{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T14:43:52Z","timestamp":1779201832529,"version":"3.51.4"},"reference-count":57,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2022,7,4]],"date-time":"2022-07-04T00:00:00Z","timestamp":1656892800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Deputyship for Research and Innovation, Ministry of Education in Saudi Arabia","award":["PNU-DRI-Targeted-20-005"],"award-info":[{"award-number":["PNU-DRI-Targeted-20-005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Coming into the second year of the pandemic, the acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants continue to be a serious health hazard globally. A surge in the omicron wave, despite the discovery of the vaccines, has shifted the attention of research towards the discovery and use of bioactive compounds, being potential inhibitors of the viral structural proteins. The present study aimed at the green synthesis of zinc oxide (ZnO) nanoparticles with seed extracts of Nigella sativa and Pimpinella anisum\u2014loaded nanostructured oil carriers (NLC)\u2014using a mixture of olive and black seed essential oils. The synthesized ZnO NLC were extensively characterized. In addition, the constituent compounds in ZnO NLC were investigated as a potential inhibitor for the SARS-CoV-2 main protease (3CLpro or Mpro) where 27 bioactive constituents, along with ZnO in the nanostructure, were subjected to molecular docking studies. The resultant high-score compounds were further validated by molecular dynamics simulation. The study optimized the compounds dithymoquinone, \u03b4-hederin, oleuropein, and zinc oxide with high docking energy scores (ranging from \u22127.9 to \u22129.9 kcal\/mol). The RMSD and RMSF data that ensued also mirrored these results for the stability of proteins and ligands. RMSD and RMSF data showed no conformational change in the protein during the MD simulation. Histograms of every simulation trajectory explained the ligand properties and ligand\u2013protein contacts. Nevertheless, further experimental investigations and validation of the selected candidates are imperative to take forward the applicability of the nanostructure as a potent inhibitor of COVID-19 (Coronavirus Disease 2019) for clinical trials.<\/jats:p>","DOI":"10.3390\/molecules27134301","type":"journal-article","created":{"date-parts":[[2022,7,4]],"date-time":"2022-07-04T20:59:18Z","timestamp":1656968358000},"page":"4301","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["In Silico Studies on Zinc Oxide Based Nanostructured Oil Carriers with Seed Extracts of Nigella sativa and Pimpinella anisum as Potential Inhibitors of 3CL Protease of SARS-CoV-2"],"prefix":"10.3390","volume":"27","author":[{"given":"Awatif A.","family":"Hendi","sequence":"first","affiliation":[{"name":"Department of Physics, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4030-7651","authenticated-orcid":false,"given":"Promy","family":"Virk","sequence":"additional","affiliation":[{"name":"Department of Zoology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5294-1721","authenticated-orcid":false,"given":"Manal A.","family":"Awad","sequence":"additional","affiliation":[{"name":"King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mai","family":"Elobeid","sequence":"additional","affiliation":[{"name":"Department of Zoology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khalid M. O.","family":"Ortashi","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering, King Saud University, Riyadh 11421, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meznah M.","family":"Alanazi","sequence":"additional","affiliation":[{"name":"Department of Physics, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4776-4978","authenticated-orcid":false,"given":"Fatemah H.","family":"Alkallas","sequence":"additional","affiliation":[{"name":"Department of Physics, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3143-447X","authenticated-orcid":false,"given":"Maha Mohammad","family":"Almoneef","sequence":"additional","affiliation":[{"name":"Department of Physics, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammed Aly","family":"Abdou","sequence":"additional","affiliation":[{"name":"Department of Physics, College of Sciences, University of Bisha, Bisha 61922, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,7,4]]},"reference":[{"key":"ref_1","unstructured":"WHO (2020). 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