title: Rational optimization of drug-target residence time: insights from inhibitor binding to the Staphylococcus aureus FabI enzyme-product complex.
abstract: Drug-target kinetics has recently emerged as an especially important facet of the drug discovery process. In particular, prolonged drug-target residence times may confer enhanced efficacy and selectivity in the open in vivo system. However, the lack of accurate kinetic and structural data for a series of congeneric compounds hinders the rational design of inhibitors with decreased off-rates. Therefore, we chose the Staphylococcus aureus enoyl-ACP reductase (saFabI)--an important target for the development of new anti-staphylococcal drugs--as a model system to rationalize and optimize the drug-target residence time on a structural basis. Using our new, efficient, and widely applicable mechanistically informed kinetic approach, we obtained a full characterization of saFabI inhibition by a series of 20 diphenyl ethers complemented by a collection of 9 saFabI-inhibitor crystal structures. We identified a strong correlation between the affinities of the investigated saFabI diphenyl ether inhibitors and their corresponding residence times, which can be rationalized on a structural basis. Because of its favorable interactions with the enzyme, the residence time of our most potent compound exceeds 10 h. In addition, we found that affinity and residence time in this system can be significantly enhanced by modifications predictable by a careful consideration of catalysis. Our study provides a blueprint for investigating and prolonging drug-target kinetics and may aid in the rational design of long-residence-time inhibitors targeting the essential saFabI enzyme.
authors.affiliation: Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Chang
authors.forename: Johannes
authors.initials: J
authors.lastname: Schiebel
authors.forename: Weixuan
authors.initials: W
authors.lastname: Yu
authors.forename: Gopal R
authors.initials: GR
authors.lastname: Bommineni
authors.forename: Pan
authors.initials: P
authors.lastname: Pan
authors.forename: Michael V
authors.initials: MV
authors.lastname: Baxter
authors.forename: Avinash
authors.initials: A
authors.lastname: Khanna
authors.forename: Christoph A
authors.initials: CA
authors.lastname: Sotriffer
authors.forename: Caroline
authors.initials: C
authors.lastname: Kisker
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Tonge
mesh_terms: D002384:Catalysis; D002626:Chemistry, Pharmaceutical; D018360:Crystallography, X-Ray; D015195:Drug Design; D050745:Enoyl-(Acyl-Carrier Protein) Reductase (NADPH, B-Specific) / Q000737:chemistry*; D050753:Enoyl-(Acyl-Carrier-Protein) Reductase (NADH) / Q000737:chemistry*; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry*; D054889:Fatty Acid Synthase, Type II / Q000737:chemistry*; D005227:Fatty Acids / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D013211:Staphylococcus aureus / Q000201:enzymology*; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D004791:Enzyme Inhibitors; D029968:Escherichia coli Proteins; D005227:Fatty Acids; D050745:Enoyl-(Acyl-Carrier Protein) Reductase (NADPH, B-Specific); D050753:Enoyl-(Acyl-Carrier-Protein) Reductase (NADH); C493924:fabI protein, E coli; D054889:Fatty Acid Synthase, Type II