title: Exploring the Sn binding pockets in gingipains by newly developed inhibitors: structure-based design, chemistry, and activity.
abstract: Arg-gingipains (Rgps) and Lys-gingipain (Kgp) are cysteine proteinases secreted by Porphyromonas gingivalis, the major pathogen implicated in periodontal disease. Gingipains are essential to the bacterium for its virulence and survival, and development of inhibitors targeting these proteins provides an approach to treat periodontal diseases. Here, we present the first example of structure-based design of gingipains inhibitors, with the use of the crystal structure of RgpB and the homology model of Kgp. Chloromethyl ketones were selected as suitable compounds to explore the specificity of the Sn binding region of both enzymes. Three series of inhibitors bearing Arg or Lys at P1 and different substituents at P2 and P3 were designed, synthesized, and tested. High potency (k(obs)/[I] approximately 10(7) M(-1) s(-1)) was achieved for small ligands, such as the dipeptide analogues. The detailed analysis of Sn binding pockets revealed the molecular basis of inhibitory affinity and provided insight into the structure-activity relationship.
authors.affiliation: Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspiańskiego 27, 50-370 Wrocław, Poland.
authors.forename: Arkadiusz
authors.initials: A
authors.lastname: Białas
authors.forename: Jolanta
authors.initials: J
authors.lastname: Grembecka
authors.forename: Daniel
authors.initials: D
authors.lastname: Krowarsch
authors.forename: Jacek
authors.initials: J
authors.lastname: Otlewski
authors.forename: Jan
authors.initials: J
authors.lastname: Potempa
authors.forename: Artur
authors.initials: A
authors.lastname: Mucha
mesh_terms: D018829:Adhesins, Bacterial / Q000737:chemistry*; D000590:Amino Acid Chloromethyl Ketones / Q000737:chemistry*; D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D003546:Cysteine Endopeptidases / Q000737:chemistry*; D015853:Cysteine Proteinase Inhibitors / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry; D000080867:Gingipain Cysteine Endopeptidases; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D018829:Adhesins, Bacterial; D000590:Amino Acid Chloromethyl Ketones; D015853:Cysteine Proteinase Inhibitors; D004151:Dipeptides; D000080867:Gingipain Cysteine Endopeptidases; D003546:Cysteine Endopeptidases