Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities

Beihong Ji, Xibing He, Yuzhao Zhang, Jingchen Zhai, Viet Hoang Man, Shuhan Liu, Junmei Wang

Research output: Contribution to journalArticlepeer-review

Abstract

In this study, we developed a novel algorithm to improve the screening performance of an arbitrary docking scoring function by recalibrating the docking score of a query compound based on its structure similarity with a set of training compounds, while the extra computational cost is neglectable. Two popular docking methods, Glide and AutoDock Vina were adopted as the original scoring functions to be processed with our new algorithm and similar improvement performance was achieved. Predicted binding affinities were compared against experimental data from ChEMBL and DUD-E databases. 11 representative drug receptors from diverse drug target categories were applied to evaluate the hybrid scoring function. The effects of four different fingerprints (FP2, FP3, FP4, and MACCS) and the four different compound similarity effect (CSE) functions were explored. Encouragingly, the screening performance was significantly improved for all 11 drug targets especially when CSE = S4 (S is the Tanimoto structural similarity) and FP2 fingerprint were applied. The average predictive index (PI) values increased from 0.34 to 0.66 and 0.39 to 0.71 for the Glide and AutoDock vina scoring functions, respectively. To evaluate the performance of the calibration algorithm in drug lead identification, we also imposed an upper limit on the structural similarity to mimic the real scenario of screening diverse libraries for which query ligands are general-purpose screening compounds and they are not necessarily structurally similar to reference ligands. Encouragingly, we found our hybrid scoring function still outperformed the original docking scoring function. The hybrid scoring function was further evaluated using external datasets for two systems and we found the PI values increased from 0.24 to 0.46 and 0.14 to 0.42 for A2AR and CFX systems, respectively. In a conclusion, our calibration algorithm can significantly improve the virtual screening performance in both drug lead optimization and identification phases with neglectable computational cost.[Figure not available: see fulltext.]

Original languageEnglish (US)
Article number11
JournalJournal of Cheminformatics
Volume13
Issue number1
DOIs
StatePublished - Dec 2021
Externally publishedYes

Keywords

  • Compound similarity
  • Computer‐aided drug design
  • Docking
  • Fingerprint
  • Protein‐ligand binding
  • Scoring function
  • Virtual screening

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Library and Information Sciences

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