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Mostrando publicaciones 1-12 de 12
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A description of the epidemiological dynamics of Chagas disease via mathematical modeling
Lozada-Yavina, Rafael; Marchant, Carolina; Cancino-Faure, Beatriz ; Hernández-Rodríguez, Erix W.; Córdova-Lepe, Fernando (2023)Chagas disease is caused by the protozoan Trypanosoma cruzi, which parasitizes many mammals, including humans. Its vectors are blood-feeding hematophagous triatomine insects of different species, which vary according to ...
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A study of the cis–trans isomerization preference of N-alkylated peptides containing phosphorus in the side chain and backbone
De la Torre, Alexander F.; Ali, Akbar; Concepción, Odette; Montero-Alejo, Ana L.; Muñiz, Francisco M.; Jiménez, Claudio A.; Belmar, Julio; Velázquez-Libera, José Luis; Hernández-Rodríguez, Erix W.; Caballero, Julio (2019)The current work provides a study on the cis–trans isomerization behaviour of N-alkylated peptides decorated with phosphonate ester groups. A Ugi four-component reaction was chosen for the synthesis of N-alkylated peptides, ...
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BitClust: fast geometrical clustering of long molecular dynamics simulations
González-Alemán, Roy; Hernández-Castillo, David; Rodríguez-Serradet, Alejandro; Caballero, Julio; Hernández-Rodríguez, Erix W.; Montero-Cabrera, Luis (2020)The growing computational capacity allows the investigation of large biomolecular systems by increasingly extensive molecular dynamics simulations. The resulting huge trajectories demand efficient partition methods to ...
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Calcium-alginate-chitosan nanoparticle as a potential solution for pesticide removal, a computational approach
Yáñez, Osvaldo; Alegría-Arcos, Melissa; Suardiaz, Reynier; Morales-Quintana, Luis; Castro, Ricardo I.; Palma-Olate, Jonathan; Galarza, Christian; Catagua-González, Ángel; Rojas-Pérez, Víctor; Urra, Gabriela; Hernández-Rodríguez, Erix W.; Bustos, Daniel (2023)Pesticides have a significant negative impact on the environment, non-target organisms, and human health. To address these issues, sustainable pest management practices and government regulations are necessary. However, ...
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Elucidating the structural basis of the intracellular pH sensing mechanism of TASK-2 K2P channels
Bustos, Daniel; Bedoya, Mauricio; Ramírez, David; Concha, Guierdy; Zúñiga, Leandro; Decher, Niels; Hernández-Rodríguez, Erix W.; Sepúlveda, Francisco V.; Martínez, Leandro; González, Wendy (2020)Two-pore domain potassium (K2P) channels maintain the cell’s background conductance by stabilizing the resting membrane potential. They assemble as dimers possessing four transmembrane helices in each subunit. K2P channels ...
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MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics
González-Alemán, Roy; Platero-Rochart, Daniel; Rodríguez-Serradet, Alejandro; Hernández-Rodríguez, Erix W.; Caballero, Julio; Leclerc, Fabrice; Montero-Cabrera, Luis (2022)Motivation The term clustering designates a comprehensive family of unsupervised learning methods allowing to group similar elements into sets called clusters. Geometrical clustering of molecular dynamics (MD) trajectories ...
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Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins
Hernández-Rodríguez, Erix W.; Escorcia, Andrés M.; van der Kamp, Marc W.; Montero-Alejo, Ana L.; Caballero, Julio (2020)Evaluating the availability of molecular oxygen (O2 ) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and ...
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On the nature of the enzyme–substrate complex and the reaction mechanism in human Arginase I. A combined molecular dynamics and QM/MM study
Velázquez-Libera, José Luis; Caballero, Julio; Tuñón, Iñaki; Hernández-Rodríguez, Erix W.; Ruiz-Pernía, J. Javier (2020)We present here a complete detailed theoretical analysis of l-arginine hydrolysis catalyzed by human arginase I (HARGI). Our study combines classical molecular dynamics (MD) simulations of different models for the ...
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Physicochemical and computational analysis of the melamine resin derivative for the glyphosate absorption from water using Langmuir-type model
Morales-Quintana, Luis; Bustos, Daniel; Gallego, J.; Valdes, O.; Guzmán, L.; Nachtigall, Fabiane M.; Marican, Adolfo; Hernández-Rodríguez, Erix W.; Avila-Salas, Fabian; Bueno-Silva, W.; Santos, Leonardo S.; Castro, R. I. (2022)Conventional pesticides are biosynthetic chemicals that are effectively used for the control of weeds, diseases, and pests worldwide. Among them, glyphosate, one of the most commonly used broad-spectrum herbicides, might ...
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Rationalizing the stability and interactions of 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2-hydroxy-3,5-dinitrobenzoate salt
Nawaz Tahir, Muhammad; Ashfaq, Muhammad; Caballero, Julio; Hernández-Rodríguez, Erix W.; Ali, Akbar; De la Torre, Alexander F. (2019)The crystal structure of the salt produced by the reaction of pyrimethamine (an antimalarial drug) with 2-hydroxy-3,5-dinitrobenzoic acid [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2-hydroxy- ...
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Structure/activity analysis of TASK-3 channel antagonists based on a 5,6,7,8 tetrahydropyrido[4,3-d]pyrimidine
Ramírez, David; Bedoya, Mauricio; Kiper, Aytug K.; Rinné, Susanne; Morales-Navarro, Samuel; Hernández-Rodríguez, Erix W.; Sepúlveda, Francisco V.; Drecher, Niels; González, Wendy (2019)TASK-3 potassium (K+) channels are highly expressed in the central nervous system, regulating the membrane potential of excitable cells. TASK-3 is involved in neurotransmitter action and has been identified as an oncogenic ...
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Unveiling novel urease inhibitors for Helicobacter pylori: A multi-methodological approach from virtual screening and ADME to molecular dynamics simulations
Valenzuela-Hormazabal, Paulina; Sepúlveda, Romina V.; Alegría-Arcos, Melissa; Valdés-Muñoz, Elizabeth; Rojas-Pérez, Víctor; González-Bonet, Ileana; Suardíaz, Reynier; Galarza, Christian; Morales, Natalia; Leddermann, Verónica; Castro, Ricardo I.; Benso, Bruna; Urra, Gabriela; Hernández-Rodríguez, Erix W.; Bustos, Daniel (2024)Helicobacter pylori (Hp) infections pose a global health challenge demanding innovative therapeutic strategies by which to eradicate them. Urease, a key Hp virulence factor hydrolyzes urea, facilitating bacterial survival ...