{"id":"https://openalex.org/W7126087738","doi":"https://doi.org/10.1109/bibm66473.2025.11356373","title":"In Silico Screening, Docking, and Redesigning of Traditional Chinese Medicinal Compounds Against Monkeypox Virus DNA Polymerase Holoenzyme and mRNA-Capping Enzyme","display_name":"In Silico Screening, Docking, and Redesigning of Traditional Chinese Medicinal Compounds Against Monkeypox Virus DNA Polymerase Holoenzyme and mRNA-Capping Enzyme","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126087738","doi":"https://doi.org/10.1109/bibm66473.2025.11356373"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356373","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356373","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5124285125","display_name":"John Luise T. Martinez","orcid":null},"institutions":[{"id":"https://openalex.org/I5791819","display_name":"University of the Philippines Manila","ror":"https://ror.org/01rrczv41","country_code":"PH","type":"education","lineage":["https://openalex.org/I103911934","https://openalex.org/I5791819"]}],"countries":["PH"],"is_corresponding":true,"raw_author_name":"John Luise T. Martinez","raw_affiliation_strings":["University of the Philippines Manila,Department of Biology,Manila,Philippines"],"affiliations":[{"raw_affiliation_string":"University of the Philippines Manila,Department of Biology,Manila,Philippines","institution_ids":["https://openalex.org/I5791819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124221132","display_name":"Katrina Rose R. Loreto","orcid":null},"institutions":[{"id":"https://openalex.org/I5791819","display_name":"University of the Philippines Manila","ror":"https://ror.org/01rrczv41","country_code":"PH","type":"education","lineage":["https://openalex.org/I103911934","https://openalex.org/I5791819"]}],"countries":["PH"],"is_corresponding":false,"raw_author_name":"Katrina Rose R. Loreto","raw_affiliation_strings":["University of the Philippines Manila,Department of Biology,Manila,Philippines"],"affiliations":[{"raw_affiliation_string":"University of the Philippines Manila,Department of Biology,Manila,Philippines","institution_ids":["https://openalex.org/I5791819"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061115264","display_name":"Enrique Jose L. Frio","orcid":"https://orcid.org/0000-0003-1385-3750"},"institutions":[{"id":"https://openalex.org/I5791819","display_name":"University of the Philippines Manila","ror":"https://ror.org/01rrczv41","country_code":"PH","type":"education","lineage":["https://openalex.org/I103911934","https://openalex.org/I5791819"]}],"countries":["PH"],"is_corresponding":false,"raw_author_name":"Enrique Jose L. Frio","raw_affiliation_strings":["University of the Philippines Manila,Department of Biology,Manila,Philippines"],"affiliations":[{"raw_affiliation_string":"University of the Philippines Manila,Department of Biology,Manila,Philippines","institution_ids":["https://openalex.org/I5791819"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046491778","display_name":"Marla A. Endriga","orcid":"https://orcid.org/0000-0002-5594-6480"},"institutions":[{"id":"https://openalex.org/I5791819","display_name":"University of the Philippines Manila","ror":"https://ror.org/01rrczv41","country_code":"PH","type":"education","lineage":["https://openalex.org/I103911934","https://openalex.org/I5791819"]}],"countries":["PH"],"is_corresponding":false,"raw_author_name":"Marla A. Endriga","raw_affiliation_strings":["University of the Philippines Manila,Department of Biology,Manila,Philippines"],"affiliations":[{"raw_affiliation_string":"University of the Philippines Manila,Department of Biology,Manila,Philippines","institution_ids":["https://openalex.org/I5791819"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5124285125"],"corresponding_institution_ids":["https://openalex.org/I5791819"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.69721799,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"6738","last_page":"6745"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.8486999869346619,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11767","display_name":"Poxvirus research and outbreaks","score":0.8486999869346619,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.025100000202655792,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.02449999935925007,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7943000197410583},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.5733000040054321},{"id":"https://openalex.org/keywords/monkeypox","display_name":"Monkeypox","score":0.5133000016212463},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.49219998717308044},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4424999952316284},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.421999990940094},{"id":"https://openalex.org/keywords/adme","display_name":"ADME","score":0.41909998655319214},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.40119999647140503},{"id":"https://openalex.org/keywords/polymerase","display_name":"Polymerase","score":0.3869999945163727},{"id":"https://openalex.org/keywords/dna-polymerase","display_name":"DNA polymerase","score":0.3720000088214874}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7943000197410583},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5928000211715698},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.5733000040054321},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5659999847412109},{"id":"https://openalex.org/C2778011067","wikidata":"https://www.wikidata.org/wiki/Q382370","display_name":"Monkeypox","level":5,"score":0.5133000016212463},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.49219998717308044},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4424999952316284},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.421999990940094},{"id":"https://openalex.org/C69366308","wikidata":"https://www.wikidata.org/wiki/Q2272286","display_name":"ADME","level":3,"score":0.41909998655319214},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.40230000019073486},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.40119999647140503},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.3869999945163727},{"id":"https://openalex.org/C2756471","wikidata":"https://www.wikidata.org/wiki/Q206286","display_name":"DNA polymerase","level":3,"score":0.3720000088214874},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.36890000104904175},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.35899999737739563},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3465000092983246},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.33730000257492065},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3343000113964081},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.33230000734329224},{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.3100999891757965},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.303600013256073},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.30230000615119934},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.29910001158714294},{"id":"https://openalex.org/C25166345","wikidata":"https://www.wikidata.org/wiki/Q4914012","display_name":"Binding domain","level":3,"score":0.2903999984264374},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.2867000102996826},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.2856000065803528},{"id":"https://openalex.org/C2777752112","wikidata":"https://www.wikidata.org/wiki/Q903238","display_name":"Lead compound","level":3,"score":0.2806999981403351},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2797999978065491},{"id":"https://openalex.org/C2779756493","wikidata":"https://www.wikidata.org/wiki/Q846227","display_name":"Antiviral drug","level":3,"score":0.27140000462532043},{"id":"https://openalex.org/C161223559","wikidata":"https://www.wikidata.org/wiki/Q138864","display_name":"Helicase","level":4,"score":0.26809999346733093},{"id":"https://openalex.org/C41258723","wikidata":"https://www.wikidata.org/wiki/Q2919111","display_name":"RNA-dependent RNA polymerase","level":4,"score":0.26570001244544983},{"id":"https://openalex.org/C2779315201","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Sequence homology","level":4,"score":0.2596000134944916},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2542000114917755}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356373","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356373","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7398455739021301,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1574994167","https://openalex.org/W1980892321","https://openalex.org/W2008059340","https://openalex.org/W2008982036","https://openalex.org/W2074656576","https://openalex.org/W2099861795","https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2151882149","https://openalex.org/W2263138261","https://openalex.org/W2796456578","https://openalex.org/W2885192023","https://openalex.org/W2906506692","https://openalex.org/W2954396852","https://openalex.org/W2991090734","https://openalex.org/W2995718460","https://openalex.org/W3083556913","https://openalex.org/W3087769169","https://openalex.org/W3099179819","https://openalex.org/W3168436232","https://openalex.org/W4245907439","https://openalex.org/W4254073994","https://openalex.org/W4283643760","https://openalex.org/W4294719209","https://openalex.org/W4296285989","https://openalex.org/W4307231743","https://openalex.org/W4310064627","https://openalex.org/W4311556607","https://openalex.org/W4317676357","https://openalex.org/W4319160725","https://openalex.org/W4322617927","https://openalex.org/W4328055011","https://openalex.org/W4366274270","https://openalex.org/W4366382766","https://openalex.org/W4386422290","https://openalex.org/W4386694139","https://openalex.org/W4387764928","https://openalex.org/W4388900300","https://openalex.org/W4390268340","https://openalex.org/W4392401766","https://openalex.org/W4396721167","https://openalex.org/W4399680371","https://openalex.org/W4400272321"],"related_works":[],"abstract_inverted_index":{"The":[0,172,191,205],"recent":[1],"outbreak":[2],"of":[3,18,56,70,86,98,107,111,126,140,150,184,202],"the":[4,42,90,94,99,104,108,112,132,141,246],"monkeypox":[5],"virus":[6],"(MPXV)":[7],"clade":[8],"IIb":[9],"has":[10],"affected":[11],"over":[12],"100,000":[13],"individuals":[14],"globally,":[15],"with":[16,58,147,219,268],"35%":[17],"cases":[19],"leading":[20],"to":[21,76,152,163,260],"hospitalization.":[22],"Current":[23],"drugs":[24,252],"like":[25],"tecovirimat":[26],"and":[27,38,78,103,135,161,236,243,263],"cidofovir,":[28],"initially":[29],"developed":[30],"for":[31,44,118,159,170],"other":[32],"orthopoxviruses,":[33],"are":[34],"hindered":[35],"by":[36],"toxicity":[37],"resistance":[39],"issues,":[40],"underscoring":[41],"need":[43],"novel":[45],"therapeutics.":[46],"Traditional":[47],"Chinese":[48],"medicine":[49],"(TCM)":[50],"offers":[51],"a":[52,83,199],"structurally":[53],"diverse":[54],"array":[55],"compounds":[57,88,144],"drug":[59,71,276],"development":[60],"potential,":[61],"while":[62,214],"in":[63,121,241,253],"silico":[64],"approaches":[65],"enable":[66],"rapid,":[67],"cost-efficient":[68],"identification":[69],"candidates.":[72],"This":[73],"study":[74],"aimed":[75],"identify":[77],"optimize":[79],"antiviral":[80],"hits":[81,146],"from":[82,89],"curated":[84,142],"set":[85],"6,699":[87],"TCMSP":[91],"database":[92],"targeting":[93],"E4":[95],"interacting":[96],"region":[97],"F8":[100,160,174,206],"DNA":[101],"polymerase":[102],"active":[105],"site":[106],"MTase":[109],"domain":[110],"D1":[113,122,193,215],"mRNA-capping":[114],"enzyme.":[115],"Homology":[116],"modeling":[117],"missing":[119],"residues":[120,270],"yielded":[123,145],"an":[124,180],"RMSD":[125],"<tex":[127,153,164,185],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[128,154,165,186],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$0.393":[129],"\\AA$</tex>":[130],"between":[131],"AlphaFold":[133],"model":[134],"PDB:":[136],"4":[137],"CKB.":[138],"Docking":[139],"TCM":[143],"binding":[148,182,200,254],"affinities":[149],"8.395":[151],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$-8.002":[155],"\\text{kcal}":[156,167,188],"/":[157,168,189],"\\text{mol}$</tex>":[158,169],"\u221212.26":[162],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$-10.91":[166],"D1.":[171],"final":[173,192],"redesigned":[175,194,207,216,227,247],"ligand,":[176,195],"R3A:":[177],"PKGVYFZOMHMCCP-GXONGKDUSA-N,":[178],"had":[179,198,229],"improved":[181,230],"affinity":[183,201,255],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$-9.10":[187],"\\text{mol}$</tex>.":[190],"R2B:":[196],"UAINZROWGPJQLF-YZUYAPEUSA-N,":[197],"\u221211.81":[203],"kcal/mol.":[204],"ligands":[208,217,228,248],"blocked":[209],"key":[210],"protein":[211],"interaction":[212],"sites,":[213],"interacted":[218],"catalytic":[220],"residues,":[221],"indicating":[222],"potential":[223,273],"functional":[224],"inhibition.":[225],"All":[226],"pharmacokinetic":[231,264],"properties,":[232],"such":[233],"as":[234,274],"distribution":[235],"excretion,":[237],"but":[238,256],"showed":[239],"limitations":[240],"absorption":[242],"toxicology.":[244],"Overall,":[245],"outperformed":[249],"current":[250],"mpox":[251],"require":[257],"further":[258],"optimization":[259],"improve":[261],"physicochemical":[262],"properties.":[265],"Their":[266],"interactions":[267],"target":[269],"highlight":[271],"their":[272],"MPXV":[275],"leads.":[277]},"counts_by_year":[],"updated_date":"2026-02-01T03:34:12.195049","created_date":"2026-01-30T00:00:00"}