Predicting Accurate Lead Structures for Screening Molecular Libraries: A Quantum Crystallographic Approach

Molecules. 2021 Apr 29;26(9):2605. doi: 10.3390/molecules26092605.

Abstract

Optimization of lead structures is crucial for drug discovery. However, the accuracy of such a prediction using the traditional molecular docking approach remains a major concern. Our study demonstrates that the employment of quantum crystallographic approach-counterpoise corrected kernel energy method (KEM-CP) can improve the accuracy by and large. We select human aldose reductase at 0.66 Å, cyclin dependent kinase 2 at 2.0 Å and estrogen receptor β at 2.7 Å resolutions with active site environment ranging from highly hydrophilic to moderate to highly hydrophobic and several of their known ligands. Overall, the use of KEM-CP alongside the GoldScore resulted superior prediction than the GoldScore alone. Unlike GoldScore, the KEM-CP approach is neither environment-specific nor structural resolution dependent, which highlights its versatility. Further, the ranking of the ligands based on the KEM-CP results correlated well with that of the experimental IC50 values. This computationally inexpensive yet simple approach is expected to ease the process of virtual screening of potent ligands, and it would advance the drug discovery research.

Keywords: kernel energy method; lead structure; molecular docking; protein-ligand interaction; quantum crystallography; scoring function.

Publication types

  • Meta-Analysis

MeSH terms

  • Binding Sites
  • Biomarkers
  • Crystallography
  • Drug Discovery / methods*
  • Humans
  • Ligands
  • Models, Molecular*
  • Molecular Conformation
  • Protein Binding
  • Quantitative Structure-Activity Relationship*
  • Small Molecule Libraries*

Substances

  • Biomarkers
  • Ligands
  • Small Molecule Libraries