title: Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.
abstract: There is growing awareness of the link between drug-target residence time and in vivo drug activity, and there are increasing efforts to determine the molecular factors that control the lifetime of a drug-target complex. Rational alterations in the drug-target residence time require knowledge of both the ground and transition states on the inhibition reaction coordinate, and we have determined the structure-kinetic relationship for 22 ethyl- or hexyl-substituted diphenyl ethers that are slow-binding inhibitors of bpFabI1, the enoyl-ACP reductase FabI1 from Burkholderia pseudomallei. Analysis of enzyme inhibition using a two-dimensional kinetic map demonstrates that the ethyl and hexyl diphenyl ethers fall into two distinct clusters. Modifications to the ethyl diphenyl ether B ring result in changes to both on and off rates, where residence times of up to ∼700 min (∼11 h) are achieved by either ground state stabilization (PT444) or transition state destabilization (slower on rate) (PT404). By contrast, modifications to the hexyl diphenyl ether B ring result in residence times of 300 min (∼5 h) through changes in only ground state stabilization (PT119). Structural analysis of nine enzyme:inhibitor complexes reveals that the variation in structure-kinetic relationships can be rationalized by structural rearrangements of bpFabI1 and subtle changes to the orientation of the inhibitor in the binding pocket. Finally, we demonstrate that three compounds with residence times on bpFabI1 from 118 min (∼2 h) to 670 min (∼11 h) have in vivo efficacy in an acute B. pseudomallei murine infection model using the virulent B. pseudomallei strain Bp400.
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Carla
authors.initials: C
authors.lastname: Neckles
authors.affiliation: Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Eltschkner
authors.affiliation: Rocky Mountain Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research and Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-0922, United States.
authors.forename: Jason E
authors.initials: JE
authors.lastname: Cummings
authors.affiliation: Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany.
authors.forename: Maria
authors.initials: M
authors.lastname: Hirschbeck
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Fereidoon
authors.initials: F
authors.lastname: Daryaee
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Gopal R
authors.initials: GR
authors.lastname: Bommineni
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Lauren
authors.initials: L
authors.lastname: Spagnuolo
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Weixuan
authors.initials: W
authors.lastname: Yu
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Shabnam
authors.initials: S
authors.lastname: Davoodi
authors.affiliation: Rocky Mountain Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research and Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-0922, United States.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Slayden
authors.affiliation: Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany.
authors.forename: Caroline
authors.initials: C
authors.lastname: Kisker
authors.affiliation: Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
authors.forename: Peter J
authors.identifier: 0000-0003-1606-3471
authors.initials: PJ
authors.lastname: Tonge
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000494:pharmacology; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D016957:Burkholderia pseudomallei / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics / Q000254:growth & development; D015169:Colony Count, Microbial; D018360:Crystallography, X-Ray; D050753:Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D005260:Female; D015870:Gene Expression; D007700:Kinetics; D008168:Lung / Q000187:drug effects / Q000382:microbiology; D008554:Melioidosis / Q000178:diet therapy* / Q000188:drug therapy / Q000382:microbiology; D051379:Mice; D008807:Mice, Inbred BALB C; D008826:Microbial Sensitivity Tests; D056004:Molecular Dynamics Simulation; D010647:Phenyl Ethers / Q000737:chemistry* / Q000494:pharmacology; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013154:Spleen / Q000187:drug effects / Q000382:microbiology; D013329:Structure-Activity Relationship
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D010647:Phenyl Ethers; D050753:Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)