Virtual Screening to Identify Novel Antimicrobial Agents against Porphyromonas gingivalis

Objective: While the oral cavity contains over 700 species of microorganisms, few are known to contribute to the onset of progressive periodontal disease. However, Porphyromonas gingivalis has long been implicated as a contributor, recently being identified as a “keystone” pathogen. We recently identified the enzyme diaminopimelate dehydrogenase as a pathogen-specific target for P. gingivalis within the oral microbial environment. By targeting one of the primary pathogens one could potentially reduce the destructive factors triggering periodontitis while maintaining a person’s healthy flora. The objective of this study was to use a computer-based drug design method to identify potential target-specific antimicrobial agents against P. gingivalis.

Method: Modeling studies were done using Tripos SYBYL X 1.3. Based on the crystal structure data accessed from the Protein Data Bank, a 3-D virtual model of the target was generated. The protein structure was cleaned and the target binding site identified for a high throughput virtual screen. Several compound database libraries containing over 500,000 unique compounds were screened. To investigate the intermolecular binding interactions, GOLD 5.1 docking program was used. Compounds were tested for antimicrobial properties by standard broth microdilution MIC assays in 96-well format. 

Result: The virtual screen resulted in over 300 unique compound “hits” which were visually inspected and docked into the binding pocket. 67 of the commercially available top-ranking compounds were selected and obtained for in vitro studies. Screening of the compounds showed MIC values ranging from >5000ug/mL to .0095ug/mL.  

Conclusion: A novel in silico screen was employed to identify inhibitors of a P. gingivalis target enzyme. A library of candidate compounds is currently being screened to verify the mode of action and to identify potential therapeutic agents.