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Artículo

Solvent Sites Improve Docking Performance of Protein-Protein Complexes and Protein-Protein Interface-Targeted Drugs

Mayol, Gonzalo FedericoIcon ; Defelipe, Lucas AlfredoIcon ; Arcon, Juan PabloIcon ; Turjanski, AdrianIcon ; Marti, Marcelo AdrianIcon
Fecha de publicación: 08/2022
Editorial: American Chemical Society
Revista: Journal of Chemical Information and Modeling
ISSN: 1549-9596
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Físico-Química, Ciencia de los Polímeros, Electroquímica

Resumen

Protein-protein interactions (PPIs) are essential, and modulating their function through PPI-targeted drugs is an important research field. PPI sites are shallow protein surfaces readily accessible to the solvent, thus lacking a proper pocket to fit a drug, while their lack of endogenous ligands prevents drug design by chemical similarity. The development of PPI-blocking compounds is, therefore, a tough challenge. Mixed solvent molecular dynamics has been shown to reveal protein-ligand interaction hot spots in protein active sites by identifying solvent sites (SSs). Furthermore, our group has shown that SSs significantly improve protein-ligand docking. In the present work, we extend our analysis to PPI sites. In particular, we analyzed water, ethanol, and phenol-derived sites in terms of their capacity to predict protein-drug and protein-protein interactions. Subsequently, we show how this information can be incorporated to improve both protein-ligand and protein-protein docking. Finally, we highlight the presence of aromatic clusters as key elements of the corresponding interactions.
Palabras clave: docking
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info:eu-repo/semantics/restrictedAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/213824
DOI: http://dx.doi.org/10.1021/acs.jcim.2c00264
Colecciones
Articulos(IQUIBICEN)
Articulos de INSTITUTO DE QUIMICA BIOLOGICA DE LA FACULTAD DE CS. EXACTAS Y NATURALES
Citación
Mayol, Gonzalo Federico; Defelipe, Lucas Alfredo; Arcon, Juan Pablo; Turjanski, Adrian; Marti, Marcelo Adrian; Solvent Sites Improve Docking Performance of Protein-Protein Complexes and Protein-Protein Interface-Targeted Drugs; American Chemical Society; Journal of Chemical Information and Modeling; 62; 15; 8-2022; 3577-3588
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