{"id":"https://openalex.org/W7172000252","doi":"https://doi.org/10.1080/08927022.2026.2711335","title":"Molecular dynamics characterization of marine alkaloid binding to the SARS-CoV-2 KP.2 receptor-binding domain","display_name":"Molecular dynamics characterization of marine alkaloid binding to the SARS-CoV-2 KP.2 receptor-binding domain","publication_year":2026,"publication_date":"2026-07-31","ids":{"openalex":"https://openalex.org/W7172000252","doi":"https://doi.org/10.1080/08927022.2026.2711335"},"language":"en","primary_location":{"id":"doi:10.1080/08927022.2026.2711335","doi":"https://doi.org/10.1080/08927022.2026.2711335","is_oa":false,"landing_page_url":"https://doi.org/10.1080/08927022.2026.2711335","pdf_url":null,"source":{"id":"https://openalex.org/S45504773","display_name":"Molecular Simulation","issn_l":"0892-7022","issn":["0892-7022","1026-7638","1029-0435"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Molecular Simulation","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5144119741","display_name":"Chuang Ma","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4405281053","display_name":"Changchun Medical College","ror":"https://ror.org/03t28bg72","country_code":"CN","type":"education","lineage":["https://openalex.org/I4405281053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuang Ma","raw_affiliation_strings":["Changchun Medical College","Jilin University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Changchun Medical College","institution_ids":["https://openalex.org/I4405281053"]},{"raw_affiliation_string":"Jilin University","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5144143075","display_name":"Mengmeng Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengmeng Wang","raw_affiliation_strings":["Jilin University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jilin University","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090928843","display_name":"Xueli Zang","orcid":"https://orcid.org/0009-0002-3532-9570","observed_orcids":["https://orcid.org/0009-0002-3532-9570"]},"institutions":[{"id":"https://openalex.org/I4405281053","display_name":"Changchun Medical College","ror":"https://ror.org/03t28bg72","country_code":"CN","type":"education","lineage":["https://openalex.org/I4405281053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueli Zang","raw_affiliation_strings":["Changchun Medical College"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Changchun Medical College","institution_ids":["https://openalex.org/I4405281053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072206502","display_name":"Sennan Qiao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sennan Qiao","raw_affiliation_strings":["Jilin University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jilin University","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102957254","display_name":"Hansi Zhang","orcid":"https://orcid.org/0000-0002-8341-5468","observed_orcids":["https://orcid.org/0000-0002-8341-5468"]},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hansi Zhang","raw_affiliation_strings":["Jilin University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jilin University","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000094065","display_name":"Zhenyan Jiang","orcid":"https://orcid.org/0000-0003-4594-7065","observed_orcids":["https://orcid.org/0000-0003-4594-7065"]},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhenyan Jiang","raw_affiliation_strings":["Jilin University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jilin University","institution_ids":["https://openalex.org/I194450716"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5000094065","https://openalex.org/A5102957254"],"corresponding_institution_ids":["https://openalex.org/I194450716"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"52","issue":"14","first_page":"1256","last_page":"1265"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6880000233650208,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6880000233650208,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.23929999768733978,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.024900000542402267,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/receptor-binding-motif","display_name":"receptor-binding motif","score":0.8769999742507935},{"id":"https://openalex.org/keywords/ligand-binding","display_name":"ligand binding","score":0.8090000152587891},{"id":"https://openalex.org/keywords/antiviral-drug-candidates","display_name":"antiviral drug candidates","score":0.7269999980926514},{"id":"https://openalex.org/keywords/ligand-binding-free-energy","display_name":"ligand binding free energy","score":0.5830000042915344},{"id":"https://openalex.org/keywords/protein-ligand-binding","display_name":"protein-ligand binding","score":0.5740000009536743}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7031999826431274},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6880999803543091},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5927000045776367},{"id":"https://openalex.org/C2780841128","wikidata":"https://www.wikidata.org/wiki/Q5073781","display_name":"Characterization (materials science)","level":2,"score":0.5827999711036682},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.367000013589859},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.36010000109672546},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.33880001306533813},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.32089999318122864},{"id":"https://openalex.org/C2777667214","wikidata":"https://www.wikidata.org/wiki/Q70702","display_name":"Alkaloid","level":2,"score":0.31769999861717224},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3107999861240387},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2802000045776367},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.2761000096797943},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.2727999985218048},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.26829999685287476},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.2660999894142151},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.26600000262260437},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.26429998874664307},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2621999979019165}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1080/08927022.2026.2711335","doi":"https://doi.org/10.1080/08927022.2026.2711335","is_oa":false,"landing_page_url":"https://doi.org/10.1080/08927022.2026.2711335","pdf_url":null,"source":{"id":"https://openalex.org/S45504773","display_name":"Molecular Simulation","issn_l":"0892-7022","issn":["0892-7022","1026-7638","1029-0435"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","jufo-1","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Molecular Simulation","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W2015688756","https://openalex.org/W2035687084","https://openalex.org/W2045683699","https://openalex.org/W2057477511","https://openalex.org/W2067174909","https://openalex.org/W2130479394","https://openalex.org/W2131288855","https://openalex.org/W2134967712","https://openalex.org/W2161605421","https://openalex.org/W2169678694","https://openalex.org/W2171268876","https://openalex.org/W2566677301","https://openalex.org/W2763159985","https://openalex.org/W3035076119","https://openalex.org/W3089574919","https://openalex.org/W3121906900","https://openalex.org/W3138447431","https://openalex.org/W3168436232","https://openalex.org/W3199985483","https://openalex.org/W3216551753","https://openalex.org/W4292248467","https://openalex.org/W4295753526","https://openalex.org/W4390038031","https://openalex.org/W4391970775","https://openalex.org/W4398147734","https://openalex.org/W4400066840","https://openalex.org/W4400725699","https://openalex.org/W4400978204","https://openalex.org/W4401154289","https://openalex.org/W4402261641","https://openalex.org/W4410958408","https://openalex.org/W4413021811","https://openalex.org/W4417227798","https://openalex.org/W7124832206"],"related_works":["https://openalex.org/W7223096323","https://openalex.org/W3165205080","https://openalex.org/W4312114516","https://openalex.org/W4312818705","https://openalex.org/W4403414543","https://openalex.org/W3177806095","https://openalex.org/W3205555860","https://openalex.org/W4205925122","https://openalex.org/W3213223478","https://openalex.org/W3047616897"],"abstract_inverted_index":{"The":[0,51],"KP.2":[1,72],"receptor-binding":[2,11],"domain":[3],"(RBD)":[4],"contains":[5],"the":[6,10,39,65,70,93,101,106,130],"F456L":[7],"substitution":[8],"within":[9],"motif":[12],"(RBM),":[13],"where":[14],"ligand":[15,110],"binding":[16,192],"was":[17],"evaluated":[18,43],"in":[19,62,80],"this":[20],"study.":[21],"Three":[22],"marine":[23],"fungal":[24],"alkaloids,":[25],"Versiquinazoline":[26],"A":[27,30],"(VQA),":[28],"Spirobrocazine":[29],"(SBA),":[31],"and":[32,42,54,64,85,114,142,150,154,182,194],"Notoamide":[33],"O":[34],"(NTO),":[35],"were":[36,57,75],"selected":[37],"from":[38],"CMNPD":[40],"library":[41],"by":[44],"triplicate":[45],"all-atom":[46],"molecular":[47],"dynamics":[48],"(MD)":[49],"simulations.":[50],"KP.2-L456":[52],"Apo":[53],"ligand-bound":[55],"systems":[56],"simulated":[58,76],"for":[59,77],"400":[60],"ns":[61,79],"triplicate,":[63],"corresponding":[66],"F456":[67],"controls":[68],"on":[69,179],"same":[71],"sequence":[73],"background":[74],"300":[78],"triplicate.":[81],"Protein":[82],"backbone":[83],"RMSD":[84],"radius":[86],"of":[87,92],"gyration":[88],"analyses":[89],"showed":[90,105,138,158],"preservation":[91],"global":[94],"RBD":[95],"fold":[96],"across":[97],"all":[98],"systems.":[99],"In":[100],"L456":[102],"background,":[103],"VQA":[104,137,160,173],"lowest":[107],"late-stage":[108],"ensemble-average":[109],"RMSD,":[111],"whereas":[112],"SBA":[113],"NTO":[115,128],"exhibited":[116],"greater":[117],"replicate-dependent":[118],"pose":[119,180],"variability.":[120],"MM/PBSA":[121],"calculations":[122],"yielded":[123],"overlapping":[124],"replicate-level":[125],"energy":[126],"distributions;":[127],"had":[129],"most":[131],"negative":[132],"mean":[133],"total-energy":[134],"estimate,":[135],"while":[136],"more":[139],"persistent":[140],"poses":[141],"concentrated":[143],"distance":[144],"distributions":[145],"involving":[146],"residue":[147],"456,":[148],"TYR473,":[149],"TYR488.":[151],"Common-basis":[152],"PCA":[153],"free-energy":[155],"landscape":[156],"analysis":[157],"that":[159],"increased":[161],"projected":[162],"RBM":[163],"conformational":[164],"dispersion":[165],"relative":[166],"to":[167,190],"Apo.":[168],"Overall,":[169],"these":[170],"results":[171],"prioritise":[172],"as":[174],"a":[175],"computational":[176],"candidate":[177],"based":[178],"persistence":[181],"residue-contact":[183],"distributions,":[184],"although":[185],"experimental":[186],"validation":[187],"is":[188],"required":[189],"determine":[191],"affinity":[193],"antiviral":[195],"activity.":[196]},"counts_by_year":[],"updated_date":"2026-09-21T07:43:02.447757","created_date":"2026-08-01T00:00:00"}
