Substituent-controlled photocyclization pathways of 3H-azepines: insights from TD-DFT and bonding evolution theory Cristian J. Guerra, Leandro Ayarde-Henríquez, Patricia Pérez, Eduardo Chamorro, Jorge Soto-Delgado, et al. New Journal of Chemistry, 2026 The photocyclization of 3 H -azepines exhibits a striking substituent-dependent preference toward the formation of the 2-azabicyclo[3.2.0]hepta-2,6-diene isomer, in agreement with experimental findings, while 6-substituted analogues remain unobserved.
Photochemical Rearrangements of Pyridine N-Oxides: Pathways to Oxaziridine Derivatives Cristian J. Guerra, Yeray A. Rodríguez-Núñez, Efraín Polo-Cuadrado, Mitchell Bacho, Jorge Soto-Delgado, et al. Molecules, 2025 The photochemical behavior of substituted pyridine N-Oxides is characterized by complex rearrangements culminating in the formation of valuable photoproducts. The CAS(10,8)/cc-pVDZ approach with NEVPT2 corrections is applied to investigate geometric distortions associated with the S1 excited state, conical intersections, and the ultimate transformation of pyridine N-Oxides into oxaziridine-like derivative formations. Our results reveal that the deactivation of the S1 excited state is driven by an out-of-plane rotation of the N-O oxygen atom, resulting in the formation of a lone pair over the nitrogen atom. Along this excited-state reaction pathway, the N-O bond undergoes significant weakening, while a C=C double bond emerges mainly in the excited state. The deactivation at the minimum-energy conical intersection leading to the ground state reveals the formation of an oxaziridine-like intermediate, which subsequently converts into a 1,2-oxazepine derivative.
Comprehensive Structure-Activity Relationship Analysis of Benzamide Derivatives as Histone Deacetylase 1 (HDAC1) Inhibitors Jorge Soto-Delgado, Yeray A. Rodríguez-Núñez, Cristian Guerra, Luis Prent-Peñaloza, Mitchell Bacho International Journal of Molecular Sciences, 2025 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.
Metabolite profiling-based characterization and antibacterial activity of sea cucumber Isostichopus sp. aff. badionotus from the Colombian Caribbean Sea Manuel E Taborda-Martínez, Adriana Rodríguez-Forero, Mitchell Bacho, Fabián Espitia-Almeida, Ericsson Coy-Barrera, et al. Science Progress, 2025 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.
From BN-Dewar benzene to BN-benzvalene: a computational exploration of photoisomerization mechanisms Cristian J. Guerra, Yeray A. Rodríguez-Núñez, Efraín Polo-Cuadrado, Leandro Ayarde-Henríquez, Diana B. Ramírez, et al. Organic and Biomolecular Chemistry, 2025 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.
Design of Hybrid Quinoline–Chalcone Compounds Against Leishmania amazonensis Based on Computational Techniques: 2D- and 3D-QSAR with Experimental Validation Marcos Lorca, Gisela C. Muscia, Jaime Mella, Luciana Thomaz, Jenicer K. Yokoyama-Yasunaka, et al. Pharmaceuticals, 2025 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.
A novel quinine derivative as a PIM-1 kinase inhibitor induces apoptosis via mitochondrial depolarization with selective cytotoxicity in acute lymphoblastic leukemia cells V Donoso-Bustamante, EH Osorio, GC Torres, JA López-Saenz, ... Frontiers in Pharmacology 17, 1799674 , 2026 2026
Harnessing Conical Intersections for Synthesizing BN-Valence Isomers CJ Guerra, YA Rodríguez-Núñez, LA Henríquez 2026
Combined experimental and computational investigation of a novel naphthalene-based VEGFR-2 inhibitor with nonlinear optical activity E Polo-Cuadrado, C Jiménez, C Rojas-Peña, K Cobos-Montes, ... Journal of Molecular Structure, 145753 , 2026 2026
Targeting Bothrops asper Venom Enzymes: Steroidal Derivatives as potential Inhibitors of Phospholipase A2, Serine proteinases, and metalloproteinases. M Bacho, YA Rodriguez-Núñez, CJ Guerra, E Polo-Cuadrado, ... bioRxiv, 2026.04. 15.718639 , 2026 2026
Multimodal characterization of a pyrazolo [3, 4-b] pyridine aldehyde: quantum chemical insights, NLO activity and VEGFR-2 docking/molecular dynamics K Acosta-Quiroga, CA Jiménez, K Cobos-Montes, YA Rodríguez-Núñez, ... RSC Advances 16 (8), 7648-7658 , 2026 2026
Substituent-controlled photocyclization pathways of 3 H-azepines: insights from TD-DFT and bonding evolution theory CJ Guerra, L Ayarde-Henríquez, P Pérez, E Chamorro, J Soto-Delgado, ... New Journal of Chemistry 50 (7), 3332-3340 , 2026 2026 Citations: 5
Photochemical Rearrangements of Pyridine N-Oxides: Pathways to Oxaziridine Derivatives CJ Guerra, YA Rodríguez-Núñez, E Polo-Cuadrado, M Bacho, ... Molecules 30 (24), 4776 , 2025 2025 Citations: 6
Design of Hybrid Quinoline–Chalcone Compounds Against Leishmania amazonensis Based on Computational Techniques: 2D- and 3D-QSAR with Experimental … M Lorca, GC Muscia, J Mella, L Thomaz, JK Yokoyama-Yasunaka, ... Pharmaceuticals 18 (10), 1567 , 2025 2025
Comprehensive Structure-Activity Relationship Analysis of Benzamide Derivatives as Histone Deacetylase 1 (HDAC1) Inhibitors J Soto-Delgado, YA Rodríguez-Núñez, C Guerra, L Prent-Peñaloza, ... International Journal of Molecular Sciences 26 (20), 9970 , 2025 2025 Citations: 2
Metabolite profiling-based characterization and antibacterial activity of sea cucumber Isostichopus sp. aff. badionotus from the Colombian Caribbean Sea ME Taborda-Martínez, A Rodríguez-Forero, M Bacho, F Espitia-Almeida, ... Science Progress 108 (4), 00368504251407127 , 2025 2025
Exploring pyridinium-based inhibitors of cholinesterases: A review of synthesis, efficacy, and structural insights E Polo-Cuadrado, C Rojas-Peña, K Acosta-Quiroga, L Camargo-Ayala, ... European Journal of Medicinal Chemistry Reports 14, 100270 , 2025 2025 Citations: 4
Topological bonding fingerprints in photochemically substituted [2+ 2] cycloaddition C Guerra, YA Rodríguez-Núñez, E Polo-Cuadrado, A Ensuncho Journal of Photochemistry and Photobiology A: Chemistry 459, 116038 , 2025 2025 Citations: 2
From BN-Dewar benzene to BN-benzvalene: a computational exploration of photoisomerization mechanisms CJ Guerra, YA Rodríguez-Núñez, E Polo-Cuadrado, L Ayarde-Henríquez, ... Organic & Biomolecular Chemistry 23 (38), 8769-8777 , 2025 2025 Citations: 8
Mechanistic insights on the Lewis acid-catalyzed three-component cationic Povarov reaction: synthesis of N-propargyl 1, 2, 3, 4-tetrahydroquinolines YA Rodríguez-Núñez, J Sánchez-Márquez, J Quintero-Saumeth, ... RSC advances 15 (15), 11799-11810 , 2025 2025 Citations: 3
Regioselective cyclocondensations with thiobarbituric acid: spirocyclic and azocine products, X-ray characterization, and antioxidant evaluation E Polo-Cuadrado, K Acosta-Quiroga, C Rojas-Peña, ... RSC advances 15 (11), 8609-8621 , 2025 2025 Citations: 2
Unexpected discovery:“A new 3, 3′-bipyrazolo [3, 4-b] pyridine scaffold and its comprehensive analysis” E Polo-Cuadrado, K Ferrer, J Sánchez-Márquez, A Charris-Molina, ... Heliyon 10 (11) , 2024 2024 Citations: 3
Role of Triplet States in the Photolysis of Proteogenic Amino Acids C Guerra, YA Rodríguez‐Núñez, AE Ensuncho ChemPhysChem 25 (3), e202300655 , 2024 2024 Citations: 1
Theoretical exploration of the 4π-photocyclization mechanism of α-tropone derivatives C Guerra, YA Rodríguez-Núñez, ME Taborda-Martínez, M Bacho, ... New Journal of Chemistry 48 (40), 17633-17640 , 2024 2024 Citations: 3
Elucidating the N− N and C− N Bond‐breaking Mechanism in the Photoinduced Formation of Nitrile Imine C Guerra, L Ayarde‐Henríquez, YA Rodríguez‐Núñez, A Ensuncho, ... ChemPhysChem 24 (11), e202200867 , 2023 2023 Citations: 30
Phenolic Profile and Cholinesterase Inhibitory Properties of Three Chilean Altiplano Plants: Clinopodium gilliesii (Benth.) Kuntze [Lamiaceae], Mutisia acuminata Ruiz & Pav … C Fernández-Galleguillos, F Jiménez-Aspee, D Mieres-Castro, ... Plants 12 (4), 819 , 2023 2023 Citations: 11
MOST CITED SCHOLAR PUBLICATIONS
Novel N ‐allyl/propargyl tetrahydroquinolines: Synthesis via Three‐component Cationic Imino Diels–Alder Reaction, Binding Prediction, and Evaluation as … YA Rodríguez, M Gutiérrez, D Ramírez, J Alzate‐Morales, CC Bernal, ... Chemical biology & drug design 88 (4), 498-510 , 2016 2016 Citations: 68
Catalytic Divergent [3+ 3]‐and [3+ 2]‐Cycloaddition by Discrimination Between Diazo Compounds Y Deng, LA Massey, YA Rodriguez Núñez, H Arman, MP Doyle Angewandte Chemie 129 (40), 12460-12464 , 2017 2017 Citations: 58
Preparation of hydrogel/silver nanohybrids mediated by tunable-size silver nanoparticles for potential antibacterial applications YA Rodriguez Nunez, RI Castro, FA Arenas, ZE López-Cabaña, ... Polymers 11 (4), 716 , 2019 2019 Citations: 55
Elucidating the N− N and C− N Bond‐breaking Mechanism in the Photoinduced Formation of Nitrile Imine C Guerra, L Ayarde‐Henríquez, YA Rodríguez‐Núñez, A Ensuncho, ... ChemPhysChem 24 (11), e202200867 , 2023 2023 Citations: 30
Rational Development of a Novel Hydrogel as a pH-Sensitive Controlled Release System for Nifedipine F Avila-Salas, YA Rodriguez Nuñez, A Marican, RI Castro, J Villaseñor, ... polymers 10 (7), 806 , 2018 2018 Citations: 27
Caracterización fisicoquímica y evaluación de la actividad antioxidante de propóleos recolectados en el departamento del Atlántico, Colombia Y Rodríguez, F Sánchez-Catalán, B Rojano, D Durango, J Gil, ... Revista UDCA Actualidad & Divulgación Científica 15 (2), 303-311 , 2012 2012 Citations: 23
Antioxidant activity and total phenolics of plants used in traditional medicine in Ecuador A Jara, Y Rodriguez, J Cornejo, ME Cazar, M Gutierrez, L Astudillo The 17th International Electronic Conference on Synthetic Organic Chemistry … , 2013 2013 Citations: 22
Mechanistic insights into benzyne formation via 1, 2-di-iodobenzene photolysis C Guerra, L Ayarde-Henríquez, YA Rodriguez-Nuñez, E Chamorro, ... New Journal of Chemistry 47 (46), 21270-21275 , 2023 2023 Citations: 21
Molecular modeling and structural analysis of some tetrahydroindazole and cyclopentanepyrazole derivatives as COX-2 inhibitors E Polo-Cuadrado, K Acosta-Quiroga, C Rojas-Pena, ... Arabian Journal of Chemistry 15 (2), 103540 , 2022 2022 Citations: 20
Efficient synthesis and antioxidant activity of novel N-propargyl tetrahydroquinoline derivatives through the cationic Povarov reaction YA Rodríguez Núñez, M Norambuena, AR Romero Bohorquez, ... Heliyon 5 (8) , 2019 2019 Citations: 13
Design, synthesis, theoretical study, antioxidant, and anticholinesterase activities of new pyrazolo-fused phenanthrolines E Polo-Cuadrado, C Rojas-Pena, K Acosta-Quiroga, L Camargo-Ayala, ... RSC advances 12 (51), 33032-33048 , 2022 2022 Citations: 12
Phenolic Profile and Cholinesterase Inhibitory Properties of Three Chilean Altiplano Plants: Clinopodium gilliesii (Benth.) Kuntze [Lamiaceae], Mutisia acuminata Ruiz & Pav … C Fernández-Galleguillos, F Jiménez-Aspee, D Mieres-Castro, ... Plants 12 (4), 819 , 2023 2023 Citations: 11
Microwave-assisted synthesis, biological assessment, and molecular modeling of aza-heterocycles: Potential inhibitory capacity of cholinergic enzymes to Alzheimer's disease E Polo, L Prent-Peñaloza, YAR Núñez, L Valdés-Salas, J Trilleras, ... Journal of Molecular Structure 1224, 129307 , 2021 2021 Citations: 11
Tetrahydroquinoline-isoxazole/isoxazoline hybrid compounds as potential cholinesterases inhibitors: Synthesis, enzyme inhibition assays, and molecular modeling studies YA Rodríguez Núñez, M Gutíerrez, J Alzate-Morales, F Adasme-Carreño, ... International Journal of Molecular Sciences 21 (1), 5 , 2019 2019 Citations: 11
Theoretical and experimental approaches aimed at drug design targeting neurodegenerative diseases S Morales-Navarro, L Prent-Peñaloza, YA Rodríguez Núñez, ... Processes 7 (12), 940 , 2019 2019 Citations: 9
From BN-Dewar benzene to BN-benzvalene: a computational exploration of photoisomerization mechanisms CJ Guerra, YA Rodríguez-Núñez, E Polo-Cuadrado, L Ayarde-Henríquez, ... Organic & Biomolecular Chemistry 23 (38), 8769-8777 , 2025 2025 Citations: 8
Crystal structure, Hirshfeld surface analysis, and molecular dynamics simulations of two isostructural N-propargyl-4-(2-oxopyrrolidin-1-yl)-1, 2, 3, 4-tetrahydroquinolines FM Güiza, YA Rodríguez-Núñez, D Ramírez, ARR Bohórquez, JA Henao, ... Journal of Molecular Structure 1254, 132280 , 2022 2022 Citations: 8
Photochemical Rearrangements of Pyridine N-Oxides: Pathways to Oxaziridine Derivatives CJ Guerra, YA Rodríguez-Núñez, E Polo-Cuadrado, M Bacho, ... Molecules 30 (24), 4776 , 2025 2025 Citations: 6
Substituent-controlled photocyclization pathways of 3 H-azepines: insights from TD-DFT and bonding evolution theory CJ Guerra, L Ayarde-Henríquez, P Pérez, E Chamorro, J Soto-Delgado, ... New Journal of Chemistry 50 (7), 3332-3340 , 2026 2026 Citations: 5
Exploring pyridinium-based inhibitors of cholinesterases: A review of synthesis, efficacy, and structural insights E Polo-Cuadrado, C Rojas-Peña, K Acosta-Quiroga, L Camargo-Ayala, ... European Journal of Medicinal Chemistry Reports 14, 100270 , 2025 2025 Citations: 4
