Predicting the binding free energy of the inclusion process of 2-hydroxypropyl-β-cyclodextrin and small molecules by means of the MM/3D-RISM method. (25th July 2016)

• Record Type: Journal Article
• Authors: Sugita, Masatake; Hirata, Fumio
• Is Part Of: Journal of physics. Volume 28:Number 38(2016)
• Publication Date: 2016-07-25
• Subjects: 3D-RISM -- binding free energy -- cyclodextrin -- supramolecules -- molecular dynamics -- fluctuation; Condensed matter -- Periodicals; Matière condensée -- Périodiques; Vaste stoffen; Vloeistoffen; Natuurkunde; Electronic journals; Computer network resources; 530.4105
• DOI: 10.1088/0953-8984/28/38/384002
• Languages: English
• ISSNs: 0953-8984

Abstract

Abstract: A protocol to calculate the binding free energy of a host–guest system is proposed based on the MM/3D-RISM method, taking cyclodextrin derivatives and their ligands as model systems. The protocol involves the procedure to identify the most probable binding mode (MPBM) of receptors and ligands by means of the umbrella sampling method. The binding free energies calculated by the MM/3D-RISM method for the complexes of the seven ligands with the MPBM of the cyclodextrin, and with the fluctuated structures around it, are in agreement with the corresponding experimental data in a semi-quantitative manner. It suggests that the protocol proposed here is promising for predicting the binding affinity of a small ligand to a relatively rigid receptor such as cyclodextrin.