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Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens.
Tse, Megan W; Zhu, Meilin; Peters, Benjamin; Hamami, Efrat; Chen, Julie; Davis, Kathleen P; Nitz, Samuel; Weller, Juliane; Warrier, Thulasi; Hunt, Diana K; Morales, Yoelkys; Kawate, Tomohiko; Gaulin, Jeffrey L; Come, Jon H; Hernandez-Bird, Juan; Huo, Wenwen; Neisewander, Isabelle; Kiessling, Laura L; Hung, Deborah T; Mecsas, Joan; Aldridge, Bree B; Isberg, Ralph R; Blainey, Paul C.
Affiliation
  • Tse MW; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
  • Zhu M; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Peters B; These authors contributed equally.
  • Hamami E; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
  • Chen J; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Davis KP; These authors contributed equally.
  • Nitz S; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Weller J; These authors contributed equally.
  • Warrier T; Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111.
  • Hunt DK; These authors contributed equally.
  • Morales Y; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
  • Kawate T; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Gaulin JL; Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139.
  • Come JH; Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111.
  • Hernandez-Bird J; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
  • Huo W; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Neisewander I; Tri-Institutional Program in Computational Biology and Medicine, New York, New York, 10065.
  • Kiessling LL; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
  • Hung DT; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Mecsas J; Wellcome Sanger Institute, Hinxton, Saffron Walden CB10 1RQ, United Kingdom.
  • Aldridge BB; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Isberg RR; Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114.
  • Blainey PC; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
bioRxiv ; 2024 Mar 26.
Article in En | MEDLINE | ID: mdl-38585790
ABSTRACT
Antibiotic resistance, especially in multidrug-resistant ESKAPE pathogens, remains a worldwide problem. Combination antimicrobial therapies may be an important strategy to overcome resistance and broaden the spectrum of existing antibiotics. However, this strategy is limited by the ability to efficiently screen large combinatorial chemical spaces. Here, we deployed a high-throughput combinatorial screening platform, DropArray, to evaluate the interactions of over 30,000 compounds with up to 22 antibiotics and 6 strains of Gram-negative ESKAPE pathogens, totaling to over 1.3 million unique strain-antibiotic-compound combinations. In this dataset, compounds more frequently exhibited synergy with known antibiotics than single-agent activity. We identified a compound, P2-56, and developed a more potent analog, P2-56-3, which potentiated rifampin (RIF) activity against Acinetobacter baumannii and Klebsiella pneumoniae. Using phenotypic assays, we showed P2-56-3 disrupts the outer membrane of A. baumannii. To identify pathways involved in the mechanism of synergy between P2-56-3 and RIF, we performed genetic screens in A. baumannii. CRISPRi-induced partial depletion of lipooligosaccharide transport genes (lptA-D, lptFG) resulted in hypersensitivity to P2-56-3/RIF treatment, demonstrating the genetic dependency of P2-56-3 activity and RIF sensitization on lpt genes in A. baumannii. Consistent with outer membrane homeostasis being an important determinant of P2-56-3/RIF tolerance, knockout of maintenance of lipid asymmetry complex genes and overexpression of certain resistance-nodulation-division efflux pumps - a phenotype associated with multidrug-resistance - resulted in hypersensitivity to P2-56-3. These findings demonstrate the immense scale of phenotypic antibiotic combination screens using DropArray and the potential for such approaches to discover new small molecule synergies against multidrug-resistant ESKAPE strains.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: BioRxiv Year: 2024 Document type: Article
Fulltext
Add to My VHL
Print
XML
PubMed Links
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: BioRxiv Year: 2024 Document type: Article