articleMolecular Systems BiologySep 1, 2022GOLD OA

Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

FWFelix WongAKAarti KrishnanEJErica J. ZhengHSH. StärkALAbigail L. Manson

Broad Institute · Massachusetts Institute of Technology · +2 more institutions

PubMed
Indexed incrossrefdoajpubmed

Abstract

Efficient identification of drug mechanisms of action remains a challenge. Computational docking approaches have been widely used to predict drug binding targets; yet, such approaches depend on existing protein structures, and accurate structural predictions have only recently become available from AlphaFold2. Here, we combine AlphaFold2 with molecular docking simulations to predict protein-ligand interactions between 296 proteins spanning Escherichia coli's essential proteome, and 218 active antibacterial compounds and 100 inactive compounds, respectively, pointing to widespread compound and protein promiscuity. We benchmark model performance by measuring enzymatic activity for 12 essential proteins treated…

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265
total citations
FWCI
35.01
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100%
References
53
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Authors

8

Topics & keywords

Topics
Keywords
  • Biology
  • Benchmarking
  • Computational biology
  • Docking (animal)
  • Antibiotics
  • Microbiology
  • Medicine
UN Sustainable Development Goals
  • Good health and well-being
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