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Ultra-large library docking for discovering new chemotypes.

Jiankun Lyu1,2, Sheng Wang3,4, Trent E Balius1

  • 1Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.

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This study unlocks access to billions of novel chemical compounds using structure-based docking. Researchers discovered potent AmpC beta-lactamase inhibitors and D4 dopamine receptor ligands, expanding drug discovery possibilities.

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Area of Science:

  • Medicinal Chemistry
  • Computational Chemistry
  • Drug Discovery

Background:

  • Vast chemical libraries are crucial for drug discovery but remain largely inaccessible.
  • Make-on-demand synthesis offers a route to novel chemical entities.

Purpose of the Study:

  • To investigate the feasibility of structure-based docking for large, make-on-demand compound libraries.
  • To identify novel inhibitors of AmpC beta-lactamase and ligands for the D4 dopamine receptor.

Main Methods:

  • Structure-based docking simulations were performed on 170 million make-on-demand compounds.
  • Synthesized and tested top-ranking compounds against AmpC and the D4 dopamine receptor.
  • Utilized X-ray crystallography to validate docking predictions.

Main Results:

  • Identified a novel class of AmpC beta-lactamase inhibitors, with one optimized to 77 nM potency.
  • Discovered 453,000 potential D4 dopamine receptor ligands, including 81 new chemotypes.
  • Found 30 compounds with submicromolar activity, including a 180 pM subtype-selective D4 dopamine receptor agonist.

Conclusions:

  • Structure-based docking of large, make-on-demand libraries is an effective strategy for chemical space expansion.
  • This approach successfully identified potent inhibitors and novel ligands for therapeutic targets.
  • The methodology provides a powerful platform for accelerating drug discovery.