{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T06:40:23Z","timestamp":1764139223089,"version":"3.46.0"},"reference-count":35,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T00:00:00Z","timestamp":1764115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Pharmacol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The continuous mutations of SARS-CoV-2 have enhanced its transmissibility and immune escape capabilities. Its invasion into cells relies on the binding of the receptor-binding domain (RBD) of the spike (S) protein to host receptors, while NRP1, as a key host cofactor, promotes viral attachment and internalization by recognizing the S protein. Therefore, dual targeting of RBD and NRP1 represents a potentially effective antiviral strategy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      In this study, a multi-step screening strategy combining molecular docking, MST assays, molecular dynamics simulations, pseudovirus neutralization assays, MTT assays, and\n                      <jats:italic>in vivo<\/jats:italic>\n                      experiments in mice was used to discover dual-targeting inhibitors of SARS-CoV-2 RBD and NRP1.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Five peptide inhibitors (peptides 1\u20135) that simultaneously target RBD and NRP1 were identified through structure-based virtual screening. MST assays showed that peptides 1\u20135 all exhibited nanomolar affinity for both RBD and NRP1, with peptide-1 showing the strongest affinity for RBD (\n                      <jats:italic>K<\/jats:italic>\n                      <jats:sub>d<\/jats:sub>\n                      = 19\u00a0nM) and NRP1 (\n                      <jats:italic>K<\/jats:italic>\n                      <jats:sub>d<\/jats:sub>\n                      = 32\u00a0nM). Molecular dynamics simulations indicated that peptide-1 can stably bind to RBD and NRP1 proteins. Importantly, peptide-1 exerted efficient antiviral activity against the SARS-CoV-2 Omicron XBB.1.5 (EC\n                      <jats:sub>50<\/jats:sub>\n                      = 0.62 \u00b1 0.03\u00a0\u03bcM) and exhibited no obvious toxicity to normal human alveolar cells. Furthermore,\n                      <jats:italic>in vivo<\/jats:italic>\n                      assays indicated that peptide-1 had effective antiviral activity without severe side effects.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>In conclusion, peptide-1 is a highly effective and low-toxicity antiviral inhibitor that dual-targets RBD and NRP1.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fphar.2025.1691679","type":"journal-article","created":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T06:35:23Z","timestamp":1764138923000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification of a novel dual-targeting peptide inhibitor of SARS-CoV-2 RBD and NRP1 through structure-based virtual screening"],"prefix":"10.3389","volume":"16","author":[{"given":"Nan","family":"Yao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lixia","family":"Guan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Feng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuting","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miao-Miao","family":"Niu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mei","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengnan","family":"Yin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,11,26]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"779","DOI":"10.2174\/1389557043403675","article-title":"Virtual screening in structure-based drug discovery","volume":"4","author":"Barril","year":"2004","journal-title":"Mini Rev. Med. Chem."},{"key":"B2","doi-asserted-by":"publisher","first-page":"856","DOI":"10.1126\/science.abd2985","article-title":"Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity","volume":"370","author":"Cantuti-Castelvetri","year":"2020","journal-title":"Science"},{"key":"B3","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1038\/s41586-022-05644-7","article-title":"Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution","volume":"614","author":"Cao","year":"2023","journal-title":"Nature"},{"key":"B4","doi-asserted-by":"publisher","first-page":"3840","DOI":"10.1021\/acs.jpclett.2c00469","article-title":"Omicron BA.2 (B.1.1.529.2): high potential for becoming the next dominant variant","volume":"13","author":"Chen","year":"2022","journal-title":"J. Phys. Chem. Lett."},{"key":"B5","doi-asserted-by":"publisher","first-page":"2399","DOI":"10.1007\/s10528-023-10518-2","article-title":"A comprehensive analysis of NRP1 in malignancies provide therapeutic implication for treating cancer patients infected with SARS-CoV-2","volume":"62","author":"Chen","year":"2024","journal-title":"Biochem. Genet."},{"key":"B6","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1126\/science.abd3072","article-title":"Neuropilin-1 is a host factor for SARS-CoV-2 infection","volume":"370","author":"Daly","year":"2020","journal-title":"Science"},{"key":"B7","doi-asserted-by":"publisher","first-page":"80","DOI":"10.3390\/futurepharmacol3010006","article-title":"SARS-CoV-2 mpro inhibitors: achieved diversity, developing resistance and future strategies","volume":"3","author":"Fischer","year":"2023","journal-title":"Future Pharmacol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"eabi6226","DOI":"10.1126\/science.abi6226","article-title":"Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity","volume":"373","author":"Gobeil","year":"2021","journal-title":"Science"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2772","DOI":"10.3390\/jcm10132772","article-title":"The role of Neuropilin-1 (NRP-1) in SARS-CoV-2 infection: review","volume":"10","author":"Gudowska-Sawczuk","year":"2021","journal-title":"J. Clin. Med."},{"key":"B10","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","article-title":"SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor","volume":"181","author":"Hoffmann","year":"2020","journal-title":"Cell"},{"key":"B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/pcmedi\/pbab001","article-title":"Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs","volume":"4","author":"Hosseini","year":"2021","journal-title":"Precis. Clin. Med."},{"key":"B12","doi-asserted-by":"publisher","first-page":"107576","DOI":"10.1016\/j.compbiomed.2023.107576","article-title":"Impact of BA.1, BA.2, and BA.4\/BA.5 Omicron mutations on therapeutic monoclonal antibodies","volume":"167","author":"Jawad","year":"2023","journal-title":"Comput. Biol. Med."},{"key":"B13","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/s41392-020-00460-9","article-title":"Not only ACE2\u2014the quest for additional host cell mediators of SARS-CoV-2 infection: Neuropilin-1 (NRP1) as a novel SARS-CoV-2 host cell entry mediator implicated in COVID-19","volume":"6","author":"Kyrou","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"B14","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/s41586-020-2180-5","article-title":"Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor","volume":"581","author":"Lan","year":"2020","journal-title":"Nature"},{"key":"B15","doi-asserted-by":"publisher","first-page":"2908","DOI":"10.3390\/cells10112908","article-title":"Novel peptide therapeutic approaches for cancer treatment","volume":"10","author":"Li","year":"2021","journal-title":"Cells"},{"key":"B16","doi-asserted-by":"publisher","first-page":"640","DOI":"10.3390\/v14030640","article-title":"Mutations and evolution of the SARS-CoV-2 spike protein","volume":"14","author":"Magazine","year":"2022","journal-title":"Viruses"},{"key":"B17","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s12982-024-00140-x","article-title":"Evolution and implications of SARS-CoV-2 variants in the post-pandemic era","volume":"21","author":"Manirambona","year":"2024","journal-title":"Discov. Public Health"},{"key":"B18","doi-asserted-by":"publisher","first-page":"864","DOI":"10.1126\/science.abn8652","article-title":"Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement","volume":"375","author":"McCallum","year":"2022","journal-title":"Science"},{"key":"B19","doi-asserted-by":"publisher","first-page":"175","DOI":"10.7774\/cevr.2024.13.3.175","article-title":"The influence of Omicron on vaccine efficacy and durability: a neurology perspective","volume":"13","author":"Muruganantham","year":"2024","journal-title":"Clin. Experimental Vaccine Res."},{"key":"B20","doi-asserted-by":"publisher","first-page":"6815","DOI":"10.3390\/ijms26146815","article-title":"Innovative peptide therapeutics in the pipeline: transforming cancer detection and treatment","volume":"26","author":"Nsereko","year":"2025","journal-title":"Int. J. Mol. Sci."},{"key":"B21","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/s41586-022-04856-1","article-title":"Characterization and antiviral susceptibility of SARS-CoV-2 Omicron BA.2","volume":"607","author":"Uraki","year":"2022","journal-title":"Nature"},{"key":"B22","doi-asserted-by":"publisher","first-page":"11157","DOI":"10.1073\/pnas.1708727114","article-title":"Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion","volume":"114","author":"Walls","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B23","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.cell.2020.02.058","article-title":"Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein","volume":"181","author":"Walls","year":"2020","journal-title":"Cell"},{"key":"B24","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1038\/s41467-020-16256-y","article-title":"A human monoclonal antibody blocking SARS-CoV-2 infection","volume":"11","author":"Wang","year":"2020","journal-title":"Nat. Commun."},{"key":"B25","doi-asserted-by":"publisher","first-page":"2103","DOI":"10.1016\/j.cell.2022.04.035","article-title":"Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike","volume":"185","author":"Yamasoba","year":"2022","journal-title":"Cell"},{"key":"B26","doi-asserted-by":"publisher","first-page":"1904969","DOI":"10.1002\/adfm.201904969","article-title":"A redox-triggered bispecific supramolecular nanomedicine based on peptide self-assembly for high-efficacy and low-toxic cancer therapy","volume":"30","author":"Yang","year":"2020","journal-title":"Adv. Funct. Mater."},{"key":"B27","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.3390\/pr10071420","article-title":"Virtual screening of drug proteins based on the prediction classification model of imbalanced data mining","volume":"10","author":"Yin","year":"2022","journal-title":"Processes"},{"key":"B28","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1038\/s41392-020-00318-0","article-title":"Receptor-binding domain-specific human neutralizing monoclonal antibodies against SARS-CoV and SARS-CoV-2","volume":"5","author":"Yu","year":"2020","journal-title":"Signal Transduct. Target. Ther."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1038\/s41564-021-00954-4","article-title":"SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution","volume":"6","author":"Zahradn\u00edk","year":"2021","journal-title":"Nat. Microbiol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1007\/s42514-021-00086-5","article-title":"Molecular docking-based computational platform for high-throughput virtual screening","volume":"4","author":"Zhang","year":"2022","journal-title":"CCF Trans. High Perform. Comput."},{"key":"B31","doi-asserted-by":"publisher","first-page":"15702","DOI":"10.1021\/acs.jmedchem.1c00932","article-title":"Discovery of a dual tubulin and Poly(ADP-Ribose) Polymerase-1 inhibitor by structure-based pharmacophore modeling, virtual screening, molecular docking, and biological evaluation","volume":"64","author":"Zheng","year":"2021","journal-title":"J. Med. Chem."},{"key":"B32","doi-asserted-by":"publisher","first-page":"16187","DOI":"10.1021\/acs.jmedchem.3c01572","article-title":"Discovery of a dual tubulin and Neuropilin-1 (NRP1) inhibitor with potent in vivo anti-tumor activity via pharmacophore-based docking screening, structure optimization, and biological evaluation","volume":"66","author":"Zheng","year":"2023","journal-title":"J. Med. Chem."},{"key":"B33","doi-asserted-by":"publisher","first-page":"7130","DOI":"10.1021\/acs.jmedchem.3c02433","article-title":"Discovery of a potent dual son of sevenless 1 (SOS1) and epidermal growth factor receptor (EGFR) inhibitor for the treatment of prostate cancer","volume":"67","author":"Zheng","year":"2024","journal-title":"J. Med. Chem."},{"key":"B34","doi-asserted-by":"publisher","first-page":"e2002197","DOI":"10.1002\/adhm.202002197","article-title":"An NRP1\/MDM2-Targeted D-Peptide supramolecular nanomedicine for high-efficacy and low-toxic liver cancer therapy","volume":"10","author":"Zhou","year":"2021","journal-title":"Adv. Healthc. Mater."},{"key":"B35","doi-asserted-by":"publisher","first-page":"7117","DOI":"10.1021\/jacs.1c12075","article-title":"Highly potent, selective, biostable, and cell-permeable cyclic D-Peptide for dual-targeting therapy of lung cancer","volume":"144","author":"Zhou","year":"2022","journal-title":"J. Am. Chem. Soc."}],"container-title":["Frontiers in Pharmacology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphar.2025.1691679\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T06:35:24Z","timestamp":1764138924000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fphar.2025.1691679\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,26]]},"references-count":35,"alternative-id":["10.3389\/fphar.2025.1691679"],"URL":"https:\/\/doi.org\/10.3389\/fphar.2025.1691679","relation":{},"ISSN":["1663-9812"],"issn-type":[{"value":"1663-9812","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,26]]},"article-number":"1691679"}}