{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:42:14Z","timestamp":1785426134500,"version":"3.56.0"},"reference-count":84,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T00:00:00Z","timestamp":1777507200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Scientific and Technological Research Council of T\u00fcrkiye (T\u00dcB\u0130TAK),","award":["123Z076"],"award-info":[{"award-number":["123Z076"]}]},{"award":["123Z076"],"award-info":[{"award-number":["123Z076"]}],"id":[{"id":"https:\/\/ror.org\/04w9kkr77","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The plague, caused by Yersinia pestis, has resulted in significant mortality over the past century. Despite advances in antimicrobial therapy, plague remains a re-emerging infectious disease with ongoing outbreaks and increasing concerns regarding antimicrobial resistance. Today, plague cases are still being reported, and the loss of effectiveness of treatment methods remains a major challenge. Therefore, effective treatment strategies are needed. In this study, we aimed to develop aptamers specific to Yersinia outer protein M (YopM), a key immunosuppressive protein that is essential for virulence. Our goal was to develop an aptamer that binds to YopM and inhibits its interaction with the human DEAD-box helicase 3 (DDX3) protein. YopM-DDX3 protein interaction was targeted because of its key role in nucleocytoplasmic shuttling of YopM. To achieve this, we developed the YopM16 aptamer using magnetic bead-based (Systematic Evolution of Ligands by Exponential Enrichment) (SELEX). The selected YopM16 aptamer exhibited a half-maximal inhibitory concentration(IC50) value of 103.3 \u00b1 2 nM and effectively inhibited the interaction between YopM and DDX3. The inhibitory effect of the aptamer on protein interaction was confirmed using a pull-down assay and colorimetric test. Given that protein\u2013protein interaction surfaces are considered undruggable, YopM16 is a promising inhibitor with the potential to serve as a molecular tool to investigate the virulence mechanism of YopM, as well as a novel antibacterial agent upon validation of its inhibition in cellular models.<\/jats:p>","DOI":"10.3390\/ijms27094038","type":"journal-article","created":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T14:35:53Z","timestamp":1777559753000},"page":"4038","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Targeting Undruggable Protein Interactions with DNA Aptamers: Inhibition of the Interaction Between Yersinia Outer Protein M and Human DEAD-Box Helicase 3"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4991-2310","authenticated-orcid":false,"given":"O\u011fuz","family":"G\u00f6k","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Faculty of Science, Ege University, 35100 Izmir, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2204-0831","authenticated-orcid":false,"given":"\u00d6zge","family":"U\u011furlu","sequence":"additional","affiliation":[{"name":"Department of Medical Services and Techniques, Hatay Vocational School of Health Services, Hatay Mustafa Kemal University, 31060 Hatay, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Canan","family":"\u00d6zyurt","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Chemical Processing Technologies, Lapseki Vocational School, Canakkale Onsekiz Mart University, 17800 Canakkale, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6676-4888","authenticated-orcid":false,"given":"Serap","family":"Evran","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Faculty of Science, Ege University, 35100 Izmir, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Grygiel-G\u00f3rniak, B. 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