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This Chlamydia-related bacterium is an emergent pathogen that causes human miscarriages and ruminant abortions, which results in financial losses<jats:italic>.<\/jats:italic> Despite the years of efforts, the underlying mechanism behind the pathogenesis of <jats:italic>W. chondrophila<\/jats:italic> is little known which hindered the development of novel treatment options. In the framework of current study, computational approaches were used to identify novel inhibitors (phytocompounds) and drug targets against <jats:italic>W. chondrophila<\/jats:italic>. At first, RNA polymerase sigma factor SigA and 3-deoxy-<jats:sc>d<\/jats:sc>-manno-octulosonic acid transferase were identified through subtractive proteomics pipeline. Afterwards, extensive docking and simulation analyses were conducted to optimize potentially novel phytocompounds by assessing their binding affinity to target proteins. A 100ns molecular dynamics simulation well complimented the compound's binding affinity and indicated strong stability of predicted compounds at the docked site. The calculation of binding free energies with MMGBSA corroborated the significant binding affinity between phytocompounds and target protein binding sites. The proposed phytocompounds may be a viable treatment option for patients infected with <jats:italic>W. chondrophila<\/jats:italic>; however, further research is required to ensure their safety.<\/jats:p>","DOI":"10.1038\/s41598-024-63555-1","type":"journal-article","created":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T06:01:54Z","timestamp":1718172114000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila"],"prefix":"10.1038","volume":"14","author":[{"given":"Sidra","family":"Aslam","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hossam M.","family":"Aljawdah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mutee","family":"Murshed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geidy E.","family":"Serrano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,6,12]]},"reference":[{"key":"63555_CR1","doi-asserted-by":"publisher","first-page":"s3","DOI":"10.1016\/S0966-842X(02)02428-9","volume":"10","author":"ME Woolhouse","year":"2002","unstructured":"Woolhouse, M. 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