{"id":"https://openalex.org/W4405997820","doi":"https://doi.org/10.1021/acs.jcim.4c01875","title":"How Do Microbial Metabolites Interact with Their Protein Targets?","display_name":"How Do Microbial Metabolites Interact with Their Protein Targets?","publication_year":2025,"publication_date":"2025-01-02","ids":{"openalex":"https://openalex.org/W4405997820","doi":"https://doi.org/10.1021/acs.jcim.4c01875","pmid":"https://pubmed.ncbi.nlm.nih.gov/39743764"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01875","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01875","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/A5114279655","display_name":"Mario Astigarraga","orcid":null},"institutions":[{"id":"https://openalex.org/I105140100","display_name":"Madrid Institute for Advanced Studies","ror":"https://ror.org/027pk6j83","country_code":"ES","type":"education","lineage":["https://openalex.org/I105140100"]},{"id":"https://openalex.org/I4210143378","display_name":"IMDEA Food","ror":"https://ror.org/04g4ezh90","country_code":"ES","type":"facility","lineage":["https://openalex.org/I105140100","https://openalex.org/I4210143378"]},{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Mario Astigarraga","raw_affiliation_strings":["Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain"],"affiliations":[{"raw_affiliation_string":"Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain","institution_ids":["https://openalex.org/I4210143378","https://openalex.org/I105140100","https://openalex.org/I63634437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031336297","display_name":"Andr\u00e9s S\u00e1nchez-Ruiz","orcid":"https://orcid.org/0000-0001-7393-542X"},"institutions":[{"id":"https://openalex.org/I105140100","display_name":"Madrid Institute for Advanced Studies","ror":"https://ror.org/027pk6j83","country_code":"ES","type":"education","lineage":["https://openalex.org/I105140100"]},{"id":"https://openalex.org/I4210143378","display_name":"IMDEA Food","ror":"https://ror.org/04g4ezh90","country_code":"ES","type":"facility","lineage":["https://openalex.org/I105140100","https://openalex.org/I4210143378"]},{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Andr\u00e9s S\u00e1nchez-Ruiz","raw_affiliation_strings":["Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain"],"affiliations":[{"raw_affiliation_string":"Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain","institution_ids":["https://openalex.org/I4210143378","https://openalex.org/I105140100","https://openalex.org/I63634437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114279656","display_name":"Aminata Diop-Aw","orcid":null},"institutions":[{"id":"https://openalex.org/I105140100","display_name":"Madrid Institute for Advanced Studies","ror":"https://ror.org/027pk6j83","country_code":"ES","type":"education","lineage":["https://openalex.org/I105140100"]},{"id":"https://openalex.org/I4210143378","display_name":"IMDEA Food","ror":"https://ror.org/04g4ezh90","country_code":"ES","type":"facility","lineage":["https://openalex.org/I105140100","https://openalex.org/I4210143378"]},{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Aminata Diop-Aw","raw_affiliation_strings":["Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain"],"affiliations":[{"raw_affiliation_string":"Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain","institution_ids":["https://openalex.org/I4210143378","https://openalex.org/I105140100","https://openalex.org/I63634437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109785832","display_name":"R. Quintero","orcid":null},"institutions":[{"id":"https://openalex.org/I105140100","display_name":"Madrid Institute for Advanced Studies","ror":"https://ror.org/027pk6j83","country_code":"ES","type":"education","lineage":["https://openalex.org/I105140100"]},{"id":"https://openalex.org/I4210143378","display_name":"IMDEA Food","ror":"https://ror.org/04g4ezh90","country_code":"ES","type":"facility","lineage":["https://openalex.org/I105140100","https://openalex.org/I4210143378"]},{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Raquel Quintero","raw_affiliation_strings":["Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain"],"affiliations":[{"raw_affiliation_string":"Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain","institution_ids":["https://openalex.org/I4210143378","https://openalex.org/I105140100","https://openalex.org/I63634437"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019277106","display_name":"Gonzalo Colmenarejo","orcid":"https://orcid.org/0000-0002-8249-4547"},"institutions":[{"id":"https://openalex.org/I105140100","display_name":"Madrid Institute for Advanced Studies","ror":"https://ror.org/027pk6j83","country_code":"ES","type":"education","lineage":["https://openalex.org/I105140100"]},{"id":"https://openalex.org/I4210143378","display_name":"IMDEA Food","ror":"https://ror.org/04g4ezh90","country_code":"ES","type":"facility","lineage":["https://openalex.org/I105140100","https://openalex.org/I4210143378"]},{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gonzalo Colmenarejo","raw_affiliation_strings":["Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain"],"affiliations":[{"raw_affiliation_string":"Biostatistics and Bioinformatics Unit, IMDEA Food CEI UAM+CSIC, Madrid E28049, Spain","institution_ids":["https://openalex.org/I4210143378","https://openalex.org/I105140100","https://openalex.org/I63634437"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5019277106"],"corresponding_institution_ids":["https://openalex.org/I105140100","https://openalex.org/I4210143378","https://openalex.org/I63634437"],"apc_list":null,"apc_paid":null,"fwci":4.1945,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.9284584,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"65","issue":"1","first_page":"201","last_page":"213"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9986000061035156,"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"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9743000268936157,"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/metabolite","display_name":"Metabolite","score":0.7364107966423035},{"id":"https://openalex.org/keywords/rational-design","display_name":"Rational design","score":0.6440486907958984},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6145378947257996},{"id":"https://openalex.org/keywords/drug-design","display_name":"Drug design","score":0.48961740732192993},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.48799437284469604},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4230790138244629},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.4108172357082367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3835037648677826},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3216100335121155},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12335559725761414}],"concepts":[{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.7364107966423035},{"id":"https://openalex.org/C53105671","wikidata":"https://www.wikidata.org/wiki/Q14777816","display_name":"Rational design","level":2,"score":0.6440486907958984},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6145378947257996},{"id":"https://openalex.org/C192071366","wikidata":"https://www.wikidata.org/wiki/Q2991682","display_name":"Drug design","level":2,"score":0.48961740732192993},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.48799437284469604},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4230790138244629},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4108172357082367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3835037648677826},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3216100335121155},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12335559725761414}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c01875","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01875","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:39743764","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39743764","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":[{"id":"https://metadata.un.org/sdg/2","score":0.49000000953674316,"display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G1957123162","display_name":null,"funder_award_id":"PIPF-2022/SAL-GL-26278","funder_id":"https://openalex.org/F4320313831","funder_display_name":"Comunidad de Madrid"},{"id":"https://openalex.org/G5158502759","display_name":null,"funder_award_id":"PEJ-2020-AI/BIO-17904","funder_id":"https://openalex.org/F4320313831","funder_display_name":"Comunidad de Madrid"},{"id":"https://openalex.org/G8970324513","display_name":null,"funder_award_id":"PID2021-127318OB-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320313831","display_name":"Comunidad de Madrid","ror":null},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W610870486","https://openalex.org/W1965443741","https://openalex.org/W1978709058","https://openalex.org/W2001900040","https://openalex.org/W2105649494","https://openalex.org/W2167115266","https://openalex.org/W2168172687","https://openalex.org/W2183050958","https://openalex.org/W2280564115","https://openalex.org/W2296686360","https://openalex.org/W2548357532","https://openalex.org/W2622206241","https://openalex.org/W2731629763","https://openalex.org/W2790856964","https://openalex.org/W2797413896","https://openalex.org/W2933530798","https://openalex.org/W2939645883","https://openalex.org/W2949223833","https://openalex.org/W2952831634","https://openalex.org/W2960868815","https://openalex.org/W2964536928","https://openalex.org/W2989934249","https://openalex.org/W2990249310","https://openalex.org/W2994651836","https://openalex.org/W3000719530","https://openalex.org/W3006796998","https://openalex.org/W3009682272","https://openalex.org/W3012279685","https://openalex.org/W3014111203","https://openalex.org/W3019201575","https://openalex.org/W3036012425","https://openalex.org/W3042595256","https://openalex.org/W3049052172","https://openalex.org/W3088203083","https://openalex.org/W3094525251","https://openalex.org/W3098935468","https://openalex.org/W3107083588","https://openalex.org/W3113757303","https://openalex.org/W3129925389","https://openalex.org/W3138215020","https://openalex.org/W3153952626","https://openalex.org/W3180679829","https://openalex.org/W4205599589","https://openalex.org/W4206447491","https://openalex.org/W4206517007","https://openalex.org/W4210919704","https://openalex.org/W4212820549","https://openalex.org/W4220938887","https://openalex.org/W4223632224","https://openalex.org/W4248107770","https://openalex.org/W4290643769","https://openalex.org/W4299878816","https://openalex.org/W4309908854","https://openalex.org/W4321377195","https://openalex.org/W4323347906","https://openalex.org/W4362471972","https://openalex.org/W4380551368","https://openalex.org/W4381250551","https://openalex.org/W4385431647","https://openalex.org/W4387609745","https://openalex.org/W4388615774","https://openalex.org/W4401728707","https://openalex.org/W4405292966"],"related_works":["https://openalex.org/W2375593122","https://openalex.org/W2142728655","https://openalex.org/W36558656","https://openalex.org/W1974559214","https://openalex.org/W2040535930","https://openalex.org/W2090043682","https://openalex.org/W3211004259","https://openalex.org/W4386165652","https://openalex.org/W2021528276","https://openalex.org/W2527383792"],"abstract_inverted_index":{"The":[0,112],"design":[1,50,151],"of":[2,24,51,71,82,109,119,138,152],"drugs":[3],"and":[4,32,74,101],"nutraceutics":[5],"that":[6,18,26],"mimic":[7],"microbial":[8,33,37],"metabolites":[9,38],"is":[10,44,114],"an":[11],"emerging":[12],"drug":[13],"modality":[14],"in":[15,79,93,136],"medicinal":[16],"chemistry":[17],"attempts":[19],"to":[20,46,130],"modulate":[21],"the":[22,59,68,75,89,94,117,132,149],"myriad":[23],"interactions":[25,76,87],"these":[27,72,110],"molecules":[28,54,73,156],"establish":[29],"with":[30,40],"host":[31],"proteins.":[34],"Understanding":[35],"how":[36],"interact":[39],"their":[41,98,102],"target":[42],"proteins":[43],"key":[45],"perform":[47],"a":[48,80],"rational":[49,150],"metabolite":[52,154],"mimetic":[53,155],"for":[55,106,116,157],"therapeutic":[56,158],"usage.":[57],"In":[58],"present":[60],"work,":[61],"we":[62,127],"address":[63],"this":[64],"question":[65],"by":[66],"analyzing":[67],"functional":[69,95,140],"groups":[70],"they":[77],"display":[78],"set":[81],"more":[83],"than":[84],"71K":[85],"protein-metabolite":[86],"from":[88],"PDB.":[90],"Significant":[91],"differences":[92],"group":[96,141],"distributions,":[97],"chemical":[99],"features,":[100],"co-occurrences":[103],"are":[104,128],"observed":[105,133,139],"distinct":[107],"subsets":[108],"molecules.":[111],"same":[113],"true":[115],"distributions":[118],"interaction":[120,134],"types.":[121],"By":[122],"correlating":[123],"both":[124],"data":[125],"sets,":[126],"able":[129],"explain":[131],"patterns":[135],"terms":[137],"patterns.":[142],"These":[143],"results":[144],"will":[145],"shed":[146],"light":[147],"on":[148],"novel":[153],"purposes.":[159]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
