{"id":"https://openalex.org/W4408787988","doi":"https://doi.org/10.1021/acs.jcim.5c00126","title":"Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations","display_name":"Mechanistic Study of Protein Interaction with Natto Inhibitory Peptides Targeting Xanthine Oxidase: Insights from Machine Learning and Molecular Dynamics Simulations","publication_year":2025,"publication_date":"2025-03-24","ids":{"openalex":"https://openalex.org/W4408787988","doi":"https://doi.org/10.1021/acs.jcim.5c00126","pmid":"https://pubmed.ncbi.nlm.nih.gov/40125929"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00126","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00126","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100721952","display_name":"Minghao Liu","orcid":"https://orcid.org/0000-0003-1235-5127"},"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":"Minghao Liu","raw_affiliation_strings":["Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115597247","display_name":"Kaiyu Wang","orcid":"https://orcid.org/0009-0007-8805-1839"},"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":"Kaiyu Wang","raw_affiliation_strings":["Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100456227","display_name":"Yan Zhang","orcid":"https://orcid.org/0000-0002-2947-1629"},"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":"Yan Zhang","raw_affiliation_strings":["Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045617155","display_name":"Xue Zhou","orcid":"https://orcid.org/0000-0002-3675-9479"},"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":"Xue Zhou","raw_affiliation_strings":["Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072301534","display_name":"Wannan Li","orcid":"https://orcid.org/0000-0001-6983-4343"},"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":"Wannan Li","raw_affiliation_strings":["Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001913247","display_name":"Weiwei Han","orcid":"https://orcid.org/0000-0002-1931-9316"},"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":"Weiwei Han","raw_affiliation_strings":["Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001913247","https://openalex.org/A5072301534"],"corresponding_institution_ids":["https://openalex.org/I194450716"],"apc_list":null,"apc_paid":null,"fwci":5.8297,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.95861337,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"65","issue":"7","first_page":"3682","last_page":"3696"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11139","display_name":"Gout, Hyperuricemia, Uric Acid","score":0.9900000095367432,"subfield":{"id":"https://openalex.org/subfields/2727","display_name":"Nephrology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11139","display_name":"Gout, Hyperuricemia, Uric Acid","score":0.9900000095367432,"subfield":{"id":"https://openalex.org/subfields/2727","display_name":"Nephrology"},"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/T11150","display_name":"Endoplasmic Reticulum Stress and Disease","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T11482","display_name":"RNA modifications and cancer","score":0.9879000186920166,"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/xanthine-oxidase","display_name":"Xanthine oxidase","score":0.6617531776428223},{"id":"https://openalex.org/keywords/inhibitory-postsynaptic-potential","display_name":"Inhibitory postsynaptic potential","score":0.5367693901062012},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5137289762496948},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.47973743081092834},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4303886294364929},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.36971479654312134},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23786437511444092},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.21725738048553467},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.10436192154884338},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.08419543504714966}],"concepts":[{"id":"https://openalex.org/C2778102346","wikidata":"https://www.wikidata.org/wiki/Q412509","display_name":"Xanthine oxidase","level":3,"score":0.6617531776428223},{"id":"https://openalex.org/C17077164","wikidata":"https://www.wikidata.org/wiki/Q1185869","display_name":"Inhibitory postsynaptic potential","level":2,"score":0.5367693901062012},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5137289762496948},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.47973743081092834},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4303886294364929},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.36971479654312134},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23786437511444092},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.21725738048553467},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.10436192154884338},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.08419543504714966}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001412","descriptor_name":"Bacillus subtilis","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014969","descriptor_name":"Xanthine Oxidase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D014969","descriptor_name":"Xanthine Oxidase","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D014969","descriptor_name":"Xanthine Oxidase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014969","descriptor_name":"Xanthine Oxidase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014969","descriptor_name":"Xanthine Oxidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014969","descriptor_name":"Xanthine Oxidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00126","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00126","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40125929","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40125929","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1124642266","https://openalex.org/W1969046853","https://openalex.org/W1979308174","https://openalex.org/W2003530350","https://openalex.org/W2067174909","https://openalex.org/W2095719702","https://openalex.org/W2137825366","https://openalex.org/W2149801992","https://openalex.org/W2160451368","https://openalex.org/W2332712348","https://openalex.org/W2417567863","https://openalex.org/W2418524920","https://openalex.org/W2606410529","https://openalex.org/W2621699830","https://openalex.org/W2783351753","https://openalex.org/W2892525055","https://openalex.org/W2899110998","https://openalex.org/W2901189851","https://openalex.org/W2903009925","https://openalex.org/W2921808963","https://openalex.org/W2947027538","https://openalex.org/W2947126983","https://openalex.org/W2948869054","https://openalex.org/W2989052455","https://openalex.org/W2996960886","https://openalex.org/W3007029501","https://openalex.org/W3049076550","https://openalex.org/W3080330343","https://openalex.org/W3084070158","https://openalex.org/W3127135885","https://openalex.org/W3128376482","https://openalex.org/W3135098857","https://openalex.org/W3135534391","https://openalex.org/W3153418506","https://openalex.org/W3164213165","https://openalex.org/W3164821738","https://openalex.org/W3198775852","https://openalex.org/W3215229494","https://openalex.org/W3216794067","https://openalex.org/W4200082066","https://openalex.org/W4289274885","https://openalex.org/W4294204348","https://openalex.org/W4295419414","https://openalex.org/W4302773722","https://openalex.org/W4309094308","https://openalex.org/W4310712976","https://openalex.org/W4315784590","https://openalex.org/W4365134756","https://openalex.org/W4366236822","https://openalex.org/W4379932151","https://openalex.org/W4382538610","https://openalex.org/W4386306002","https://openalex.org/W4387440676","https://openalex.org/W4389434277","https://openalex.org/W4391943071","https://openalex.org/W4392234099","https://openalex.org/W4392663253","https://openalex.org/W4396721167","https://openalex.org/W4396815409","https://openalex.org/W4401572054","https://openalex.org/W4401753793"],"related_works":["https://openalex.org/W2126425357","https://openalex.org/W2465839450","https://openalex.org/W2412975142","https://openalex.org/W2974163011","https://openalex.org/W2036001456","https://openalex.org/W40952352","https://openalex.org/W2037381935","https://openalex.org/W1781578531","https://openalex.org/W2791883561","https://openalex.org/W2050756181"],"abstract_inverted_index":{"Bioactive":[0],"peptides":[1,98,125],"from":[2,52],"food":[3],"sources":[4],"offer":[5],"a":[6,34,106],"safe":[7,127],"and":[8,24,48,57,68,80,128],"biocompatible":[9],"approach":[10,38],"to":[11,28],"enzyme":[12,101],"inhibition,":[13],"with":[14,63,103],"potential":[15,137],"applications":[16],"in":[17],"managing":[18],"metabolic":[19,139],"disorders":[20],"such":[21],"as":[22,59,126],"hyperuricemia":[23],"gout,":[25],"conditions":[26],"linked":[27],"excessive":[29],"xanthine":[30,60,132],"oxidase":[31,61],"activity.":[32],"Using":[33],"machine":[35],"learning-based":[36],"screening":[37],"inspired":[39],"by":[40],"the":[41,53],"bioactivity":[42],"of":[43,66,131],"natto,":[44],"two":[45],"peptides,":[46],"ECFK":[47,104],"FECK,":[49],"were":[50],"identified":[51],"<i>Bacillus":[54],"subtilis</i>":[55],"proteome":[56],"validated":[58],"inhibitors":[62,130],"IC<sub>50</sub>":[64],"values":[65],"37.36":[67],"71.57":[69],"mM,":[70],"respectively.":[71],"Further":[72],"experiments":[73],"confirmed":[74],"their":[75,85,90],"safety":[76],"through":[77],"cytotoxicity":[78],"assays,":[79],"electronic":[81],"tongue":[82],"analysis":[83],"demonstrated":[84],"mild":[86],"sensory":[87],"properties,":[88],"supporting":[89],"edibility.":[91],"Molecular":[92],"dynamics":[93],"simulations":[94],"revealed":[95],"that":[96],"these":[97],"stabilize":[99],"critical":[100],"regions,":[102],"showing":[105],"higher":[107],"dissociation":[108],"energy":[109],"barrier":[110],"(52.08":[111],"kcal/mol)":[112],"than":[113],"FECK":[114],"(46.39":[115],"kcal/mol),":[116],"indicating":[117],"strong,":[118],"stable":[119],"interactions.":[120],"This":[121],"study":[122],"highlights":[123],"food-derived":[124],"natural":[129],"oxidase,":[133],"offering":[134],"promising":[135],"therapeutic":[136],"for":[138],"disorder":[140],"management.":[141]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2025-12-19T19:40:27.379048","created_date":"2025-10-10T00:00:00"}