Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score.
J Comput Aided Mol Des
; 37(4): 217-225, 2023 04.
Article
in En
| MEDLINE
| ID: mdl-36943644
ABSTRACT
Membrane proteins are attractive targets for drug discovery due to their crucial roles in various biological processes. Studying the binding poses of amphipathic molecules to membrane proteins is essential for understanding the functions of membrane proteins and docking simulations can facilitate the screening of protein-ligand complexes at low computational costs. However, identifying docking poses for a ligand in non-aqueous environments such as lipid bilayers can be challenging. To address this issue, we propose a new docking score called logP-corrected membrane docking (LoCoMock) score. To screen putative protein-ligand complexes embedded in a membrane, the LoCoMock score considers the affinity between a target ligand and the membrane. It combines the docking score of the protein-ligand complex with the logP of the target ligand. In demonstrations using several model ligands, the LoCoMock score screened more putative complexes than the conventional docking score. As extended docking, the LoCoMock score makes it possible to screen membrane proteins more effectively as drug targets than the conventional docking.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Lipid Bilayers
/
Membrane Proteins
Type of study:
Diagnostic_studies
/
Prognostic_studies
/
Screening_studies
Language:
En
Journal:
J Comput Aided Mol Des
Journal subject:
BIOLOGIA MOLECULAR
/
ENGENHARIA BIOMEDICA
Year:
2023
Document type:
Article
Affiliation country:
Japón