24 results on '"Yorley Duarte"'
Search Results
2. Increased Absorption of Thyroxine in a Murine Model of Hypothyroidism Using Water/CO2 Nanobubbles
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Maria Cecilia Opazo, Osvaldo Yañez, Valeria Márquez-Miranda, Johana Santos, Maximiliano Rojas, Ingrid Araya-Durán, Daniel Aguayo, Matías Leal, Yorley Duarte, Jorge Kohanoff, and Fernando D. González-Nilo
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thyroxine ,nanobubbles ,drug delivery ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Thyroxine (T4) is a drug extensively utilized for the treatment of hypothyroidism. However, the oral absorption of T4 presents certain limitations. This research investigates the efficacy of CO2 nanobubbles in water as a potential oral carrier for T4 administration to C57BL/6 hypothyroid mice. Following 18 h of fasting, the formulation was administered to the mice, demonstrating that the combination of CO2 nanobubbles and T4 enhanced the drug’s absorption in blood serum by approximately 40%. To comprehend this observation at a molecular level, we explored the interaction mechanism through which T4 engages with the CO2 nanobubbles, employing molecular simulations, semi-empirical quantum mechanics, and PMF calculations. Our simulations revealed a high affinity of T4 for the water–gas interface, driven by additive interactions between the hydrophobic region of T4 and the gas phase and electrostatic interactions of the polar groups of T4 with water at the water–gas interface. Concurrently, we observed that at the water–gas interface, the cluster of T4 formed in the water region disassembles, contributing to the drug’s bioavailability. Furthermore, we examined how the gas within the nanobubbles aids in facilitating the drug’s translocation through cell membranes. This research contributes to a deeper understanding of the role of CO2 nanobubbles in drug absorption and subsequent release into the bloodstream. The findings suggest that utilizing CO2 nanobubbles could enhance T4 bioavailability and cell permeability, leading to more efficient transport into cells. Additional research opens the possibility of employing lower concentrations of this class of drugs, thereby potentially reducing the associated side effects due to poor absorption.
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- 2024
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3. Multicomponent synthesis and photophysical study of novel α,β-unsaturated carbonyl depsipeptides and peptoids
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Ricelia González, Juliana Murillo-López, Walter Rabanal-León, Luis Prent-Peñaloza, Odette Concepción, Pedro Olivares, Yorley Duarte, Alexander F. de la Torre, Margarita Gutiérrez, and Julio Caballero
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multicomponent reactions ,depsipeptides ,peptoids ,time-dependent density functional theory (TD-DFT) ,peptidomimetics ,Chemistry ,QD1-999 - Abstract
Multicomponent reactions were performed to develop novel α,β-unsaturated carbonyl depsipeptides and peptoids incorporating various chromophores such as cinnamic, coumarin, and quinolines. Thus, through the Passerini and Ugi multicomponent reactions (P-3CR and U-4CR), we obtained thirteen depsipeptides and peptoids in moderate to high yield following the established protocol and fundamentally varying the electron-rich carboxylic acid as reactants. UV/Vis spectroscopy was utilized to study the photophysical properties of the newly synthesized compounds. Differences between the carbonyl-substituted chromophores cause differences in electron delocalization that can be captured in the spectra. The near UV regions of all the compounds exhibited strong absorption bands. Compounds P2, P5, U2, U5, and U7 displayed absorption bands in the range of 250–350 nm, absorbing radiation in this broad region of the electromagnetic spectrum. A photostability study for U5 showed that its molecular structure does not change after exposure to UV radiation. Fluorescence analysis showed an incipient emission of U5, while U6 showed blue fluorescence under UV radiation. The photophysical properties and electronic structure were also determined by TD-DFT theoretical study.
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- 2023
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4. Gut microbiota short-chain fatty acids and their impact on the host thyroid function and diseases
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María José Mendoza-León, Ashutosh K. Mangalam, Alejandro Regaldiz, Enrique González-Madrid, Ma. Andreina Rangel-Ramírez, Oscar Álvarez-Mardonez, Omar P. Vallejos, Constanza Méndez, Susan M. Bueno, Felipe Melo-González, Yorley Duarte, Ma. Cecilia Opazo, Alexis M. Kalergis, and Claudia A. Riedel
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thyroid disorders ,metabolic diseases ,gut microbiota ,dysbiosis ,metabolism and endocrinology ,Short-chain Fatty Acids (SCFAs) ,Diseases of the endocrine glands. Clinical endocrinology ,RC648-665 - Abstract
Thyroid disorders are clinically characterized by alterations of L-3,5,3’,5’-tetraiodothyronine (T4), L-3,5,3’-triiodothyronine (T3), and/or thyroid-stimulating hormone (TSH) levels in the blood. The most frequent thyroid disorders are hypothyroidism, hyperthyroidism, and hypothyroxinemia. These conditions affect cell differentiation, function, and metabolism. It has been reported that 40% of the world’s population suffers from some type of thyroid disorder and that several factors increase susceptibility to these diseases. Among them are iodine intake, environmental contamination, smoking, certain drugs, and genetic factors. Recently, the intestinal microbiota, composed of more than trillions of microbes, has emerged as a critical player in human health, and dysbiosis has been linked to thyroid diseases. The intestinal microbiota can affect host physiology by producing metabolites derived from dietary fiber, such as short-chain fatty acids (SCFAs). SCFAs have local actions in the intestine and can affect the central nervous system and immune system. Modulation of SCFAs-producing bacteria has also been connected to metabolic diseases, such as obesity and diabetes. In this review, we discuss how alterations in the production of SCFAs due to dysbiosis in patients could be related to thyroid disorders. The studies reviewed here may be of significant interest to endocrinology researchers and medical practitioners.
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- 2023
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5. Insights into Early Steps of Decanoic Acid Self-Assemblies under Prebiotic Temperatures Using Molecular Dynamics Simulations
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Romina V. Sepulveda, Christopher Sbarbaro, Ma Cecilia Opazo, Yorley Duarte, Fernando González-Nilo, and Daniel Aguayo
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prebiotic membranes ,decanoic acids ,peptide–membrane interactions ,molecular dynamics simulations ,Chemical technology ,TP1-1185 ,Chemical engineering ,TP155-156 - Abstract
The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life.
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- 2023
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6. Direct Oral FXa Inhibitors Binding to Human Serum Albumin: Spectroscopic, Calorimetric, and Computational Studies
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Nory Mariño-Ocampo, Diego F. Rodríguez, Daniel Guerra Díaz, Daniel Zúñiga-Núñez, Yorley Duarte, Denis Fuentealba, and Flavia C. Zacconi
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FXa inhibitors ,human serum albumin ,fluorescence ,isothermal titration calorimetry ,molecular modeling ,direct oral FXa inhibitors ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Direct FXa inhibitors are an important class of bioactive molecules (rivaroxaban, apixaban, edoxaban, and betrixaban) applied for thromboprophylaxis in diverse cardiovascular pathologies. The interaction of active compounds with human serum albumin (HSA), the most abundant protein in blood plasma, is a key research area and provides crucial information about drugs’ pharmacokinetics and pharmacodynamic properties. This research focuses on the study of the interactions between HSA and four commercially available direct oral FXa inhibitors, applying methodologies including steady-state and time-resolved fluorescence, isothermal titration calorimetry (ITC), and molecular dynamics. The HSA complexation of FXa inhibitors was found to occur via static quenching, and the complex formation in the ground states affects the fluorescence of HSA, with a moderate binding constant of 104 M−1. However, the ITC studies reported significantly different binding constants (103 M−1) compared with the results obtained through spectrophotometric methods. The suspected binding mode is supported by molecular dynamics simulations, where the predominant interactions were hydrogen bonds and hydrophobic interactions (mainly π–π stacking interactions between the phenyl ring of FXa inhibitors and the indole moiety of Trp214). Finally, the possible implications of the obtained results regarding pathologies such as hypoalbuminemia are briefly discussed.
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- 2023
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7. Development of a PHBV nanoparticle as a peptide vehicle for NOD1 activation
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Mauricio Cabaña-Brunod, Pablo A. Herrera, Valeria Márquez-Miranda, Felipe M. Llancalahuen, Yorley Duarte, Danilo González-Nilo, Juan A. Fuentes, Cristián Vilos, Luis Velásquez, and Carolina Otero
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nanoparticles ,macrophage ,innate immunity ,nod1 agonist ,phbv ,Therapeutics. Pharmacology ,RM1-950 - Abstract
NOD1 is an intracellular receptor that, when activated, induces gene expression of pro-inflammatory factors promoting macrophages and neutrophils recruitment at the infection site. However, iE-DAP, the dipeptide agonist that promotes this receptor's activation, cannot permeate cell membranes. To develop a nanocarrier capable of achieving a high and prolonged activation over time, iE-DAP was encapsulated in nanoparticles (NPs) made of poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). The physicochemical properties, colloidal stability, encapsulation efficiency, and cellular uptake of iE-DAP-loaded PHVB NPs were analyzed. Results evidenced that physicochemical properties of iE-DAP-loaded NPs remained stable over time, and NPs were efficiently internalized into cells, a process that depends on time and concentration. Moreover, our results showed that NPs elicited a controlled cargo release in vitro, and the encapsulated agonist response was higher than its free form, suggesting the possibility of activating intracellular receptors triggering an immune response through the release of NOD1 agonist.
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- 2021
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8. Molecular modeling and structural analysis of some tetrahydroindazole and cyclopentanepyrazole derivatives as COX-2 inhibitors
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Efraín Polo-Cuadrado, Karen Acosta-Quiroga, Cristian Rojas-Peña, Yeray A. Rodriguez-Nuñez, Yorley Duarte, Iván Brito, Jonathan Cisterna, and Margarita Gutiérrez
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Tetrahydroindazole ,Pyrazole ,COX-2 enzyme ,Molecular Docking ,Molecular dynamics simulation ,Crystal structure ,Chemistry ,QD1-999 - Abstract
In an attempt to rationalize the search for new potential anti-inflammatory compounds on the COX-2 enzyme, we carried out an in silico protocol that successfully combines the prediction of physicochemical and pharmacokinetic properties, molecular docking, molecular dynamic simulation, and free energy calculation. Starting from a small library of compounds synthesized previously, it was found that 70% of the compounds analyzed satisfy with the associated values to physicochemical principles as key evaluation parameters for the drug-likeness; all the compounds presented good gastrointestinal absorption and cerebral permeability and they showed an interaction with the Arg 106 residue of the COX-2 isoenzyme. Finally, it was obtained that compound 3ab has a binding mode, binding energy, and stability in the active site of COX-2 like the reference drug celecoxib, suggesting that this compound could become a powerful candidate in the inhibition of the COX-2 enzyme. In addition, we realized the crystallographic analysis of compounds 3j, 3r, and 3t defining the crystal parameters and the Packing interactions.
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- 2022
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9. The TGA Transcription Factors from Clade II Negatively Regulate the Salicylic Acid Accumulation in Arabidopsis
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Alejandro Fonseca, Tomás Urzúa, Joanna Jelenska, Christopher Sbarbaro, Aldo Seguel, Yorley Duarte, Jean T. Greenberg, Loreto Holuigue, Francisca Blanco-Herrera, and Ariel Herrera-Vásquez
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salicylic acid ,TGA transcription factors ,Pseudomonas syringae ,AvrRPM1 ,UV-C ,tga256 ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Salicylic acid (SA) is a hormone that modulates plant defenses by inducing changes in gene expression. The mechanisms that control SA accumulation are essential for understanding the defensive process. TGA transcription factors from clade II in Arabidopsis, which include the proteins TGA2, TGA5, and TGA6, are known to be key positive mediators for the transcription of genes such as PR-1 that are induced by SA application. However, unexpectedly, stress conditions that induce SA accumulation, such as infection with the avirulent pathogen P. syringae DC3000/AvrRPM1 and UV-C irradiation, result in enhanced PR-1 induction in plants lacking the clade II TGAs (tga256 plants). Increased PR-1 induction was accompanied by enhanced isochorismate synthase-dependent SA production as well as the upregulation of several genes involved in the hormone’s accumulation. In response to avirulent P. syringae, PR-1 was previously shown to be controlled by both SA-dependent and -independent pathways. Therefore, the enhanced induction of PR-1 (and other defense genes) and accumulation of SA in the tga256 mutant plants is consistent with the clade II TGA factors providing negative feedback regulation of the SA-dependent and/or -independent pathways. Together, our results indicate that the TGA transcription factors from clade II negatively control SA accumulation under stress conditions that induce the hormone production. Our study describes a mechanism involving old actors playing new roles in regulating SA homeostasis under stress.
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- 2022
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10. Novel TRPV1 Channel Agonists With Faster and More Potent Analgesic Properties Than Capsaicin
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Yorley Duarte, Javier Cáceres, Romina V. Sepúlveda, Diego Arriagada, Pedro Olivares, Ignacio Díaz-Franulic, Jimmy Stehberg, and Fernando González-Nilo
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transient receptor potential vanilloid 1 channels ,TRPV1 ,drug discovery ,capsaicin ,analgesic ,carrageenan ,Therapeutics. Pharmacology ,RM1-950 - Abstract
The transient receptor potential vanilloid 1 (TRPV1) ion channel is a member of the family of Transient Receptor Potential (TRP) channels that acts as a molecular detector of noxious signals in primary sensory neurons. Activated by capsaicin, heat, voltage and protons, it is also well known for its desensitization, which led to the medical use of topically applied TRPV1 agonist capsaicin for its long-lasting analgesic effects. Here we report three novel small molecules, which were identified using a Structure-Based Virtual Screening for TRPV1 from the ZINC database. The three compounds were tested using electrophysiological assays, which confirmed their capsaicin-like agonist activity. von Frey filaments were used to measure the analgesic effects of the compounds applied topically on tactile allodynia induced by intra-plantar carrageenan. All compounds had anti-nociceptive activity, but two of them showed faster and longer lasting analgesic effects than capsaicin. The present results suggest that TRPV1 agonists different from capsaicin could be used to develop topical analgesics with faster onset and more potent effects.
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- 2020
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11. Green by Design: Convergent Synthesis, Computational Analyses, and Activity Evaluation of New FXa Inhibitors Bearing Peptide Triazole Linking Units
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Diego F. Rodríguez, Francisca Durán-Osorio, Yorley Duarte, Pedro Olivares, Yanina Moglie, Kamal Dua, and Flavia C. Zacconi
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FXa inhibitors ,DOACs ,green chemistry ,microwave synthesis ,click chemistry ,drug discovery ,Pharmacy and materia medica ,RS1-441 - Abstract
Green chemistry implementation has led to promising results in waste reduction in the pharmaceutical industry. However, the early sustainable development of pharmaceutically active compounds and ingredients remains a considerable challenge. Herein, we wish to report a green synthesis of new pharmaceutically active peptide triazoles as potent factor Xa inhibitors, an important drug target associated with the treatment of diverse cardiovascular diseases. The new inhibitors were synthesized in three steps, featuring cycloaddition reactions (high atom economy), microwave-assisted organic synthesis (energy efficiency), and copper nanoparticle catalysis, thus featuring Earth-abundant metals. The molecules obtained showed FXa inhibition, with IC50-values as low as 17.2 μM and no associated cytotoxicity in HEK293 and HeLa cells. These results showcase the environmental potential and chemical implications of the applied methodologies for the development of new molecules with pharmacological potential.
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- 2021
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12. Different Classes of Antidepressants Inhibit the Rat α7 Nicotinic Acetylcholine Receptor by Interacting within the Ion Channel: A Functional and Structural Study
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Yorley Duarte, Maximiliano Rojas, Jonathan Canan, Edwin G. Pérez, Fernando González-Nilo, and Jesús García-Colunga
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α7 nicotinic acetylcholine receptors ,biological activity ,hippocampus ,antidepressants ,in silico studies ,allosteric modulators ,Organic chemistry ,QD241-441 - Abstract
Several antidepressants inhibit nicotinic acetylcholine receptors (nAChRs) in a non-competitive and voltage-dependent fashion. Here, we asked whether antidepressants with a different structure and pharmacological profile modulate the rat α7 nAChR through a similar mechanism by interacting within the ion-channel. We applied electrophysiological (recording of the ion current elicited by choline, ICh, which activates α7 nAChRs from rat CA1 hippocampal interneurons) and in silico approaches (homology modeling of the rat α7 nAChR, molecular docking, molecular dynamics simulations, and binding free energy calculations). The antidepressants inhibited ICh with the order: norfluoxetine ~ mirtazapine ~ imipramine < bupropion ~ fluoxetine ~ venlafaxine ~ escitalopram. The constructed homology model of the rat α7 nAChR resulted in the extracellular vestibule and the channel pore is highly negatively charged, which facilitates the permeation of cations and the entrance of the protonated form of antidepressants. Molecular docking and molecular dynamics simulations were carried out within the ion−channel of the α7 nAChR, revealing that the antidepressants adopt poses along the receptor channel, with slightly different binding-free energy values. Furthermore, the inhibition of ICh and free energy values for each antidepressant-receptor complex were highly correlated. Thus, the α7 nAChR is negatively modulated by a variety of antidepressants interacting in the ion−channel.
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- 2021
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13. Stretch-Induced Activation of Pannexin 1 Channels Can Be Prevented by PKA-Dependent Phosphorylation
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Ximena López, Rosalba Escamilla, Paola Fernández, Yorley Duarte, Fernando González-Nilo, Nicolás Palacios-Prado, Agustín D. Martinez, and Juan C. Sáez
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protein phosphorylation ,site-directed mutation ,dye uptake ,adenosine ,cAMP ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Pannexin 1 channels located in the cell membrane are permeable to ions, metabolites, and signaling molecules. While the activity of these channels is known to be modulated by phosphorylation on T198, T308, and S206, the possible involvement of other putative phosphorylation sites remains unknown. Here, we describe that the activity of Panx1 channels induced by mechanical stretch is reduced by adenosine via a PKA-dependent pathway. The mechanical stretch-induced activity—measured by changes in DAPI uptake—of Panx1 channels expressed in HeLa cell transfectants was inhibited by adenosine or cAMP analogs that permeate the cell membrane. Moreover, inhibition of PKA but not PKC, p38 MAPK, Akt, or PKG prevented the effects of cAMP analogs, suggesting the involvement of Panx1 phosphorylation by PKA. Accordingly, alanine substitution of T302 or S328, two putative PKA phosphorylation sites, prevented the inhibitory effect of cAMP analogs. Moreover, phosphomimetic mutation of either T302 or S328 to aspartate prevented the mechanical stretch-induced activation of Panx1 channels. A molecular dynamics simulation revealed that T302 and S328 are located in the water–lipid interphase near the lateral tunnel of the intracellular region, suggesting that their phosphorylation could promote conformational changes in lateral tunnels. Thus, Panx1 phosphorylation via PKA could be modulated by G protein-coupled receptors associated with the Gs subunit.
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- 2020
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14. Innovative Three-Step Microwave-Promoted Synthesis of N-Propargyltetrahydroquinoline and 1,2,3-Triazole Derivatives as a Potential Factor Xa (FXa) Inhibitors: Drug Design, Synthesis, and Biological Evaluation
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Fabián Santana-Romo, Carlos F. Lagos, Yorley Duarte, Francisco Castillo, Yanina Moglie, Miguel A. Maestro, Nitin Charbe, and Flavia C. Zacconi
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factor xa inhibitors ,microwave-assisted synthesis ,n-propargyltetrahydroquinoline ,1,2,3-triazole ,cell viability assay ,coagulation parameters ,Organic chemistry ,QD241-441 - Abstract
The coagulation cascade is the process of the conversion of soluble fibrinogen to insoluble fibrin that terminates in production of a clot. Factor Xa (FXa) is a serine protease involved in the blood coagulation cascade. Moreover, FXa plays a vital role in the enzymatic sequence which ends with the thrombus production. Thrombosis is a common causal pathology for three widespread cardiovascular syndromes: acute coronary syndrome (ACS), venous thromboembolism (VTE), and strokes. In this research a series of N-propargyltetrahydroquinoline and 1,2,3-triazole derivatives as a potential factor Xa (FXa) inhibitor were designed, synthesized, and evaluated for their FXa inhibitor activity, cytotoxicity activity and coagulation parameters. Rational design for the desired novel molecules was performed through protein-ligand complexes selection and ligand clustering. The microwave-assisted synthetic strategy of selected compounds was carried out by using Ullmann-Goldberg, N-propargylation, Mannich addition, Friedel-Crafts, and 1,3-dipolar cycloaddition type reactions under microwave irradiation. The microwave methodology proved to be an efficient way to obtain all novel compounds in high yields (73−93%). Furthermore, a thermochemical analysis, optimization and reactivity indexes such as electronic chemical potential (µ), chemical hardness (η), and electrophilicity (ω) were performed to understand the relationship between the structure and the energetic behavior of all the series. Then, in vitro analysis showed that compounds 27, 29−31, and 34 exhibited inhibitory activity against FXa and the corresponding half maximal inhibitory concentration (IC50) values were calculated. Next, a cell viability assay in HEK293 and HepG2 cell lines, and coagulation parameters (anti FXa, Prothrombin time (PT), activated Partial Thromboplastin Time (aPTT)) of the most active novel molecules were performed to determine the corresponding cytotoxicity and possible action on clotting pathways. The obtained results suggest that compounds 27 and 29 inhibited FXa targeting through coagulation factors in the intrinsic and extrinsic pathways. However, compound 34 may target coagulation FXa mainly by the extrinsic and common pathway. Interestingly, the most active compounds in relation to the inhibition activity against FXa and coagulation parameters did not show toxicity at the performed coagulation assay concentrations. Finally, docking studies confirmed the preferential binding mode of N-propargyltetrahydroquinoline and 1,2,3-triazole derivatives inside the active site of FXa.
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- 2020
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15. Synthesis of Bistetrahydroquinolines as Potential Anticholinesterasic Agents by Double Diels-Alder Reactions
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Natalia Valdés, Jans Alzate-Morales, Luis Astudillo, Yorley Duarte, and Margarita Gutiérrez
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bistetrahydroquinolines ,Diels-Alder reaction ,AChE and BuChE inhibitors ,molecular docking ,MM-GBSA ,Organic chemistry ,QD241-441 - Abstract
The tetrahydroquinoline ring system is a unit found in many biologically active natural products and pharmacologically relevant therapeutic agents. A new series of bistetrahydroquinolines (bis-THQs) was synthesized using imino Diels-Alder reactions between dialdehydes, anilines and N-vinyl-2-pyrrolidone (NVP). The notable features of this procedure are mild reaction conditions, greater selectivity and good yields of products. In addition, the inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) of some selected derivatives is reported. The feasible binding modes of these active compounds, within AChE and BuChE binding sites, were predicted by molecular docking experiments and their binding affinity was estimated by means of free energy calculations through the MM-GBSA approximation.
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- 2013
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16. X-ray and Hydrogen-bonding Properties of 1-((1H-benzotriazol-1-yl)methyl)naphthalen-2-ol
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Jaime Ríos-Motta, Guillermo Zaragoza, Diego González-Salas, Yorley Duarte, and Augusto Rivera
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Mannich bases ,Benzotriazole ,Intra-intermolecular hydrogen bond ,1-((1H-benzotriazol-1-yl)methyl)naphthalen-2-ol ,Single crystal X-ray diffraction ,Organic chemistry ,QD241-441 - Abstract
The solid state structure of 1-((1H-benzotriazol-1-yl)methyl)naphthalen-2-ol, C17H13N3O, shows that this Mannich base crystallizes forming intermolecular N···HO hydrogen bonds, rather than intramolecular ones. Factors contributing to this choice of hydrogen-bonding mode are discussed. The compound crystallizes in the monoclinic system, P21/c space group, with lattice constants: a = 11.7934(9) Å, b = 14.3002(14) Å, c = 8.4444(8) Å, β = 106.243(5) deg, V = 1367.3(2) Å3, Z = 4, F(000) = 576, R1 = 6.96%, wR2 = 11.4%.
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- 2009
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17. Molecular modeling and structural analysis of some tetrahydroindazole and cyclopentanepyrazole derivatives as COX-2 inhibitors
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Karen Acosta-Quiroga, Cristian Rojas-Peña, Efraín Polo-Cuadrado, Iván Brito, Yeray A. Rodriguez-Nuñez, Yorley Duarte, Jonathan Cisterna, and Margarita Gutiérrez
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chemistry.chemical_classification ,biology ,Molecular model ,Chemistry ,General Chemical Engineering ,In silico ,Crystal structure ,Binding energy ,Active site ,General Chemistry ,Reference drug ,Tetrahydroindazole ,Molecular Docking ,Molecular dynamics ,Residue (chemistry) ,Enzyme ,Computational chemistry ,COX-2 enzyme ,Pyrazole ,Molecular dynamics simulation ,biology.protein ,QD1-999 - Abstract
In an attempt to rationalize the search for new potential anti-inflammatory compounds on the COX-2 enzyme, we carried out an in silico protocol that successfully combines the prediction of physicochemical and pharmacokinetic properties, molecular docking, molecular dynamic simulation, and free energy calculation. Starting from a small library of compounds synthesized previously, it was found that 70% of the compounds analyzed satisfy with the associated values to physicochemical principles as key evaluation parameters for the drug-likeness; all the compounds presented good gastrointestinal absorption and cerebral permeability and they showed an interaction with the Arg 106 residue of the COX-2 isoenzyme. Finally, it was obtained that compound 3ab has a binding mode, binding energy, and stability in the active site of COX-2 like the reference drug celecoxib, suggesting that this compound could become a powerful candidate in the inhibition of the COX-2 enzyme. In addition, we realized the crystallographic analysis of compounds 3j, 3r, and 3t defining the crystal parameters and the Packing interactions.
- Published
- 2022
18. Experimental and Theoretical Approaches in the Study of Phenanthroline‐Tetrahydroquinolines for Alzheimer's Disease
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Jans Alzate-Morales, Yorley Duarte, Rocío Álvarez, Jorge Soto-Delgado, and Margarita Gutiérrez
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tetrahydroquinolines ,Phenanthroline ,Substituent ,Activation energy ,010402 general chemistry ,01 natural sciences ,lcsh:Chemistry ,chemistry.chemical_compound ,Pyridine ,density functional theory ,Cholinesterase ,biology ,Full Paper ,010405 organic chemistry ,Biological activity ,General Chemistry ,acetylcholinesterase ,Full Papers ,Combinatorial chemistry ,Acetylcholinesterase ,Alzheimer's disease imino-Diels-Alder ,0104 chemical sciences ,chemistry ,lcsh:QD1-999 ,Yield (chemistry) ,biology.protein - Abstract
The imino‐Diels‐Alder reaction is one of the most common strategies in organic chemistry and is an important tool for providing a broad spectrum of biologically active heterocyclic systems. A combined theoretical and experimental study of the imino‐Diels‐Alder reaction is described. The new phenanthroline‐tetrahydroquinolines were evaluated as cholinesterase inhibitors. Their cytotoxicity in human neuroblastoma SH‐SY5Y cells was also evaluated. The theoretical results suggest that compounds formation in stages can be explained by endo cycloadducts under the established reaction conditions, thereby confirming experimental results obtained for percentage yield. These results allowed us to establish that pyridine substituent remarkably influences activation energy and reaction yield, as well as in acetylcholinesterase (AChE) activity. Among these derivatives, compounds with 4‐pyridyl and 4‐nitrophenyl showed favorable AChE activity and proved to be non‐cytotoxic.
- Published
- 2019
19. Different Classes of Antidepressants Inhibit the Rat α7 Nicotinic Acetylcholine Receptor by Interacting within the Ion Channel: A Functional and Structural Study
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Maximiliano Rojas, Edwin G. Pérez, Fernando D. González-Nilo, Jesús García-Colunga, Jonathan Canan, and Yorley Duarte
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0301 basic medicine ,alpha7 Nicotinic Acetylcholine Receptor ,hippocampus ,Pharmaceutical Science ,biological activity ,Molecular Dynamics Simulation ,Imipramine ,Ion Channels ,Article ,Choline ,Analytical Chemistry ,lcsh:QD241-441 ,Structure-Activity Relationship ,03 medical and health sciences ,0302 clinical medicine ,lcsh:Organic chemistry ,Interneurons ,Drug Discovery ,mental disorders ,medicine ,Animals ,Homology modeling ,Physical and Theoretical Chemistry ,Ion channel ,Acetylcholine receptor ,Bupropion ,Chemistry ,musculoskeletal, neural, and ocular physiology ,Organic Chemistry ,Biological activity ,Antidepressive Agents ,Rats ,Molecular Docking Simulation ,Electrophysiology ,030104 developmental biology ,Nicotinic agonist ,nervous system ,in silico studies ,Structural Homology, Protein ,Chemistry (miscellaneous) ,antidepressants ,Biophysics ,Thermodynamics ,Molecular Medicine ,α7 nicotinic acetylcholine receptors ,allosteric modulators ,Ion Channel Gating ,030217 neurology & neurosurgery ,medicine.drug - Abstract
Several antidepressants inhibit nicotinic acetylcholine receptors (nAChRs) in a non-competitive and voltage-dependent fashion. Here, we asked whether antidepressants with a different structure and pharmacological profile modulate the rat α7 nAChR through a similar mechanism by interacting within the ion-channel. We applied electrophysiological (recording of the ion current elicited by choline, ICh, which activates α7 nAChRs from rat CA1 hippocampal interneurons) and in silico approaches (homology modeling of the rat α7 nAChR, molecular docking, molecular dynamics simulations, and binding free energy calculations). The antidepressants inhibited ICh with the order: norfluoxetine ~ mirtazapine ~ imipramine <, bupropion ~ fluoxetine ~ venlafaxine ~ escitalopram. The constructed homology model of the rat α7 nAChR resulted in the extracellular vestibule and the channel pore is highly negatively charged, which facilitates the permeation of cations and the entrance of the protonated form of antidepressants. Molecular docking and molecular dynamics simulations were carried out within the ion−channel of the α7 nAChR, revealing that the antidepressants adopt poses along the receptor channel, with slightly different binding-free energy values. Furthermore, the inhibition of ICh and free energy values for each antidepressant-receptor complex were highly correlated. Thus, the α7 nAChR is negatively modulated by a variety of antidepressants interacting in the ion−channel.
- Published
- 2021
- Full Text
- View/download PDF
20. Stretch-Induced Activation of Pannexin 1 Channels Can Be Prevented by PKA-Dependent Phosphorylation
- Author
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Rosalba Escamilla, Fernando D. González-Nilo, Agustín Martínez, Paola Fernández, Yorley Duarte, Nicolás Palacios-Prado, Juan C. Sáez, and Ximena López
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Dye uptake ,Models, Molecular ,Adenosine ,Protein Conformation ,Mechanotransduction, Cellular ,Connexins ,Cell membrane ,lcsh:Chemistry ,Palps ,Protein phosphorylation ,Phosphorylation ,lcsh:QH301-705.5 ,Spectroscopy ,Probenecid ,Chemistry ,General Medicine ,Pannexin ,Computer Science Applications ,medicine.anatomical_structure ,dye uptake ,adenosine ,Ion Channel Gating ,Intracellular ,medicine.drug ,Cell signaling ,Nerve Tissue Proteins ,Catalysis ,Article ,Inorganic Chemistry ,Structure-Activity Relationship ,Pannexins ,cAMP ,medicine ,Humans ,Physical and Theoretical Chemistry ,Molecular Biology ,Protein kinase C ,Site-directed mutation ,Organic Chemistry ,Cyclic AMP-Dependent Protein Kinases ,protein phosphorylation ,lcsh:Biology (General) ,lcsh:QD1-999 ,Biophysics ,Mutagenesis, Site-Directed ,CAMP ,site-directed mutation ,HeLa Cells - Abstract
Pannexin 1 channels located in the cell membrane are permeable to ions, metabolites, and signaling molecules. While the activity of these channels is known to be modulated by phosphorylation on T198, T308, and S206, the possible involvement of other putative phosphorylation sites remains unknown. Here, we describe that the activity of Panx1 channels induced by mechanical stretch is reduced by adenosine via a PKA-dependent pathway. The mechanical stretch-induced activity&mdash, measured by changes in DAPI uptake&mdash, of Panx1 channels expressed in HeLa cell transfectants was inhibited by adenosine or cAMP analogs that permeate the cell membrane. Moreover, inhibition of PKA but not PKC, p38 MAPK, Akt, or PKG prevented the effects of cAMP analogs, suggesting the involvement of Panx1 phosphorylation by PKA. Accordingly, alanine substitution of T302 or S328, two putative PKA phosphorylation sites, prevented the inhibitory effect of cAMP analogs. Moreover, phosphomimetic mutation of either T302 or S328 to aspartate prevented the mechanical stretch-induced activation of Panx1 channels. A molecular dynamics simulation revealed that T302 and S328 are located in the water&ndash, lipid interphase near the lateral tunnel of the intracellular region, suggesting that their phosphorylation could promote conformational changes in lateral tunnels. Thus, Panx1 phosphorylation via PKA could be modulated by G protein-coupled receptors associated with the Gs subunit.
- Published
- 2020
21. Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites
- Author
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Miguel Holmgren, Fernando D. González-Nilo, Ignacio Diaz-Franulic, Maximiliano Rojas, Valeria Márquez-Miranda, Yorley Duarte, and Raul E. Cachau
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chemistry.chemical_compound ,Transmembrane domain ,Molecular dynamics ,Membrane ,chemistry ,Tetramer ,Dimer ,Beta sheet ,Biophysics ,Protomer ,Ion channel ,Article - Abstract
SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. ORF3a assemblies as homotetramers, which are stabilized by residue C133. A recent cryoEM structure of a homodimeric complex of ORF3a has been released. A lower-resolution cryoEM map of the tetramer suggests two dimers form it, arranged side by side. The dimer’s cryoEM structure revealed that each protomer contains three transmembrane helices arranged in a clockwise configuration forming a six helices transmembrane domain. This domain’s potential permeation pathway has six constrictions narrowing to about 1 Å in radius, suggesting the structure solved is in a closed or inactivated state. At the cytosol end, the permeation pathway encounters a large and polar cavity formed by multiple beta strands from both protomers, which opens to the cytosolic milieu. We modeled the tetramer following the arrangement suggested by the low-resolution tetramer cryoEM map. Molecular dynamics simulations of the tetramer embedded in a membrane and solvated with 0.5 M of KCl were performed. Our simulations show the cytosolic cavity is quickly populated by both K+ and Cl-, yet with different dynamics. K+ ions moved relatively free inside the cavity without forming proper coordination sites. In contrast, Cl- ions enter the cavity, and three of them can become stably coordinated near the intracellular entrance of the potential permeation pathway by an inter-subunit network of positively charged amino acids. Consequently, the central cavity’s electrostatic potential changed from being entirely positive at the beginning of the simulation to more electronegative at the end.
- Published
- 2020
22. Novel TRPV1 Channel Agonists With Faster and More Potent Analgesic Properties Than Capsaicin
- Author
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Javier Cáceres, Ignacio Diaz-Franulic, Fernando D. González-Nilo, Yorley Duarte, Pedro Olivares, Romina V. Sepúlveda, Diego Arriagada, and Jimmy Stehberg
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0301 basic medicine ,Agonist ,von frey ,medicine.drug_class ,Analgesic ,TRPV1 ,Pharmacology ,capsaicin ,drug discovery ,03 medical and health sciences ,Transient receptor potential channel ,chemistry.chemical_compound ,0302 clinical medicine ,Desensitization (telecommunications) ,medicine ,Pharmacology (medical) ,Original Research ,allodynia ,transient receptor potential vanilloid 1 channels ,lcsh:RM1-950 ,analgesic ,Electrophysiology ,030104 developmental biology ,Allodynia ,lcsh:Therapeutics. Pharmacology ,chemistry ,Capsaicin ,030220 oncology & carcinogenesis ,carrageenan ,lipids (amino acids, peptides, and proteins) ,medicine.symptom - Abstract
Indexación: Scopus. The transient receptor potential vanilloid 1 (TRPV1) ion channel is a member of the family of Transient Receptor Potential (TRP) channels that acts as a molecular detector of noxious signals in primary sensory neurons. Activated by capsaicin, heat, voltage and protons, it is also well known for its desensitization, which led to the medical use of topically applied TRPV1 agonist capsaicin for its long-lasting analgesic effects. Here we report three novel small molecules, which were identified using a Structure-Based Virtual Screening for TRPV1 from the ZINC database. The three compounds were tested using electrophysiological assays, which confirmed their capsaicin-like agonist activity. von Frey filaments were used to measure the analgesic effects of the compounds applied topically on tactile allodynia induced by intra-plantar carrageenan. All compounds had anti-nociceptive activity, but two of them showed faster and longer lasting analgesic effects than capsaicin. The present results suggest that TRPV1 agonists different from capsaicin could be used to develop topical analgesics with faster onset and more potent effects. © Copyright © 2020 Duarte, Cáceres, Sepúlveda, Arriagada, Olivares, Díaz-Franulic, Stehberg and González-Nilo. https://www.frontiersin.org/articles/10.3389/fphar.2020.01040/full
- Published
- 2020
23. Synthesis of Bistetrahydroquinolines as Potential Anticholinesterasic Agents by Double Diels-Alder Reactions
- Author
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Yorley Duarte, Luis Astudillo, Margarita Gutiérrez, Jans Alzate-Morales, and Natalia Valdés
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Stereochemistry ,Pharmaceutical Science ,bistetrahydroquinolines ,Molecular Docking Simulation ,Article ,Analytical Chemistry ,lcsh:QD241-441 ,chemistry.chemical_compound ,lcsh:Organic chemistry ,AChE and BuChE inhibitors ,Catalytic Domain ,Drug Discovery ,Animals ,Humans ,Diels-Alder reaction ,molecular docking ,MM-GBSA ,Physical and Theoretical Chemistry ,Binding site ,Butyrylcholinesterase ,Diels–Alder reaction ,Cycloaddition Reaction ,Drug discovery ,Organic Chemistry ,Biological activity ,Acetylcholinesterase ,chemistry ,Chemistry (miscellaneous) ,Quinolines ,Molecular Medicine ,Thermodynamics ,Cholinesterase Inhibitors ,Selectivity ,Protein Binding - Abstract
The tetrahydroquinoline ring system is a unit found in many biologically active natural products and pharmacologically relevant therapeutic agents. A new series of bistetrahydroquinolines (bis-THQs) was synthesized using imino Diels-Alder reactions between dialdehydes, anilines and N-vinyl-2-pyrrolidone (NVP). The notable features of this procedure are mild reaction conditions, greater selectivity and good yields of products. In addition, the inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) of some selected derivatives is reported. The feasible binding modes of these active compounds, within AChE and BuChE binding sites, were predicted by molecular docking experiments and their binding affinity was estimated by means of free energy calculations through the MM-GBSA approximation.
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- 2013
24. Experimental and Theoretical Approaches in the Study of Phenanthroline‐Tetrahydroquinolines for Alzheimer's Disease
- Author
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Dr. Yorley Duarte, Dr. Margarita Gutierrez, Dr. Rocío Álvarez, Dr. Jans H. Alzate‐Morales, and Dr. Jorge Soto‐Delgado
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Alzheimer's disease imino-Diels-Alder ,acetylcholinesterase ,tetrahydroquinolines ,density functional theory ,Chemistry ,QD1-999 - Abstract
Abstract The imino‐Diels‐Alder reaction is one of the most common strategies in organic chemistry and is an important tool for providing a broad spectrum of biologically active heterocyclic systems. A combined theoretical and experimental study of the imino‐Diels‐Alder reaction is described. The new phenanthroline‐tetrahydroquinolines were evaluated as cholinesterase inhibitors. Their cytotoxicity in human neuroblastoma SH‐SY5Y cells was also evaluated. The theoretical results suggest that compounds formation in stages can be explained by endo cycloadducts under the established reaction conditions, thereby confirming experimental results obtained for percentage yield. These results allowed us to establish that pyridine substituent remarkably influences activation energy and reaction yield, as well as in acetylcholinesterase (AChE) activity. Among these derivatives, compounds with 4‐pyridyl and 4‐nitrophenyl showed favorable AChE activity and proved to be non‐cytotoxic.
- Published
- 2019
- Full Text
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