{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:34:01Z","timestamp":1787027641020,"version":"build-2736575974"},"reference-count":46,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,9,7]],"date-time":"2022-09-07T00:00:00Z","timestamp":1662508800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"King Khalid University","award":["RGP.2\/70\/43"],"award-info":[{"award-number":["RGP.2\/70\/43"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Bioengineering"],"abstract":"<jats:p>Staphylococcus lugdunensis is a coagulase-negative, Gram-positive, and human pathogenic bacteria. S. lugdunensis is the causative agent of diseases, such as native and prosthetic valve endocarditis, meningitis, septic arthritis, skin abscesses, brain abscess, breast abscesses, spondylodiscitis, post-surgical wound infections, bacteremia, and peritonitis. S. lugdunensis displays resistance to beta-lactam antibiotics due to the production of beta-lactamases. This study aimed to identify potential novel essential, human non-homologous, and non-gut flora drug targets in the S. lugdunensis strain N920143, and to evaluate the potential inhibitors of drug targets. The method was concerned with a homology search between the host and the pathogen proteome. Various tools, including the DEG (database of essential genes) for the essentiality of proteins, the KEGG for pathways analysis, CELLO V.2.5 for cellular localization prediction, and the drug bank database for predicting the druggability potential of proteins, were used. Furthermore, a similarity search with gut flora proteins was performed. A DNA-binding response-regulator protein was identified as a novel drug target against the N920143 strain of S. lugdunensis. The three-dimensional structure of the drug target was modelled and validated with the help of online tools. Furthermore, ten thousand drug-like compounds were retrieved from the ZINC15 database. The molecular docking approach for the DNA-binding response-regulator protein identified ZINC000020192004 and ZINC000020530348 as the most favorable compounds to interact with the active site residues of the drug target. These two compounds were subjected to an MD simulation study. Our analysis revealed that the identified compounds revealed more stable behavior when bound to the drug target DNA-binding response-regulator protein than the apostate.<\/jats:p>","DOI":"10.3390\/bioengineering9090451","type":"journal-article","created":{"date-parts":[[2022,9,7]],"date-time":"2022-09-07T20:52:03Z","timestamp":1662583923000},"page":"451","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Identification of New Drug Target in Staphylococcus lugdunensis by Subtractive Genomics Analysis and Their Inhibitors through Molecular Docking and Molecular Dynamic Simulation Studies"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8368-9047","authenticated-orcid":false,"given":"Yahya","family":"Alhamhoom","sequence":"first","affiliation":[{"name":"Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4643-0922","authenticated-orcid":false,"given":"Umme","family":"Hani","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0981-3959","authenticated-orcid":false,"given":"Fatima Ezzahra","family":"Bennani","sequence":"additional","affiliation":[{"name":"Laboratory of Pharmacology and Toxicology, Bio Pharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and pharmacy, Mohammed V University in Rabat, BP6203 Rabat, Morocco"},{"name":"Laboratory of Medicinal Chemistry, Faculty of Medicine and pharmacy, Mohammed V University in Rabat, BP6203 Rabat, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7062-2302","authenticated-orcid":false,"given":"Noor","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9404-5186","authenticated-orcid":false,"given":"Md Abdur","family":"Rashid","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Naseer","family":"Abbas","sequence":"additional","affiliation":[{"name":"Department of Pharmacy, Kohat University of Science and Technology (KUST), Kohat 26000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0718-5450","authenticated-orcid":false,"given":"Luca","family":"Rastrelli","sequence":"additional","affiliation":[{"name":"Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II, 84084 Fisciano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,7]]},"reference":[{"key":"ref_1","first-page":"168","article-title":"Staphylococcus lugdunensis sp. nov. and Staphylococcus schleiferi sp. nov., Two Species from Human Clinical Specimens","volume":"38","author":"Freney","year":"1988","journal-title":"Int. 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