title: In silico identification of a therapeutic target for photo-activated disinfection with indocyanine green: Modeling and virtual screening analysis of Arg-gingipain from Porphyromonas gingivalis.
abstract: BACKGROUND
  Porphyromonas gingivalis is a momentous bacterial etiological agent associated with periodontitis, peri-implantitis as well as endodontic infections. The potential advantage of Photo-activated disinfection (PAD) as a promising novel approach is the choice of a suitable target site, specific photosensitizer, and wavelength of light for delivery of the light from source to target. Since Arg-gingipain is a cysteine proteinase that is involved in the virulence of P. gingivalis, it was evaluated as a target site for PAD with indocyanine green (ICG) as a photosensitizer.
  
  
  METHODS
  In this study, we used a range of in silico strategies, bioinformatics tools, biological databases, and computer simulation molecular modeling to evaluate the capacity of Arg-gingipain.
  
  
  RESULTS
  The predicted structure of Arg-gingipain indicated that it is located outside the cell and has nine domains and 17 ligands, including two calcium ions and three sodium ions with positive charges which can be a site of interaction for anionic ICG.
  
  
  CONCLUSIONS
  Based on the results of this study, anionic ICG desires to bind and interact with residues of Arg-gingipain during PAD as a main site to enhance the yield of treatment of endo-periodontal lesions.
authors.affiliation: Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
authors.forename: Maryam
authors.initials: M
authors.lastname: Pourhajibagher
authors.affiliation: Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Laser Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran. Electronic address: abahador@sina.tums.ac.ir.
authors.forename: Abbas
authors.initials: A
authors.lastname: Bahador
mesh_terms: D018829:Adhesins, Bacterial / Q000378:metabolism*; D003198:Computer Simulation; D003546:Cysteine Endopeptidases / Q000378:metabolism*; D004203:Disinfection / Q000379:methods; D004305:Dose-Response Relationship, Drug; D004307:Dose-Response Relationship, Radiation; D004353:Drug Evaluation, Preclinical / Q000379:methods; D000080867:Gingipain Cysteine Endopeptidases; D007208:Indocyanine Green / Q000008:administration & dosage* / Q000494:pharmacology*; D008954:Models, Biological; D058990:Molecular Targeted Therapy / Q000379:methods; D010778:Photochemotherapy / Q000379:methods*; D017319:Photosensitizing Agents / Q000008:administration & dosage / Q000493:pharmacokinetics; D016966:Porphyromonas gingivalis / Q000187:drug effects* / Q000378:metabolism* / Q000528:radiation effects; D016896:Treatment Outcome; D014584:User-Computer Interface
chemical_list: D018829:Adhesins, Bacterial; D000080867:Gingipain Cysteine Endopeptidases; D017319:Photosensitizing Agents; D003546:Cysteine Endopeptidases; D007208:Indocyanine Green
keywords: Arg-gingipain; Bioinformatics; Endodontic infections; Indocyanine green; Periodontitis; Photo-activated disinfection; Porphyromonas gingivalis; in silico