Bioorganic Chemistry最新文献

{"title":"Synthesis and antitumoral evaluation of 3',4'-unsaturated nucleoside analogues bearing a chlorinated remdesivir-like base.","authors":"Song Wang, Jing Yang, Xinyue Yang, Hao Huang, Haiyang Zou, Yu Zhang, Xushan Zhang, Congcong Luo, Bing Zhao, Feng-Wu Liu, Piet Herdewijn","doi":"10.1016/j.bioorg.2026.110389","DOIUrl":"10.1016/j.bioorg.2026.110389","url":null,"abstract":"<p><p>Nucleoside analogues are traditionally developed as antimetabolites that interfere with nucleic acid synthesis after intracellular phosphorylation. In this study, inspired by the 3',4'-unsaturated sugar scaffold of ddhCTP, we designed and synthesized a series of 3',4'-unsaturated nucleoside analogues to explore their antiproliferative potential and possible non-classical cellular effects. Among the synthesized compounds, 17k, a C-nucleoside bearing both a 3',4'-unsaturated sugar moiety and a chlorinated remdesivir-like base, exhibited potent antiproliferative activity against HepG2 cells, with an IC₅₀ value of 2.27 ± 0.36 μM, lower than that of gemcitabine under the same assay conditions. In the nonmalignant GES-1 epithelial cell line, 17k showed an IC₅₀ value of 34.26 ± 3.45 μM, corresponding to a selectivity index of 15.1 relative to HepG2 cells. Closely related compounds 12 and 17j showed no detectable activity, indicating a narrow structure-activity relationship. Exploratory single-concentration kinase profiling at 20 μM showed strong inhibition of several transcription-associated CDK/cyclin complexes (CDK13/CycK, CDK12/CycK, CDK9/CycT1, CDK19/CycC, and CDK8/CycC) and selected receptor tyrosine kinases (KDR/VEGFR2, RET, EPHA1, and FLT3). Compound 17k also suppressed colony formation and wound closure, induced apoptosis, and caused S-phase accumulation in HepG2 cells. These findings identify 17k as a nucleoside analogue with unanticipated antiproliferative activity and suggest that kinase modulation may contribute to its cellular effects.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110389"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of pentagalloylglucose as a dual GSTP1/ P-gp inhibitor uncovered by integrated computational and experimental approaches.","authors":"Gaiqian Song, Ayixia Abudula, Moyisa Simayi, Hongning Liu, Hao Lin","doi":"10.1016/j.bioorg.2026.110395","DOIUrl":"10.1016/j.bioorg.2026.110395","url":null,"abstract":"<p><p>Taxol remains a cornerstone therapy for non-small cell lung cancer, however, the development of acquired resistance continues to pose a significant clinical hurdle. Glutathione S-transferase P1 (GSTP1) and P-glycoprotein (P-gp) have been identified as key mediators of this multi-drug resistance phenotype. Consequently, the dual-target inhibition of these proteins represents a promising therapeutic strategy to circumvent chemoresistance. Here, pentagalloylglucose has been identified as a potential dual GSTP1/P-gp inhibitor through virtual screening. Molecular dynamics simulations validated the stable binding conformations of pentagalloylglucose with both target proteins. Furthermore, microscale thermophoresis and cellular thermal shift assays confirmed the direct binding interaction between pentagalloylglucose and GSTP1, while enzymatic assays demonstrated its potent inhibitory efficacy against the enzyme. Notably, treatment with pentagalloylglucose significantly enhanced the intracellular accumulation of Rhodamine 123, thereby indicating effective inhibition of P-gp mediated efflux. This effect culminated in a marked restoration of taxol sensitivity in A549/Taxol resistant cells. Additionally, pentagalloylglucose treatment inhibited cell metastasis in a concentration-dependent manner, accompanied by the down-regulation of epithelial-mesenchymal transition-related genes. Transcriptomic analysis further revealed that pentagalloylglucose modulates multiple signaling pathways implicated in cell proliferation and metastasis. Collectively, these findings establish pentagalloylglucose as a promising dual-target inhibitor for overcoming taxol resistance. The strategy of simultaneously targeting GSTP1 and P-gp offers a viable approach for the treatment of drug-resistant lung adenocarcinoma, providing a robust scientific foundation for future drug development and structural optimization.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110395"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A near-infrared fluorescent probe for imaging sulfite-associated changes in experimental renal injury.","authors":"Kai Wang, Shu-Yi Zou, Yi-Xuan Bo, Han Liu, Zi-Rui Luo, Hong-Rui Zhan","doi":"10.1016/j.bioorg.2026.110403","DOIUrl":"10.1016/j.bioorg.2026.110403","url":null,"abstract":"<p><p>Dissolved S(IV), present mainly as sulfite/bisulfite under near-physiological conditions, participates in sulfur metabolism and redox homeostasis, but its association with renal injury remains difficult to visualize. Here, we describe HD-ZHR, a hemicyanine-based near-infrared turn-on probe in which a levulinate masking group suppresses fluorescence until sulfite/bisulfite-triggered deprotection restores the emissive chromophore. In PBS (10 mM, pH 7.4, 1% DMSO), HD-ZHR produced an approximately 100-fold fluorescence increase at 740 nm under 670 nm excitation, showed a linear response over 0-10 μM, reached a plateau near 40 μM, and achieved a buffer-based detection limit of 0.20 μM with a response time of approximately 120 s. The probe was evaluated in cellular imaging experiments and in mouse models of cisplatin- or gentamicin-induced nephrotoxic injury, hyperuricemic nephropathy, and diabetic kidney disease. Renal-region and ex vivo kidney fluorescence differed between control and injury groups and decreased in losartan- or metformin-treated groups, with parallel group-level changes in serum creatinine and blood urea nitrogen. Because intact probe, fluorescent product, biodistribution, clearance, and tissue sulfite were not independently quantified, these signals are interpreted as sulfite-responsive fluorescence patterns associated with experimental renal injury rather than sulfite-specific in vivo quantification or kidney targeting. HD-ZHR therefore provides a preclinical optical tool for investigating disease-associated S(IV)-responsive fluorescence, while further chemical, analytical, and pharmacokinetic validation is required.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110403"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and synthesis of long-acting prodrugs of SEP-363856 with sustained antipsychotic-like activity.","authors":"Wenjing Gao, Yunlin Xue, Jiyang Zhang, Haoyun Chen, Boyang Yu, Shuo Liu, Yin Chen, Jiaying Xiong, Tao Zhuang","doi":"10.1016/j.bioorg.2026.110390","DOIUrl":"10.1016/j.bioorg.2026.110390","url":null,"abstract":"<p><p>Schizophrenia is a chronic and disabling neuropsychiatric disorder that requires sustained therapeutic exposure to achieve stable symptom control and prevent relapse. SEP-363856, a promising investigational antipsychotic, exhibits robust antipsychotic-like efficacy and safety; however, relatively high clearance may constrain the persistence of its pharmacological effects. To circumvent these drawbacks, three series of prodrugs of SEP-363856 featuring carbamate, amide, and sulfonamide linkages were designed and synthesized. In mouse liver microsomes, prodrug 15 showed markedly prolonged half-lives (57.8 min) relative to SEP-363856 (4.2 min), while gradually releasing the parent drug through metabolic conversion. In two mouse models of schizophrenia, SEP-363856 suppressed schizophrenia-like behaviors only through approximately 90 min, whereas prodrug 15 remained effective at later assessments up to approximately 150 min. These results collectively support prodrug design as a viable strategy for extending the antipsychotic-like effects of SEP-363856.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110390"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148811636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of quinazoline-based dual RET/Aurora B inhibitors for non-small cell lung cancer.","authors":"Maha Hanafi, Baha'a Jabali, Daniel Armstrong, Eva R Palmer, Gavin Hargrove, Baku Acharya, Halle Morgan, Emily Kanwischer, Ashton Hale, Paige Spicer, Brendan Frett","doi":"10.1016/j.bioorg.2026.110399","DOIUrl":"10.1016/j.bioorg.2026.110399","url":null,"abstract":"<p><p>RET and Aurora B (AurB) kinases play critical roles in tumor growth and survival in non-small cell lung cancer (NSCLC), yet monotherapy approaches are frequently undermined by acquired resistance and tumor heterogeneity. Here, we report the discovery of dual RET/AurB inhibitors with potent activity in NSCLC cells. Structure-activity relationship (SAR) studies identified compound 47 as a lead candidate with nanomolar cellular potency. Compound 47 directly inhibits RET and Aurora B kinases in enzymatic assays and effectively suppresses their signaling in cells, as demonstrated by reduced phosphorylation levels. Mechanistic studies involving molecular modeling and kinetic analyses indicate that compound 47 functions as a type II RET inhibitor. In addition, compound 47 demonstrates favorable solubility at therapeutically relevant concentrations, which is further enhanced through salt formation. Collectively, these findings establish a dual-targeted RET/AurB inhibition strategy that addresses complementary oncogenic vulnerabilities in NSCLC and provides a strong foundation for continued optimization and development.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110399"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148823499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, antileukemic activity, and predicted ABL kinase binding dynamics of novel oleanolic acid derivatives in BCR::ABL-positive K562 cells.","authors":"Melek Pehlivan, Burcu Çerçi, Merve Karaman, Süleyman Selim Çınaroğlu, Tülay Kılıçaslan Ayna, Bengüsu Aydın, Nefise Demir, Mustafa Soyöz, Tuba Öz, Mustafa Can, Hakkı Ogün Sercan","doi":"10.1016/j.bioorg.2026.110345","DOIUrl":"10.1016/j.bioorg.2026.110345","url":null,"abstract":"<p><p>Chronic myeloid leukemia (CML) is a hematological malignancy driven by the BCR::ABL fusion protein. Although tyrosine kinase inhibitors such as imatinib have markedly improved clinical outcomes, treatment resistance remains a major challenge. Natural product-derived compounds may offer alternative therapeutic opportunities. This study investigated the antiproliferative and pro-apoptotic effects of newly synthesized oleanolic acid (OA) derivatives in K562 cells and evaluated their predicted interactions with the ABL kinase domain. OA derivatives were synthesized and characterized by FT-IR and NMR. Cytotoxicity was assessed using the WST-8 assay. Apoptosis, mitochondrial membrane potential, and cell-cycle distribution were analyzed by flow cytometry. Expression levels of BCL2, BAX, Caspase-3, Caspase-8, and Caspase-9 were determined by qPCR, whereas BCR::ABL protein levels were assessed by Western blotting. Boltz-2 complex prediction, molecular dynamics simulations, and MM/PBSA calculations were used to evaluate predicted binding stability, interaction patterns, and energetics. OA-Acid showed the lowest IC₅₀, whereas OACN showed the highest value . Apoptosis was highest in imatinib- and OACN-treated cells, and mitochondrial membrane potential decreased significantly in both groups. OA-Acid and MCM35 produced the greatest G0/G1 accumulation. Apoptosis-related gene expression was altered in a compound-dependent manner. OA-Acid showed the greatest decrease in BCR::ABL protein level. Computational analyses supported conformationally stable predicted interactions of OA, OA-Acid, and OACN within the ABL ATP-binding region. OA derivatives produced distinct cytotoxic, apoptotic, mitochondrial, cell-cycle, and molecular effects in K562 cells. Computational findings supported predicted interactions within the ABL kinase domain, warranting further chemical and mechanistic evaluation.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110345"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design, synthesis, and biological evaluation of secondary amine-containing flavonoids with anti-osteosarcoma activity associated with modulation of AKT signaling and EMT-related gene expression.","authors":"Isabela Santos, Hélio M T Albuquerque, José Miguel P Ferreira de Oliveira, Eduarda Fernandes","doi":"10.1016/j.bioorg.2026.110433","DOIUrl":"10.1016/j.bioorg.2026.110433","url":null,"abstract":"<p><p>The development of more effective therapeutics for osteosarcoma is frequently hindered by chemoresistance, metastatic progression, and chemotherapy-associated toxicity. Targeting key oncogenic signaling pathways, such as the PI3K/AKT axis - a key driver of osteosarcoma progression, migration, EMT-like processes, and chemoresistance - represents a rational therapeutic strategy for improving treatment outcomes. In this study, five flavonoid-based derivatives bearing a trimethoxy moiety on the B-ring and distinct secondary amines at C-7 of the A-ring were designed, synthesized, and screened against the 143B osteosarcoma cell line with high propensity to metastasize. Derivatives 6a and 6b demonstrated potent anticancer activity, exhibiting high selectivity toward the osteosarcoma cell line and low toxicity toward non-malignant MRC-5 lung fibroblasts. Interestingly, both compounds synergistically interacted with doxorubicin, substantially reducing the required dose of the chemotherapeutic agent. Mechanistically, both compounds, as single agents and in combination with doxorubicin, were associated with reduced AKT phosphorylation and downregulation of downstream mediators associated with tumor progression and epithelial-mesenchymal transition (EMT), including ZEB1, MMP2, and MMP9. Collectively, these findings show that 6a and 6b exert anti-osteosarcoma effects that are consistent with modulation of the AKT signaling pathway and EMT-related gene expression. Here, we demonstrate that secondary amine functionalities in the flavonoid backbone provide a rational framework for the development of targeted therapeutic strategies for osteosarcoma.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110433"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148849488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design, synthesis, anticancer evaluation, and molecular dynamics-based computational investigation of novel pyrimidine-benzothiazole/phenyl hybrid-based VEGFR-2-targeted derivatives with antioxidant, DNA nicking, DNA interaction, and cytotoxicity studies.","authors":"Karan A Kamle, Shreyansh R Mevada, Reena H Hirani, Shailesh Vanshiya, Nishith Gamit, Ravi K Barad, Nigam Bhanugariya, Muskan Goswami, Milan Thakar, Gaurang Shindhav, Shilpa Kumari, Kanu Priya, Himanshu Vasava, Rakesh Panchal, Nandan Dixit, Saumya Patel, Dilip V Vasava","doi":"10.1016/j.bioorg.2026.110422","DOIUrl":"10.1016/j.bioorg.2026.110422","url":null,"abstract":"<p><p>A series of novel pyrimidine-based benzothiazole/phenyl hybrids was rationally designed and synthesized via molecular hybridization to develop promising anticancer agents. The compounds were evaluated against human lung carcinoma (A549) and breast adenocarcinoma (MCF-7) cell lines, while HEK-293 cells were used to assess selectivity toward normal cells. Among the derivatives, K12, K5, and K4 showed potent activity against A549 cells, with IC₅₀ values of 6.18, 7.01, and 7.54 μM, respectively. K5 and K12 also showed significant activity against MCF-7 cells, with IC₅₀ values of 8.33 and 9.30 μM, respectively. All compounds displayed minimal cytotoxicity toward HEK-293 cells, indicating favorable selectivity for cancer cells. UV-Vis DNA-binding studies suggested a probable intercalative binding mode, while DNA nicking assays demonstrated protection against oxidative DNA damage. K12 showed the strongest DNA-binding affinity and DNA-protective activity. Molecular docking against the VEGFR-2 kinase domain (PDB ID: 4ASD), followed by 501 ns MD simulations, revealed stable protein-ligand complexes, supported by RMSD, RMSF, DCCM, PCA, and free energy landscape analyses. MM/GBSA calculations indicated favorable binding free energies, dominated by van der Waals interactions. Overall, K12 emerged as the most promising lead compound, combining potent antiproliferative activity, high selectivity, efficient DNA-binding characteristics, and robust computational performance, highlighting its potential for further development as a novel anticancer agent.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110422"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148816926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design, synthesis and biological evaluation of piroctone olamine-derived iron chelators as HIF-1α stabilizers for diabetic wound healing.","authors":"Liying Zhou, Lijuan Wu, Kangkang Qi, Xiaozhuang Li, Lu Lu, Rilei Yu, Jinbo Yang, Lu Han, Shengbiao Wan, Peiju Qiu","doi":"10.1016/j.bioorg.2026.110378","DOIUrl":"10.1016/j.bioorg.2026.110378","url":null,"abstract":"<p><p>Hyperglycemia-induced iron overload and oxidative stress impair HIF-α stabilization and transcriptional activation, thereby suppressing neovascularization and delaying diabetic wound healing. Targeting iron-associated oxidative stress and reactivating HIF signaling therefore represents a promising therapeutic strategy for diabetic wound healing. In this study, inspired by the strong iron-chelating capacity of cyclic hydroxamate scaffolds, we designed and synthesized a novel series of 29 piroctone olamine-derived iron chelators through pharmacophore-guided optimization of the cyclic hydroxamate moiety and strategic incorporation of 2-oxoglutarate-mimetic motifs. Systematic structure-activity relationship analysis revealed that the free cyclic hydroxamate moiety, terminal aromatic substitution, and linker length were key determinants of iron-chelating potency, ROS-suppressive activity, cellular efficacy, and safety. Among these derivatives, compound 17b displayed the most favorable pharmacological profile, including potent iron-chelating activity, effective suppression of hyperglycemia-induced ROS accumulation, low cytotoxicity, and rapid stabilization of HIF-1α under high-glucose stress conditions. Further mechanistic investigations demonstrated that 17b activated HIF-dependent transcription, as reflected by increased expression of VEGFA and GLUT1. Functionally, 17b promoted fibroblast migration in vitro, supporting its role in key cellular processes involved in wound repair. In a Pseudomonas aeruginosa-infected diabetic rat wound model, 17b significantly accelerated wound closure, accompanied by enhanced neovascularization and collagen deposition. Collectively, these findings identify 17b as a promising piroctone olamine-derived HIF-1α stabilizer and an iron-chelating compound that may alleviate iron-associated oxidative stress under diabetic stress conditions, providing a novel chemical scaffold for the development of iron chelator-based therapeutics for diabetic wound management.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110378"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Activity cliffs resist prediction within and across protein kinases: a leakage-controlled machine-learning analysis of structure-potency discontinuities.","authors":"Samuel S Agboola, Oluwaseun E Agboola, Oluwaseun Ruth Olasehinde, Temitope C Aribigbola, Anuoluwapo Bukola Shaleye, I Adefolake Alebiosu, Zainab A Ayinla, Babatunji E Oyinloye, Olutosin S Ilesanmi, Idowu O Omotuyi, Abel Kolawole Oyebamiji","doi":"10.1016/j.bioorg.2026.110406","DOIUrl":"10.1016/j.bioorg.2026.110406","url":null,"abstract":"<p><p>Activity cliffs, that is pairs of closely related molecules with large potency differences, limit the reliability of structure-activity models, and it is commonly assumed that the chemistry responsible for a cliff carries information that generalizes to other targets. We tested this assumption directly across the protein kinase family using machine-learning models trained on measured bioactivity data. From 16,897 Ki and Kd measurements for 20 human kinases (8661 unique standardized structures) we generated 186,663 single-cut matched molecular pairs and labelled 116,845 as activity cliffs (|ΔpActivity| ≥ 2.0) or smooth pairs (≤0.5). Three findings emerged. First, cliff-forming transformations rarely recur across targets: 97.1% occurred on a single kinase, and agreement among those that did recur was indistinguishable from zero (median r = -0.058, 95% CI -0.13 to 0.41). Second, leave-one-kinase-out random forests exceeded both a prevalence baseline (average precision 0.111) and a transformation-frequency baseline (0.149), reaching 0.238. Third, the apparent advantage of within-target learning proved to be a validation artefact: under leakage-controlled grouped cross-validation, within-kinase performance fell from 0.821 to 0.309 (scaffold grouping) and 0.211 (molecular-component grouping) and became statistically indistinguishable from cross-kinase performance (p = 0.31 and p = 0.17). Activity cliffs are therefore difficult to predict in general rather than specifically difficult to transfer, and inferences about target specificity are highly sensitive to how within-target validation is grouped.</p>","PeriodicalId":257,"journal":{"name":"Bioorganic Chemistry","volume":"181 ","pages":"110406"},"PeriodicalIF":5.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148786253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}