Toward Simple, Predictive Understanding of Protein-Ligand Interactions: Electronic Structure Calculations on Torpedo Californica Acetylcholinesterase Join Forces with the Chemist's Intuition

Sci Rep. 2020 Jun 8;10(1):9218. doi: 10.1038/s41598-020-65984-0.

Abstract

Contemporary efforts for empirically-unbiased modeling of protein-ligand interactions entail a painful tradeoff - as reliable information on both noncovalent binding factors and the dynamic behavior of a protein-ligand complex is often beyond practical limits. We demonstrate that information drawn exclusively from static molecular structures can be used for reproducing and predicting experimentally-measured binding affinities for protein-ligand complexes. In particular, inhibition constants (Ki) were calculated for seven different competitive inhibitors of Torpedo californica acetylcholinesterase using a multiple-linear-regression-based model. The latter, incorporating five independent variables - drawn from QM cluster, DLPNO-CCSD(T) calculations and LED analyses on the seven complexes, each containing active amino-acid residues found within interacting distance (3.5 Å) from the corresponding ligand - is shown to recover 99.9% of the sum of squares for measured Ki values, while having no statistically-significant residual errors. Despite being fitted to a small number of data points, leave-one-out cross-validation statistics suggest that it possesses surprising predictive value (Q2LOO=0.78, or 0.91 upon removal of a single outlier). This thus challenges ligand-invariant definitions of active sites, such as implied in the lock-key binding theory, as well as in alternatives highlighting shape-complementarity without taking electronic effects into account. Broader implications of the current work are discussed in dedicated appendices.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylcholinesterase / chemistry
  • Acetylcholinesterase / metabolism*
  • Animals
  • Cholinesterase Inhibitors / chemistry
  • Cholinesterase Inhibitors / metabolism
  • Kinetics
  • Ligands*
  • Linear Models
  • Models, Molecular
  • Torpedo / metabolism

Substances

  • Cholinesterase Inhibitors
  • Ligands
  • Acetylcholinesterase