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This study explored CDK-related pathways in\n                      <jats:italic>N. fowleri<\/jats:italic>\n                      using a focused CDK inhibitor library and structure-based analysis of a selected CDK-like protein.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A library of 126 CDK inhibitors was screened against\n                      <jats:italic>N. fowleri<\/jats:italic>\n                      trophozoites using a luminescence-based ATP viability assay, and active compounds were further evaluated in dose\u2013response assays. Human CDK1\u20139 sequences were used for BLASTp searches against the\n                      <jats:italic>N. fowleri<\/jats:italic>\n                      proteome, followed by comparative sequence analysis with\n                      <jats:italic>Trypanosoma brucei<\/jats:italic>\n                      cdc2-related kinases (CRKs). Nf_CDK-like protein1 (FDP41_013684) was selected for homology modeling, molecular docking, and 100-ns molecular dynamics simulations.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Screening identified 23 active CDK inhibitors with IC\n                      <jats:sub>50<\/jats:sub>\n                      values\u2009\u2264\u200910\u00a0\u03bcM against\n                      <jats:italic>N. fowleri<\/jats:italic>\n                      , including five prioritized compounds with submicromolar activity: AZD5438, GSK-3 inhibitor IX, milciclib, roniciclib, and SU9516 (IC\n                      <jats:sub>50<\/jats:sub>\n                      , 0.30\u20130.88\u00a0\u03bcM). Sequence analysis identified five CDK-like proteins in the\n                      <jats:italic>N. fowleri<\/jats:italic>\n                      proteome, among which Nf_CDK-like protein1 showed the highest similarity to\n                      <jats:italic>T. brucei<\/jats:italic>\n                      CRK3 and shared approximately 58\u201361% sequence identity with human CDK1\/2. Conserved kinase features, including the glycine-rich loop, \u03b1C-helix, hinge region, DFG motif, and activation loop, were retained in Nf_CDK-like protein1. Docking analysis placed all five prioritized compounds within the predicted ATP-binding cleft, with shared interactions around Lys60, Tyr42, Asp113, and the hinge-proximal residues Ile110 and Asp111. Molecular dynamics simulations showed generally stable protein backbones and ligand poses over 100\u00a0ns.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      This study identified multiple CDK inhibitor scaffolds with potent in vitro activity against\n                      <jats:italic>N. fowleri<\/jats:italic>\n                      and supports Nf_CDK-like protein1 as a plausible CDK-like kinase target candidate through integrated phenotypic and structure-based analyses, with direct biochemical validation needed in future studies. These findings suggest that CDK-like pathways may represent a relevant molecular axis in\n                      <jats:italic>N. fowleri<\/jats:italic>\n                      and provide a basis for future structure-guided optimization of anti-amoebic candidates.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13071-026-07525-8","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T17:26:31Z","timestamp":1782321991000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cyclin-dependent kinase-inhibitor screening and structural analysis identify a CDK-like kinase candidate in Naegleria fowleri"],"prefix":"10.1186","volume":"19","author":[{"given":"Min-Jeong","family":"Kim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joo Hwan","family":"No","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,24]]},"reference":[{"key":"7525_CR1","doi-asserted-by":"publisher","first-page":"6677","DOI":"10.1128\/AAC.01293-15","volume":"59","author":"E Grace","year":"2015","unstructured":"Grace E, Asbill S, Virga K. 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