{"id":"https://openalex.org/W2889800404","doi":"https://doi.org/10.1080/07391102.2018.1526117","title":"Investigation of selective binding of inhibitors to PTP1B and TCPTP by accelerated molecular dynamics simulations","display_name":"Investigation of selective binding of inhibitors to PTP1B and TCPTP by accelerated molecular dynamics simulations","publication_year":2018,"publication_date":"2018-09-21","ids":{"openalex":"https://openalex.org/W2889800404","doi":"https://doi.org/10.1080/07391102.2018.1526117","mag":"2889800404","pmid":"https://pubmed.ncbi.nlm.nih.gov/30238851"},"language":"en","primary_location":{"id":"doi:10.1080/07391102.2018.1526117","doi":"https://doi.org/10.1080/07391102.2018.1526117","is_oa":false,"landing_page_url":"https://doi.org/10.1080/07391102.2018.1526117","pdf_url":null,"source":{"id":"https://openalex.org/S178711970","display_name":"Journal of Biomolecular Structure and Dynamics","issn_l":"0739-1102","issn":["0739-1102","1538-0254"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","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":"Journal of Biomolecular Structure and Dynamics","raw_type":"journal-article"},"volume":null,"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/A5100329932","display_name":"Xi Chen","orcid":"https://orcid.org/0000-0002-3160-614X","observed_orcids":["https://orcid.org/0000-0002-3160-614X"]},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4405259188","display_name":"State Key Laboratory of Explosion Science and Safety Protection","ror":"https://ror.org/01w9z6890","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4405259188"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xi Chen","raw_affiliation_strings":["State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4405259188"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101640830","display_name":"Qiang Gan","orcid":"https://orcid.org/0000-0003-2214-2723","observed_orcids":["https://orcid.org/0000-0003-2214-2723"]},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4405259188","display_name":"State Key Laboratory of Explosion Science and Safety Protection","ror":"https://ror.org/01w9z6890","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4405259188"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qiang Gan","raw_affiliation_strings":["State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4405259188"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Changgen Feng","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4405259188","display_name":"State Key Laboratory of Explosion Science and Safety Protection","ror":"https://ror.org/01w9z6890","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4405259188"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Changgen Feng","raw_affiliation_strings":["State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4405259188"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049779153","display_name":"Xia Liu","orcid":"https://orcid.org/0000-0002-3110-9602","observed_orcids":["https://orcid.org/0000-0002-3110-9602","https://orcid.org/0000-0003-1136-4742"]},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xia Liu","raw_affiliation_strings":["College of Science, China Agricultural University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Science, China Agricultural University, Beijing, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100401630","display_name":"Qian Zhang","orcid":"https://orcid.org/0000-0002-2959-0863","observed_orcids":["https://orcid.org/0000-0002-2959-0863"]},"institutions":[{"id":"https://openalex.org/I125839683","display_name":"Beijing Institute of Technology","ror":"https://ror.org/01skt4w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I125839683","https://openalex.org/I890469752"]},{"id":"https://openalex.org/I4405259188","display_name":"State Key Laboratory of Explosion Science and Safety Protection","ror":"https://ror.org/01w9z6890","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4405259188"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qian Zhang","raw_affiliation_strings":["State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Explosion Science and Technology, Beijing Institute of Technology, Beijing, China;","institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4405259188"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101640830"],"corresponding_institution_ids":["https://openalex.org/I125839683","https://openalex.org/I4405259188"],"apc_list":null,"apc_paid":null,"fwci":0.4445,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.58511106,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"37","issue":"14","first_page":"3697","last_page":"3706"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12104","display_name":"Protein Tyrosine Phosphatases","score":0.9961000084877014,"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/T12104","display_name":"Protein Tyrosine Phosphatases","score":0.9961000084877014,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.002099999925121665,"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":0.00139999995008111,"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/ptp1b","display_name":"PTP1B","score":0.8799999952316284},{"id":"https://openalex.org/keywords/tcptp","display_name":"TCPTP","score":0.949999988079071},{"id":"https://openalex.org/keywords/protein-tyrosine-phosphatase-inhibitors","display_name":"protein tyrosine phosphatase inhibitors","score":0.9079999923706055},{"id":"https://openalex.org/keywords/inhibitor-selectivity","display_name":"inhibitor selectivity","score":0.8379999995231628},{"id":"https://openalex.org/keywords/conformational-change","display_name":"conformational change","score":0.6639999747276306},{"id":"https://openalex.org/keywords/wpd-loop","display_name":"WPD loop","score":0.6930000185966492},{"id":"https://openalex.org/keywords/r-loops","display_name":"R-loops","score":0.8899999856948853},{"id":"https://openalex.org/keywords/binding-free-energy","display_name":"binding free energy","score":0.8820000290870667},{"id":"https://openalex.org/keywords/mm-pbsa","display_name":"MM-PBSA","score":0.6980000138282776},{"id":"https://openalex.org/keywords/alanine-scanning","display_name":"alanine scanning","score":0.8790000081062317},{"id":"https://openalex.org/keywords/insulin-signaling","display_name":"insulin signaling","score":0.6510000228881836},{"id":"https://openalex.org/keywords/type-2-diabetes","display_name":"type 2 diabetes","score":0.8989999890327454}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6455791592597961},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.487102746963501},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.4522569179534912},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.16570249199867249},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16460534930229187},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D054562","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 1","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054578","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 2","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D054578","descriptor_name":"Protein Tyrosine Phosphatase, Non-Receptor Type 2","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}],"locations_count":2,"locations":[{"id":"doi:10.1080/07391102.2018.1526117","doi":"https://doi.org/10.1080/07391102.2018.1526117","is_oa":false,"landing_page_url":"https://doi.org/10.1080/07391102.2018.1526117","pdf_url":null,"source":{"id":"https://openalex.org/S178711970","display_name":"Journal of Biomolecular Structure and Dynamics","issn_l":"0739-1102","issn":["0739-1102","1538-0254"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","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":"Journal of Biomolecular Structure and Dynamics","raw_type":"journal-article"},{"id":"pmid:30238851","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30238851","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,"listed_in":[],"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 biomolecular structure & dynamics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5683000087738037,"display_name":"Good health and well-being"}],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/7","score":0.75,"display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1497274503","https://openalex.org/W1499420960","https://openalex.org/W1963529746","https://openalex.org/W1978164637","https://openalex.org/W1980586346","https://openalex.org/W1987114890","https://openalex.org/W1991175412","https://openalex.org/W1996908796","https://openalex.org/W2000613080","https://openalex.org/W2006816012","https://openalex.org/W2009488815","https://openalex.org/W2011223348","https://openalex.org/W2015688756","https://openalex.org/W2019619651","https://openalex.org/W2021650763","https://openalex.org/W2022786966","https://openalex.org/W2025395236","https://openalex.org/W2026671374","https://openalex.org/W2027685123","https://openalex.org/W2028046413","https://openalex.org/W2035266068","https://openalex.org/W2042924462","https://openalex.org/W2044529125","https://openalex.org/W2049126566","https://openalex.org/W2062767127","https://openalex.org/W2063484479","https://openalex.org/W2067174909","https://openalex.org/W2075392233","https://openalex.org/W2083164919","https://openalex.org/W2087482176","https://openalex.org/W2088892296","https://openalex.org/W2099220382","https://openalex.org/W2099854272","https://openalex.org/W2105332853","https://openalex.org/W2105398220","https://openalex.org/W2105668062","https://openalex.org/W2106140689","https://openalex.org/W2115681043","https://openalex.org/W2122586120","https://openalex.org/W2123229219","https://openalex.org/W2124876030","https://openalex.org/W2132629607","https://openalex.org/W2134486592","https://openalex.org/W2136805944","https://openalex.org/W2144288821","https://openalex.org/W2145501578","https://openalex.org/W2147993766","https://openalex.org/W2149201695","https://openalex.org/W2150533499","https://openalex.org/W2154319440","https://openalex.org/W2168640804","https://openalex.org/W2169585787","https://openalex.org/W2330799739","https://openalex.org/W2332712348","https://openalex.org/W2469324777","https://openalex.org/W2599326125"],"related_works":["https://openalex.org/W2911020401","https://openalex.org/W2444256618","https://openalex.org/W2085289891","https://openalex.org/W2808633495","https://openalex.org/W2107995523","https://openalex.org/W2765612488","https://openalex.org/W2124876030","https://openalex.org/W3208654454","https://openalex.org/W4366428227","https://openalex.org/W4386884159"],"abstract_inverted_index":{"Protein":[0],"tyrosine":[1,40],"phosphatase":[2,41],"1B":[3],"(PTP1B),":[4],"a":[5,16],"key":[6],"negative":[7],"regulator":[8],"in":[9,123],"insulin":[10],"signaling":[11],"pathways,":[12],"is":[13,46],"regarded":[14],"as":[15],"potential":[17],"target":[18],"for":[19,185],"the":[20,29,32,49,58,71,81,103,130,140,144,159,162,170,186,210],"treatment":[21],"of":[22,34,64,84,108,117,134,147,166,188,196,199],"type":[23],"II":[24],"diabetes":[25],"and":[26,54,57,86,113,143,169,180,203],"obesity.":[27],"However,":[28],"mechanism":[30],"underlying":[31],"selectivity":[33,187],"PTP1B":[35,53,85,202],"inhibitors":[36,95,177,200],"against":[37],"T-cell":[38],"protein":[39],"(TCPTP)":[42],"remains":[43],"controversial,":[44],"which":[45,205],"due":[47],"to":[48,79,105,182,201,209],"high":[50],"similarity":[51],"between":[52],"TCPTP":[55,65,87],"sequence":[56],"fact":[59],"that":[60,88,129],"no":[61],"ligand-protein":[62],"complex":[63],"has":[66],"been":[67],"established":[68],"yet.":[69],"Here,":[70],"accelerated":[72],"molecular":[73],"dynamics":[74,83],"(aMD)":[75],"method":[76],"was":[77],"used":[78],"investigate":[80],"structural":[82],"are":[89],"bound":[90],"by":[91,153,176,216],"two":[92],"chemically":[93],"similar":[94],"with":[96,139],"distinct":[97],"selectivity.":[98],"The":[99],"conformational":[100,164],"transitions":[101],"during":[102],"\"open\"":[104],"\"close\"":[106],"states":[107,136],"four":[109,160],"complexes":[110],"were":[111,121,137,150,178],"captured,":[112],"free":[114,132],"energy":[115],"profiles":[116],"important":[118,148],"residue":[119],"pairs":[120],"analyzed":[122],"detail.":[124],"Additional":[125],"MM-PBSA":[126],"calculations":[127],"confirmed":[128],"binding":[131,173,198],"energies":[133],"final":[135],"consistent":[138],"experimental":[141],"results,":[142],"energetic":[145],"contributions":[146],"residues":[149],"further":[151,211],"investigated":[152],"alanine":[154],"scanning":[155],"mutagenesis.":[156],"By":[157],"comparing":[158],"complexes,":[161],"different":[163],"behavior":[165],"WPD-loop,":[167],"R-loop,":[168],"second":[171],"pTyr":[172],"site":[174],"induced":[175],"featured":[179],"found":[181],"be":[183,207],"crucial":[184],"inhibitors.":[189],"This":[190],"study":[191],"provides":[192],"new":[193],"mechanistic":[194],"insights":[195],"specific":[197],"TCPTP,":[204],"can":[206],"exploited":[208],"structural-based":[212],"inhibitor":[213],"design.":[214],"Communicated":[215],"Ramaswamy":[217],"H.":[218],"Sarma.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2018-09-27T00:00:00"}