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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding Sites

Ligand Binding Sites

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Protein Folding

Protein Folding

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Ligand Binding and Linkage

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Published on: June 20, 2025

Embarque de proteínas flexible con empaquetado de cadenas laterales basado en difusión

Runze Zhang^1,2, Xinyu Jiang^1,2, Duanhua Cao^1,3

¹Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Proceedings of the National Academy of Sciences of the United States of America

|December 24, 2025

Resumen

Este resumen es generado por máquina.

PackDock, un nuevo marco, utiliza IA y física para modelar la flexibilidad de las proteínas y las interacciones, mejorando el descubrimiento de fármacos al identificar compuestos potentes y revelar cambios moleculares cruciales.

Palabras clave:

aprendizaje automático acoplamiento molecular predicción de estructura de proteínas

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Área de la Ciencia:

Biología computacional
Biología estructural
Descubrimiento de fármacos

Sus antecedentes:

La flexibilidad de las proteínas es fundamental para la función biológica y el diseño de fármacos, pero los métodos tradicionales tienen dificultades para capturarla.
El modelado preciso de las interacciones proteína-ligando requiere tener en cuenta los cambios conformacionales dinámicos.

Objetivo del estudio:

Presentar PackDock, un marco novedoso que integra el aprendizaje profundo y el modelado basado en la física para el análisis de la interacción proteína-ligando.
Abordar las limitaciones de los modelos estáticos capturando la flexibilidad de las proteínas y los cambios conformacionales inducidos por el ligando.

Principales métodos:

PackDock utiliza modelos de difusión (PackPocket) para muestrear diversas conformaciones del bolsillo de unión.
La validación implicó experimentos de empaquetado de cadenas laterales, redocking y cross-docking.
El marco integra el aprendizaje profundo con simulaciones basadas en la física.

Principales resultados:

PackDock abordó con éxito los desafíos de flexibilidad de proteínas en varios experimentos computacionales.
El marco identificó compuestos novedosos de afinidad nanomolar con andamios únicos para una proteína diana.
Se dilucidaron cambios conformacionales clave de aminoácidos inducidos por la unión del ligando.

Conclusiones:

PackDock ofrece un enfoque potente para modelar las interacciones proteína-ligando, representando con precisión la dinámica de las proteínas.
El marco mejora la comprensión de los mecanismos de reconocimiento molecular.
PackDock proporciona perspectivas valiosas para avanzar en la investigación biológica básica y los esfuerzos de descubrimiento de fármacos.