Biological and Medicinal Chemistry

AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High Throughput Screens

Authors

  • Kate Stafford Atomwise Inc., San Francisco, CA 94103 USA ,
  • Brandon M. Anderson Atomwise Inc., San Francisco, CA 94103 USA ,
  • Jon Sorenson Atomwise Inc., San Francisco, CA 94103 USA ,
  • Henry van den Bedem Atomwise Inc. San Francisco, CA 94103 USA & Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.

Abstract

Structure-based, virtual High Throughput Screening (vHTS) methods for predicting ligand activity in drug discovery are important when there are no or relatively few known compounds that interact with a therapeutic target of interest. State-of-the-art computational vHTS necessarily relies on effective methods for pose sampling and docking to generate an accurate affinity score from the docked poses. However, proteins are dynamic; in vivo, ligands bind to a conformational ensemble. In silico docking to the single conformation represented by a crystal structure can adversely affect the pose quality. Here we introduce AtomNet PoseRanker, a graph convolutional network trained to identify, and re-rank crystal-like ligand poses from a sampled ensemble of protein conformations and ligand poses. In contrast to conventional vHTS methods that incorporate receptor flexibility, a deep learning approach can internalize valid cognate and non-cognate binding modes corresponding to distinct receptor conformations. AtomNet PoseRanker significantly enriched pose quality in docking to cognate and non-cognate receptors of the PDBbind v2019 dataset. Improved pose rankings that better represent experimentally observed ligand binding modes improve hit rates in vHTS campaigns, and thereby advance computational drug discovery, especially for novel therapeutic targets or novel binding sites.

Content

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