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Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation
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DOI：10.1021/acs.jctc.3c00300.png)
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Abstract
En 中文
Here, we develop an empirical energy function based onquantummechanical data for the interaction between methane and benzene thatcaptures the contribution from CH-& pi; interactions. Suchinteractions are frequently observed in protein-ligand crystalstructures, particularly for carbohydrate ligands, but have been hardto quantify due to the absence of a model for CH-& pi; interactionsin typical molecular mechanical force fields or docking scoring functions.The CH-& pi; term was added to the AutoDock Vina (AD VINA)scoring function enabling its performance to be evaluated againsta cohort of more than 1600 occurrences in 496 experimental structuresof protein-ligand complexes. By employing a conformationalgrid search algorithm, inclusion of the CH-& pi; term wasshown to improve the prediction of the preferred orientation of flexibleligands in protein-binding sites and to enhance the detection of carbohydrate-bindingsites that display CH-& pi; interactions. Last but not least,this term was also shown to improve docking performance for the CASF-2016benchmark set and a carbohydrate set.
Keywords:
CENTER-DOT-PI
BENZENE
PATTERN
MODEL
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