{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T03:39:34Z","timestamp":1788925174367,"version":"build-2803163510"},"reference-count":33,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T00:00:00Z","timestamp":1748390400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016190","name":"Trond Mohn Foundation","doi-asserted-by":"publisher","award":["TMS2019TMT07"],"award-info":[{"award-number":["TMS2019TMT07"]}],"id":[{"id":"10.13039\/100016190","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pharmaceuticals"],"abstract":"<jats:p>Background\/Objectives: Colony stimulating factor 1 receptor kinase (CSF1R) is a well-validated molecular target in drug discovery for various reasons. Based on the structure of an early lead molecule identified in our lab and the marketed drug Pexidartinib (PLX3397), we merged fragments of Pexidartinib with our pyrrolo[2,3-d]pyrimidine nucleus, and the idea was supported by initial molecular docking studies. Thus, several new compounds were synthesized with Pexidartinib fragments on C4, C5, and C6 on the pyrrolopyrimidine scaffold using molecular hybridization. Methods: Nine final products were synthesized using a combination of Buchwald-Hartwig and Suzuki-Miyaura cross-coupling reactions in three to four steps and in good yields. The analogues were subsequently profiled as CSF1R inhibitors in enzymatic and cellular assays, and ADME properties were evaluated for some derivatives. Results: N-Methyl-N-(3-methylbenzyl)-6-(6-((pyridin-3-ylmethyl)amino)pyridin-3-yl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (12b) emerged as the most potent CSF1R inhibitor, showing low-nanomolar enzymatic activity, cellular efficacy, and favorable ADME properties, highlighting its promise as a lead compound for further development. Conclusions: These findings suggest that combining structural elements from previously reported CSF1R inhibitors such as Pexidartinib could guide the development of improved drug candidates targeting this kinase.<\/jats:p>","DOI":"10.3390\/ph18060814","type":"journal-article","created":{"date-parts":[[2025,5,29]],"date-time":"2025-05-29T04:46:38Z","timestamp":1748493998000},"page":"814","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Design and Synthesis of Pyridine-Based Pyrrolo[2,3-d]pyrimidine Analogs as CSF1R Inhibitors: Molecular Hybridization and Scaffold Hopping Approach"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7814-0965","authenticated-orcid":false,"given":"Srinivasulu","family":"Cherukupalli","sequence":"first","affiliation":[{"name":"Department of Chemistry, Norwegian University of Science and Technology (NTNU), H\u00f8gskoleringen 5, NO-7491 Trondheim, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carsten","family":"Degenhart","sequence":"additional","affiliation":[{"name":"Lead Discovery Center GmbH (LDC), Otto-Hahn-Strasse 15, 44227 Dortmund, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1251-264X","authenticated-orcid":false,"given":"Peter","family":"Habenberger","sequence":"additional","affiliation":[{"name":"Lead Discovery Center GmbH (LDC), Otto-Hahn-Strasse 15, 44227 Dortmund, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1288-3763","authenticated-orcid":false,"given":"Anke","family":"Unger","sequence":"additional","affiliation":[{"name":"Lead Discovery Center GmbH (LDC), Otto-Hahn-Strasse 15, 44227 Dortmund, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5537-438X","authenticated-orcid":false,"given":"Jan","family":"Eickhoff","sequence":"additional","affiliation":[{"name":"Lead Discovery Center GmbH (LDC), Otto-Hahn-Strasse 15, 44227 Dortmund, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7859-7810","authenticated-orcid":false,"given":"B\u00e5rd Helge","family":"Hoff","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Norwegian University of Science and Technology (NTNU), H\u00f8gskoleringen 5, NO-7491 Trondheim, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eirik","family":"Sundby","sequence":"additional","affiliation":[{"name":"Department of Material Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.biopha.2018.04.046","article-title":"Recent advances in colony stimulating factor-1 receptor\/c-FMS as an emerging target for various therapeutic implications","volume":"103","author":"Kumari","year":"2018","journal-title":"Biomed. Pharmacother."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"106566","DOI":"10.1016\/j.phrs.2022.106566","article-title":"Targeting CSF-1R represents an effective strategy in modulating inflammatory diseases","volume":"187","author":"Xiang","year":"2023","journal-title":"Pharmacol. Res."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Barca, C., Foray, C., Hermann, S., Herrlinger, U., Remory, I., Laoui, D., Schaefers, M., Grauer, O.M., Zinnhardt, B., and Jacobs, A.H. (2021). The Colony Stimulating Factor-1 Receptor (CSF-1R)-Mediated Regulation of Microglia\/Macrophages as a Target for Neurological Disorders (Glioma, Stroke). Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.787307"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1046\/j.1365-2141.2003.04108.x","article-title":"Mutational analysis of class III receptor tyrosine kinases (C-KIT, C-FMS, FLT3) in idiopathic myelofibrosis","volume":"120","author":"Goodeve","year":"2003","journal-title":"Br. J. Haematol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1007\/s10787-022-00958-4","article-title":"Colony-stimulating factor 1 receptor signaling in the central nervous system and the potential of its pharmacological inhibitors to halt the progression of neurological disorders","volume":"30","author":"Tarale","year":"2022","journal-title":"Inflammopharmacology"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1080\/13543776.2021.1839414","article-title":"Small-molecule CSF1R kinase inhibitors; review of patents 2015-present","volume":"31","author":"Denny","year":"2021","journal-title":"Expert Opin. Ther. Pat."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1056\/NEJMoa1411366","article-title":"Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor","volume":"373","author":"Tap","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2098","DOI":"10.1158\/1535-7163.MCT-21-0361","article-title":"Vimseltinib: A Precision CSF1R Therapy for Tenosynovial Giant Cell Tumors and Diseases Promoted by Macrophages","volume":"20","author":"Smith","year":"2021","journal-title":"Mol. Cancer Ther."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1500","DOI":"10.1016\/S1470-2045(20)30496-4","article-title":"Surufatinib in advanced extrapancreatic neuroendocrine tumours (SANET-ep): A randomised, double-blind, placebo-controlled, phase 3 study","volume":"21","author":"Xu","year":"2020","journal-title":"Lancet Oncol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"114884","DOI":"10.1016\/j.ejmech.2022.114884","article-title":"CSF1R inhibitors are emerging immunotherapeutic drugs for cancer treatment","volume":"245","author":"Wen","year":"2023","journal-title":"Eur. J. Med. Chem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1693","DOI":"10.2147\/DDDT.S253232","article-title":"Pexidartinib, a Novel Small Molecule CSF-1R Inhibitor in Use for Tenosynovial Giant Cell Tumor: A Systematic Review of Pre-Clinical and Clinical Development","volume":"14","author":"Benner","year":"2020","journal-title":"Drug Des. Dev. Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1758835919854238","DOI":"10.1177\/1758835919854238","article-title":"Phase Ib study of the combination of pexidartinib (PLX3397), a CSF-1R inhibitor, and paclitaxel in patients with advanced solid tumors","volume":"11","author":"Wesolowski","year":"2019","journal-title":"Ther. Adv. Med. Oncol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1634\/theoncologist.2019-0418","article-title":"A Phase I Study of Binimetinib (MEK162) Combined with Pexidartinib (PLX3397) in Patients with Advanced Gastrointestinal Stromal Tumor","volume":"24","author":"Rosenbaum","year":"2019","journal-title":"Oncologist"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1016\/S1470-2045(20)30493-9","article-title":"Surufatinib in advanced pancreatic neuroendocrine tumours (SANET-p): A randomised, double-blind, placebo-controlled, phase 3 study","volume":"21","author":"Xu","year":"2020","journal-title":"Lancet Oncol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"11557","DOI":"10.1200\/JCO.2022.40.16_suppl.11557","article-title":"Surufatinib in US patients with soft tissue sarcoma","volume":"40","author":"Movva","year":"2022","journal-title":"J. Clin. Oncol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Son, Y., Jeong, Y.J., Shin, N.R., Oh, S.J., Nam, K.R., Choi, H.D., Choi, J.Y., and Lee, H.J. (2020). Inhibition of Colony-Stimulating Factor 1 Receptor by PLX3397 Prevents Amyloid Beta Pathology and Rescues Dopaminergic Signaling in Aging 5xFAD Mice. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21155553"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1096\/fj.201900567RR","article-title":"Pharmacological inhibition of CSF1R by GW2580 reduces microglial proliferation and is protective against neuroinflammation and dopaminergic neurodegeneration","volume":"34","author":"Neal","year":"2020","journal-title":"FASEB J."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3243","DOI":"10.1093\/brain\/awz241","article-title":"CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice","volume":"142","author":"Mancuso","year":"2019","journal-title":"Brain"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Spiteri, A.G., Ni, D., Ling, Z.L., Macia, L., Campbell, I.L., Hofer, M.J., and King, N.J.C. (2022). PLX5622 Reduces Disease Severity in Lethal CNS Infection by Off-Target Inhibition of Peripheral Inflammatory Monocyte Production. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.851556"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1158\/1535-7163.MCT-05-0410","article-title":"Preclinical activity of ABT-869, a multitargeted receptor tyrosine kinase inhibitor","volume":"5","author":"Albert","year":"2006","journal-title":"Mol. Cancer Ther."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1111\/cas.13141","article-title":"CS2164, a novel multi-target inhibitor against tumor angiogenesis, mitosis and chronic inflammation with anti-tumor potency","volume":"108","author":"Zhou","year":"2017","journal-title":"Cancer Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1016\/S1470-2045(17)30764-7","article-title":"Anti-VEGFR, PDGFR, and CSF1R tyrosine kinase inhibitor CM082 (X-82) in combination with everolimus for treatment of metastatic renal cell carcinoma: A phase 1 clinical trial","volume":"18","author":"Yan","year":"2017","journal-title":"Lancet Oncol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"6959","DOI":"10.1021\/acs.jmedchem.3c00428","article-title":"Synthesis and Development of Highly Selective Pyrrolo[2,3- d]pyrimidine CSF1R Inhibitors Targeting the Autoinhibited Form","volume":"66","author":"Aarhus","year":"2023","journal-title":"J. Med. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"115344","DOI":"10.1016\/j.ejmech.2023.115344","article-title":"A highly selective purine-based inhibitor of CSF1R potently inhibits osteoclast differentiation","volume":"255","author":"Aarhus","year":"2023","journal-title":"Eur. J. Med. Chem."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e202300052","DOI":"10.1002\/ejoc.202300052","article-title":"Negishi Cross-Coupling in the Preparation of Benzyl Substituted Pyrrolo[2,3-d]pyrimidine Based CSF1R Inhibitors","volume":"26","author":"Aarhus","year":"2023","journal-title":"Eur. J. Org. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"116053","DOI":"10.1016\/j.ejmech.2023.116053","article-title":"Pyrrolopyrimidine based CSF1R inhibitors: Attempted departure from Flatland","volume":"265","author":"Havik","year":"2024","journal-title":"Eur. J. Med. Chem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1517\/17460441.2016.1135125","article-title":"An overview of molecular hybrids in drug discovery","volume":"11","year":"2016","journal-title":"Expert Opin. Drug Discov."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"113768","DOI":"10.1016\/j.ejmech.2021.113768","article-title":"Molecular hybrids: A five-year survey on structures of multiple targeted hybrids of protein kinase inhibitors for cancer therapy","volume":"225","author":"Soltan","year":"2021","journal-title":"Eur. J. Med. Chem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1021\/acs.jmedchem.6b01437","article-title":"Recent Advances in Scaffold Hopping","volume":"60","author":"Hu","year":"2017","journal-title":"J. Med. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"727","DOI":"10.37349\/etat.2023.00164","article-title":"In silico targeting of colony-stimulating factor-1 receptor: Delineating immunotherapy in cancer","volume":"4","author":"Azhar","year":"2023","journal-title":"Explor. Target. Anti-Tumor Ther."},{"key":"ref_31","unstructured":"Schr\u00f6dinger_Release_2025-1 (2025). Glide, Schr\u00f6dinger, LLC."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Reiers\u00f8lmoen, A.C., Aarhus, T.I., Eckelt, S., N\u00f8rsett, K.G., Sundby, E., and Hoff, B.H. (2019). Potent and selective EGFR inhibitors based on 5-aryl-7H-pyrrolopyrimidin-4-amines. Bioorg. Chem., 88.","DOI":"10.1016\/j.bioorg.2019.102918"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/nbt1358","article-title":"A quantitative analysis of kinase inhibitor selectivity","volume":"26","author":"Karaman","year":"2008","journal-title":"Nat. Biotechnol."}],"container-title":["Pharmaceuticals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8247\/18\/6\/814\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:42:33Z","timestamp":1760031753000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8247\/18\/6\/814"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,28]]},"references-count":33,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["ph18060814"],"URL":"https:\/\/doi.org\/10.3390\/ph18060814","relation":{},"ISSN":["1424-8247"],"issn-type":[{"value":"1424-8247","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,28]]}}}