Publicaciones de Wendy González
2024
Bedoya, Mauricio; Adasme-Carreño, Francisco; Peña-Martínez, Paula Andrea; Muñoz-Gutiérrez, Camila; Peña-Tejo, Luciano; Montesinos, José C. E. Márquez; Hernández-Rodríguez, Erix W.; González, Wendy; Martínez, Leandro; Alzate-Morales, Jans
Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods Miscelánea
2024.
@misc{bedoya_moltiverse_2024,
title = {Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods},
author = {Mauricio Bedoya and Francisco Adasme-Carreño and Paula Andrea Peña-Martínez and Camila Muñoz-Gutiérrez and Luciano Peña-Tejo and José C. E. Márquez Montesinos and Erix W. Hernández-Rodríguez and Wendy González and Leandro Martínez and Jans Alzate-Morales},
url = {https://chemrxiv.org/engage/chemrxiv/article-details/67621d996dde43c908780be8},
doi = {10.26434/chemrxiv-2024-qs0pc-v2},
year = {2024},
date = {2024-12-01},
urldate = {2025-01-03},
publisher = {Chemistry},
abstract = {Accurately predicting the diverse bound-state conformations of small molecules is crucial for successful drug discovery and design, particularly when detailed protein-ligand interactions are unknown. Established tools exist, but efficiently exploring the vast conformational space remains challenging. This work introduces Moltiverse, a novel protocol using enhanced sampling molecular dynamics (MD) simulations for conformer generation. The extended adaptive biasing force (eABF) algorithm combined with metadynamics, guided by a single collective variable (radius of gyration, RDGYR), efficiently samples the conformational landscape of a small molecule. Moltiverse demonstrates comparable accuracy and, in some cases, superior quality when benchmarked against established software like RDKit, CONFORGE, ConfGenX, Torsional diffusion, and Conformator. We present an exhaustive ranking based on eight quantitative metrics and statistical analysis for robust conformer generation algorithms comparison and provide recommendations for their improvement based on our findings. We introduce the Cofactorv1 dataset, a complementary resource for conformer generator evaluation. Unlike traditional datasets with thousands of single-conformer molecules, the Cofactorv1 dataset features only seven small molecule cofactors but with hundreds to thousands of experimental conformers per molecule (sourced from the PDB). This diversity, encompassing 15-29 rotatable bonds, poses a significant challenge for conformer generation benchmarks. Cofactorv1 is a complementary dataset that serves as a valuable resource for developing and evaluating conformer generation methods like Moltiverse, pushing the boundaries of accuracy and diversity in this relevant field.},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
Accurately predicting the diverse bound-state conformations of small molecules is crucial for successful drug discovery and design, particularly when detailed protein-ligand interactions are unknown. Established tools exist, but efficiently exploring the vast conformational space remains challenging. This work introduces Moltiverse, a novel protocol using enhanced sampling molecular dynamics (MD) simulations for conformer generation. The extended adaptive biasing force (eABF) algorithm combined with metadynamics, guided by a single collective variable (radius of gyration, RDGYR), efficiently samples the conformational landscape of a small molecule. Moltiverse demonstrates comparable accuracy and, in some cases, superior quality when benchmarked against established software like RDKit, CONFORGE, ConfGenX, Torsional diffusion, and Conformator. We present an exhaustive ranking based on eight quantitative metrics and statistical analysis for robust conformer generation algorithms comparison and provide recommendations for their improvement based on our findings. We introduce the Cofactorv1 dataset, a complementary resource for conformer generator evaluation. Unlike traditional datasets with thousands of single-conformer molecules, the Cofactorv1 dataset features only seven small molecule cofactors but with hundreds to thousands of experimental conformers per molecule (sourced from the PDB). This diversity, encompassing 15-29 rotatable bonds, poses a significant challenge for conformer generation benchmarks. Cofactorv1 is a complementary dataset that serves as a valuable resource for developing and evaluating conformer generation methods like Moltiverse, pushing the boundaries of accuracy and diversity in this relevant field.
Peña-Münzenmayer, Gaspar; George, Alvin T.; Llontop, Nuria; Mazola, Yuliet; Apablaza, Natalia; Spichiger, Carlos; Brauchi, Sebastián; Sarmiento, José; Zúñiga, Leandro; González, Wendy; Catalán, Marcelo A.
K+-Driven Cl−/HCO3− Exchange Mediated by Slc4a8 and Slc4a10 Artículo de revista
En: International Journal of Molecular Sciences, vol. 25, no 8, pp. 4575, 2024, ISSN: 1422-0067.
@article{pena-munzenmayer_k-driven_2024,
title = {K+-Driven Cl−/HCO3− Exchange Mediated by Slc4a8 and Slc4a10},
author = {Gaspar Peña-Münzenmayer and Alvin T. George and Nuria Llontop and Yuliet Mazola and Natalia Apablaza and Carlos Spichiger and Sebastián Brauchi and José Sarmiento and Leandro Zúñiga and Wendy González and Marcelo A. Catalán},
url = {https://www.mdpi.com/1422-0067/25/8/4575},
doi = {10.3390/ijms25084575},
issn = {1422-0067},
year = {2024},
date = {2024-04-01},
urldate = {2024-12-14},
journal = {International Journal of Molecular Sciences},
volume = {25},
number = {8},
pages = {4575},
abstract = {Slc4a genes encode various types of transporters, including Na+-HCO3− cotransporters, Cl−/HCO3− exchangers, or Na+-driven Cl−/HCO3− exchangers. Previous research has revealed that Slc4a9 (Ae4) functions as a Cl−/HCO3− exchanger, which can be driven by either Na+ or K+, prompting investigation into whether other Slc4a members facilitate cation-dependent anion transport. In the present study, we show that either Na+ or K+ drive Cl−/HCO3− exchanger activity in cells overexpressing Slc4a8 or Slc4a10. Further characterization of cation-driven Cl−/HCO3− exchange demonstrated that Slc4a8 and Slc4a10 also mediate Cl− and HCO3−-dependent K+ transport. Full-atom molecular dynamics simulation on the recently solved structure of Slc4a8 supports the coordination of K+ at the Na+ binding site in S1. Sequence analysis shows that the critical residues coordinating monovalent cations are conserved among mouse Slc4a8 and Slc4a10 proteins. Together, our results suggest that Slc4a8 and Slc4a10 might transport K+ in the same direction as HCO3− ions in a similar fashion to that described for Na+ transport in the rat Slc4a8 structure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Slc4a genes encode various types of transporters, including Na+-HCO3− cotransporters, Cl−/HCO3− exchangers, or Na+-driven Cl−/HCO3− exchangers. Previous research has revealed that Slc4a9 (Ae4) functions as a Cl−/HCO3− exchanger, which can be driven by either Na+ or K+, prompting investigation into whether other Slc4a members facilitate cation-dependent anion transport. In the present study, we show that either Na+ or K+ drive Cl−/HCO3− exchanger activity in cells overexpressing Slc4a8 or Slc4a10. Further characterization of cation-driven Cl−/HCO3− exchange demonstrated that Slc4a8 and Slc4a10 also mediate Cl− and HCO3−-dependent K+ transport. Full-atom molecular dynamics simulation on the recently solved structure of Slc4a8 supports the coordination of K+ at the Na+ binding site in S1. Sequence analysis shows that the critical residues coordinating monovalent cations are conserved among mouse Slc4a8 and Slc4a10 proteins. Together, our results suggest that Slc4a8 and Slc4a10 might transport K+ in the same direction as HCO3− ions in a similar fashion to that described for Na+ transport in the rat Slc4a8 structure.
2022
Arévalo, Bárbara; Bedoya, Mauricio; Kiper, Aytug K.; Vergara, Fernando; Ramírez, David; Mazola, Yuliet; Bustos, Daniel; Zúñiga, Rafael; Cikutovic, Rocio; Cayo, Angel; Rinné, Susanne; Ramirez-Apan, M. Teresa; Sepúlveda, Francisco V.; Cerda, Oscar; López-Collazo, Eduardo; Decher, Niels; Zúñiga, Leandro; Gutierrez, Margarita; González, Wendy
Selective TASK-1 Inhibitor with a Defined Structure–Activity Relationship Reduces Cancer Cell Proliferation and Viability Artículo de revista
En: Journal of Medicinal Chemistry, vol. 65, no 22, pp. 15014–15027, 2022, ISSN: 0022-2623, 1520-4804.
@article{arevalo_selective_2022,
title = {Selective TASK-1 Inhibitor with a Defined Structure–Activity Relationship Reduces Cancer Cell Proliferation and Viability},
author = {Bárbara Arévalo and Mauricio Bedoya and Aytug K. Kiper and Fernando Vergara and David Ramírez and Yuliet Mazola and Daniel Bustos and Rafael Zúñiga and Rocio Cikutovic and Angel Cayo and Susanne Rinné and M. Teresa Ramirez-Apan and Francisco V. Sepúlveda and Oscar Cerda and Eduardo López-Collazo and Niels Decher and Leandro Zúñiga and Margarita Gutierrez and Wendy González},
url = {https://pubs.acs.org/doi/10.1021/acs.jmedchem.1c00378},
doi = {10.1021/acs.jmedchem.1c00378},
issn = {0022-2623, 1520-4804},
year = {2022},
date = {2022-11-01},
urldate = {2024-12-14},
journal = {Journal of Medicinal Chemistry},
volume = {65},
number = {22},
pages = {15014–15027},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zúñiga, Rafael; Mancilla, Daniel; Rojas-Rocco, Tamara; Vergara, Fernando; González, Wendy; Catalán, Marcelo A.; Zúñiga, Leandro
A Direct Interaction between Cyclodextrins and TASK Channels Decreases the Leak Current in Cerebellar Granule Neurons Artículo de revista
En: Biology, vol. 11, no 8, pp. 1097, 2022, ISSN: 2079-7737, (Publisher: MDPI AG).
@article{zuniga_direct_2022,
title = {A Direct Interaction between Cyclodextrins and TASK Channels Decreases the Leak Current in Cerebellar Granule Neurons},
author = {Rafael Zúñiga and Daniel Mancilla and Tamara Rojas-Rocco and Fernando Vergara and Wendy González and Marcelo A. Catalán and Leandro Zúñiga},
url = {http://dx.doi.org/10.3390/biology11081097},
doi = {10.3390/biology11081097},
issn = {2079-7737},
year = {2022},
date = {2022-07-01},
urldate = {2022-07-01},
journal = {Biology},
volume = {11},
number = {8},
pages = {1097},
note = {Publisher: MDPI AG},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Mazola, Yuliet; Montesinos, José C. E. Márquez; Ramírez, David; Zúñiga, Leandro; Decher, Niels; Ravens, Ursula; Yarov-Yarovoy, Vladimir; González, Wendy
Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational Approach Artículo de revista
En: Pharmaceutics, vol. 14, no 7, pp. 1356, 2022, ISSN: 1999-4923.
@article{mazola_common_2022,
title = {Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational Approach},
author = {Yuliet Mazola and José C. E. Márquez Montesinos and David Ramírez and Leandro Zúñiga and Niels Decher and Ursula Ravens and Vladimir Yarov-Yarovoy and Wendy González},
url = {https://www.mdpi.com/1999-4923/14/7/1356},
doi = {10.3390/pharmaceutics14071356},
issn = {1999-4923},
year = {2022},
date = {2022-06-01},
urldate = {2024-12-14},
journal = {Pharmaceutics},
volume = {14},
number = {7},
pages = {1356},
abstract = {Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that a combined blockade of Nav1.5 (and its current, INa) and Kv1.5 (and its current, IKur) ion channels yield a synergistic anti-arrhythmic effect without alterations in ventricles. We focused on Kv1.5 and Nav1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD) as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We present a computational workflow for a flecainide BS comparison in a flecainide-Kv1.5 docking model and a solved structure of the flecainide-Nav1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the central cavity and consists of a hydrophobic patch and a polar region, involving residues from the S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that a combined blockade of Nav1.5 (and its current, INa) and Kv1.5 (and its current, IKur) ion channels yield a synergistic anti-arrhythmic effect without alterations in ventricles. We focused on Kv1.5 and Nav1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD) as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We present a computational workflow for a flecainide BS comparison in a flecainide-Kv1.5 docking model and a solved structure of the flecainide-Nav1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the central cavity and consists of a hydrophobic patch and a polar region, involving residues from the S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.
