{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T04:07:19Z","timestamp":1787371639360,"version":"build-2736575974"},"reference-count":34,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2022,9,9]],"date-time":"2022-09-09T00:00:00Z","timestamp":1662681600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["21-14-00381"],"award-info":[{"award-number":["21-14-00381"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Rheumatoid arthritis belongs to the group of chronic systemic autoimmune diseases characterized by the development of destructive synovitis and extra-articular manifestations. Cytokines regulate a wide range of inflammatory processes involved in the pathogenesis of rheumatoid arthritis and contribute to the induction of autoimmunity and chronic inflammation. Janus-associated kinase (JAK) and signal transducer and activator of transcription (STAT) proteins mediate cell signaling from cytokine receptors, and are involved in the pathogenesis of autoimmune and inflammatory diseases. Targeted small-molecule drugs that inhibit the functional activity of JAK proteins are used in clinical practice for the treatment of rheumatoid arthritis. In our study, we modeled the interactions of the small-molecule drug ruxolitinib with JAK1 and JAK2 isoforms and determined the binding selectivity using molecular docking. Molecular modeling data show that ruxolitinib selectively binds the JAK1 and JAK2 isoforms with a binding affinity of \u22128.3 and \u22128.0 kcal\/mol, respectively. The stabilization of ligands in the cavity of kinases occurs primarily through hydrophobic interactions. The amino acid residues of the protein globules of kinases that are responsible for the correct positioning of the drug ruxolitinib and its retention have been determined.<\/jats:p>","DOI":"10.3390\/ijms231810466","type":"journal-article","created":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T22:53:46Z","timestamp":1663023226000},"page":"10466","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Atomic Simulation of the Binding of JAK1 and JAK2 with the Selective Inhibitor Ruxolitinib"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6717-4206","authenticated-orcid":false,"given":"Maxim","family":"Kondratyev","sequence":"first","affiliation":[{"name":"Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir R.","family":"Rudnev","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"},{"name":"Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirill S.","family":"Nikolsky","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9113-9440","authenticated-orcid":false,"given":"Alexander A.","family":"Stepanov","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denis V.","family":"Petrovsky","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liudmila I.","family":"Kulikova","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"},{"name":"Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia"},{"name":"Institute of Mathematical Problems of Biology RAS\u2014The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7199-372X","authenticated-orcid":false,"given":"Arthur T.","family":"Kopylov","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9404-1660","authenticated-orcid":false,"given":"Kristina A.","family":"Malsagova","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4472-2016","authenticated-orcid":false,"given":"Anna L.","family":"Kaysheva","sequence":"additional","affiliation":[{"name":"Biobanking Group, Branch of Institute of Biomedical Chemistry \u201cScientific and Education Center\u201d, 109028 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,9,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"20150876","DOI":"10.1098\/rsif.2015.0876","article-title":"Fold and Flexibility: What Can Proteins\u2019 Mechanical Properties Tell Us about Their Folding Nucleus?","volume":"12","year":"2015","journal-title":"J. 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