{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T12:45:11Z","timestamp":1791809111046,"version":"4.3.4"},"reference-count":41,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T00:00:00Z","timestamp":1790985600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T00:00:00Z","timestamp":1790985600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["T2425029"],"award-info":[{"award-number":["T2425029"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["T2425029"],"award-info":[{"award-number":["T2425029"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Shaanxi Provincial Natural Science Basic Research Program","award":["2026JC-YBMS-0072"],"award-info":[{"award-number":["2026JC-YBMS-0072"]}]},{"name":"Open Project Program of the State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases","award":["SKLD2025M04"],"award-info":[{"award-number":["SKLD2025M04"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Carnitine palmitoyltransferase 1A (CPT1A) catalyzes a rate-limiting step in fatty acid \u03b2-oxidation and is a target for studies of metabolic disease and cancer. However, the structural dynamics of CPT1A remain poorly understood due to the lack of full-length structure. In this study, we employed an integrated computational approach combining molecular dynamics (MD) simulations, Markov state models (MSMs), and binding free energy calculations to elucidate the conformational landscape of human CPT1A. We performed an all-atom MD simulation of CPT1A embedded in a realistic outer mitochondrial membrane, and root-mean-square fluctuation (RMSF)-guided local region analysis coupled with MSM transition-path analysis and GROMOS clustering convergently identified a representative conformation. The pathway probabilities reported here describe dominant local transitions within specific mobile segments rather than the global equilibrium population of the full-length protein. Using this representative conformation, we performed a virtual screening of over 1.23 million compounds from the ChemDiv library, followed by Lipinski filtering, yielding five candidates with docking scores below \u221210 kcal\/mol. Subsequent MD simulations and binding free energy calculations confirmed stable binding, with Compound 2 exhibiting the most favorable free energy of \u221225.99 kcal\/mol. Principal component analysis (PCA) and secondary-structure analyses revealed ligand-specific modulation of CPT1A dynamics. A preliminary in vitro CPT1 activity assay revealed candidate-specific responses, and the free-energy and activity data were partially consistent. These results provide a dynamically informed structural basis for CPT1A ligand recognition, identify candidates with distinct energetic and functional profiles, and establish an integrated strategy for ligand discovery in structurally uncharacterized proteins.<\/jats:p>","DOI":"10.3390\/ijms27198840","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T12:31:31Z","timestamp":1791203491000},"page":"8840","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Conformational Sampling of CPT1A Enables Dynamic Structure-Based Ligand Screening"],"prefix":"10.3390","volume":"27","author":[{"given":"Sijia","family":"Zhang","sequence":"first","affiliation":[{"name":"MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi\u2019an Jiaotong University, Xi\u2019an 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingbo","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Xi\u2019an Jiaotong University, Xi\u2019an 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiasheng","family":"Zhao","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi\u2019an Jiaotong University, Xi\u2019an 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8074-957X","authenticated-orcid":false,"given":"Jiangang","family":"Long","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Xi\u2019an Jiaotong University, Xi\u2019an 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4880-824X","authenticated-orcid":false,"given":"Lei","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi\u2019an Jiaotong University, Xi\u2019an 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6969-8177","authenticated-orcid":false,"given":"Zhiwei","family":"Yang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi\u2019an Jiaotong University, Xi\u2019an 710049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,10,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1038\/s41574-019-0176-8","article-title":"Obesity: Global Epidemiology and Pathogenesis","volume":"15","year":"2019","journal-title":"Nat. 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