Mechanisms of Specific versus Nonspecific Interactions of Aggregation-Prone Inhibitors and Attenuators

J Med Chem. 2019 May 23;62(10):5063-5079. doi: 10.1021/acs.jmedchem.9b00258. Epub 2019 May 10.

Abstract

A common source of false positives in drug discovery is ligand self-association into large colloidal assemblies that nonspecifically inhibit target proteins. However, the mechanisms of aggregation-based inhibition (ABI) and ABI-attenuation by additives, such as Triton X-100 (TX) and human serum albumin (HSA), are not fully understood. Here, we investigate the molecular basis of ABI and ABI-attenuation through the lens of NMR and coupled thermodynamic cycles. We unexpectedly discover a new class of aggregating ligands that exhibit negligible interactions with proteins but act as competitive sinks for the free inhibitor, resulting in bell-shaped dose-response curves. TX attenuates ABI by converting inhibitory, protein-binding aggregates into nonbinding coaggregates, whereas HSA minimizes nonspecific ligand interactions by functioning as a reservoir for free inhibitor and preventing self-association. Hence, both TX and HSA are useful tools to minimize false positives arising from nonspecific binding but at the cost of potentially introducing false negatives due to suppression of specific interactions.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Buffers
  • Dose-Response Relationship, Drug
  • Drug Discovery / methods*
  • False Positive Reactions
  • Humans
  • Light
  • Magnetic Resonance Spectroscopy
  • Octoxynol / pharmacology
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / pharmacology*
  • Scattering, Radiation
  • Serum Albumin, Human / chemistry
  • Serum Albumin, Human / drug effects
  • Spectrometry, Mass, Electrospray Ionization
  • Surface Plasmon Resonance
  • Thermodynamics

Substances

  • Buffers
  • Protein Kinase Inhibitors
  • Octoxynol
  • Serum Albumin, Human