{"id":"https://openalex.org/W4408893259","doi":"https://doi.org/10.1021/acs.jcim.4c02420","title":"Stacking Interactions of Druglike Heterocycles with Nucleobases","display_name":"Stacking Interactions of Druglike Heterocycles with Nucleobases","publication_year":2025,"publication_date":"2025-03-27","ids":{"openalex":"https://openalex.org/W4408893259","doi":"https://doi.org/10.1021/acs.jcim.4c02420","pmid":"https://pubmed.ncbi.nlm.nih.gov/40146533"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c02420","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02420","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c02420?ref=article_openPDF","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c02420?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114991570","display_name":"Audrey V. Conner","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Audrey V. Conner","raw_affiliation_strings":["Department of Chemistry","University of Georgia","Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of Georgia","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006987023","display_name":"Lauren M. Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lauren M. Kim","raw_affiliation_strings":["Department of Chemistry","University of Georgia","Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of Georgia","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023930929","display_name":"Phoebe Fagan","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick A. Fagan","raw_affiliation_strings":["Department of Chemistry","University of Georgia","Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of Georgia","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085714025","display_name":"Drew P. Harding","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Drew P. Harding","raw_affiliation_strings":["Department of Chemistry","University of Georgia","Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of Georgia","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007309417","display_name":"Steven E. Wheeler","orcid":"https://orcid.org/0000-0001-7824-6906"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven E. Wheeler","raw_affiliation_strings":["Department of Chemistry","University of Georgia","Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of Georgia","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5007309417"],"corresponding_institution_ids":["https://openalex.org/I165733156"],"apc_list":null,"apc_paid":null,"fwci":3.8127,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.92879417,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"65","issue":"7","first_page":"3502","last_page":"3516"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9977999925613403,"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/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/stacking","display_name":"Stacking","score":0.9500715136528015},{"id":"https://openalex.org/keywords/nucleobase","display_name":"Nucleobase","score":0.9103202223777771},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.456184059381485},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4377390146255493},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.43367999792099},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.42001867294311523},{"id":"https://openalex.org/keywords/basis-set","display_name":"Basis set","score":0.41517531871795654},{"id":"https://openalex.org/keywords/density-functional-theory","display_name":"Density functional theory","score":0.40701091289520264},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.07662653923034668}],"concepts":[{"id":"https://openalex.org/C33347731","wikidata":"https://www.wikidata.org/wiki/Q285210","display_name":"Stacking","level":2,"score":0.9500715136528015},{"id":"https://openalex.org/C61234307","wikidata":"https://www.wikidata.org/wiki/Q422960","display_name":"Nucleobase","level":3,"score":0.9103202223777771},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.456184059381485},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4377390146255493},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.43367999792099},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.42001867294311523},{"id":"https://openalex.org/C65956243","wikidata":"https://www.wikidata.org/wiki/Q2664086","display_name":"Basis set","level":3,"score":0.41517531871795654},{"id":"https://openalex.org/C152365726","wikidata":"https://www.wikidata.org/wiki/Q1048589","display_name":"Density functional theory","level":2,"score":0.40701091289520264},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.07662653923034668},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006571","descriptor_name":"Heterocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006571","descriptor_name":"Heterocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006571","descriptor_name":"Heterocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006571","descriptor_name":"Heterocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c02420","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02420","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c02420?ref=article_openPDF","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40146533","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40146533","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12004538","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12004538","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c02420","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02420","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.4c02420?ref=article_openPDF","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408893259.pdf"},"referenced_works_count":91,"referenced_works":["https://openalex.org/W1554563779","https://openalex.org/W1931081986","https://openalex.org/W1983693962","https://openalex.org/W1988091937","https://openalex.org/W1988920524","https://openalex.org/W1989474096","https://openalex.org/W1990566970","https://openalex.org/W1992921903","https://openalex.org/W2005212066","https://openalex.org/W2009846017","https://openalex.org/W2018674598","https://openalex.org/W2037535298","https://openalex.org/W2043592573","https://openalex.org/W2048631643","https://openalex.org/W2050890227","https://openalex.org/W2063021257","https://openalex.org/W2065294654","https://openalex.org/W2067102689","https://openalex.org/W2069006374","https://openalex.org/W2069385410","https://openalex.org/W2078511427","https://openalex.org/W2084414756","https://openalex.org/W2086632126","https://openalex.org/W2087864238","https://openalex.org/W2090082574","https://openalex.org/W2104681470","https://openalex.org/W2112850441","https://openalex.org/W2117569373","https://openalex.org/W2131781277","https://openalex.org/W2147993766","https://openalex.org/W2151699909","https://openalex.org/W2165049467","https://openalex.org/W2170402416","https://openalex.org/W2172235361","https://openalex.org/W2306228802","https://openalex.org/W2316765238","https://openalex.org/W2330936115","https://openalex.org/W2338555109","https://openalex.org/W2397070557","https://openalex.org/W2407040666","https://openalex.org/W2431436481","https://openalex.org/W2440663665","https://openalex.org/W2500362036","https://openalex.org/W2508330908","https://openalex.org/W2563239084","https://openalex.org/W2739439285","https://openalex.org/W2755181646","https://openalex.org/W2792638343","https://openalex.org/W2793821032","https://openalex.org/W2820941669","https://openalex.org/W2886156228","https://openalex.org/W2902936691","https://openalex.org/W2931878065","https://openalex.org/W2932634309","https://openalex.org/W2942906220","https://openalex.org/W2943749213","https://openalex.org/W2945542316","https://openalex.org/W2953135775","https://openalex.org/W2956222435","https://openalex.org/W2978444138","https://openalex.org/W3009504459","https://openalex.org/W3013162259","https://openalex.org/W3022734398","https://openalex.org/W3034073642","https://openalex.org/W3084513853","https://openalex.org/W3086801715","https://openalex.org/W3088792251","https://openalex.org/W3112748348","https://openalex.org/W3116905955","https://openalex.org/W3146554579","https://openalex.org/W3163614504","https://openalex.org/W3164642402","https://openalex.org/W3194990567","https://openalex.org/W3198687577","https://openalex.org/W3212083998","https://openalex.org/W4229058666","https://openalex.org/W4247685997","https://openalex.org/W4255422539","https://openalex.org/W4280571115","https://openalex.org/W4280599192","https://openalex.org/W4281292940","https://openalex.org/W4290672950","https://openalex.org/W4308052782","https://openalex.org/W4308172916","https://openalex.org/W4322632297","https://openalex.org/W4376226284","https://openalex.org/W4376604306","https://openalex.org/W4377982067","https://openalex.org/W4383198444","https://openalex.org/W4385459236","https://openalex.org/W4396546066"],"related_works":["https://openalex.org/W2035329725","https://openalex.org/W1981761942","https://openalex.org/W2009254401","https://openalex.org/W2188489321","https://openalex.org/W2016562941","https://openalex.org/W2587744446","https://openalex.org/W2321366725","https://openalex.org/W4322626745","https://openalex.org/W4205201584","https://openalex.org/W2016595539"],"abstract_inverted_index":{"Stacking":[0],"interactions":[1,18,40,64,100,124,169,229,249],"contribute":[2],"significantly":[3],"to":[4,163,205],"the":[5,14,24,49,60,96,119,138,165,178,227,240],"interaction":[6,199,218],"of":[7,16,26,38,44,62,83,87,98,118,122,170,173,187,213,239],"small":[8],"molecules":[9],"with":[10,65,177,250],"RNA,":[11],"and":[12,48,71,106,129,232],"harnessing":[13],"power":[15],"these":[17,99],"will":[19],"likely":[20],"prove":[21],"important":[22],"in":[23,196,246],"development":[25],"RNA-targeting":[27],"inhibitors.":[28],"To":[29],"this":[30],"end,":[31],"we":[32,112,182],"present":[33,113],"a":[34,42,68,80,114,126,171,210,233],"comprehensive":[35],"computational":[36,222],"analysis":[37],"stacking":[39,63,84,123,168,198,217,228,248],"between":[41,125,230],"set":[43,82,172],"54":[45],"druglike":[46,175],"heterocycles":[47,73,176],"natural":[50,179],"nucleobases.":[51,180,253],"We":[52,224],"first":[53],"show":[54,183],"that":[55,72,77,95,131,184,237],"heterocycle":[56,128],"choice":[57],"can":[58,143],"tune":[59],"strength":[61,121],"nucleobases":[66],"over":[67],"large":[69],"range":[70],"favor":[74],"stacked":[75],"geometries":[76],"cluster":[78],"around":[79,202],"discrete":[81],"loci":[85],"characteristic":[86],"each":[88],"nucleobase.":[89],"Symmetry-adapted":[90],"perturbation":[91],"theory":[92,150],"results":[93],"indicate":[94],"strengths":[97],"are":[101],"modulated":[102],"primarily":[103],"by":[104],"electrostatic":[105,139],"dispersion":[107],"effects.":[108],"Based":[109],"on":[110,133],"this,":[111],"multivariate":[115],"predictive":[116],"model":[117,160],"maximum":[120,166],"given":[127],"nucleobase":[130],"depends":[132],"molecular":[134,190],"descriptors":[135,142],"derived":[136],"from":[137,154,201],"potential.":[140],"These":[141],"be":[144],"readily":[145],"computed":[146],"using":[147,220],"density":[148],"functional":[149],"or":[151],"predicted":[152,197],"directly":[153],"atom":[155],"connectivity":[156],"(e.g.,":[157],"SMILES).":[158],"This":[159],"is":[161],"used":[162],"predict":[164],"possible":[167],"1854":[174],"Finally,":[181],"trivial":[185],"modifications":[186],"standard":[188],"(fixed-charge)":[189],"mechanics":[191],"force":[192],"fields":[193],"reduce":[194],"errors":[195],"energies":[200,219],"2":[203],"kcal/mol":[204],"below":[206],"1":[207],"kcal/mol,":[208],"providing":[209],"pragmatic":[211],"means":[212],"predicting":[214],"more":[215],"reliable":[216],"existing":[221],"workflows.":[223],"also":[225],"analyze":[226],"ribocil":[231],"bacterial":[234],"riboswitch,":[235],"showing":[236],"two":[238],"three":[241],"aromatic":[242],"heterocyclic":[243],"components":[244],"engage":[245],"near-optimal":[247],"binding":[251],"site":[252]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
