1. Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor
- Author
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Tibisay Guevara, Anna M. Lasica, Miroslaw Ksiazek, Barbara Potempa, F. Xavier Gomis-Rüth, Arturo Rodríguez-Banqueri, Jan Potempa, National Institutes of Health (US), Ministry of Science and Higher Education (Poland), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Fundació La Marató de TV3, and Ministerio de Ciencia, Innovación y Universidades (España)
- Subjects
0301 basic medicine ,Benzylamines ,Virulence Factors ,Virulence ,lcsh:Medicine ,Crystallography, X-Ray ,Article ,Structure-Activity Relationship ,03 medical and health sciences ,0302 clinical medicine ,Drug Development ,Protein Domains ,Catalytic Domain ,Hydrolase ,Bacteroidaceae Infections ,Structure–activity relationship ,Protease Inhibitors ,Periodontitis ,lcsh:Science ,Pathogen ,Porphyromonas gingivalis ,Gingipain K ,X-ray crystallography ,Bacterial structural biology ,Multidisciplinary ,biology ,Chemistry ,lcsh:R ,biology.organism_classification ,3. Good health ,Hydrazines ,030104 developmental biology ,Biochemistry ,Enzyme mechanisms ,Gingipain Cysteine Endopeptidases ,lcsh:Q ,Carbamates ,Salt bridge ,Hydrophobic and Hydrophilic Interactions ,030217 neurology & neurosurgery ,Cysteine - Abstract
© The Author(s) 2019., Porphyromonas gingivalis is a member of the dysbiotic oral microbiome and a “keystone pathogen” that causes severe periodontal disease, which is among the most prevalent infectious diseases. Part of the virulence factors secreted by P. gingivalis are the essential cysteine peptidases gingipain K (Kgp) and R (RgpA and RgpB), which account for 85% of the extracellular proteolytic activity of the pathogen and are thus prime targets for inhibition. We report the high-resolution (1.20 Å) complex structure of Kgp with KYT-36, a peptide-derived, potent, bioavailable and highly selective inhibitor, which is widely used for studies in vitro, in cells and in vivo. Sub-nanomolar inhibition of Kgp is achieved by tight binding to the active-site cleft, which is covered for its sub-sites S3 through S1’ under establishment of nine hydrophobic interactions, 14 hydrogen bonds and one salt bridge. In addition, an inhibitor carbonyl carbon that mimics the scissile carbonyl of substrates is pyramidalized and just 2.02 Å away from the catalytic nucleophile of Kgp, C477Sγ. Thus, the crystal structure emulates a reaction intermediate of the first nucleophilic attack during catalysis of cysteine peptidases. The present study sets the pace for the development of tailored next-generation drugs to tackle P. gingivalis., This study was supported in part by grants from US American (NIH/NIDCR R01 DE022597), Polish (National Science Center and Ministry of Science and Higher Education, Miniatura 2017/01/X/NZ1/01378, UMO-2015/199/N/NZ1/00322, UMO-2015/17/B/NZ1/00666, UMO-2016/21/B/NZ1/00292, and Mobility Plus 1306/MOB/IV/2015/0), Spanish (BFU2015-64487R and MDM-2014-0435), and Catalan (2017SGR3, and Fundació “La Marató de TV3” 201815) agencies. The Structural Biology Unit of IBMB is a “María de Maeztu” Unit of Excellence from the Spanish Ministry of Science, Innovation and Universities.
- Published
- 2019