Yeray Rodriguez Nunez
Verified @unab.cl
Facultad de Ciencias Exactas
Universidad Andrés Bello
RESEARCH INTERESTS
Organic synthesis
Heterocycles chemistry
Medicinal chemistry
Scopus Publications
Scholar Citations
Scholar h-index
Scholar i10-index
Scopus Publications
Jorge Soto-Delgado, Yeray A. Rodríguez-Núñez, Cristian Guerra, Luis Prent-Peñaloza, and Mitchell Bacho
MDPI AG
A three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis incorporating ligand-receptor docking alignment and molecular dynamic (MD) simulations was conducted to elucidate the potent inhibitory effects of a series of benzamide derivatives on histone deacetylase 1 (HDAC1). A comparison between ligand-based (LB) and receptor-based (RB) 3D-QSAR models using molecular docking alignment produced statistically significant results. Steric and electrostatic contour maps provided insights into the interactions surrounding the benzamide ring, revealing that an increase in electron density enhances inhibitory activity. Furthermore, MD simulations were employed to investigate protein-ligand interactions in greater detail, yielding outcomes consistent with those from 3D-QSAR and molecular docking studies. This integrated approach of molecular docking, 3D-QSAR, and energy decomposition analysis derived from MD simulations, provides a valuable framework for the rational design of more potent HDAC1 inhibitors, facilitating the synthesis of highly effective anti-tumor compounds based on benzamide scaffolds.
Manuel E Taborda-Martínez, Adriana Rodríguez-Forero, Mitchell Bacho, Fabián Espitia-Almeida, Ericsson Coy-Barrera, and Yeray A Rodríguez-Núñez
SAGE Publications
Objective Marine organisms such as sea cucumbers represent valuable sources of specialized metabolites with promising applications, making them relevant targets for exploring metabolite distribution and subsequent in-depth characterization. This study aimed to chemically and biologically characterize the parent methanolic extract and its derived fractions, obtained through sequential liquid–liquid partitioning, from the sea cucumber Isostichopus sp. aff . badionotus collected from the Colombian Caribbean Sea. Methods The extract and fractions were analyzed using ultra-high-performance liquid chromatography coupled with mass spectrometry and the Global Natural Products Social-based molecular networking platform, enabling dereplication and identification of metabolites. Additionally, the extract and fractions were evaluated against eight Gram-positive and Gram-negative bacterial strains using broth microdilution assays. Results The dichloromethane fractions exhibited the highest antibacterial activity against both Gram-positive and Gram-negative bacteria. For the first time, chemical characterization allowed the identification of a series of metabolites present in the extract and fractions. Conclusion This study provides the first report on antibacterial activity in I. sp. aff . badionotus , demonstrating that medium-polarity compounds in the dichloromethane fraction exhibited moderate bacterial inhibition, particularly against Gram-positive strains.
Cristian J. Guerra, Yeray A. Rodríguez-Núñez, Efraín Polo-Cuadrado, Leandro Ayarde-Henríquez, Diana B. Ramírez, and Adolfo E. Ensuncho
Royal Society of Chemistry (RSC)
The photoisomerization of BN-Dewar benzene to BN-benzvalene derivatives is driven by excited-state dynamics mediated by two S1/S0 minimum energy conical intersections, with bond rearrangements occurring on both the S1 and S0 surfaces.
Marcos Lorca, Gisela C. Muscia, Jaime Mella, Luciana Thomaz, Jenicer K. Yokoyama-Yasunaka, Daniel Moraga, Yeray A. Rodriguez-Nuñez, Silvia E. Asís, Mauro Cortez, and Marco Mellado
MDPI AG
Background: Leishmania amazonensis, one of the causative agents of cutaneous leishmaniasis, is responsible for a neglected tropical disease affecting nearly one million individuals worldwide. Although clinical treatments are available, their effectiveness is often compromised by high toxicity and limited selectivity. Methods: From a database, 64 chalcone derivatives were studied using Comparative Molecular Similarity Indices Analysis (CoMSIA) and Hansch analysis (2D-QSAR) to construct predictive computational models. Internal and external validation criteria were applied to identify structural determinants associated with antileishmanial activity. Based on these insights, twelve novel quinoline–chalcone hybrids were designed, synthesized, and biologically evaluated against L. amazonensis. Results: The most robust CoMSIA model combined steric and hydrogen-bond acceptor fields (CoMSIA-SA), while Hansch analysis highlighted electronic descriptors—specifically LUMO energy and the global electrophilicity index—as critical for parasite growth inhibition. Guided by these computational findings, a new series of 12 hybrid quinoline–chalcone derivatives (E001–E012) was synthesized through a two-step procedure, achieving overall yields of 43–71%. Biological assays demonstrated that four compounds displayed inhibitory activity comparable to amphotericin B. Furthermore, physicochemical profiling and in silico pharmacokinetic predictions for the most active compounds (E003, E005, E006, and E011) indicated favorable biocompatibility and drug-like properties. Conclusions: These results underscore the value of an integrative computational–experimental approach in the rational design of next-generation L. amazonensis inhibitors, reinforcing chalcone-based scaffolds as promising pharmacophoric frameworks for antileishmanial drug discovery.
Efraín Polo-Cuadrado, Cristian Rojas-Peña, Karen Acosta-Quiroga, Lorena Camargo-Ayala, Yeray A. Rodríguez-Núñez, Edison Osorio, Jhon J. López, Rhonny Brid-Cuadrado, and Margarita Gutierrez
Elsevier BV
Yeray A. Rodríguez-Núñez, Jesús Sánchez-Márquez, Jorge Quintero-Saumeth, Cristian J. Guerra, Efraín Polo-Cuadrado, David Villaman, Cristopher A. Fica-Cornejo, and Arnold R. Romero Bohórquez
Royal Society of Chemistry (RSC)
This study explored the mechanism of the Lewis acid-catalyzed Povarov cationic reaction. InCl3 showed the best performance, and the tetrahydroquinoline core is formed via a domino Mannich–Friedel Crafts reaction, discarding the terms “Diels–Alder”.
Efraín Polo-Cuadrado, Karen Acosta-Quiroga, Cristian Rojas-Peña, Yeray A. Rodriguez-Nuñez, Edgard Fabián Blanco-Acuña, Jhon J. Lopez, Iván Brito, Jonathan Cisterna, Joel B. Alderete, and Margarita Gutiérrez
Royal Society of Chemistry (RSC)
Multicomponent cyclocondensations of 5-amino-3-methyl-1-phenyl-1H-pyrazole (AMPZ), thiobarbituric acid, and p-formaldehyde under conventional thermal heating or ultrasonic irradiation were studied.
Cristian Guerra, Yeray A. Rodríguez-Núñez, Efraín Polo-Cuadrado, and Adolfo Ensuncho
Elsevier BV
Cristian Guerra, Yeray A. Rodríguez-Núñez, Manuel E. Taborda-Martínez, Mitchell Bacho, Rafael Miranda-Pastrana, and Adolfo E. Ensuncho
Royal Society of Chemistry (RSC)
We used ab initio methods to study the 4π-photocyclization of α-tropones. Acid catalysts and electron-donating groups lower energy barriers, promoting the formation of bicyclo[3.2.0]hepta-3,6-dien-2-one derivatives via T1/S0 and S1/S0 crossings.
Efraín Polo-Cuadrado, Karoll Ferrer, Jesús Sánchez-Márquez, Andrés Charris-Molina, Yeray A. Rodríguez-Núñez, Luis Espinoza-Catalán, and Margarita Gutiérrez
Elsevier BV
Cristian Guerra, Yeray A. Rodríguez‐Núñez, and Adolfo E. Ensuncho
Wiley
AbstractThis investigation delves into the UV photodissociation of pivotal amino acids (Alanine, Glycine, Leucine, Proline, and Serine) at 213 nm, providing insights into triplet‐state deactivation pathways. Utilizing a comprehensive approach involving time‐dependent density functional calculations (TD‐DFT), multi‐configurational methods, and ab‐initio molecular dynamics (AIMD) simulations, we scrutinize the excited electronic states (T1, T2, and S1) subsequent to 213 nm excitation. Our findings demonstrate that α‐carbonyl C−C bond‐breaking in triplet states exhibits markedly lower barriers than in singlet states (below 5.0 kcal mol−1). AIMD simulations corroborate the potential involvement of triplet states in amino acid fragmentation, underscoring the significance of accounting for these states in photochemistry. Chemical bonding analyses unveil distinctive patterns for S1 and T1 states, with the asymmetric redistribution of electron density characterizing the C−C breaking in triplet states, in contrast to the symmetric breaking observed in singlet states. This research complements recent experimental discoveries, enhancing our comprehension of amino acid reactions in the interstellar medium.
Cristian Guerra, Leandro Ayarde-Henríquez, Yeray A. Rodriguez-Nuñez, Eduardo Chamorro, and Adolfo E. Ensuncho
Royal Society of Chemistry (RSC)
Non-adiabatic transitions in 1,2-di-iodo benzene photolysis: radical-intermediate-free benzyne formation.
Cristian Guerra, Leandro Ayarde‐Henríquez, Yeray A. Rodríguez‐Núñez, Adolfo Ensuncho, and Eduardo Chamorro
Wiley
In this study, we revealed the significance of chemical bonding for the photochemically induced mechanism of 2-phenyl tetrazole derivatives generating nitrile imines. The correlated electron localization function shows that the formation of imine nitrile involves two key bond events: (i) the heterolytic C-N breakage taking place in the T1 state and (ii) the homolytic N-N rupture occurring in the T2 excited state. In particular, a cation-radical specie results from the C-N cleavage, whereas the N-N rupture creates a biradical resonant form of imine nitrile. Additionally, we noticed that the substantial pair delocalization of the C-C-N bonded structure could play a significant role in the conversion of the biradical imine nitrile into both the propargylic and allenic forms via the T1 →S0 deactivation.
Carlos Fernández-Galleguillos, Felipe Jiménez-Aspee, Daniel Mieres-Castro, Yeray A. Rodríguez-Núñez, Margarita Gutiérrez, Luis Guzmán, Javier Echeverría, Claudia Sandoval-Yañez, and Oscar Forero-Doria
MDPI AG
This research aimed to identify the phenolic profile and composition of the aerial parts of three native species used in traditional medicine in the Andean Altiplano of northern Chile: Clinopodium gilliesii (Benth.) Kuntze [Lamiaceae] (commonly known as Muña-Muña), Mutisia acuminata Ruiz & Pav. var. hirsuta (Meyen) Cabrera [Asteraceae] (commonly known as Chinchircoma), and Tagetes multiflora (Kunth), [Asteraceae] (commonly known as Gracilis), as well as to evaluate their potential inhibitory effects against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Polyphenolic enriched-extracts (PEEs) of the species were prepared and analyzed and the main components were quantified using HPLC-DAD. In total, 30 phenolic compounds were identified and quantified in all species, including simple phenolics, hydroxycinnamic acids, flavan-3-ols (monomers and polymers), flavanones, and flavonols. In addition, other main phenolics from the extracts were tentatively identified by ESI-MS-MS high-resolution analysis. T. multiflora extract showed the greatest anti-AChE and BChE activity in comparison with C. gilliesii and M. acuminata extracts, being the anti-AChE and BChE activity weak in all extracts in comparison to galantamine control. To comprise to better understand the interactions between cholinesterase enzymes and the main phenolics identified in T. multiflora, molecular docking analysis was conducted.
Efraín Polo-Cuadrado, Cristian Rojas-Peña, Karen Acosta-Quiroga, Lorena Camargo-Ayala, Iván Brito, Jonathan Cisterna, Félix Moncada, Jorge Trilleras, Yeray A. Rodríguez-Núñez, and Margarita Gutierrez
Royal Society of Chemistry (RSC)
Different synthetic strategies were used to optimize, obtaining a series of compounds derived from the pyrazole-fused phenanthroline system.
Fausto M. Güiza, Yeray A. Rodríguez-Núñez, David Ramírez, Arnold R. Romero Bohórquez, José Antonio Henao, Robert A. Toro, José Miguel Delgado, and Graciela Díaz de Delgado
Elsevier BV
Efraín Polo-Cuadrado, Karen Acosta-Quiroga, Cristian Rojas-Peña, Yeray A. Rodriguez-Nuñez, Yorley Duarte, Iván Brito, Jonathan Cisterna, and Margarita Gutiérrez
Elsevier BV
Efraín Polo, Luis Prent-Peñaloza, Yeray A. Rodríguez Núñez, Lady Valdés-Salas, Jorge Trilleras, Juan Ramos, José A. Henao, Antonio Galdámez, Alejandro Morales-Bayuelo, and Margarita Gutiérrez
Elsevier BV
Yeray A. Rodríguez Núñez, Margarita Gutíerrez, Jans Alzate-Morales, Francisco Adasme-Carreño, Fausto M. Güiza, Cristian C. Bernal, and Arnold R. Romero Bohórquez
MDPI AG
A series of 44 hybrid compounds that included in their structure tetrahydroquinoline (THQ) and isoxazole/isoxazoline moieties were synthesized through the 1,3-dipolar cycloaddition reaction (1,3-DC) from the corresponding N-allyl/propargyl THQs, previously obtained via cationic Povarov reaction. In vitro cholinergic enzymes inhibition potential of all compounds was tested. Enzyme inhibition assays showed that some hybrids exhibited significant potency to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Especially, the hybrid compound 5n presented the more effective inhibition against AChE (4.24 µM) with an acceptable selectivity index versus BChE (SI: 5.19), while compound 6aa exhibited the greatest inhibition activity on BChE (3.97 µM) and a significant selectivity index against AChE (SI: 0.04). Kinetic studies were carried out for compounds with greater inhibitory activity of cholinesterases. Structure–activity relationships of the molecular hybrids were analyzed, through computational models using a molecular cross-docking algorithm and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy approach, which indicated a good correlation between the experimental inhibition values and the predicted free binding energy.
Samuel Morales-Navarro, Luis Prent-Peñaloza, Yeray A. Rodríguez Núñez, Laura Sánchez-Aros, Oscar Forero-Doria, Wendy González, Nuria E. Campilllo, Miguel Reyes-Parada, Ana Martínez, and David Ramírez
MDPI AG
In recent years, green chemistry has been strengthening, showing how basic and applied sciences advance globally, protecting the environment and human health. A clear example of this evolution is the synergy that now exists between theoretical and computational methods to design new drugs in the most efficient possible way, using the minimum of reagents and obtaining the maximum yield. The development of compounds with potential therapeutic activity against multiple targets associated with neurodegenerative diseases/disorders (NDD) such as Alzheimer’s disease is a hot topic in medical chemistry, where different scientists from various disciplines collaborate to find safe, active, and effective drugs. NDD are a public health problem, affecting mainly the population over 60 years old. To generate significant progress in the pharmacological treatment of NDD, it is necessary to employ different experimental strategies of green chemistry, medical chemistry, and molecular biology, coupled with computational and theoretical approaches such as molecular simulations and chemoinformatics, all framed in the rational drug design targeting NDD. Here, we review how green chemistry and computational approaches have been used to develop new compounds with the potential application against NDD, as well as the challenges and new directions of the drug development multidisciplinary process.
Yeray A. Rodriguez Núñez, Maximiliano Norambuena, Arnold R. Romero Bohorquez, Alejandro Morales-Bayuelo, and Margarita Gutíerrez
Elsevier BV
Yeray Rodríguez Nuñez, Ricardo Castro, Felipe Arenas, Zoraya López-Cabaña, Gustavo Carreño, Verónica Carrasco-Sánchez, Adolfo Marican, Jorge Villaseñor, Esteban Vargas, Leonardo Santos,et al.
MDPI AG
In this study, a versatile synthesis of silver nanoparticles of well-defined size by using hydrogels as a template and stabilizer of nanoparticle size is reported. The prepared hydrogels are based on polyvinyl alcohol and maleic acid as crosslinker agents. Three hydrogels with the same nature were synthesized, however, the crosslinking degree was varied. The silver nanoparticles were synthesized into each prepared hydrogel matrix achieving three significant, different-sized nanoparticles that were spherical in shape with a narrow size distribution. It is likely that the polymer network stabilized the nanoparticles. It was determined that the hydrogel network structure can control the size and shape of the nanoparticles. The hydrogel/silver nanohybrids were characterized by swelling degree, Thermal Gravimetric Analysis (TGA), Fourier Transform Infrared (FT-IR), Scanning Electron Microscopy (SEM) and Transmission Electron Microscope (TEM). Antibacterial activity against Staphylococcus aureus was evaluated, confirming antimicrobial action of the encapsulated silver nanoparticles into the hydrogels.
Fabián Avila-Salas, Yeray Rodriguez Nuñez, Adolfo Marican, Ricardo Castro, Jorge Villaseñor, Leonardo Santos, Sergio Wehinger, and Esteban Durán-Lara
MDPI AG
This work depicts the rational development (in-silico design, synthesis, characterization and in-vitro evaluation) of polyvinyl alcohol hydrogels (PVAH) cross-linked with maleic acid (MA) and linked to γ-cyclodextrin molecules (γ-CDPVAHMA) as systems for the controlled and sustained release of nifedipine (NFD). Through computational studies, the structural blocks (PVA chain + dicarboxylic acid + γ-CD) of 20 different hydrogels were evaluated to test their interaction energies (ΔE) with NFD. According to the ΔE obtained, the hydrogel cross-linked with maleic acid was selected. To characterize the intermolecular interactions between NFD and γ-CDPVAHMA, molecular dynamics simulation studies were carried out. Experimentally, three hydrogel formulations with different proportions of γ-CD (2.43%, 3.61% and 4.76%) were synthesized and characterized. Both loading and release of NFD from the hydrogels were evaluated at acid and basic pH. The computational and experimental results show that γ-CDs linked to the hydrogels were able to form 1:1 inclusion complexes with NFD molecules. Finally, γ-CDPVAHMA-3 demonstrated to be the best pH-sensitive release platform for nifedipine. Its effectiveness could significantly reduce the adverse effects caused by the anticipated release of NFD in the stomach of patients.
Yongming Deng, Lynée A. Massey, Yeray A. Rodriguez Núñez, Hadi Arman, and Michael P. Doyle
Wiley
Highly selective divergent cycloaddition reactions of enoldiazo compounds and α-diazocarboximides catalyzed by copper(I) or dirhodium(II) have been developed. With tetrakis(acetonitrile)copper(I) tetrafluoroborate as the catalyst epoxypyrrolo[1,2-a]azepine derivatives were prepared in good yields and excellent diastereoselectivities through the first reported [3+3]-cycloaddition of a carbonyl ylide. Use of Rh2 (pfb)4 or Rh2 (esp)2 directs the reactants to regioselective [3+2]-cycloaddition generating cyclopenta[2,3]pyrrolo[2,1-b]oxazoles with good yields and excellent diastereoselectivities.
Yeray A. Rodríguez, Margarita Gutiérrez, David Ramírez, Jans Alzate‐Morales, Cristian C. Bernal, Fausto M. Güiza, and Arnold R. Romero Bohórquez
Wiley
New N‐allyl/propargyl 4‐substituted 1,2,3,4‐tetrahydroquinolines derivatives were efficiently synthesized using acid‐catalyzed three components cationic imino Diels–Alder reaction (70–95%). All compounds were tested in vitro as dual acetylcholinesterase and butyryl‐cholinesterase inhibitors and their potential binding modes, and affinity, were predicted by molecular docking and binding free energy calculations (∆G) respectively. The compound 4af (IC50 = 72 μm) presented the most effective inhibition against acetylcholinesterase despite its poor selectivity (SI = 2), while the best inhibitory activity on butyryl‐cholinesterase was exhibited by compound 4ae (IC50 = 25.58 μm) with considerable selectivity (SI = 0.15). Molecular docking studies indicated that the most active compounds fit in the reported acetylcholinesterase and butyryl‐cholinesterase active sites. Moreover, our computational data indicated a high correlation between the calculated ∆G and the experimental activity values in both targets.