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Structure-based design of an aromatic helical foldamer-protein interface.

Lingfei Wang1, Céline Douat1, Johannes Sigl1

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Researchers modified aromatic foldamers to better interact with human carbonic anhydrase II (HCAII). While modifications improved protein interface contacts and helix control, they did not significantly increase binding affinity to HCAII.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Medicinal Chemistry

Background:

  • Human carbonic anhydrase II (HCAII) is a validated drug target.
  • Aromatic foldamers offer a scaffold for designing enzyme inhibitors.
  • Controlling foldamer structure and protein interactions is key for drug development.

Purpose of the Study:

  • To design and synthesize modified aromatic foldamers with enhanced interactions with HCAII.
  • To investigate the impact of foldamer modifications on protein-ligand interface and helix handedness.
  • To assess the binding affinity of modified foldamers to HCAII.

Main Methods:

  • Solid-state structure determination of HCAII-foldamer complexes.
  • Computational analysis of protein-ligand interactions.
  • Molecular dynamics simulations.
  • Solid-phase synthesis of novel foldamer sequences.
  • RP-HPLC purification.
  • Fluorescence competition assay for binding affinity (K_D) determination.

Main Results:

  • Foldamer-protein interface was extended through predictable side-chain modifications.
  • Side-chain alterations did not affect main-chain behavior, allowing independent implementation.
  • Main-chain units derived from various aromatic δ-amino acids were interchangeable without altering helix curvature.
  • Despite design improvements, binding affinity (K_D) to HCAII did not significantly improve.

Conclusions:

  • Predictable modification of foldamer side chains can enhance protein interface interactions.
  • Aromatic foldamer scaffolds allow for independent tuning of side-chain and main-chain properties.
  • Further optimization is needed to translate improved structural interactions into enhanced binding affinity for HCAII inhibition.