title: Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.
abstract: CBR hydroxamidines are small-molecule inhibitors of bacterial RNA polymerase (RNAP) discovered through high-throughput screening of synthetic-compound libraries. CBR pyrazoles are structurally related RNAP inhibitors discovered through scaffold hopping from CBR hydroxamidines. CBR hydroxamidines and pyrazoles selectively inhibit Gram-negative bacterial RNAP and exhibit selective antibacterial activity against Gram-negative bacteria. Here, we report crystal structures of the prototype CBR hydroxamidine, CBR703, and a CBR pyrazole in complex with E. coli RNAP holoenzyme. In addition, we define the full resistance determinant for CBR703, show that the binding site and resistance determinant for CBR703 do not overlap the binding sites and resistance determinants of other characterized RNAP inhibitors, show that CBR703 exhibits no or minimal cross-resistance with other characterized RNAP inhibitors, and show that co-administration of CBR703 with other RNAP inhibitors results in additive antibacterial activities. The results set the stage for structure-based optimization of CBR inhibitors as antibacterial drugs.
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Feng
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: David
authors.initials: D
authors.lastname: Degen
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Xinyue
authors.initials: X
authors.lastname: Wang
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Gigliotti
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Shuang
authors.initials: S
authors.lastname: Liu
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Deepankar
authors.initials: D
authors.lastname: Das
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Michalchuk
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Yon W
authors.initials: YW
authors.lastname: Ebright
authors.affiliation: Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA.
authors.forename: Meliza
authors.initials: M
authors.lastname: Talaue
authors.affiliation: Center for Biodefense, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Connell
authors.affiliation: Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Electronic address: ebright@waksman.rutgers.edu.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
mesh_terms: D000578:Amidines / Q000737:chemistry / Q000494:pharmacology*; D000595:Amino Acid Sequence; D000818:Animals; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology*; D001665:Binding Sites; D002522:Chlorocebus aethiops; D018360:Crystallography, X-Ray; D012321:DNA-Directed RNA Polymerases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics; D004357:Drug Synergism; D004926:Escherichia coli / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D006898:Hydroxylamines / Q000737:chemistry / Q000494:pharmacology*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000201:enzymology / Q000235:genetics; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011720:Pyrazoles / Q000737:chemistry / Q000494:pharmacology*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D014158:Transcription, Genetic / Q000187:drug effects*; D014709:Vero Cells
chemical_list: D000578:Amidines; D000900:Anti-Bacterial Agents; C478598:CBR 703; D029968:Escherichia coli Proteins; D006898:Hydroxylamines; D008024:Ligands; D011720:Pyrazoles; D011994:Recombinant Proteins; D012321:DNA-Directed RNA Polymerases