{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T19:37:51Z","timestamp":1784921871481,"version":"3.55.0"},"reference-count":81,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,6,7]],"date-time":"2025-06-07T00:00:00Z","timestamp":1749254400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"Training Program of the Major Research Plan of the National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["92370133"],"award-info":[{"award-number":["92370133"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Training Program of the Major Research Plan of the National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["2022016"],"award-info":[{"award-number":["2022016"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011408","name":"State Key Laboratory of Medicinal Chemical Biology","doi-asserted-by":"publisher","award":["92370133"],"award-info":[{"award-number":["92370133"]}],"id":[{"id":"10.13039\/501100011408","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011408","name":"State Key Laboratory of Medicinal Chemical Biology","doi-asserted-by":"publisher","award":["2022016"],"award-info":[{"award-number":["2022016"]}],"id":[{"id":"10.13039\/501100011408","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Instrumentation Open Sharing Fund of Huazhong University of Science and Technology","award":["92370133"],"award-info":[{"award-number":["92370133"]}]},{"name":"Instrumentation Open Sharing Fund of Huazhong University of Science and Technology","award":["2022016"],"award-info":[{"award-number":["2022016"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The COVID-19 infection, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has evoked a worldwide pandemic. Even though vaccines have been developed on an enormous scale, but due to regular mutations in the viral gene and the emergence of new strains could pose a more significant problem for the population. Therefore, new treatments are always necessary to combat future pandemics. Utilizing an antiviral peptide as a model biomolecule, we trained a generative deep learning algorithm on a database of known antiviral peptides to design novel peptide sequences with antiviral activity. Using artificial intelligence (AI), specifically variational autoencoders (VAE) and Wasserstein autoencoders (WAE), we were able to generate a latent space plot that can be surveyed for peptides with known properties and interpolated across a predictive vector between two defined points to identify novel peptides that exhibit dose-responsive antiviral activity. Two hundred peptide sequences were generated from the trained latent space and the top peptides were subjected to a molecular docking study. The docking analysis revealed that the top four peptides (MSK-1, MSK-2, MSK-3, and MSK-4) exhibited the strongest binding affinity, with docking scores of \u2212106.4, \u2212126.2, \u2212125.7, and \u2212127.8, respectively. Molecular dynamics simulations lasting 500 ns were performed to assess their stability and binding interactions. Further analyses, including MMGBSA, RMSD, RMSF, and hydrogen bond analysis, confirmed the stability and strong binding interactions of the peptide\u2013protein complexes, suggesting that MSK-4 is a promising therapeutic agent for further development. We believe that the peptides generated through AI and MD simulations in the current study could be potential inhibitors in natural systems that can be utilized in designing therapeutic strategies against SARS-CoV-2.<\/jats:p>","DOI":"10.3390\/v17060828","type":"journal-article","created":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T08:22:34Z","timestamp":1749457354000},"page":"828","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Synergizing Attribute-Guided Latent Space Exploration (AGLSE) with Classical Molecular Simulations to Design Potent Pep-Magnet Peptide Inhibitors to Abrogate SARS-CoV-2 Host Cell Entry"],"prefix":"10.3390","volume":"17","author":[{"given":"Farhan","family":"Ullah","sequence":"first","affiliation":[{"name":"Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China"},{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430030, China"},{"name":"Lab for Computational and Structural Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aobo","family":"Xiao","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence & Automation, Huazhong University of Science and Technology, Wuhan 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6694-5590","authenticated-orcid":false,"given":"Shahid","family":"Ullah","sequence":"additional","affiliation":[{"name":"S-Khan Lab Takht Bhai, Takht-i-Bahi 55100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6956-6630","authenticated-orcid":false,"given":"Na","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Lei","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Chen","sequence":"additional","affiliation":[{"name":"Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China"},{"name":"Urology Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2509-6761","authenticated-orcid":false,"given":"Sheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430030, China"},{"name":"Lab for Computational and Structural Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430030, China"},{"name":"State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"9561","DOI":"10.1080\/07391102.2023.2256864","article-title":"A molecular dynamics simulations analysis of repurposing drugs for COVID-19 using bioinformatics methods","volume":"42","author":"Ullah","year":"2024","journal-title":"J. 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