title: Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening.
abstract: To identify specific bacterial thymidylate synthase (TS) inhibitors, we exploited phenolphthalein (PTH), which inhibits both bacterial and human enzymes. The X-ray crystal structure of Lactobacillus casei TS (LcTS) that binds PTH showed multiple binding modes of the inhibitor, which prevented a classical structure-based drug design approach. To overcome this issue, we synthesized two phthalimidic libraries that were tested against TS enzymes and then we performed X-ray crystallographic screening of the active compounds. Compounds 6A, 8A, and 12A showed 40-fold higher affinity for bacterial TS than human TS. The X-ray crystallographic screening characterized the binding mode of six inhibitors in complexes with LcTS. Of these, 20A, 23A, and 24A showed a common unique binding mode, whereas 8A showed a different, unique binding mode. A comparative analysis of the LcTS X-ray complexes that were obtained with the pathogenic TS enabled the selection of compounds 8A and 23A as specific compounds and starting points to be exploited for the specific inhibition of pathogen enzymes.
authors.affiliation: Dipartimento di Scienze Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Modena, Italy. mangani@unisi.it
authors.forename: Stefano
authors.initials: S
authors.lastname: Mangani
authors.forename: Laura
authors.initials: L
authors.lastname: Cancian
authors.forename: Rosalida
authors.initials: R
authors.lastname: Leone
authors.forename: Cecilia
authors.initials: C
authors.lastname: Pozzi
authors.forename: Sandra
authors.initials: S
authors.lastname: Lazzari
authors.forename: Rosaria
authors.initials: R
authors.lastname: Luciani
authors.forename: Stefania
authors.initials: S
authors.lastname: Ferrari
authors.forename: M Paola
authors.initials: MP
authors.lastname: Costi
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D015195:Drug Design; D013293:Enterococcus faecalis / Q000201:enzymology; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D004926:Escherichia coli / Q000201:enzymology; D006801:Humans; D007780:Lacticaseibacillus casei / Q000201:enzymology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020113:Phenolphthalein / Q000494:pharmacology; D010797:Phthalimides / Q000138:chemical synthesis / Q000494:pharmacology*; D011485:Protein Binding; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D013940:Thymidylate Synthase / Q000037:antagonists & inhibitors*
chemical_list: D004791:Enzyme Inhibitors; D010797:Phthalimides; C037430:N-phenylphthalimide; D020113:Phenolphthalein; D013940:Thymidylate Synthase