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Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors.
Calderón, Jacqueline C; Plut, Eva; Keller, Max; Cabrele, Chiara; Reiser, Oliver; Gervasio, Francesco L; Clark, Timothy.
Afiliación
  • Calderón JC; Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, Erlangen 91052, Germany.
  • Plut E; Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany.
  • Keller M; Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg D-93040, Germany.
  • Cabrele C; Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany.
  • Reiser O; Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany.
  • Gervasio FL; Pharmaceutical Sciences, University of Geneva, Geneva CH-1211, Switzerland.
  • Clark T; Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, Erlangen 91052, Germany.
J Chem Inf Model ; 64(1): 205-218, 2024 01 08.
Article en En | MEDLINE | ID: mdl-38150388
ABSTRACT
A metadynamics protocol is presented to characterize the binding and unbinding of peptide ligands to class A G-protein-coupled receptors (GPCRs). The protocol expands on the one previously presented for binding and unbinding small-molecule ligands to class A GPCRs and accounts for the more demanding nature of the peptide binding-unbinding process. It applies to almost all class A GPCRs. Exemplary simulations are described for subtypes Y1R, Y2R, and Y4R of the neuropeptide Y receptor family, vasopressin binding to the vasopressin V2 receptor (V2R), and oxytocin binding to the oxytocin receptor (OTR). Binding free energies and the positions of alternative binding sites are presented and, where possible, compared with the experiment.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Vasopresinas / Receptores Acoplados a Proteínas G Idioma: En Revista: J Chem Inf Model Asunto de la revista: INFORMATICA MEDICA / QUIMICA Año: 2024 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Estados Unidos
Texto completo
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XML
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Vasopresinas / Receptores Acoplados a Proteínas G Idioma: En Revista: J Chem Inf Model Asunto de la revista: INFORMATICA MEDICA / QUIMICA Año: 2024 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Estados Unidos