{"id":"https://openalex.org/W4241220693","doi":"https://doi.org/10.26434/chemrxiv.12622667.v1","title":"Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2","display_name":"Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2","publication_year":2020,"publication_date":"2020-07-09","ids":{"openalex":"https://openalex.org/W4241220693","doi":"https://doi.org/10.26434/chemrxiv.12622667.v1"},"language":"en","primary_location":{"id":"doi:10.26434/chemrxiv.12622667.v1","doi":"https://doi.org/10.26434/chemrxiv.12622667.v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.12622667.v1","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d88469df489d0f442e1/original/adaptive-evolution-of-peptide-inhibitors-for-mutating-sars-co-v-2.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d88469df489d0f442e1/original/adaptive-evolution-of-peptide-inhibitors-for-mutating-sars-co-v-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027424609","display_name":"Lela Vukovi\u0107","orcid":"https://orcid.org/0000-0002-9053-5708","observed_orcids":["https://orcid.org/0000-0002-9053-5708"]},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lela Vukovic","raw_affiliation_strings":["University of Texas at El Paso"],"raw_orcid":"https://orcid.org/0000-0002-9053-5708","affiliations":[{"raw_affiliation_string":"University of Texas at El Paso","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030799118","display_name":"Yanxiao Han","orcid":"https://orcid.org/0000-0002-1684-6073","observed_orcids":["https://orcid.org/0000-0002-1684-6073"]},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanxiao Han","raw_affiliation_strings":["Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States and","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076291344","display_name":"Parth Chaturvedi","orcid":"https://orcid.org/0000-0003-4560-0977","observed_orcids":["https://orcid.org/0000-0003-4560-0977"]},"institutions":[{"id":"https://openalex.org/I164936912","display_name":"The University of Texas at El Paso","ror":"https://ror.org/04d5vba33","country_code":"US","type":"education","lineage":["https://openalex.org/I164936912"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Parth Chaturvedi","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States","institution_ids":["https://openalex.org/I164936912"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029247141","display_name":"Petr Kr\u00e1l","orcid":"https://orcid.org/0000-0003-2992-9027","observed_orcids":["https://orcid.org/0000-0003-2992-9027"]},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Petr Kral","raw_affiliation_strings":["Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States and","institution_ids":["https://openalex.org/I39422238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.8446999788284302,"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"}},"topics":[{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.8446999788284302,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.06459999829530716,"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":0.03200000151991844,"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/sars-cov-2","display_name":"SARS-CoV-2","score":0.9980000257492065},{"id":"https://openalex.org/keywords/peptide-inhibitors","display_name":"peptide inhibitors","score":0.7889999747276306},{"id":"https://openalex.org/keywords/adaptive-evolution","display_name":"adaptive evolution","score":0.8690000176429749},{"id":"https://openalex.org/keywords/receptor-binding-domain","display_name":"receptor binding domain","score":0.7670000195503235},{"id":"https://openalex.org/keywords/ace2","display_name":"ACE2","score":0.9369999766349792},{"id":"https://openalex.org/keywords/viral-mutations","display_name":"viral mutations","score":0.703000009059906},{"id":"https://openalex.org/keywords/antiviral-agents","display_name":"antiviral agents","score":0.7919999957084656},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.5109999775886536},{"id":"https://openalex.org/keywords/monte-carlo-optimization","display_name":"Monte Carlo optimization","score":0.8109999895095825},{"id":"https://openalex.org/keywords/peptide-library-design","display_name":"peptide library design","score":0.4480000138282776}],"concepts":[{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.6473450660705566},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.5783702731132507},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5283967852592468},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5082497000694275},{"id":"https://openalex.org/C3006700255","wikidata":"https://www.wikidata.org/wiki/Q81068910","display_name":"2019-20 coronavirus outbreak","level":3,"score":0.48980093002319336},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.476166695356369},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.44623899459838867},{"id":"https://openalex.org/C2908542902","wikidata":"https://www.wikidata.org/wiki/Q440681","display_name":"Directed Molecular Evolution","level":5,"score":0.43680715560913086},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.33356067538261414},{"id":"https://openalex.org/C9418097","wikidata":"https://www.wikidata.org/wiki/Q440681","display_name":"Directed evolution","level":4,"score":0.3008783757686615},{"id":"https://openalex.org/C116675565","wikidata":"https://www.wikidata.org/wiki/Q3241045","display_name":"Outbreak","level":2,"score":0.2925882041454315},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.2570619583129883},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2441290318965912},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24187305569648743},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.20942768454551697},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17654138803482056},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13877740502357483},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.26434/chemrxiv.12622667.v1","doi":"https://doi.org/10.26434/chemrxiv.12622667.v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.12622667.v1","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d88469df489d0f442e1/original/adaptive-evolution-of-peptide-inhibitors-for-mutating-sars-co-v-2.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv.12622667.v1","doi":"https://doi.org/10.26434/chemrxiv.12622667.v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.12622667.v1","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d88469df489d0f442e1/original/adaptive-evolution-of-peptide-inhibitors-for-mutating-sars-co-v-2.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.46810001134872437}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4241220693.pdf","grobid_xml":"https://content.openalex.org/works/W4241220693.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W3014714014","https://openalex.org/W6604377271","https://openalex.org/W6605784485","https://openalex.org/W6631008485"],"related_works":["https://openalex.org/W4280572789","https://openalex.org/W3193682077","https://openalex.org/W7144314872","https://openalex.org/W3160073929","https://openalex.org/W7139973475","https://openalex.org/W4312211932","https://openalex.org/W4304196012","https://openalex.org/W7131221023","https://openalex.org/W2090139119","https://openalex.org/W4317735670"],"abstract_inverted_index":{"The":[0,137],"SARS-CoV-2":[1,65,149],"virus":[2],"is":[3],"currently":[4],"causing":[5],"a":[6,45,152],"worldwide":[7],"pandemic":[8],"with":[9,29],"dramatic":[10],"societal":[11],"consequences":[12],"for":[13,35],"the":[14,17,95,119,126,148],"humankind.":[15],"In":[16,110],"last":[18],"decades,":[19],"disease":[20],"outbreaks":[21],"due":[22],"to":[23,48,70],"such":[24],"zoonotic":[25],"pathogens":[26],"have":[27],"appeared":[28],"an":[30,36],"accelerated":[31],"rate,":[32],"which":[33,129],"calls":[34],"urgent":[37],"development":[38],"ofadaptive":[39],"(smart)":[40],"therapeutics.":[41],"Here,":[42],"we":[43,92],"develop":[44],"computational":[46,138],"strategy":[47],"adaptively":[49],"evolve":[50],"peptides":[51],"that":[52,104],"could":[53],"selectively":[54],"inhibit":[55],"mutating":[56],"S":[57],"protein":[58],"receptor":[59],"binding":[60,69],"domains":[61],"(RBDs)":[62],"of":[63,118,146],"different":[64],"viral":[66],"strains":[67],"from":[68,80],"their":[71,106],"human":[72],"host":[73],"receptor,":[74],"angiotensin-converting":[75],"enzyme":[76],"2":[77],"(ACE2).":[78],"Starting":[79],"suitable":[81],"peptide":[82,127],"templates,":[83],"based":[84],"on":[85,151],"selected":[86],"ACE2":[87],"segments":[88],"(natural":[89],"RBD":[90],"binder),":[91],"gradually":[93],"modify":[94],"templates":[96],"by":[97,125],"random":[98],"mutations,":[99,128],"while":[100],"retaining":[101],"those":[102],"mutations":[103],"maximize":[105],"RBD-binding":[107],"free":[108],"energies.":[109],"this":[111],"adaptive":[112],"evolution,":[113],"atomistic":[114],"molecular":[115],"dynamics":[116],"simulations":[117],"template-RBD":[120],"complexes":[121],"are":[122,130],"iteratively":[123],"perturbed":[124],"retained":[131],"under":[132],"favorable":[133],"Monte":[134],"Carlo":[135],"decisions.":[136],"search":[139],"will":[140],"provide":[141],"librariesof":[142],"optimized":[143],"therapeutics":[144],"capable":[145],"reducing":[147],"infection":[150],"global":[153],"scale.":[154]},"counts_by_year":[],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2022-05-12T00:00:00"}