Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference.
Most existing antibiotics were discovered through screens of environmental microbes, particularly the streptomycetes, for the capacity to prevent the growth of pathogenic bacteria. This "activity-guided screening" method has been largely abandoned because it repeatedly rediscovers those compounds that are highly expressed during laboratory culture. Most of these metabolites have already been biochemically characterized. However, the sequencing of streptomycete genomes has revealed a large number of "cryptic" secondary metabolic genes that are either poorly expressed in the laboratory or that have biological activities that cannot be discovered through standard activity-guided screens. Methods that reveal these uncharacterized compounds, particularly methods that are not biased in favor of the highly expressed metabolites, would provide direct access to a large number of potentially useful biologically active small molecules. To address this need, we have devised a discovery method in which a chemical elicitor called Cl-ARC is used to elevate the expression of cryptic biosynthetic genes. We show that the resulting change in product yield permits the direct discovery of secondary metabolites without requiring knowledge of their biological activity. We used this approach to identify three rare secondary metabolites and find that two of them target eukaryotic cells and not bacterial cells. In parallel, we report the first paired use of cheminformatic inference and chemical genetic epistasis in yeast to identify the target. In this way, we demonstrate that oxohygrolidin, one of the eukaryote-active compounds we identified through activity-independent screening, targets the V1 ATPase in yeast and human cells and secondarily HSP90.
Department of Biochemistry, Medical Sciences Building, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
Sheila M
SM
Pimentel-Elardo
Department of Chemistry and Chemical Biology, McMaster University , 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada.
Dan
D
Sørensen
Department of Biochemistry, Medical Sciences Building, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
Louis
L
Ho
Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada.
Mikaela
M
Ziko
Molecular Structure & Function Program, The Hospital for Sick Children Research Institute , 686 Bay St., Toronto, Ontario M5G 0A4, Canada.
Stephanie A
SA
Bueler
Keenan Research Centre for Biomedical Sciences, St. Michael's Hospital , 30 Bond St., Toronto, Ontario M5B 1W8, Canada.
Stella
S
Lu
Department of Biochemistry & Biophysics, University of California at San Francisco , Mission Bay, Genentech Hall 600 16th St., San Francisco, California 94158-2517, United States.
Joe
J
Tao
Advanced Chemistry Development Inc. , 8 King St. East, Suite 107, Toronto, Ontario M5C 1B5, Canada.
Arvin
A
Moser
Advanced Chemistry Development Inc. , 8 King St. East, Suite 107, Toronto, Ontario M5C 1B5, Canada.
Richard
R
Lee
Department of Biochemistry & Biophysics, University of California at San Francisco , Mission Bay, Genentech Hall 600 16th St., San Francisco, California 94158-2517, United States.
David
D
Agard
Keenan Research Centre for Biomedical Sciences, St. Michael's Hospital , 30 Bond St., Toronto, Ontario M5B 1W8, Canada.
Greg
G
Fairn
Department of Biochemistry, Medical Sciences Building, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.|Molecular Structure & Function Program, The Hospital for Sick Children Research Institute , 686 Bay St., Toronto, Ontario M5G 0A4, Canada.
John L
JL
Rubinstein
Department of Pharmaceutical Chemistry, University of California, San Francisco , 1700 4th St., Byers Hall Suite 508D, San Francisco California 94158-2550, United States.
Brian K
BK
Shoichet
Department of Biochemistry, Medical Sciences Building, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
Justin R
JR
Nodwell
D000083:Acetanilides / Q000737:chemistry* / Q000494:pharmacology; D039903:Actinobacteria / Q000737:chemistry* / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D000900:Anti-Bacterial Agents / Q000096:biosynthesis* / Q000737:chemistry / Q000302:isolation & purification* / Q000494:pharmacology; D001419:Bacteria / Q000187:drug effects; D001688:Biological Products / Q000737:chemistry* / Q000378:metabolism; D002853:Chromatography, Liquid; D055808:Drug Discovery / Q000379:methods*; D018841:HSP90 Heat-Shock Proteins / Q000037:antagonists & inhibitors; D018942:Macrolides / Q000737:chemistry* / Q000494:pharmacology; D010647:Phenyl Ethers / Q000737:chemistry* / Q000494:pharmacology
D000083:Acetanilides; D000900:Anti-Bacterial Agents; D001688:Biological Products; D018841:HSP90 Heat-Shock Proteins; D018942:Macrolides; C000610772:N-(4-(4-chlorophenoxy)phenyl)acetamide; D010647:Phenyl Ethers; C000610771:oxohygrolidin