title: Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum.
abstract: The efficient application of nitrogenous fertilizers is urgently required, as their excessive and inefficient use is causing substantial economic loss and environmental pollution. A significant amount of applied nitrogen in agricultural soils is lost as nitrous oxide (N2O) in the environment due to the microbial denitrification process. The widely distributed fungus Fusarium oxysporum is a major denitrifier in agricultural soils and its denitrification activity could be targeted to reduce nitrogen loss in the form of N2O from agricultural soils. Here, we report the discovery of first small molecule inhibitors of copper nitrite reductase (NirK) from F. oxysporum, which is a key enzyme in the fungal denitrification process. The inhibitors were discovered by a hierarchical in silico screening approach consisting of pharmacophore modeling and molecular docking. In vitro evaluation of F. oxysporum NirK activity revealed several pyrimidone and triazinone based compounds with potency in the low micromolar range. Some of these compounds suppressed the fungal denitrification in vivo as well. The compounds reported here could be used as starting points for the development of nitrogenous fertilizer supplements and coatings as a means to prevent nitrogen loss by targeting fungal denitrification.
authors.affiliation: Chemical Genomics Research Group, Center for Sustainable Resource Science, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Matsuoka
authors.affiliation: Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN , 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN , 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Muddassar
authors.affiliation: Chemical Genomics Research Group, Center for Sustainable Resource Science, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.|Chemical Genetics Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Akihisa
authors.initials: A
authors.lastname: Matsuyama
authors.affiliation: Chemical Genomics Research Group, Center for Sustainable Resource Science, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.|Chemical Genetics Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.|CREST Research Project, Japan Science and Technology Corporation , 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
authors.forename: Minoru
authors.initials: M
authors.lastname: Yoshida
authors.affiliation: Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN , 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Kam Y J
authors.identifier: 0000-0002-9282-8045
authors.initials: KY
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D058440:Denitrification / Q000187:drug effects*; D055808:Drug Discovery; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D005670:Fusarium / Q000187:drug effects* / Q000378:metabolism*; D062105:Molecular Docking Simulation; D009572:Nitrite Reductases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
chemical_list: D004791:Enzyme Inhibitors; D009572:Nitrite Reductases; C052695:nitrite reductase, copper-containing