{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T05:24:46Z","timestamp":1789709086894,"version":"4.0.1"},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:00:00Z","timestamp":1767916800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:00:00Z","timestamp":1767916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Arch Virol"],"published-print":{"date-parts":[[2026,2]]},"DOI":"10.1007\/s00705-025-06517-w","type":"journal-article","created":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T13:56:14Z","timestamp":1767966974000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Virtual screening, molecular dynamics simulations, and antiviral evaluation of Ocimum basilicum phytoconstituents against Japanese encephalitis virus"],"prefix":"10.1007","volume":"171","author":[{"given":"Selamu Kebamo","family":"Abate","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4235-3926","authenticated-orcid":false,"given":"Debapriya","family":"Garabadu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,1,9]]},"reference":[{"issue":"9","key":"6517_CR1","doi-asserted-by":"publisher","first-page":"e2830","DOI":"10.21769\/BioProtoc.2830","volume":"8","author":"C Aoki-Utsubo","year":"2018","unstructured":"Aoki-Utsubo C, Chen M, Hotta H (2018) Time-of-addition and temperature-shift assays to determine particular step(s) in the viral life cycle that is blocked by antiviral substance(s). Bio-Protocol 8(9):e2830. https:\/\/doi.org\/10.21769\/BioProtoc.2830","journal-title":"Bio-Protocol"},{"key":"6517_CR2","doi-asserted-by":"publisher","first-page":"52065","DOI":"10.3791\/52065-v","volume":"93","author":"A Baer","year":"2014","unstructured":"Baer A, Kehn-Hall K (2014) Viral concentration determination through plaque assays: Using traditional and novel overlay systems. J Visualized Experiments 93:52065. https:\/\/doi.org\/10.3791\/52065-v","journal-title":"J Visualized Experiments"},{"key":"6517_CR3","doi-asserted-by":"publisher","first-page":"103753","DOI":"10.1016\/j.sjbs.2023.103753","volume":"30","author":"ZK Bagewadi","year":"2023","unstructured":"Bagewadi ZK, Khan Y, Gangadharappa TM, Kamalapurkar B, Shamsudeen AM, S., Yaraguppi DA (2023) Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target of Micrococcus luteus with secondary metabolites from Bacillus licheniformis recognized by genome mining approach. Saudi J Biol Sci 30:103753. https:\/\/doi.org\/10.1016\/j.sjbs.2023.103753","journal-title":"Saudi J Biol Sci"},{"key":"6517_CR4","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235\u2013242. https:\/\/doi.org\/10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"6517_CR5","doi-asserted-by":"publisher","first-page":"2320","DOI":"10.1039\/c1mb05038a","volume":"7","author":"M Bhattacharyya","year":"2011","unstructured":"Bhattacharyya M, Vishveshwara S (2011) Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein\u2013ligand interactions. Mol Biosyst 7(7):2320. https:\/\/doi.org\/10.1039\/c1mb05038a","journal-title":"Mol Biosyst"},{"issue":"6","key":"6517_CR6","doi-asserted-by":"publisher","first-page":"8759","DOI":"10.1007\/s11356-021-16229-8","volume":"29","author":"S Bhimaneni","year":"2022","unstructured":"Bhimaneni S, Kumar A (2022) Abscisic acid and aloe-emodin against NS2B-NS3A protease of Japanese encephalitis virus. Environ Sci Pollut Res 29(6):8759\u20138766. https:\/\/doi.org\/10.1007\/s11356-021-16229-8","journal-title":"Environ Sci Pollut Res"},{"key":"6517_CR7","doi-asserted-by":"publisher","first-page":"100043","DOI":"10.1016\/j.crphar.2021.100043","volume":"2","author":"S Bhosale","year":"2021","unstructured":"Bhosale S, Kumar A (2021) Screening of phytoconstituents of Andrographis paniculata against various targets of Japanese encephalitis virus: An in-silico and in-vitro target-based approach. Curr Res Pharmacol Drug Discovery 2:100043. https:\/\/doi.org\/10.1016\/j.crphar.2021.100043","journal-title":"Curr Res Pharmacol Drug Discovery"},{"key":"6517_CR8","doi-asserted-by":"publisher","first-page":"108695","DOI":"10.1016\/j.jmgm.2023.108695","volume":"127","author":"A Biharee","year":"2024","unstructured":"Biharee A, Singh Y, Kulkarni S, Jangid K, Kumar V, Jain AK, Thareja S (2024) An amalgamated molecular dynamic and Gaussian based 3D-QSAR study for the design of 2,4-thiazolidinediones as potential PTP1B inhibitors. J Mol Graph Model 127:108695. https:\/\/doi.org\/10.1016\/j.jmgm.2023.108695","journal-title":"J Mol Graph Model"},{"key":"6517_CR9","doi-asserted-by":"publisher","unstructured":"Bowers KJ, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the 2006 ACM\/IEEE Conference on Supercomputing - SC '06, 84. https:\/\/doi.org\/10.1145\/1188455.1188544","DOI":"10.1145\/1188455.1188544"},{"key":"6517_CR10","doi-asserted-by":"publisher","first-page":"20119","DOI":"10.1038\/s41598-019-56556-y","volume":"9","author":"HA Braz-De-Melo","year":"2019","unstructured":"Braz-De-Melo HA, Pasquarelli-do-Nascimento G, Corr\u00eaa R, das Neves Almeida R, de Oliveira Santos I, Prado PS, Picolo V, de Bem AF, Pizato N, Magalh\u00e3es KG (2019) Potential neuroprotective and anti-inflammatory effects provided by omega-3 (DHA) against zika virus infection in human SH-SY5Y cells. Sci Rep 9:20119. https:\/\/doi.org\/10.1038\/s41598-019-56556-y","journal-title":"Sci Rep"},{"issue":"10","key":"6517_CR11","doi-asserted-by":"publisher","first-page":"766","DOI":"10.2471\/BLT.10.085233","volume":"89","author":"GL Campbell","year":"2011","unstructured":"Campbell GL, Hills SL, Fischer M, Jacobson JA, Hoke CH, Hombach JM, Marfin AA, Solomon T, Tsai TF, Tsu VD (2011) Estimated global incidence of Japanese encephalitis: A systematic review. Bull World Health Organ 89(10):766\u2013774. https:\/\/doi.org\/10.2471\/BLT.10.085233","journal-title":"Bull World Health Organ"},{"issue":"5","key":"6517_CR12","doi-asserted-by":"publisher","first-page":"e0004686","DOI":"10.1371\/journal.pntd.0004686","volume":"10","author":"L Cao","year":"2016","unstructured":"Cao L, Fu S, Gao X, Li M, Cui S, Li X, Cao Y, Lei W, Lu Z, He Y, Wang H, Yan J, Gao GF, Liang G (2016) Low Protective Efficacy of the Current Japanese Encephalitis Vaccine against the Emerging Genotype 5 Japanese Encephalitis Virus. PLoS Negl Trop Dis 10(5):e0004686. https:\/\/doi.org\/10.1371\/journal.pntd.0004686","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"6517_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13737-016-0030-7","volume":"5","author":"A Castellaneta","year":"2016","unstructured":"Castellaneta A, Massaro A, Rendina M, D\u2019Errico F, Carparelli S, Rizzi SF, Thomson AW, Di Leo A (2016) Immunomodulating effects of the antiviral agent Silibinin in liver transplant patients with HCV recurrence. Transplantation Res 5(1):1. https:\/\/doi.org\/10.1186\/s13737-016-0030-7","journal-title":"Transplantation Res"},{"issue":"6","key":"6517_CR14","doi-asserted-by":"publisher","first-page":"101957","DOI":"10.1016\/j.jbc.2022.101957","volume":"298","author":"H-H Chen","year":"2022","unstructured":"Chen H-H, Lin C-J, Anand A, Lin H-J, Lin H-Y, Mao J-Y, Wang P-H, Tseng YJ, Tzou W-S, Huang C-C, Wang RYL (2022) Development of antiviral carbon quantum dots that target the Japanese encephalitis virus envelope protein. J Biol Chem 298(6):101957. https:\/\/doi.org\/10.1016\/j.jbc.2022.101957","journal-title":"J Biol Chem"},{"issue":"4","key":"6517_CR15","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1007\/s10126-011-9428-x","volume":"14","author":"Y-H Chiu","year":"2012","unstructured":"Chiu Y-H, Chan Y-L, Li T-L, Wu C-J (2012) Inhibition of Japanese Encephalitis Virus Infection by the Sulfated Polysaccharide Extracts from Ulva lactuca. Mar Biotechnol 14(4):468\u2013478. https:\/\/doi.org\/10.1007\/s10126-011-9428-x","journal-title":"Mar Biotechnol"},{"issue":"8","key":"6517_CR16","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.1016\/j.chembiol.2018.05.011","volume":"25","author":"M de Wispelaere","year":"2018","unstructured":"de Wispelaere M, Lian W, Potisopon S, Li P-C, Jang J, Ficarro SB, Clark MJ, Zhu X, Kaplan JB, Pitts JD, Wales TE, Wang J, Engen JR, Marto JA, Gray NS, Yang PL (2018) Inhibition of Flaviviruses by Targeting a Conserved Pocket on the Viral Envelope Protein. Cell Chem Biology 25(8):1006\u20131016e8. https:\/\/doi.org\/10.1016\/j.chembiol.2018.05.011","journal-title":"Cell Chem Biology"},{"issue":"1","key":"6517_CR17","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1080\/87559129.2021.1900230","volume":"39","author":"K Dhama","year":"2023","unstructured":"Dhama K, Sharun K, Gugjoo MB, Tiwari R, Alagawany M, Yatoo I, Thakur M, Iqbal P, Chaicumpa HMN, Michalak W, Elnesr I, S. S., Farag MR (2023) A Comprehensive Review on Chemical Profile and Pharmacological Activities of Ocimum basilicum. Food Reviews Int 39(1):119\u2013147. https:\/\/doi.org\/10.1080\/87559129.2021.1900230","journal-title":"Food Reviews Int"},{"issue":"3","key":"6517_CR18","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1007\/s11626-022-00666-x","volume":"58","author":"SK Dutta","year":"2022","unstructured":"Dutta SK, Sengupta S, Tripathi A (2022) In silico and in vitro evaluation of silibinin: A promising anti-Chikungunya agent. Vitro Cell Dev Biology - Anim 58(3):255\u2013267. https:\/\/doi.org\/10.1007\/s11626-022-00666-x","journal-title":"Vitro Cell Dev Biology - Anim"},{"issue":"21","key":"6517_CR19","doi-asserted-by":"publisher","first-page":"6177","DOI":"10.1021\/jm051256o","volume":"49","author":"RA Friesner","year":"2006","unstructured":"Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein\u2009\u2013\u2009ligand complexes. J Med Chem 49(21):6177\u20136196. https:\/\/doi.org\/10.1021\/jm051256o","journal-title":"J Med Chem"},{"issue":"4","key":"6517_CR20","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1007\/s13337-015-0276-6","volume":"26","author":"RK Ganjhu","year":"2015","unstructured":"Ganjhu RK, Mudgal PP, Maity H, Dowarha D, Devadiga S, Nag S, Arunkumar G (2015) Herbal plants and plant preparations as remedial approach for viral diseases. VirusDisease 26(4):225\u2013236. https:\/\/doi.org\/10.1007\/s13337-015-0276-6","journal-title":"VirusDisease"},{"key":"6517_CR21","doi-asserted-by":"publisher","DOI":"10.1007\/s11030-023-10797-2","author":"SD Ghate","year":"2024","unstructured":"Ghate SD, Pinto L, Alva S, Srinivasa MG, Vangala RK, Naik P, Revanasiddappa BC, Rao RS P (2024) In silico identification of potential phytochemical inhibitors for mpox virus: Molecular docking, MD simulation, and ADMET studies. Mol Diversity. https:\/\/doi.org\/10.1007\/s11030-023-10797-2","journal-title":"Mol Diversity"},{"issue":"4","key":"6517_CR22","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1007\/s13721-013-0040-z","volume":"2","author":"SK Gupta","year":"2013","unstructured":"Gupta SK, Singh S, Nischal A, Pant KK, Seth PK (2013) Molecular docking and simulation studies towards exploring antiviral compounds against envelope protein of Japanese encephalitis virus. Netw Model Anal Health Inf Bioinf 2(4):231\u2013243. https:\/\/doi.org\/10.1007\/s13721-013-0040-z","journal-title":"Netw Model Anal Health Inf Bioinf"},{"key":"6517_CR23","doi-asserted-by":"publisher","first-page":"100894","DOI":"10.1016\/j.imu.2022.100894","volume":"29","author":"MM Hasan","year":"2022","unstructured":"Hasan MM, Khan Z, Chowdhury MS, Khan MA, Moni MA, Rahman MH (2022) In silico molecular docking and ADME\/T analysis of Quercetin compound with its evaluation of broad-spectrum therapeutic potential against particular diseases. Inf Med Unlocked 29:100894. https:\/\/doi.org\/10.1016\/j.imu.2022.100894","journal-title":"Inf Med Unlocked"},{"key":"6517_CR24","doi-asserted-by":"publisher","unstructured":"Ishag HZA, Ishag HZA, Li C, Li C, Li Huang, Huang L, Sun M-X, Sun M, Wang F, Wang F, Ni B, Ni B, Malik T, Malik T, Chen Pu-yan, Chen P, Mao X, Mao X (2013) Griffithsin inhibits Japanese encephalitis virus infection in vitro and in vivo. Archives of Virology, 158(2), 349\u2013358. https:\/\/doi.org\/10.1007\/s00705-012-1489-2","DOI":"10.1007\/s00705-012-1489-2"},{"issue":"22","key":"6517_CR25","doi-asserted-by":"publisher","first-page":"579","DOI":"10.15585\/mmwr.mm6622a3","volume":"66","author":"JD Heffelfinger","year":"2017","unstructured":"Heffelfinger JD, Li X, Batmunkh N, Grabovac V, Diorditsa S, Liyanage JB, Pattamadilok S, Bahl S, Vannice KS, Hyde TB, Chu SY, Fox KK, Hills SL, Marfin AA (2017) Japanese Encephalitis Surveillance and Immunization\u2014Asia and Western Pacific Regions, 2016. MMWR Morb Mortal Wkly Rep 66(22):579\u2013583. https:\/\/doi.org\/10.15585\/mmwr.mm6622a3","journal-title":"MMWR Morb Mortal Wkly Rep"},{"issue":"5","key":"6517_CR26","doi-asserted-by":"publisher","first-page":"860","DOI":"10.4269\/ajtmh.23-0036","volume":"108","author":"SL Hills","year":"2023","unstructured":"Hills SL, Netravathi M, Solomon T (2023) Japanese Encephalitis among Adults: A Review. Am J Trop Med Hyg 108(5):860\u2013864. https:\/\/doi.org\/10.4269\/ajtmh.23-0036","journal-title":"Am J Trop Med Hyg"},{"issue":"1","key":"6517_CR27","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1080\/22221751.2021.1941276","volume":"10","author":"L Huang","year":"2021","unstructured":"Huang L, Li H, Ye Z, Xu Q, Fu Q, Sun W, Qi W, Yue J (2021) Berbamine inhibits Japanese encephalitis virus (JEV) infection by compromising TPRMLs-mediated endolysosomal trafficking of low-density lipoprotein receptor (LDLR). Emerg Microbes Infections 10(1):1257\u20131271. https:\/\/doi.org\/10.1080\/22221751.2021.1941276","journal-title":"Emerg Microbes Infections"},{"key":"6517_CR28","doi-asserted-by":"publisher","first-page":"1833","DOI":"10.2147\/IDR.S210890","volume":"12","author":"C Jasso-Miranda","year":"2019","unstructured":"Jasso-Miranda C, Herrera-Camacho I, Flores-Mendoza LK, Dominguez F, Vallejo-Ruiz V, Sanchez-Burgos GG, Pando-Robles V, Santos-Lopez G, Reyes-Leyva J (2019) Antiviral and immunomodulatory effects of polyphenols on macrophages infected with dengue virus serotypes 2 and 3 enhanced or not with antibodies. Infect Drug Resist 12:1833\u20131852. https:\/\/doi.org\/10.2147\/IDR.S210890","journal-title":"Infect Drug Resist"},{"issue":"2","key":"6517_CR29","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1007\/s43440-022-00355-2","volume":"74","author":"S Joe","year":"2022","unstructured":"Joe S, Salam AAA, Neogi U, N, N. B., Mudgal PP (2022) Antiviral drug research for Japanese encephalitis: An updated review. Pharmacol Rep 74(2):273\u2013296. https:\/\/doi.org\/10.1007\/s43440-022-00355-2","journal-title":"Pharmacol Rep"},{"issue":"12","key":"6517_CR30","doi-asserted-by":"publisher","first-page":"16785","DOI":"10.3390\/ijms131216785","volume":"13","author":"J Johari","year":"2012","unstructured":"Johari J, Kianmehr A, Mustafa M, Abubakar S, Zandi K (2012) Antiviral Activity of Baicalein and Quercetin against the Japanese Encephalitis Virus. Int J Mol Sci 13(12):16785\u201316795. https:\/\/doi.org\/10.3390\/ijms131216785","journal-title":"Int J Mol Sci"},{"key":"6517_CR31","doi-asserted-by":"publisher","first-page":"16785","DOI":"10.3390\/ijms131216785","volume":"13","author":"J Johari","year":"2012","unstructured":"Johari J, Kianmehr A, Mustafa MR, AbuBakar S, Zandi K (2012) Antiviral activity of baicalein and quercetin against the Japanese encephalitis virus. Int J Mol Sci 13:16785\u201316795. https:\/\/doi.org\/10.3390\/ijms131216785","journal-title":"Int J Mol Sci"},{"key":"6517_CR32","doi-asserted-by":"publisher","first-page":"60682","DOI":"10.3791\/60682-v","volume":"160","author":"H Kim","year":"2020","unstructured":"Kim H, Xue X (2020) Detection of Total Reactive Oxygen Species in Adherent Cells by 2',7\u2019-Dichlorodihydrofluorescein Diacetate Staining. J Visualized Experiments 160:60682. https:\/\/doi.org\/10.3791\/60682-v","journal-title":"J Visualized Experiments"},{"issue":"D1","key":"6517_CR33","doi-asserted-by":"publisher","first-page":"D1388","DOI":"10.1093\/nar\/gkaa971","volume":"49","author":"S Kim","year":"2021","unstructured":"Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE (2021) PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Res 49(D1):D1388\u2013D1395. https:\/\/doi.org\/10.1093\/nar\/gkaa971","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"6517_CR34","doi-asserted-by":"publisher","first-page":"166","DOI":"10.4314\/ajtcam.v11i3.24","volume":"11","author":"GA Koffuor","year":"2014","unstructured":"Koffuor GA, Dickson R, Gbedema SY, Ekuadzi E, Dapaah G, Otoo LF (2014) The immunostimulatory and antimicrobial property of two herbal decoctions used in the management of HIV\/AIDS in Ghana. Afr J Tradit Complement Altern Med 11(3):166\u2013172. https:\/\/doi.org\/10.4314\/ajtcam.v11i3.24","journal-title":"Afr J Tradit Complement Altern Med"},{"issue":"4","key":"6517_CR35","doi-asserted-by":"publisher","first-page":"e0249866","DOI":"10.1371\/journal.pone.0249866","volume":"16","author":"S Kumar","year":"2021","unstructured":"Kumar S, Deshpande PA (2021) Structural and thermodynamic analysis of factors governing the stability and thermal folding\/unfolding of SazCA. PLoS ONE 16(4):e0249866. https:\/\/doi.org\/10.1371\/journal.pone.0249866","journal-title":"PLoS ONE"},{"issue":"9","key":"6517_CR36","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1007\/s00705-022-05481-z","volume":"167","author":"S Kumar","year":"2022","unstructured":"Kumar S, Verma A, Yadav P, Dubey SK, Azhar EI, Maitra SS, Dwivedi VD (2022) Molecular pathogenesis of Japanese encephalitis and possible therapeutic strategies. Arch Virol 167(9):1739\u20131762. https:\/\/doi.org\/10.1007\/s00705-022-05481-z","journal-title":"Arch Virol"},{"issue":"1","key":"6517_CR37","doi-asserted-by":"publisher","first-page":"4833","DOI":"10.1038\/s41598-019-41302-1","volume":"9","author":"N Lannes","year":"2019","unstructured":"Lannes N, Garcia-Nicol\u00e0s O, D\u00e9moulins T, Summerfield A, Filgueira L (2019) CX3CR1-CX3CL1-dependent cell-to-cell japanese encephalitis virus transmission by human microglial cells. Sci Rep 9(1):4833. https:\/\/doi.org\/10.1038\/s41598-019-41302-1","journal-title":"Sci Rep"},{"issue":"1","key":"6517_CR38","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s12974-017-0931-5","volume":"14","author":"N Lannes","year":"2017","unstructured":"Lannes N, Summerfield A, Filgueira L (2017) Regulation of inflammation in Japanese encephalitis. J Neuroinflamm 14(1):158. https:\/\/doi.org\/10.1186\/s12974-017-0931-5","journal-title":"J Neuroinflamm"},{"issue":"15","key":"6517_CR39","doi-asserted-by":"publisher","first-page":"8271","DOI":"10.1128\/JVI.78.15.8271-8280.2004","volume":"78","author":"E Lee","year":"2004","unstructured":"Lee E, Hall RA, Lobigs M (2004) Common E Protein Determinants for Attenuation of Glycosaminoglycan-Binding Variants of Japanese Encephalitis and West Nile Viruses. J Virol 78(15):8271\u20138280. https:\/\/doi.org\/10.1128\/JVI.78.15.8271-8280.2004","journal-title":"J Virol"},{"key":"6517_CR40","doi-asserted-by":"publisher","first-page":"100026","DOI":"10.1016\/j.medntd.2019.100026","volume":"3","author":"D Li","year":"2019","unstructured":"Li D, Ji B (2019) Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine. Med Novel Technol Devices 3:100026. https:\/\/doi.org\/10.1016\/j.medntd.2019.100026","journal-title":"Med Novel Technol Devices"},{"issue":"3","key":"6517_CR41","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1021\/acsinfecdis.8b00322","volume":"5","author":"P-C Li","year":"2019","unstructured":"Li P-C, Jang J, Hsia C-Y, Groomes PV, Lian W, De Wispelaere M, Pitts JD, Wang J, Kwiatkowski N, Gray NS, Yang PL (2019) Small Molecules Targeting the Flavivirus E Protein with Broad-Spectrum Activity and Antiviral Efficacy in Vivo. ACS Infect Dis 5(3):460\u2013472. https:\/\/doi.org\/10.1021\/acsinfecdis.8b00322","journal-title":"ACS Infect Dis"},{"issue":"4","key":"6517_CR42","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1134\/S0026893308040195","volume":"42","author":"MY Lobanov","year":"2008","unstructured":"Lobanov MY, Bogatyreva NS, Galzitskaya OV (2008) Radius of gyration as an indicator of protein structure compactness. Mol Biol 42(4):623\u2013628. https:\/\/doi.org\/10.1134\/S0026893308040195","journal-title":"Mol Biol"},{"issue":"4","key":"6517_CR43","doi-asserted-by":"publisher","first-page":"2337","DOI":"10.1128\/JVI.06072-11","volume":"86","author":"VC Luca","year":"2012","unstructured":"Luca VC, AbiMansour J, Nelson CA, Fremont DH (2012) Crystal Structure of the Japanese Encephalitis Virus Envelope Protein. J Virol 86(4):2337\u20132346. https:\/\/doi.org\/10.1128\/JVI.06072-11","journal-title":"J Virol"},{"issue":"21","key":"6517_CR44","doi-asserted-by":"publisher","first-page":"14716","DOI":"10.1021\/acs.jmedchem.3c01223","volume":"66","author":"M Mahanti","year":"2023","unstructured":"Mahanti M, Pal KB, Kumar R, Schulze M, Leffler H, Logan DT, Nilsson UJ (2023) Ligand Sulfur Oxidation State Progressively Alters Galectin-3-Ligand Complex Conformations To Induce Affinity-Influencing Hydrogen Bonds. J Med Chem 66(21):14716\u201314723. https:\/\/doi.org\/10.1021\/acs.jmedchem.3c01223","journal-title":"J Med Chem"},{"issue":"1","key":"6517_CR45","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1016\/j.jmb.2008.10.018","volume":"385","author":"GG Maisuradze","year":"2009","unstructured":"Maisuradze GG, Liwo A, Scheraga HA (2009) Principal Component Analysis for Protein Folding Dynamics. J Mol Biol 385(1):312\u2013329. https:\/\/doi.org\/10.1016\/j.jmb.2008.10.018","journal-title":"J Mol Biol"},{"key":"6517_CR46","doi-asserted-by":"publisher","first-page":"9954","DOI":"10.1021\/jp003020w","volume":"105","author":"P Mark","year":"2001","unstructured":"Mark P, Nilsson L (2001) Structure and Dynamics of the TIP3P, SPC, and SPC\/E Water Models at 298 K. J Phys Chem A 105:9954\u20139960. https:\/\/doi.org\/10.1021\/jp003020w","journal-title":"J Phys Chem A"},{"issue":"4","key":"6517_CR47","doi-asserted-by":"publisher","first-page":"2635","DOI":"10.1063\/1.463940","volume":"97","author":"GJ Martyna","year":"1992","unstructured":"Martyna GJ, Klein ML, Tuckerman M (1992) Nos\u00e9\u2013Hoover chains: The canonical ensemble via continuous dynamics. J Chem Phys 97(4):2635\u20132643. https:\/\/doi.org\/10.1063\/1.463940","journal-title":"J Chem Phys"},{"key":"6517_CR48","doi-asserted-by":"publisher","unstructured":"Monticelli L, Tieleman DP (2013) Force Fields for Classical Molecular Dynamics. In L. Monticelli & E. Salonen (Eds.), Biomolecular Simulations (Vol. 924, pp. 197\u2013213). Humana Press. https:\/\/doi.org\/10.1007\/978-1-62703-017-5_8","DOI":"10.1007\/978-1-62703-017-5_8"},{"key":"6517_CR49","doi-asserted-by":"publisher","first-page":"1737","DOI":"10.1099\/vir.0.18883-0","volume":"84","author":"M Nawa","year":"2003","unstructured":"Nawa M, Takasaki T, Yamada K-I, Kurane I, Akatsuka T (2003) Interference in Japanese encephalitis virus infection of Vero cells by a cationic amphiphilic drug, chlorpromazine. J Gen Virol 84:1737\u20131741. https:\/\/doi.org\/10.1099\/vir.0.18883-0","journal-title":"J Gen Virol"},{"issue":"3","key":"6517_CR50","doi-asserted-by":"publisher","first-page":"713","DOI":"10.47665\/tb.37.3.713","volume":"37","author":"N Nor Rashid","year":"2020","unstructured":"Nor Rashid N, Yusof R, Rothan HA (2020) Antiviral and virucidal activities of sulphated polysaccharides against Japanese encephalitis virus. Trop Biomed 37(3):713\u2013721","journal-title":"Trop Biomed"},{"issue":"1","key":"6517_CR51","doi-asserted-by":"publisher","first-page":"21646","DOI":"10.1038\/s41598-022-25836-5","volume":"12","author":"A Patigo","year":"2022","unstructured":"Patigo A, Hengphasatporn K, Cao V, Paunrat W, Vijara N, Chokmahasarn T, Maitarad P, Rungrotmongkol T, Shigeta Y, Boonyasuppayakorn S, Khotavivattana T (2022) Design, synthesis, in vitro, in silico, and SAR studies of flavone analogs towards anti-dengue activity. Sci Rep 12(1):21646. https:\/\/doi.org\/10.1038\/s41598-022-25836-5","journal-title":"Sci Rep"},{"key":"6517_CR52","unstructured":"Release Schr\u00f6dinger & Maestro 2021-2. (2021). Schr\u00f6dinger, LLC. New York, NY, USA"},{"issue":"1","key":"6517_CR53","doi-asserted-by":"publisher","first-page":"71","DOI":"10.3390\/pr9010071","volume":"9","author":"OMH Salo-Ahen","year":"2020","unstructured":"Salo-Ahen OMH, Alanko I, Bhadane R, Bonvin AMJJ, Honorato RV, Hossain S, Juffer AH, Kabedev A, Lahtela-Kakkonen M, Larsen AS, Lescrinier E, Marimuthu P, Mirza MU, Mustafa G, Nunes-Alves A, Pantsar T, Saadabadi A, Singaravelu K, Vanmeert M (2020) Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development. Processes 9(1):71. https:\/\/doi.org\/10.3390\/pr9010071","journal-title":"Processes"},{"issue":"8","key":"6517_CR54","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1517\/13543784.2013.805744","volume":"22","author":"S Sharma","year":"2013","unstructured":"Sharma S, Ali A, Ali J, Sahni JK, Baboota S (2013) Rutin: Therapeutic potential and recent advances in drug delivery. Expert Opin Investig Drugs 22(8):1063\u20131079. https:\/\/doi.org\/10.1517\/13543784.2013.805744","journal-title":"Expert Opin Investig Drugs"},{"issue":"7","key":"6517_CR55","doi-asserted-by":"publisher","first-page":"2196","DOI":"10.1007\/s11064-023-03898-9","volume":"48","author":"G Singh","year":"2023","unstructured":"Singh G, Kumar A (2023) Japanese Encephalitis Virus Infection Causes an Imbalance in the Activation of Mitochondrial Fusion\/Fission Genes and Triggers the Activation of NOX2-mediated Oxidative Stress and Neuronal Cell Death. Neurochem Res 48(7):2196\u20132205. https:\/\/doi.org\/10.1007\/s11064-023-03898-9","journal-title":"Neurochem Res"},{"key":"6517_CR56","doi-asserted-by":"publisher","first-page":"742","DOI":"10.3390\/vaccines11040742","volume":"11","author":"KS Srivastava","year":"2023","unstructured":"Srivastava KS, Jeswani V, Pal N, Bohra B, Vishwakarma V, Bapat AA, Patnaik YP, Khanna N, Shukla R (2023) Japanese Encephalitis Virus: An Update on the Potential Antivirals and Vaccines. Vaccines 11:742. https:\/\/doi.org\/10.3390\/vaccines11040742","journal-title":"Vaccines"},{"key":"6517_CR57","doi-asserted-by":"publisher","first-page":"10546","DOI":"10.1038\/s41598-018-28373-2","volume":"8","author":"S Sunandan Mukherjee, Mukherjee","year":"2018","unstructured":"Sunandan Mukherjee, Mukherjee S, Ranjit Prasad Bahadur, Bahadur RP (2018) An account of solvent accessibility in protein-RNA recognition. Sci Rep 8:10546\u201310546. https:\/\/doi.org\/10.1038\/s41598-018-28373-2","journal-title":"Sci Rep"},{"issue":"9","key":"6517_CR58","doi-asserted-by":"publisher","first-page":"3367","DOI":"10.1128\/AAC.00041-07","volume":"51","author":"V Swarup","year":"2007","unstructured":"Swarup V, Ghosh J, Ghosh S, Saxena A, Basu A (2007) Antiviral and Anti-Inflammatory Effects of Rosmarinic Acid in an Experimental Murine Model of Japanese Encephalitis. Antimicrob Agents Chemother 51(9):3367\u20133370. https:\/\/doi.org\/10.1128\/AAC.00041-07","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"6517_CR59","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1186\/s12917-024-04053-4","volume":"396","author":"S Tajima","year":"2010","unstructured":"Tajima S, Nerome R, Nukui Y, Kato F, Takasaki T, Kurane I (2010) A single mutation in the Japanese encephalitis virus E protein (S123R) increases its growth rate in mouse neuroblastoma cells and its pathogenicity in mice. Virology 396(2):298\u2013304. https:\/\/doi.org\/10.1186\/s12917-024-04053-4","journal-title":"Virology"},{"key":"6517_CR60","doi-asserted-by":"publisher","first-page":"1314","DOI":"10.3389\/fmicb.2017.01314","volume":"8","author":"\u00c1 V\u00e1zquez-Calvo","year":"2017","unstructured":"V\u00e1zquez-Calvo \u00c1, De Jim\u00e9nez N, Mart\u00edn-Acebes MA, Garcia-Moruno E, Saiz J-C (2017) Antiviral Properties of the Natural Polyphenols Delphinidin and Epigallocatechin Gallate against the Flaviviruses West Nile Virus, Zika Virus, and Dengue Virus. Front Microbiol 8:1314. https:\/\/doi.org\/10.3389\/fmicb.2017.01314","journal-title":"Front Microbiol"},{"key":"6517_CR61","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.virusres.2018.06.009","volume":"253","author":"C-Y Wang","year":"2018","unstructured":"Wang C-Y, Hour M-J, Lai H-C, Chen C-H, Chang P-J, Huang S-H, Lin C-W (2018) Epigallocatechin-3-gallate inhibits the early stages of Japanese encephalitis virus infection. Virus Res 253:140\u2013146. https:\/\/doi.org\/10.1016\/j.virusres.2018.06.009","journal-title":"Virus Res"},{"issue":"4","key":"6517_CR62","doi-asserted-by":"publisher","first-page":"2031","DOI":"10.3390\/ijms23042031","volume":"23","author":"N Wang","year":"2022","unstructured":"Wang N, Li R, Feng B, Cheng Y, Guo Y, Qian H (2022) Chicoric Acid Prevents Neuroinflammation and Neurodegeneration in a Mouse Parkinson's Disease Model: Immune Response and Transcriptome Profile of the Spleen and Colon. Int J Mol Sci 23(4):2031. https:\/\/doi.org\/10.3390\/ijms23042031","journal-title":"Int J Mol Sci"},{"key":"6517_CR63","doi-asserted-by":"crossref","unstructured":"Wang S, Liu Y, Guo J, Wang P, Zhang L, Xiao G, Wang W (2017) Screening of FDA-Approved Drugs for Inhibitors of Japanese Encephalitis Virus Infection. J Virol 91(21). 10.1128\/jvi.01055-17","DOI":"10.1128\/JVI.01055-17"},{"issue":"57","key":"6517_CR64","doi-asserted-by":"publisher","first-page":"36149","DOI":"10.1039\/C7RA06325C","volume":"7","author":"Y Wang","year":"2017","unstructured":"Wang Y, Diao Z, Li J, Ren B, Zhu D, Liu Q, Liu Z, Liu X (2017) Chicoric acid supplementation ameliorates cognitive impairment induced by oxidative stress via promotion of antioxidant defense system. RSC Adv 7(57):36149\u201336162. https:\/\/doi.org\/10.1039\/C7RA06325C","journal-title":"RSC Adv"},{"issue":"22","key":"6517_CR65","doi-asserted-by":"publisher","first-page":"6596","DOI":"10.1021\/jm0608210","volume":"49","author":"A Weis","year":"2006","unstructured":"Weis A, Katebzadeh K, S\u00f6derhjelm P, Nilsson I, Ryde U (2006) Ligand affinities predicted with the MM\/PBSA method: Dependence on the simulation method and the force field. J Med Chem 49(22):6596\u20136606. https:\/\/doi.org\/10.1021\/jm0608210","journal-title":"J Med Chem"},{"key":"6517_CR66","unstructured":"WHO, W (2019) Japanese encephalitis. Japanese Encephalitis. https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/japanese-encephalitis"},{"issue":"1","key":"6517_CR67","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.antiviral.2014.01.011","volume":"104","author":"XT Xiangyang Zu, Zu","year":"2014","unstructured":"Xiangyang Zu, Zu XT, Yang Liu, Liu Y, Liu Y, Liu Y, Wang S, Wang S, Jin R, Jin R, Zhou Z, Zhou Z, Liu H, Liu H, Gong R, Gong R, Xiao G, Xiao G, Wang W-J, Wang W (2014) Peptide inhibitor of Japanese encephalitis virus infection targeting envelope protein domain III. Antiviral Res 104(1):7\u201314. https:\/\/doi.org\/10.1016\/j.antiviral.2014.01.011","journal-title":"Antiviral Res"},{"key":"6517_CR68","doi-asserted-by":"publisher","first-page":"952","DOI":"10.3390\/life12070952","volume":"12","author":"P Yadav","year":"2022","unstructured":"Yadav P, El-Kafrawy SA, Mai M, El-Daly, Alghafari WT, Arwa A, Faizo SK, Jha, Dwivedi VD, Dwivedi VD, Azhar EI (2022) Discovery of Small Molecules from Echinacea angustifolia Targeting RNA-Dependent RNA Polymerase of Japanese Encephalitis Virus. Life 12:952. https:\/\/doi.org\/10.3390\/life12070952","journal-title":"Life"},{"issue":"5","key":"6517_CR69","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1021\/acsinfecdis.9b00376","volume":"6","author":"J Yang","year":"2020","unstructured":"Yang J, Xu Y, Yan Y, Li W, Zhao L, Dai Q, Li Y, Li S, Zhong J, Cao R, Zhong W (2020) Small Molecule Inhibitor of ATPase Activity of HSP70 as a Broad-Spectrum Inhibitor against Flavivirus Infections. ACS Infect Dis 6(5):832\u2013843. https:\/\/doi.org\/10.1021\/acsinfecdis.9b00376","journal-title":"ACS Infect Dis"},{"issue":"10","key":"6517_CR70","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.3390\/ph16101459","volume":"16","author":"C Yao","year":"2023","unstructured":"Yao C, Shen Z, Shen L, Kadier K, Zhao J, Guo Y, Xu L, Cao J, Dong X, Yang B (2023) Identification of Potential JNK3 Inhibitors: A Combined Approach Using Molecular Docking and Deep Learning-Based Virtual Screening. Pharmaceuticals 16(10):1459. https:\/\/doi.org\/10.3390\/ph16101459","journal-title":"Pharmaceuticals"},{"issue":"3","key":"6517_CR71","doi-asserted-by":"publisher","first-page":"68","DOI":"10.3390\/pathogens7030068","volume":"7","author":"S-I Yun","year":"2018","unstructured":"Yun S-I, Lee Y-M (2018) Early Events in Japanese Encephalitis Virus Infection: Viral Entry. Pathogens 7(3):68. https:\/\/doi.org\/10.3390\/pathogens7030068","journal-title":"Pathogens"},{"issue":"1","key":"6517_CR72","doi-asserted-by":"publisher","first-page":"20","DOI":"10.3934\/microbiol.2023002","volume":"9","author":"MI Zapata-Cardona","year":"2023","unstructured":"Zapata-Cardona MI, Florez-Alvarez L, Guerra-Sandoval AL, Chvatal-Medina M, Guerra-Almonacid CM, Hincapie-Garcia J, Hernandez JC, Rugeles MT, Zapata-Builes W (2023) In vitro and in silico evaluation of antiretrovirals against SARS-CoV-2: A drug repurposing approach. AIMS Microbiol 9(1):20\u201340. https:\/\/doi.org\/10.3934\/microbiol.2023002","journal-title":"AIMS Microbiol"},{"key":"6517_CR73","doi-asserted-by":"publisher","first-page":"199120","DOI":"10.1016\/j.virusres.2023.199120","volume":"331","author":"Y Zhu","year":"2023","unstructured":"Zhu Y, He Z, Qi Z (2023) Virus-host Interactions in Early Japanese Encephalitis Virus Infection. Virus Res 331:199120. https:\/\/doi.org\/10.1016\/j.virusres.2023.199120","journal-title":"Virus Res"}],"container-title":["Archives of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00705-025-06517-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00705-025-06517-w","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00705-025-06517-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T17:24:00Z","timestamp":1770312240000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00705-025-06517-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,9]]},"references-count":73,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["6517"],"URL":"https:\/\/doi.org\/10.1007\/s00705-025-06517-w","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-4888640\/v1","asserted-by":"object"}]},"ISSN":["0304-8608","1432-8798"],"issn-type":[{"value":"0304-8608","type":"print"},{"value":"1432-8798","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,9]]},"assertion":[{"value":"9 August 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 August 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 January 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that there is no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"48"}}