title: Structure guided development of novel thymidine mimetics targeting Pseudomonas aeruginosa thymidylate kinase: from hit to lead generation.
abstract: Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of an essential component, thymidine triphosphate, in DNA replication. All reported TMK inhibitors are thymidine analogues, which might retard their development as potent therapeutics due to cell permeability and off-target activity against human TMK. A small molecule hit (1, IC(50) = 58 μM), which has reasonable inhibition potency against Pseudomonas aeruginosa TMK (PaTMK), was identified by the analysis of the binding mode of thymidine or TP(5)A in a PaTMK homology model. This hit (1) was cocrystallized with PaTMK, and several potent PaTMK inhibitors (leads, 46, 47, 48, and 56, IC(50) = 100-200 nM) were synthesized using computer-aided design approaches including virtual synthesis/screening, which was used to guide the design of inhibitors. The binding mode of the optimized leads in PaTMK overlaps with that of other bacterial TMKs but not with human TMK, which shares few common features with the bacterial enzymes. Therefore, the optimized TMK inhibitors described here should be useful for the development of antibacterial agents targeting TMK without undesired off-target effects. In addition, an inhibition mechanism associated with the LID loop, which mimics the process of phosphate transfer from ATP to dTMP, was proposed based on X-ray cocrystal structures, homology models, and structure-activity relationship results.
authors.affiliation: Department of Chemistry, Scripps Florida, Jupiter, Florida 33458, United States.
authors.forename: Jun Yong
authors.initials: JY
authors.lastname: Choi
authors.forename: Mark S
authors.initials: MS
authors.lastname: Plummer
authors.forename: Jeremy
authors.initials: J
authors.lastname: Starr
authors.forename: Charlene R
authors.initials: CR
authors.lastname: Desbonnet
authors.forename: Holly
authors.initials: H
authors.lastname: Soutter
authors.forename: Jeanne
authors.initials: J
authors.lastname: Chang
authors.forename: J Richard
authors.initials: JR
authors.lastname: Miller
authors.forename: Keith
authors.initials: K
authors.lastname: Dillman
authors.forename: Alita A
authors.initials: AA
authors.lastname: Miller
authors.forename: William R
authors.initials: WR
authors.lastname: Roush
mesh_terms: D000900:Anti-Bacterial Agents / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology; D018360:Crystallography, X-Ray; D006801:Humans; D007093:Imidazoles / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology; D008826:Microbial Sensitivity Tests; D008958:Models, Molecular; D008968:Molecular Conformation; D018716:Molecular Mimicry; D009703:Nucleoside-Phosphate Kinase / Q000037:antagonists & inhibitors* / Q000737:chemistry; D011485:Protein Binding; D011550:Pseudomonas aeruginosa / Q000187:drug effects / Q000201:enzymology*; D011725:Pyridines / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology; D011743:Pyrimidines / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology; D016415:Sequence Alignment; D013936:Thymidine / Q000737:chemistry*
chemical_list: D000900:Anti-Bacterial Agents; D007093:Imidazoles; D011725:Pyridines; D011743:Pyrimidines; D009703:Nucleoside-Phosphate Kinase; C020093:dTMP kinase; D013936:Thymidine