{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T05:06:08Z","timestamp":1781586368080,"version":"3.54.5"},"reference-count":48,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2021,4,12]],"date-time":"2021-04-12T00:00:00Z","timestamp":1618185600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009381","name":"International Medical University","doi-asserted-by":"publisher","award":["IMU JC grant #485\/2020"],"award-info":[{"award-number":["IMU JC grant #485\/2020"]}],"id":[{"id":"10.13039\/501100009381","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>To determine whether quaternary ammonium (k21) binds to Severe Acute Respiratory Syndrome\u2013Coronavirus 2 (SARS-CoV-2) spike protein via computational molecular docking simulations, the crystal structure of the SARS-CoV-2 spike receptor-binding domain complexed with ACE-2 (PDB ID: 6LZG) was downloaded from RCSB PD and prepared using Schrodinger 2019-4. The entry of SARS-CoV-2 inside humans is through lung tissues with a pH of 7.38\u20137.42. A two-dimensional structure of k-21 was drawn using the 2D-sketcher of Maestro 12.2 and trimmed of C18 alkyl chains from all four arms with the assumption that the core moiety k-21 was without C18. The immunogenic potential of k21\/QA was conducted using the C-ImmSim server for a position-specific scoring matrix analyzing the human host immune system response. Therapeutic probability was shown using prediction models with negative and positive control drugs. Negative scores show that the binding of a quaternary ammonium compound with the spike protein\u2019s binding site is favorable. The drug molecule has a large Root Mean Square Deviation fluctuation due to the less complex geometry of the drug molecule, which is suggestive of a profound impact on the regular geometry of a viral protein. There is high concentration of Immunoglobulin M\/Immunoglobulin G, which is concomitant of virus reduction. The proposed drug formulation based on quaternary ammonium to characterize affinity to the SARS-CoV-2 spike protein using simulation and computational immunological methods has shown promising findings.<\/jats:p>","DOI":"10.3390\/molecules26082214","type":"journal-article","created":{"date-parts":[[2021,4,12]],"date-time":"2021-04-12T11:05:06Z","timestamp":1618225506000},"page":"2214","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Molecular Dynamic Simulation Search for Possible Amphiphilic Drug Discovery for Covid-19"],"prefix":"10.3390","volume":"26","author":[{"given":"Umer","family":"Daood","sequence":"first","affiliation":[{"name":"Division Clinical Dentistry, School of Dentistry, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, Kuala Lumpur 57000, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4279-7420","authenticated-orcid":false,"given":"Divya","family":"Gopinath","sequence":"additional","affiliation":[{"name":"Oral Diagnostics and Surgical Sciences, School of Dentistry, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, Kuala Lumpur 57000, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malikarjuna Rao","family":"Pichika","sequence":"additional","affiliation":[{"name":"School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, Kuala Lumpur 57000, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kit-Kay","family":"Mak","sequence":"additional","affiliation":[{"name":"School of Pharmacy, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, Kuala Lumpur 57000, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8390-3130","authenticated-orcid":false,"given":"Liang Lin","family":"Seow","sequence":"additional","affiliation":[{"name":"Division Clinical Dentistry, School of Dentistry, International Medical University Kuala Lumpur, 126, Jalan Jalil Perkasa 19, Bukit Jalil, Kuala Lumpur 57000, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,4,12]]},"reference":[{"key":"ref_1","unstructured":"(2020, June 13). 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