química más allá de la molécula". Se basa en procesos de ensamblaje molecular a través de fuerzas intermoleculares y ha permitido sintetizar arquitecturas fascinantes con aplicaciones muy importantes. Esta Tesis Doctoral se basa en el diseño y síntesis de nuevas moléculas pseudopeptídicas para ser usadas como bloques constituyentes en la generación de quimiotecas combinatorias dinámicas. La originalidad de la idea radica en la preparación de estructuras químicas con distinta topología molecular (monopodales, bipodales, tripodales), lo que puede conducir potencialmente a una gran diversidad estructural (lineal, cíclica, policíclica) mediante la adecuada combinación de dichos bloques constituyentes en procesos dinámicos. Con ello se planteó el objetivo de estudiar el efecto de la geometría y la topología molecular en la composición de las quimiotecas dinámicas. Tras suponer que la estabilización de un compuesto u otro es debido a las interacciones intramoleculares, se estudió el comportamiento adaptativo de estas quimiotecas dinámicas combinatorias para apoyar esta premisa. El estudio sistemático de los factores intrínsecos (estructura química y valencia del BB) y extrínseco (pH, fuerza iónica y codisolvente orgánico) proporcionó información importante sobre las interacciones intramoleculares no covalentes que dirigen estos sistemas. Los sistemas que dieron lugar a procesos de reconocimiento molecular eficiente, se estudiarían en detalle. Seguidamente y partiendo del conocimiento adquirido y los resultados obtenidos hasta el momento, se planteó modificar los correspondientes bloques constituyentes para llevar a cabo sistemas dinámicos con una aplicación práctica, la preparación de sensores químicos específicos de aminoácidos, capaces de funcionar en medios acuosos. Con ello se ha conseguido por primera vez la preparación de un sistema dinámico capaz de producir una respuesta fluorescente en presencia de la L-cisteína y, lo que es más importante, su dímero oxidado L-cistina. Este entramado molecular actúa como un sensor fluorescente selectivo de cisteína, incluso en presencia de otros aminoácidos y en fluidos biológicos, como la orina humana, con la consiguiente potencial aplicación para el diagnóstico de cistinuria, una enfermedad metabólica relacionada con el transporte deficiente de dicho aminoácido.