J
Jonathan M. Stokes
Researcher at Massachusetts Institute of Technology
Publications - 26
Citations - 2460
Jonathan M. Stokes is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Antibiotics & Medicine. The author has an hindex of 14, co-authored 22 publications receiving 1230 citations. Previous affiliations of Jonathan M. Stokes include Wyss Institute for Biologically Inspired Engineering & Broad Institute.
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Journal ArticleDOI
A Deep Learning Approach to Antibiotic Discovery
Jonathan M. Stokes,Kevin Yang,Kyle Swanson,Wengong Jin,Andres Cubillos-Ruiz,Nina M. Donghia,Craig R. MacNair,Shawn French,Lindsey A. Carfrae,Zohar Bloom-Ackermann,Victoria M. Tran,Anush Chiappino-Pepe,Ahmed H. Badran,Ian W. Andrews,Ian W. Andrews,Ian W. Andrews,Emma J. Chory,George M. Church,Eric D. Brown,Tommi S. Jaakkola,Regina Barzilay,James J. Collins +21 more
TL;DR: A deep neural network capable of predicting molecules with antibacterial activity is trained and a molecule from the Drug Repurposing Hub-halicin- is discovered that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens.
Journal ArticleDOI
Bacterial Metabolism and Antibiotic Efficacy
TL;DR: This work aims to emphasize the close relationship between bacterial metabolism and antibiotic efficacy as well as propose areas of exploration to develop novel antibiotics that optimally exploit bacterial metabolic networks.
Journal ArticleDOI
Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance.
Jonathan M. Stokes,Craig R. MacNair,Bushra Ilyas,Shawn French,Jean-Philippe Côté,Catrien Bouwman,Maya A. Farha,Arthur O. Sieron,Chris Whitfield,Brian K. Coombes,Eric D. Brown +10 more
TL;DR: An unconventional screening platform designed to enrich for non-lethal, outer-membrane-active compounds with potential as adjuvants for conventional antibiotics is described, identifying the antiprotozoal drug pentamidine6 as an effective perturbant of the Gram-negative outer membrane through its interaction with lipopolysaccharide.
Journal ArticleDOI
Overcoming mcr-1 mediated colistin resistance with colistin in combination with other antibiotics.
Craig R. MacNair,Jonathan M. Stokes,Lindsey A. Carfrae,Aline Fiebig-Comyn,Brian K. Coombes,Michael R. Mulvey,Eric D. Brown +6 more
TL;DR: The use of colistin in combination with antibiotics that are typically active against Gram-positive bacteria poses a viable therapeutic alternative for highly drug-resistant Gram-negative pathogens expressing plasmid-borne mcr-1.
Journal ArticleDOI
Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate.
Allison J. Lopatkin,Allison J. Lopatkin,Allison J. Lopatkin,Jonathan M. Stokes,Jonathan M. Stokes,Erica J. Zheng,Erica J. Zheng,Jason H. Yang,Jason H. Yang,Melissa K. Takahashi,Melissa K. Takahashi,Lingchong You,James J. Collins +12 more
TL;DR: This study provides a cohesive metabolic-dependent basis for antibiotic-mediated cell death, with implications for current treatment strategies and future drug development, and shows that metabolic state and ATP levels are better predictors of antibiotic lethality across diverse bacterial species than growth rate.