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In Silico Docking of Medicinal Herbs Against P. Gingivalis for Chronic Periodontitis Intervention Publisher Pubmed



Saini RS1 ; Vaddamanu SK1 ; Dermawan D2 ; Bavabeedu SS3 ; Khudaverdyan M4 ; Mosaddad SA5, 6, 7 ; Heboyan A5, 8, 9
Authors
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Authors Affiliations
  1. 1. Department of Dental Technology, COAMS, King Khalid University, Abha, Saudi Arabia
  2. 2. Applied Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
  3. 3. Department of Restorative Dental Sciences, College of Dentistry, King Khalid University, Abha, Saudi Arabia
  4. 4. The Center for Excellence in Dental Education, Yerevan State Medical University after Mkhitar Heratsi, Yerevan, Armenia
  5. 5. Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Tamil Nadu, Chennai, India
  6. 6. Student Research Committee, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
  7. 7. Department of Conservative Dentistry and Bucofacial Prosthesis, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
  8. 8. Department of Prosthodontics, Faculty of Stomatology, Yerevan State Medical University after Mkhitar Heratsi, Yerevan, Armenia
  9. 9. Department of Prosthodontics, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran

Source: International Dental Journal Published:2025


Abstract

Objective: This study aimed to explore the therapeutic potential of medicinal herbs for chronic periodontitis by examining the molecular interactions between specific herbal compounds and the heme-binding protein of Porphyromonas gingivalis, a key pathogen involved in the disease. Methods: The crystal structure of heme-binding protein was obtained from the Protein Data Bank. Herbal compounds were identified through an extensive literature review. Molecular docking simulations were performed to predict binding affinities, followed by Absorption, Distribution, Metabolism, and Excretion (ADME) parameter prediction. Drug-likeness was assessed based on Lipinski's Rule of Five, and pharmacophore modeling was conducted to identify key molecular interactions. Results: The molecular docking simulations revealed that chelidonine, rotenone, and myricetin exhibited significant binding affinities to the heme-binding protein, with docking scores of -6.5 kcal/mol, -6.4 kcal/mol, and -6.1 kcal/mol, respectively. These compounds formed stable interactions with key amino acid residues within the binding pocket. ADME analysis indicated that all 3 compounds had favourable pharmacokinetic properties, with no violations of Lipinski's rules and minimal predicted toxicity. Pharmacophore modeling further elucidated the interaction profiles, highlighting specific hydrogen bonds and hydrophobic interactions critical for binding efficacy. Conclusions: Chelidonine, rotenone, and myricetin emerged as promising therapeutic candidates for chronic periodontitis due to their strong binding affinities, favorable ADME profiles, and lack of significant toxicity. The detailed pharmacophore modeling provided insights into the molecular mechanisms underpinning their inhibitory effects on the heme-binding protein of P. gingivalis. These findings suggest that these compounds have the potential for further development as effective treatments for chronic periodontitis. Future research should focus on in vitro and in vivo validation of these findings to confirm the efficacy and safety of these compounds in biological systems. © 2024 The Authors
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