Molecular Networks in Dynamic Multilevel Systems

Dynamic multilevel systems can be assembled from molecular building blocks through two or more reversible reactions that form covalent bonds. Molecular networks of dynamic multilevel systems can exhibit different connectivities between nodes. The design and creation of molecular networks in multilevel systems require control of the crossed reactivity of the functional groups (how to connect nodes) and the conditions of the reactions (when to connect nodes). In recent years, the combination of orthogonal and communicating reactions, which can be simultaneous or individually activated, has produced a variety of systems that have given rise to macrocycles and cages, as well as molecular motors and multicomponent architectures on surfaces. A given set of reactions can lead to systems with unique responsiveness, compositions, and functions as a result of the relative reactivities. In this Concept article, different molecular networks from synthetic systems that can be produced by combinations of different reaction types are discussed. Moreover, applications of this chemistry are highlighted, and future perspectives are envisioned.Fil: Orrillo, Alfredo Gastón. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Escalante, Andrea Marta. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Martinez Amezaga, Maitena. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Cabezudo, Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Furlan, Ricardo Luis Eugenio. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro

Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence.Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy –performed in a large and diverse chemolibrary– complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening.Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12–20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7–45 μM).Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known “garbage in, garbage out” machine learning principle

Reacciones mediadas por metales de transición para generar diversidad molecular: Aplicación a la generación de bibliotecas de compuestos biológicamente prometedores

Las reacciones multicomponentes son una herramienta fundamental para la generación de diversidad en un solo paso. En nuestra búsqueda de obtención de complejidad estructural de manera rápida y eficiente, y como primera etapa de investigación, estudiamos la reacción tricomponente tipo-Mannich catalizada por Cu(I) o Cu(II), tanto en solución como en fase sólida y la preparación de una quimioteca de propargilaminas aplicando las condiciones optimizadas. Seguidamente, se sintetizan alenos a partir de estas aminas propargílicas mediante una transformación catalizada por Au(I), Ag(I) o In(III). En esta etapa se logró la optimización de las condiciones para la conversión completa y la obtención de buenos rendimientos de los productos. A su vez, la metodología fue transferida a la química en fase sólida, obteniéndose el aleno correspondiente, lo cual representa uno de los primeros ejemplos de síntesis de alenos inmovilizados. Para finalizar el primer período de Tesis, se llevó a cabo un análisis sistemático de la cicloadición de los alenos con ácido 2-iodobenzoico mediado por Pd, de esta manera se desarrolló una técnica eficiente mediante la cual se sintetizan una serie de estructuras de interés biológico con núcleo isocumarina.En una segunda etapa del trabajo de Tesis, se llevó a cabo un estudio sobre el acoplamiento de Suzuki-Miyaura en fase sólida. La síntesis en fase sólida es especialmente útil para la generación de diversidad molecular a través de reacciones de acoplamiento cruzado. De allí que se decidió analizar las condiciones óptimas para el acoplamiento de Suzuki-Miyaura a partir de un ácido borónico soportado, lo que hace menos favorables los procesos de homoacoplamiento y formación de boroxinas. A partir de ello, se sintetizó una quimioteca de biarilos estructuralmente muy variada que incluye heterociclos interesantes como 4-biaril-β-lactamas y 4-arilcromenonas. Para estudiar el alcance de la metodología, se utilizó un biarilo obtenido mediante esta estrategia para la exploración de nuevas derivatizaciones, como la síntesis de aminas secundarias conteniendo sistemas biarílicos, la cicloadición 1,3-dipolar para obtener una biaril-Δ2-isoxazolina y la condensación tetracomponente para obtener un derivado 4,5-difenil-1H-imidazol.Los resultados expuestos en este Trabajo representan un interesante aporte a la generación de compuestos de interés biológico y sintético, a partir de metodologías optimizadas tanto en solución, como en fase sólida.Fil: Martinez Amezaga, Maitena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; Argentin

Engineering multilayer chemical networks

Dynamic multilevel systems emerged in the last few years as new platforms to study thermodynamic systems. In this work, unprecedented fully communicated three-level systems are studied. First, different conditions were screened to selectively activate thiol/dithioacetal, thiol/thioester, and thiol/disulfide exchanges, individually or in pairs. Some of those conditions were applied, sequentially, to build multilayer dynamic systems wherein information, in the form of relative amounts of building blocks, can be directionally transmitted between different exchange pools. As far as we know, this is the first report of one synthetic dynamic chemical system where relationships between layers can be changed through network operations.Fil: Martinez Amezaga, Maitena. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Química Orgánica. Área Farmacognosia; ArgentinaFil: Orrillo, Alfredo Gastón. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Química Orgánica. Área Farmacognosia; ArgentinaFil: Furlan, Ricardo Luis Eugenio. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Química Orgánica. Área Farmacognosia; Argentin

Chemical Frustration in Dynamic Multilevel Systems

Dynamic multilevel systems constructed with sequential-communicating reactions are a poorly studied type of thermodynamic systems. Recent work of our group showed that multilevel sequential systems are history-dependent and nonconmutative, since different compositions can be attained when one cycle of reactions is carried out by affecting the order of activation. In this work, we show that compositional divergence observed in previous work is the result of trapping the composition in frustrated states placed on local minima of the energy landscape. These intermediary steps in the trajectory can be overcome by the system, when it approaches the global energy minimum of the energy landscape, as expected in usual thermodynamic systems. The behavior of the multilevel system depends on its underlying energy landscape and can be externally regulated by adjusting starting materials and reaction conditions.Fil: Martinez Amezaga, Maitena. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Química Orgánica. Área Farmacognosia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; ArgentinaFil: Orrillo, Alfredo Gastón. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Química Orgánica. Área Farmacognosia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; ArgentinaFil: Furlan, Ricardo Luis Eugenio. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Departamento de Química Orgánica. Área Farmacognosia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario; Argentin

Recent approaches toward the generation of molecular diversity based on b-lactam structures

One of the most significant strategies in the search of biologically promising structures is the generation of scaffold diversity. Varying molecular scaffolds yielded useful small molecule tools for chemical genetic studies of cellular protein functions, apart from “classic” drug discovery approaches. In this chapter, the latest developments for the transformation of b-lactam monocyclic moieties into complex and diverse structures are discussed. The significance of the 2-azetidinones as starting material for the synthesis of libraries of fused and non-fused multicyclic b-lactams, multicyclic (non-b-lactamic) scaffolds, as well as new heterocyclic derivatives of pyrroles, c-lactones, c-lactams, oxazinones, imidazolidines, piperazines, piperidines, among others. Finally, the importance of b-lactam-based hybrids as a new source of potential biologically active compounds, have been also highlighted.Fil: Delpiccolo, Carina Maria Lujan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; ArgentinaFil: Martinez Amezaga, Maitena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; ArgentinaFil: Mata, Ernesto Gabino. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; Argentin

Immobilized boronic acid for Suzuki–Miyaura coupling: application to the generation of pharmacologically relevant molecules

An synthetic strategy for the generation of a variety of biaryl and related derivatives, based on Suzuki– Miyaura coupling using immobilized boronic acid, is described. The importance of the methodology was demonstrated by its further application to biologically interesting compounds such as 4-biaryl-blactams, descripted as cholesterol absorption inhibitors and anti-MRSA active agents, neoflavonoids, imidazoles, isoxazolines, among others.This is a post-peer-review, pre-copyedit version of an article published in RSC Advances. The final authenticated version is available online at: https://doi.org/10.1039/c7ra06662gFil: Martinez-Amezaga, Maitena. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario (IQUIR -CONICET); Argentina.Fil: Delpiccolo, Carina M. L. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario (IQUIR -CONICET); Argentina.Fil: Mata, Ernesto Gabino. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario (IQUIR -CONICET); Argentina

Unprecedented Multifunctionality of Grubbs and Hoveyda–Grubbs Catalysts: Competitive Isomerization, Hydrogenation, Silylation and Metathesis Occurring in Solution and on Solid Phase

This contribution showcases the interplay of several non-metathetic reactions (isomerization, silylation and “hydrogen-free” reduction) with metathesis in systems comprising a functionalized olefin and a soluble or resin-immobilized silane. These competing, one-pot reactions occur under activation by second-generation Ru-alkylidene catalysts. Different olefinic substrates were used to study the influence of the substitution pattern on the reaction outcome. Emphasis is placed upon the rarely reported yet important transformations implying a solid phase-supported silane reagent. Catalytic species involved in and reaction pathways accounting for these concurrent processes are evidenced. An unexpected result of this research was the clearly proved partial binding of the olefin to the resin, thereby removing it from the reacting ensemble

Light modulates metabolic pathways and other novel physiological traits in the human pathogen Acinetobacter baumannii

Light sensing in chemotrophic bacteria has been relatively recently ascertained. In the human pathogen Acinetobacter baumannii, light modulates motility, biofilm formation, and virulence through the blue-light-sensing-using flavin (BLUF) photoreceptor BlsA. In addition, light can induce a reduction in susceptibility to certain antibiotics, such as minocycline and tigecycline, in a photoreceptorindependent manner. In this work, we identified new traits whose expression levels are modulated by light in this pathogen, which comprise not only important determinants related to pathogenicity and antibiotic resistance but also metabolic pathways, which represents a novel concept for chemotrophic bacteria. Indeed, the phenylacetic acid catabolic pathway and trehalose biosynthesis were modulated by light, responses that completely depend on BlsA. We further show that tolerance to some antibiotics and modulation of antioxidant enzyme levels are also influenced by light, likely contributing to bacterial persistence in adverse environments. Also, we present evidence indicating that surfactant production is modulated by light. Finally, the expression of whole pathways and gene clusters, such as genes involved in lipid metabolism and genes encoding components of the type VI secretion system, as well as efflux pumps related to antibiotic resistance, was differentially induced by light. Overall, our results indicate that light modulates global features of the A. baumannii lifestyle.Fil: Müller, Gabriela Leticia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Tuttobene, Marisel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; ArgentinaFil: Altilio, Matías. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; ArgentinaFil: Martinez Amezaga, Maitena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Química Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Química Rosario; ArgentinaFil: Nguyen, Meaghan. California State University; Estados UnidosFil: Cribb, Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Cybulski, Larisa Estefania. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Ramirez, Maria Soledad. California State University; Estados UnidosFil: Altabe, Silvia Graciela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Mussi, María Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; Argentin

Antitumor activity of new chemical compounds in triple negative mammary adenocarcinoma models

Aim: According to the need for the development of new anticancer agents, we have synthetized novel bioactive compounds and aimed to determine their antitumor action. Materials & methods: We describe in vitro studies evaluating the effect of 35 novel chemical compounds on two triple negative murine mammary adenocarcinoma tumors. Results & conclusion: Three compounds were selected because of their high antitumor activity and their low toxicity to normal cells. Their effect on tumor cells apoptosis, clonogenicity and migratory capacity, were determined. We found that the selected compounds showed inhibition of viability and clonogenic capacity, and promotion of apoptosis. They also decreased the migratory capacity of tumor cells. The results obtained suggest the likelihood of their future use as antitumor and/or antimetastatic agents.In spite of the important progress achieved in cancer therapeutics, the percentage of people dying because of cancer is still high. Hence, we need to develop new, effective and nontoxic anticancer agents. We synthetized novel compounds and tested their antitumor effect and toxicity, in order to choose those that are effective and do not affect normal cells and therefore, are suitable for human cancer therapies. We selected three out of 35 compounds that show high antitumor action and low toxicity. Also, we studied the mechanisms by which that effect was achieved. Our next goal is to develop experiments with animals in order to have preclinical data that, hopefully, will lead to the clinical use of one or more of the selected compounds.Fil: Giolito, Maria Virginia. Universidad Nacional de Rosario. Facultad de Ciencias Médicas; Argentin