Publicaciones de Erbio Díaz-Pico
2024
Valdés-Albuernes, Jorge Luis; Díaz-Pico, Erbio; Alfaro, Sergio; Caballero, Julio
Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking Artículo de revista
En: Frontiers in Molecular Biosciences, vol. 11, pp. 1374364, 2024, ISSN: 2296-889X.
@article{valdes-albuernes_modeling_2024,
title = {Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking},
author = {Jorge Luis Valdés-Albuernes and Erbio Díaz-Pico and Sergio Alfaro and Julio Caballero},
url = {https://www.frontiersin.org/articles/10.3389/fmolb.2024.1374364/full},
doi = {10.3389/fmolb.2024.1374364},
issn = {2296-889X},
year = {2024},
date = {2024-03-01},
urldate = {2024-12-14},
journal = {Frontiers in Molecular Biosciences},
volume = {11},
pages = {1374364},
abstract = {The papain-like protease (PLpro) found in coronaviruses that can be transmitted from animals to humans is a critical target in respiratory diseases linked to Severe Acute Respiratory Syndrome (SARS-CoV). Researchers have proposed designing PLpro inhibitors. In this study, a set of 89 compounds, including recently reported 2-phenylthiophenes with nanomolar inhibitory potency, were investigated as PLpro noncovalent inhibitors using advanced molecular modeling techniques. To develop the work with these inhibitors, multiple structures of the SARS-CoV-2 PLpro binding site were generated using a molecular sampling method. These structures were then clustered to select a group that represents the flexibility of the site. Subsequently, models of the protein-ligand complexes were created for the set of inhibitors within the chosen conformations. The quality of the complex models was assessed using LigRMSD software to verify similarities in the orientations of the congeneric series and interaction fingerprints to determine the recurrence of chemical interactions. With the multiple models constructed, a protocol was established to choose one per ligand, optimizing the correlation between the calculated docking energy values and the biological activities while incorporating the effect of the binding site’s flexibility. A strong correlation (R
2 = 0.922) was found when employing this flexible docking protocol.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The papain-like protease (PLpro) found in coronaviruses that can be transmitted from animals to humans is a critical target in respiratory diseases linked to Severe Acute Respiratory Syndrome (SARS-CoV). Researchers have proposed designing PLpro inhibitors. In this study, a set of 89 compounds, including recently reported 2-phenylthiophenes with nanomolar inhibitory potency, were investigated as PLpro noncovalent inhibitors using advanced molecular modeling techniques. To develop the work with these inhibitors, multiple structures of the SARS-CoV-2 PLpro binding site were generated using a molecular sampling method. These structures were then clustered to select a group that represents the flexibility of the site. Subsequently, models of the protein-ligand complexes were created for the set of inhibitors within the chosen conformations. The quality of the complex models was assessed using LigRMSD software to verify similarities in the orientations of the congeneric series and interaction fingerprints to determine the recurrence of chemical interactions. With the multiple models constructed, a protocol was established to choose one per ligand, optimizing the correlation between the calculated docking energy values and the biological activities while incorporating the effect of the binding site’s flexibility. A strong correlation (R
2 = 0.922) was found when employing this flexible docking protocol.
2 = 0.922) was found when employing this flexible docking protocol.
Dreyer, Ingo; Hernández-Rojas, Naomí; Bolua-Hernández, Yasnaya; Tapia-Castillo, Valentina De Los Angeles; Astola-Mariscal, Sadith Z.; Díaz-Pico, Erbio; Mérida-Quesada, Franko; Vergara-Valladares, Fernando; Arrey-Salas, Oscar; Rubio-Meléndez, María E.; Riedelsberger, Janin; Michard, Erwan
Homeostats: The hidden rulers of ion homeostasis in plants Artículo de revista
En: Quantitative Plant Biology, vol. 5, pp. e8, 2024, ISSN: 2632-8828.
@article{dreyer_homeostats_2024,
title = {Homeostats: The hidden rulers of ion homeostasis in plants},
author = {Ingo Dreyer and Naomí Hernández-Rojas and Yasnaya Bolua-Hernández and Valentina De Los Angeles Tapia-Castillo and Sadith Z. Astola-Mariscal and Erbio Díaz-Pico and Franko Mérida-Quesada and Fernando Vergara-Valladares and Oscar Arrey-Salas and María E. Rubio-Meléndez and Janin Riedelsberger and Erwan Michard},
url = {https://www.cambridge.org/core/product/identifier/S2632882824000080/type/journal_article},
doi = {10.1017/qpb.2024.8},
issn = {2632-8828},
year = {2024},
date = {2024-01-01},
urldate = {2024-12-14},
journal = {Quantitative Plant Biology},
volume = {5},
pages = {e8},
abstract = {Abstract
Ion homeostasis is a crucial process in plants that is closely linked to the efficiency of nutrient uptake, stress tolerance and overall plant growth and development. Nevertheless, our understanding of the fundamental processes of ion homeostasis is still incomplete and highly fragmented. Especially at the mechanistic level, we are still in the process of dissecting physiological systems to analyse the different parts in isolation. However, modelling approaches have shown that it is not individual transporters but rather transporter networks (homeostats) that control membrane transport and associated homeostatic processes in plant cells. To facilitate access to such theoretical approaches, the modelling of the potassium homeostat is explained here in detail to serve as a blueprint for other homeostats. The unbiased approach provided strong arguments for the abundant existence of electroneutral H
+
/K
+
antiporters in plants.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract
Ion homeostasis is a crucial process in plants that is closely linked to the efficiency of nutrient uptake, stress tolerance and overall plant growth and development. Nevertheless, our understanding of the fundamental processes of ion homeostasis is still incomplete and highly fragmented. Especially at the mechanistic level, we are still in the process of dissecting physiological systems to analyse the different parts in isolation. However, modelling approaches have shown that it is not individual transporters but rather transporter networks (homeostats) that control membrane transport and associated homeostatic processes in plant cells. To facilitate access to such theoretical approaches, the modelling of the potassium homeostat is explained here in detail to serve as a blueprint for other homeostats. The unbiased approach provided strong arguments for the abundant existence of electroneutral H
+
/K
+
antiporters in plants.
Ion homeostasis is a crucial process in plants that is closely linked to the efficiency of nutrient uptake, stress tolerance and overall plant growth and development. Nevertheless, our understanding of the fundamental processes of ion homeostasis is still incomplete and highly fragmented. Especially at the mechanistic level, we are still in the process of dissecting physiological systems to analyse the different parts in isolation. However, modelling approaches have shown that it is not individual transporters but rather transporter networks (homeostats) that control membrane transport and associated homeostatic processes in plant cells. To facilitate access to such theoretical approaches, the modelling of the potassium homeostat is explained here in detail to serve as a blueprint for other homeostats. The unbiased approach provided strong arguments for the abundant existence of electroneutral H
+
/K
+
antiporters in plants.
