{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T18:04:38Z","timestamp":1775585078423,"version":"3.50.1"},"reference-count":95,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,10,25]],"date-time":"2024-10-25T00:00:00Z","timestamp":1729814400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Epstein\u2013Barr virus (EBV), also known as human herpesvirus 4, is a member of the herpes virus family. EBV is a widespread virus and causes infectious mononucleosis, which manifests with symptoms such as fever, fatigue, lymphadenopathy, splenomegaly, and hepatomegaly. Additionally, EBV is associated with different lymphocyte-associated non-malignant, premalignant, and malignant diseases. So far, no effective treatment or therapeutic drug is known for EBV-induced infections and diseases. This study investigated natural compounds that inhibit EBV glycoprotein L (gL) and block EBV fusion in host cells. We utilised computational approaches, including molecular docking, in silico ADMET analysis, and molecular dynamics simulation. We docked 628 natural compounds against gL and identified the four best compounds based on binding scores and pharmacokinetic properties. These four compounds, with PubChem CIDs 4835509 (CHx-HHPD-Ac), 2870247 (Cyh-GlcNAc), 21206004 (Hep-HHPD-Ac), and 51066638 (Und-GlcNAc), showed several interactions with EBV gL. However, molecular dynamics simulations indicated that the protein\u2013ligand complexes of CID: 4835509 (CHx-HHPD-Ac) and CID: 2870247 (Cyh-GlcNAc) are more stable than those of the other two compounds. Therefore, CIDs 4835509 and 2870247 (Cyh-GlcNAc) may be potent natural inhibitors of EBV infection. These findings can open a new way for effective drug design against EBV and its associated infections and diseases.<\/jats:p>","DOI":"10.3390\/pathogens13110928","type":"journal-article","created":{"date-parts":[[2024,10,25]],"date-time":"2024-10-25T08:42:13Z","timestamp":1729845733000},"page":"928","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["An In Silico Approach to Discover Efficient Natural Inhibitors to Tie Up Epstein\u2013Barr Virus Infection"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4264-1271","authenticated-orcid":false,"given":"Ayan","family":"Das","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mumtaza","family":"Mumu","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4594-100X","authenticated-orcid":false,"given":"Tanjilur","family":"Rahman","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram 4331, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6626-4178","authenticated-orcid":false,"given":"Md Abu","family":"Sayeed","sequence":"additional","affiliation":[{"name":"National Centre for Epidemiology and Population Health (NCEPH), College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7357-9645","authenticated-orcid":false,"given":"Md Mazharul","family":"Islam","sequence":"additional","affiliation":[{"name":"Department of Animal Resources, Ministry of Municipality, Doha P.O. Box 35081, Qatar"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John I.","family":"Alawneh","sequence":"additional","affiliation":[{"name":"Plant Biosecurity and Product Integrity, Biosecurity Queensland, Department of Agriculture and Fisheries, Brisbane, QLD 4000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6495-4637","authenticated-orcid":false,"given":"Mohammad Mahmudul","family":"Hassan","sequence":"additional","affiliation":[{"name":"School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia"},{"name":"Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1016\/S0140-6736(64)91524-7","article-title":"Virus particles in cultured lymphoblasts from Burkitt\u2019s lymphoma","volume":"1","author":"Epstein","year":"1964","journal-title":"Lancet"},{"key":"ref_2","first-page":"1147","article-title":"Antibodies to Epstein-Barr Virus in Burkitt\u2019s Lymphoma and Control Groups2","volume":"43","author":"Henle","year":"1969","journal-title":"JNCI J. Natl. Cancer Inst."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1056\/NEJM198903163201103","article-title":"Hodgkin\u2019s Disease and Epstein-Barr Virus","volume":"320","author":"Mueller","year":"1989","journal-title":"N. Engl. J. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3409","DOI":"10.1128\/jvi.66.6.3409-3414.1992","article-title":"Epstein-Barr virus enters B cells and epithelial cells by different routes","volume":"66","author":"Miller","year":"1992","journal-title":"J. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1038\/sj.bjc.6600107","article-title":"Low prevalence of Epstein\u2013Barr virus in incident gastric adenocarcinomas from the United Kingdom","volume":"86","author":"Woodman","year":"2002","journal-title":"Br. J. Cancer"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1007\/s11604-008-0291-2","article-title":"Spectrum of Epstein-Barr virus-related diseases: A pictorial review","volume":"27","author":"Maeda","year":"2009","journal-title":"Jpn. J. Radiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1086\/342596","article-title":"Sexual History and Epstein-Barr Virus Infection","volume":"186","author":"Crawford","year":"2002","journal-title":"J. Infect. Dis."},{"key":"ref_8","first-page":"1211","article-title":"Incidence of Epstein-Barr virus in astronaut saliva during spaceflight","volume":"70","author":"Payne","year":"1999","journal-title":"Aviat. Space. Environ. Med."},{"key":"ref_9","first-page":"1279","article-title":"Epstein-Barr virus infectious mononucleosis","volume":"70","author":"Ebell","year":"2004","journal-title":"Am. Fam. Physician."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1128\/CMR.00044-10","article-title":"Progress and problems in understanding and managing primary Epstein-Barr virus infections","volume":"24","author":"Odumade","year":"2011","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1542\/pir.32.9.375","article-title":"Epstein-Barr virus","volume":"32","author":"Jenson","year":"2011","journal-title":"Pediatr. Rev."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"7","DOI":"10.2174\/1874357901509010007","article-title":"Epstein- Barr virus: Clinical and epidemiological revisits and genetic basis of oncogenesis","volume":"9","author":"Ali","year":"2015","journal-title":"Open Virol. J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1128\/JVI.02517-12","article-title":"Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains","volume":"87","author":"Lin","year":"2013","journal-title":"J. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/S0065-230X(08)60714-9","article-title":"Molecular epidemiology of Epstein\u2013Barr virus infection","volume":"67","author":"Gratama","year":"1995","journal-title":"Adv. Cancer Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.virol.2006.01.015","article-title":"The genome of Epstein\u2013Barr virus type 2 strain AG876","volume":"350","author":"Dolan","year":"2006","journal-title":"Virology"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1002\/ijc.2910080312","article-title":"The establishment of lymphoblastoid lines from adult and fetal human lymphoid tissue and its dependence on EBV","volume":"8","author":"Nilsson","year":"1971","journal-title":"Int. J. Cancer"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.2217\/fvl.15.80","article-title":"EBV glycoproteins: Where are we now?","volume":"10","year":"2015","journal-title":"Future Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"9628","DOI":"10.1128\/JVI.00622-06","article-title":"Antibodies to gp350\/220 enhance the ability of Epstein-Barr virus to infect epithelial cells","volume":"80","author":"Turk","year":"2006","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"13214","DOI":"10.1128\/JVI.05580-11","article-title":"Fusion of Epstein-Barr virus with epithelial cells can be triggered by \u03b1v\u03b25 in addition to \u03b1v\u03b26 and \u03b1v\u03b28, and integrin binding triggers a conformational change in glycoproteins gHgL","volume":"85","author":"Chesnokova","year":"2011","journal-title":"J. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.virol.2009.06.013","article-title":"Human antibody titers to Epstein\u2013Barr Virus (EBV) gp350 correlate with neutralization of infectivity better than antibody titers to EBV gp42 using a rapid flow cytometry-based EBV neutralization assay","volume":"391","author":"Sashihara","year":"2009","journal-title":"Virology"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"6324","DOI":"10.1128\/JVI.74.14.6324-6332.2000","article-title":"Epstein-Barr virus gH is essential for penetration of B cells but also plays a role in attachment of virus to epithelial cells","volume":"74","author":"Molesworth","year":"2000","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/nm830","article-title":"Epstein-Barr virus infection of polarized tongue and nasopharyngeal epithelial cells","volume":"9","author":"Tugizov","year":"2003","journal-title":"Nat. Med."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"5307","DOI":"10.1073\/pnas.77.9.5307","article-title":"Monoclonal antibodies against the major glycoprotein (gp350\/220) of Epstein-Barr virus neutralize infectivity","volume":"77","author":"Geilinger","year":"1980","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3987","DOI":"10.1128\/jvi.69.7.3987-3994.1995","article-title":"The Epstein-Barr virus (EBV) BZLF2 gene product associates with the gH and gL homologs of EBV and carries an epitope critical to infection of B cells but not of epithelial cells","volume":"69","author":"Li","year":"1995","journal-title":"J. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1128\/jvi.41.1.258-264.1982","article-title":"Production and characterization of monoclonal antibodies against the Epstein-Barr virus membrane antigen","volume":"41","author":"Strnad","year":"1982","journal-title":"J. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2979","DOI":"10.1073\/pnas.77.5.2979","article-title":"Monoclonal antibody against a 250,000-dalton glycoprotein of Epstein-Barr virus identifies a membrane antigen and a neutralizing antigen","volume":"77","author":"Hoffman","year":"1980","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1128\/jvi.61.4.1125-1135.1987","article-title":"Antigenic cross-reactions among herpes simplex virus types 1 and 2, Epstein-Barr virus, and cytomegalovirus","volume":"61","author":"Balachandran","year":"1987","journal-title":"J. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1016\/j.immuni.2018.03.026","article-title":"An antibody targeting the fusion machinery neutralizes dual-tropic infection and defines a site of vulnerability on Epstein-Barr virus","volume":"48","author":"Snijder","year":"2018","journal-title":"Immunity"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7825","DOI":"10.1128\/JVI.00445-07","article-title":"Epstein-Barr virus entry","volume":"81","year":"2007","journal-title":"J. Virol."},{"key":"ref_30","unstructured":"Longnecker, R.M., Kieff, E., and Cohen, J.I. (2013). Epstein-barr virus. Fields Virology, Wolters Kluwer Health Adis (ESP). [6th ed.]."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/nrmicro2548","article-title":"Fusing structure and function: A structural view of the herpesvirus entry machinery","volume":"9","author":"Connolly","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Chesnokova, L.S., Jiang, R., and Hutt-Fletcher, L.M. (2015). Viral entry. Epstein Barr Virus Volume 2: One Herpes Virus: Many Diseases, Springer.","DOI":"10.1007\/978-3-319-22834-1_7"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"12408","DOI":"10.1128\/JVI.79.19.12408-12415.2005","article-title":"The amino terminus of Epstein-Barr virus glycoprotein gH is important for fusion with epithelial and B cells","volume":"79","author":"Lev","year":"2005","journal-title":"J. Virol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"22641","DOI":"10.1073\/pnas.1011806108","article-title":"Crystal structure of the Epstein-Barr virus (EBV) glycoprotein H\/glycoprotein L (gH\/gL) complex","volume":"107","author":"Matsuura","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.coviro.2012.10.005","article-title":"Stuck in the middle: Structural insights into the role of the gH\/gL heterodimer in herpesvirus entry","volume":"3","author":"Stampfer","year":"2013","journal-title":"Curr. Opin. Virol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Sathiyamoorthy, K., Jiang, J., Hu, Y.X., Rowe, C.L., M\u00f6hl, B.S., Chen, J., Jiang, W., Mellins, E.D., Longnecker, R., and Zhou, Z.H. (2014). Assembly and architecture of the EBV B cell entry triggering complex. PLoS Pathog., 10.","DOI":"10.1371\/journal.ppat.1004309"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"9216","DOI":"10.1128\/JVI.00575-07","article-title":"Binding-site interactions between Epstein-Barr virus fusion proteins gp42 and gH\/gL reveal a peptide that inhibits both epithelial and B-cell membrane fusion","volume":"81","author":"Kirschner","year":"2007","journal-title":"J. Virol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1128\/jvi.66.4.2240-2250.1992","article-title":"A novel herpes simplex virus glycoprotein, gL, forms a complex with glycoprotein H (gH) and affects normal folding and surface expression of gH","volume":"66","author":"Hutchinson","year":"1992","journal-title":"J. Virol."},{"key":"ref_39","first-page":"3","article-title":"In-silico drug design: An approach which revolutionarised the drug discovery process","volume":"1","author":"Wadood","year":"2013","journal-title":"OA Drug Des. Deliv."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e20190105","DOI":"10.1590\/0001-3765201920190105","article-title":"The role of natural products in modern drug discovery","volume":"91","author":"Calixto","year":"2019","journal-title":"An. Acad. Bras. Ci\u00eancias"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e67","DOI":"10.1002\/cpph.67","article-title":"Natural products as a foundation for drug discovery","volume":"86","author":"Beutler","year":"2019","journal-title":"Curr. Protoc. Pharmacol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S1359-6446(99)01443-9","article-title":"The role of natural products in a modern drug discovery program","volume":"5","author":"Strohl","year":"2000","journal-title":"Drug Discov. Today"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/nchem.2479","article-title":"Counting on natural products for drug design","volume":"8","author":"Rodrigues","year":"2016","journal-title":"Nat. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"D475","DOI":"10.1093\/nar\/gks1200","article-title":"The RCSB Protein Data Bank: New resources for research and education","volume":"41","author":"Rose","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"5372","DOI":"10.1080\/07391102.2020.1871074","article-title":"In silico analysis of antiviral phytochemicals efficacy against Epstein\u2013Barr virus glycoprotein H","volume":"40","author":"Jakhmola","year":"2022","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_46","first-page":"135","article-title":"Drug Designing in Discovery Studio","volume":"14","author":"Jejurikar","year":"2021","journal-title":"Asian J. Res. Chem."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/978-1-4939-2269-7_19","article-title":"Small-molecule library screening by docking with pyrx","volume":"Volume 1263","author":"Dallakyan","year":"2015","journal-title":"Chemical Biology: Methods and Protocols"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"D1202","DOI":"10.1093\/nar\/gkv951","article-title":"PubChem substance and compound databases","volume":"44","author":"Kim","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"10024","DOI":"10.1021\/ja00051a040","article-title":"UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations","volume":"114","author":"Casewit","year":"1992","journal-title":"J. Am. Chem. Soc."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"W363","DOI":"10.1093\/nar\/gky473","article-title":"CASTp 3.0: Computed atlas of surface topography of proteins","volume":"46","author":"Tian","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/nprot.2015.043","article-title":"The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins","volume":"10","author":"Kozakov","year":"2015","journal-title":"Nat. Protoc."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1023\/A:1024582008908","article-title":"Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA","volume":"17","author":"Wolohan","year":"2003","journal-title":"J. Comput.-Aided Mol. Des."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Daina, A., Michielin, O., and Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 7.","DOI":"10.1038\/srep42717"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0169-409X(96)00423-1","article-title":"Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings","volume":"23","author":"Lipinski","year":"1997","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"4066","DOI":"10.1021\/acs.jmedchem.5b00104","article-title":"pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures","volume":"58","author":"Pires","year":"2015","journal-title":"J. Med. Chem."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1093\/bioinformatics\/bty707","article-title":"admetSAR 2.0: Web-service for prediction and optimization of chemical ADMET properties","volume":"35","author":"Yang","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_57","unstructured":"Release, S. (2017). 3: Desmond molecular dynamics system, DE Shaw research, New York, NY, 2017. Maestro-Desmond Interoperability Tools, Schr\u00f6dinger."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"100146","DOI":"10.1016\/j.medidd.2022.100146","article-title":"Deciphering antiviral efficacy of malaria box compounds against malaria exacerbating viral pathogens-Epstein Barr virus and SARS-CoV-2, an in silico study","volume":"16","author":"Indari","year":"2022","journal-title":"Med. Drug Discov."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1021\/acscombsci.0c00058","article-title":"Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy","volume":"22","author":"Goyal","year":"2020","journal-title":"ACS Comb. Sci."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.1021\/acs.jctc.8b01026","article-title":"OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules","volume":"15","author":"Roos","year":"2019","journal-title":"J. Chem. Theory Comput."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1080\/0026897021000044025","article-title":"Constant pressure-constant temperature molecular dynamics: A correct constrained NPT ensemble using the molecular virial","volume":"101","author":"Kalibaeva","year":"2003","journal-title":"Mol. Phys."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"3234","DOI":"10.1103\/PhysRevE.50.3234","article-title":"Remarks on \u201cConstant-temperature molecular dynamics with momentum conservation\u201d","volume":"50","author":"Martyna","year":"1994","journal-title":"Phys. Rev. E"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Bouback, T.A., Pokhrel, S., Albeshri, A., Aljohani, A.M., Samad, A., Alam, R., Hossen, M.S., Al-Ghamdi, K., Talukder, M.E.K., and Ahammad, F. (2021). Pharmacophore-based virtual screening, quantum mechanics calculations, and molecular dynamics simulation approaches identified potential natural antiviral drug candidates against MERS-CoV S1-NTD. Molecules, 26.","DOI":"10.3390\/molecules26164961"},{"key":"ref_64","unstructured":"Koparde, A.A., Doijad, R.C., and Magdum, C.S.J.P. (2019). Natural Products in Drug Discovery, IntechOpen."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1039\/B513504B","article-title":"Natural products: Sources and databases","volume":"23","author":"Michalsky","year":"2006","journal-title":"Nat. Prod. Rep."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"2084","DOI":"10.1021\/acs.jcim.3c01969","article-title":"Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites","volume":"64","author":"Khan","year":"2024","journal-title":"J. Chem. Inform. Model."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nrd1549","article-title":"Structure-based virtual screening and lead optimization: Methods and applications","volume":"3","author":"Kitchen","year":"2004","journal-title":"Nat. Rev Drug Discov."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Hunter, A.D. (1997). ACD\/ChemSketch 1.0 (freeware); ACD\/ChemSketch 2.0 and its Tautomers, Dictionary, and 3D Plug-ins; ACD\/HNMR 2.0; ACD\/CNMR 2.0. J. Chem. Educ., 74.","DOI":"10.1021\/ed074p905"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.ddtec.2004.11.007","article-title":"Lead- and drug-like compounds: The rule-of-five revolution","volume":"1","author":"Lipinski","year":"2004","journal-title":"Drug Discov. Today Technol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1007\/s40203-021-00113-x","article-title":"Computational identification of 2,4-disubstituted amino-pyrimidines as L858R\/T790M-EGFR double mutant inhibitors using pharmacophore mapping, molecular docking, binding free energy calculation, DFT study and molecular dynamic simulation","volume":"9","author":"Pawara","year":"2021","journal-title":"Silico Pharmacol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"100272","DOI":"10.1016\/j.jics.2021.100272","article-title":"In silico validation of anti-viral drugs obtained from marine sources as a potential target against SARS-CoV-2 Mpro","volume":"98","author":"Ghosh","year":"2021","journal-title":"J. Indian Chem. Soc."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1056\/NEJM198512193132502","article-title":"Replication of Epstein\u2013Barr virus within the epithelial cells of oral hairy leukoplakia, an AIDS-associated lesion","volume":"313","author":"Greenspan","year":"1985","journal-title":"N. Engl. J. Med."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"20464","DOI":"10.1073\/pnas.0907508106","article-title":"Fusion of epithelial cells by Epstein\u2013Barr virus proteins is triggered by binding of viral glycoproteins gHgL to integrins \u03b1v\u03b26 or \u03b1v\u03b28","volume":"106","author":"Chesnokova","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"7678","DOI":"10.1128\/JVI.00457-09","article-title":"Functional analysis of glycoprotein L (gL) from rhesus lymphocryptovirus in Epstein-Barr virus-mediated cell fusion indicates a direct role of gL in gB-induced membrane fusion","volume":"83","author":"Plate","year":"2009","journal-title":"J. Virol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1128\/jvi.71.2.1667-1670.1997","article-title":"Chaperone functions common to nonhomologous Epstein-Barr virus gL and Varicella-Zoster virus gL proteins","volume":"71","author":"Li","year":"1997","journal-title":"J. Virol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"6092","DOI":"10.1128\/JVI.72.7.6092-6103.1998","article-title":"Structural and antigenic analysis of a truncated form of the herpes simplex virus glycoprotein gH-gL complex","volume":"72","author":"Peng","year":"1998","journal-title":"J. Virol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1038\/nsmb.1837","article-title":"Crystal structure of the conserved herpesvirus fusion regulator complex gH\u2013gL","volume":"17","author":"Chowdary","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"6664","DOI":"10.1128\/JVI.00195-09","article-title":"Cleavage and Secretion of Epstein-Barr Virus Glycoprotein 42 Promote Membrane Fusion with B Lymphocytes","volume":"83","author":"Sorem","year":"2009","journal-title":"J. Virol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/S0167-6296(02)00126-1","article-title":"The price of innovation: New estimates of drug development costs","volume":"22","author":"DiMasi","year":"2003","journal-title":"J. Health Econ."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1093\/bib\/bbp023","article-title":"Recent advances in computer-aided drug design","volume":"10","author":"Song","year":"2009","journal-title":"Briefings Bioinform."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10822-013-9644-8","article-title":"Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments","volume":"27","author":"Sastry","year":"2013","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.2174\/09298673113209990001","article-title":"Virtual screening strategies in drug discovery: A critical review","volume":"20","author":"Lavecchia","year":"2013","journal-title":"Curr. Med. Chem."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"10150","DOI":"10.3390\/molecules190710150","article-title":"Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design","volume":"19","author":"Grinter","year":"2014","journal-title":"Molecules"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1208\/s12248-012-9322-0","article-title":"Structure-Based Virtual Screening for Drug Discovery: A Problem-Centric Review","volume":"14","author":"Cheng","year":"2012","journal-title":"AAPS J."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1002\/ddr.21222","article-title":"Computational approaches for drug discovery","volume":"75","author":"Hung","year":"2014","journal-title":"Drug Dev. Res."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13099-021-00443-3","article-title":"In silico molecular docking and in vitro antimicrobial efficacy of phytochemicals against multi-drug-resistant enteroaggregative Escherichia coli and non-typhoidal Salmonella spp.","volume":"13","author":"Abishad","year":"2021","journal-title":"Gut Pathog."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Alkafaas, S.S., Abdallah, A.M., Hassan, M.H., Hussien, A.M., Elkafas, S.S., Loutfy, S.A., Mikhail, A., Murad, O.G., Elsalahaty, M.I., and Hessien, M. (2024). Molecular docking as a tool for the discovery of novel insight about the role of acid sphingomyelinase inhibitors in SARS-CoV-2 infectivity. BMC Public Health, 24.","DOI":"10.1186\/s12889-024-17747-z"},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Opo, F.A.D.M., Rahman, M.M., Ahammad, F., Ahmed, I., Bhuiyan, M.A., and Asiri, A.M. (2021). Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-83626-x"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1038\/nrd941","article-title":"Integration of virtual and high-throughput screening","volume":"1","author":"Bajorath","year":"2002","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1021\/cr60274a001","article-title":"Partition coefficients and their uses","volume":"71","author":"Leo","year":"1971","journal-title":"Chem. Rev."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1021\/ci034243x","article-title":"ESOL: Estimating aqueous solubility directly from molecular structure","volume":"44","author":"Delaney","year":"2004","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Zhou, W., Wang, Y., Lu, A., and Zhang, G. (2016). Systems pharmacology in small molecular drug discovery. Int. J. Mol. Sci., 17.","DOI":"10.3390\/ijms17020246"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1016\/j.jmb.2005.01.058","article-title":"The relationship between the flexibility of proteins and their conformational states on forming protein\u2013protein complexes with an application to protein\u2013protein docking","volume":"347","author":"Smith","year":"2005","journal-title":"J. Mol. Biol."},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Ahammad, F., Alam, R., Mahmud, R., Akhter, S., Talukder, E.K., Tonmoy, A.M., Fahim, S., Al-Ghamdi, K., Samad, A., and Qadri, I. (2021). Pharmacoinformatics and molecular dynamics simulation-based phytochemical screening of neem plant (Azadiractha indica) against human cancer by targeting MCM7 protein. Briefings Bioinform., 22.","DOI":"10.1093\/bib\/bbab098"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"101522","DOI":"10.1016\/j.imu.2024.101522","article-title":"Insights into novel inhibitors intending HCMV protease a computational molecular modelling investigation for antiviral drug repurposing","volume":"48","author":"Siddiquee","year":"2024","journal-title":"Inform. Med. 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