{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T13:06:56Z","timestamp":1774012016978,"version":"3.50.1"},"reference-count":67,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,2,1]],"date-time":"2025-02-01T00:00:00Z","timestamp":1738368000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computation"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/computation13020034","type":"journal-article","created":{"date-parts":[[2025,2,3]],"date-time":"2025-02-03T08:47:57Z","timestamp":1738572477000},"page":"34","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Combining Subtractive Genomics with Computer-Aided Drug Discovery Techniques to Effectively Target S. sputigena in Periodontitis"],"prefix":"10.3390","volume":"13","author":[{"given":"Mallari","family":"Praveen","sequence":"first","affiliation":[{"name":"Department of Research and Development, Academy of Bioelectric Meridian Massage Australia (ABMMA), Noosaville, QLD 4566, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chendruru Geya","family":"Sree","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Sri Padmavati Mahila Visvavidyalayam, Tirupati, Andhra Pradesh 517502, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9375-6242","authenticated-orcid":false,"given":"Simone","family":"Brogi","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy"},{"name":"Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincenzo","family":"Calderone","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kamakshya Prasad Kanchan Prava","family":"Dalei","sequence":"additional","affiliation":[{"name":"Department of Commerce, Khaira College, Balasore, Odhissa 756019, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1074\/mcp.RA117.000394","article-title":"Flagellin Glycoproteomics of the Periodontitis Associated Pathogen Selenomonas sputigena Reveals Previously Not Described O-glycans and Rhamnose Fragment Rearrangement Occurring on the Glycopeptides","volume":"17","author":"Rath","year":"2018","journal-title":"Mol. 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