title: Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents.
abstract: MenE is an o-succinylbenzoyl-CoA (OSB-CoA) synthetase in the bacterial menaquinone biosynthesis pathway and is a promising target for the development of novel antibacterial agents. The enzyme catalyzes CoA ligation via an acyl-adenylate intermediate, and we have previously reported tight-binding inhibitors of MenE based on stable acyl-sulfonyladenosine analogues of this intermediate, including OSB-AMS (1), which has an IC50 value of ≤25 nM for Escherichia coli MenE. Herein, we show that OSB-AMS reduces menaquinone levels in Staphylococcus aureus, consistent with its proposed mechanism of action, despite the observation that the antibacterial activity of OSB-AMS is ∼1000-fold lower than the IC50 for enzyme inhibition. To inform the synthesis of MenE inhibitors with improved antibacterial activity, we have undertaken a structure-activity relationship (SAR) study stimulated by the knowledge that OSB-AMS can adopt two isomeric forms in which the OSB side chain exists either as an open-chain keto acid or a cyclic lactol. These studies revealed that negatively charged analogues of the keto acid form bind, while neutral analogues do not, consistent with the hypothesis that the negatively charged keto acid form of OSB-AMS is the active isomer. X-ray crystallography and site-directed mutagenesis confirm the importance of a conserved arginine for binding the OSB carboxylate. Although most lactol isomers tested were inactive, a novel difluoroindanediol inhibitor (11) with improved antibacterial activity was discovered, providing a pathway toward the development of optimized MenE inhibitors in the future.
authors.affiliation: Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.|Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400.
authors.forename: Joe S
authors.initials: JS
authors.lastname: Matarlo
authors.affiliation: Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Evans
authors.affiliation: Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.
authors.forename: Indrajeet
authors.initials: I
authors.lastname: Sharma
authors.affiliation: Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.
authors.forename: Lubens J
authors.initials: LJ
authors.lastname: Lavaud
authors.affiliation: Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Ngo
authors.affiliation: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400.
authors.forename: Roger
authors.initials: R
authors.lastname: Shek
authors.affiliation: NE-CAT and Department of Chemistry and Chemical Biology, Building 436E, Argonne National Laboratory, Argonne, IL 60439.
authors.forename: Kanagalaghatta R
authors.initials: KR
authors.lastname: Rajashankar
authors.affiliation: Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.|Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.|Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-3400.
authors.forename: Jarrod B
authors.initials: JB
authors.lastname: French
authors.affiliation: Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065.|Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065.
authors.forename: Derek S
authors.initials: DS
authors.lastname: Tan
authors.affiliation: Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400.|Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Tonge
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000494:pharmacology* / Q000633:toxicity; D001120:Arginine / Q000737:chemistry; D020134:Catalytic Domain / Q000235:genetics; D002522:Chlorocebus aethiops; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D055808:Drug Discovery; D048168:Escherichia coli K12 / Q000201:enzymology / Q000235:genetics; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000235:genetics; D008826:Microbial Sensitivity Tests; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D010654:Phenylbutyrates / Q000737:chemistry / Q000494:pharmacology / Q000633:toxicity; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013211:Staphylococcus aureus / Q000187:drug effects / Q000378:metabolism; D013329:Structure-Activity Relationship; D013389:Succinate-CoA Ligases / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000235:genetics; D014709:Vero Cells; D024482:Vitamin K 2 / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; D010654:Phenylbutyrates; D024482:Vitamin K 2; C013691:o-succinylbenzoic acid; D001120:Arginine; D013389:Succinate-CoA Ligases; C022693:O-succinylbenzoate - CoA ligase