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Combining Subtractive Genomics With Computer-Aided Drug Discovery Techniques to Effectively Target S. Sputigena in Periodontitis Publisher



Praveen M1 ; Sree CG2 ; Brogi S3, 4 ; Calderone V3 ; Dalei KPKP5
Authors
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Authors Affiliations
  1. 1. Department of Research and Development, Academy of Bioelectric Meridian Massage Australia (ABMMA), Noosaville, 4566, QLD, Australia
  2. 2. Department of Biotechnology, Sri Padmavati Mahila Visvavidyalayam, Andhra Pradesh, Tirupati, 517502, India
  3. 3. Department of Pharmacy, University of Pisa, Via Bonanno 6, Pisa, 56126, Italy
  4. 4. Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
  5. 5. Department of Commerce, Khaira College, Odhissa, Balasore, 756019, India

Source: Computation Published:2025


Abstract

This study aimed to provide an inclusive in silico investigation for the identification of novel drug targets that can be exploited to develop drug candidates for treating oral infections caused by S. sputigena. By coupling subtractive genomics with an in silico drug discovery approach, we identified dTDP-4-dehydrorhamnose 3,5-epimerase (UniProt ID: C9LUR0), UTP-glucose-1-phosphate uridyltransferase (UniProt ID: C9LRH1), and imidazole glycerol phosphate synthase (UniProt ID: C9LTU7) as three unique proteins crucial for the S. sputigena life cycle with no substantial similarity to human proteins. These potential drug targets served as the starting point for screening bioactive phytochemicals (1090 compounds) from the Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT) database. Among the screened natural products, cubebin (IMPHY001912) showed a higher affinity for two of the three selected targets, as evidenced by molecular docking and molecular dynamics studies. Given its favorable drug-like profile and possible multitargeting behavior, cubebin could be further exploited as an antibacterial agent for treating S. sputigena-mediated oral infections. It is worth nothing that cubebin could be the active ingredient of appropriate formulations such as mouthwash and/or toothpaste to treat S. sputigena-induced periodontitis, with the advantage of limiting the adverse effects that could affect the use of current drugs. © 2025 by the authors.
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