19/08/2026
๐ EFMC Literature Spotlight ๐
This contribution, provided by Dr Caroline Gentz (Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, Spain), discusses the recently published article โStructure-Based Design, Synthesis, and Evaluation of Novel Ponatinib Derivatives With a Significantly Altered Selectivity Profileโ by Betzholz et al., published in ChemMedChem.
Ponatinib is a third-generation tyrosine kinase inhibitor approved for the treatment of chronic myeloid leukemia, particularly in patients harboring the T315I gatekeeper mutation that confers resistance to other tyrosine kinase inhibitors. Its clinical efficacy is related to its broad kinase inhibition profile, which is able to inhibit more than 60 kinases. However, this promiscuity is also associated with severe adverse effects, including cardiovascular toxicity. In this work, Betzholz and co-workers investigated whether subtle structural modifications could reduce ponatinib's kinase promiscuity while maintaining its antiproliferative activity, using a structure-based medicinal chemistry approach.
The design was guided by crystal structures of ponatinib bound to diverse kinases, which suggested that the benzamide moiety could tolerate structural modifications without disrupting the key interactions responsible for target binding. Based on this, the authors prepared a chemo-library of twelve derivatives by varying two structural elements: the substitution pattern of the benzamide ring and the terminal basic side chain. Four regioisomeric methyl-substituted benzamides were first synthesized and coupled to either a propylamine- or a propenylamine-containing ponatinib intermediate, giving two complementary subseries (compounds 1-4 and 5-12, respectively). The modular synthetic route enabled late-stage diversification while preserving the imidazopyridazine core and the ethynyl linker, allowing the authors to directly assess how subtle steric modifications influence kinase inhibition.
The compounds were evaluated in MDA-MB-231, a breast cancer cell line that expresses many kinases that are targeted by ponatinib, using both cytotoxicity assays and long-term colony formation experiments. Interestingly, the colony formation assay proved to be more sensitive in detecting sustained antiproliferative effects, revealing differences between analogues that were less apparent in the short-term viability assay. To characterize kinase engagement, the authors employed differential scanning fluorimetry (DSF) as a primary profiling method, followed by microscale thermophoresis (MST) to quantify binding affinities for selected kinases.
One of the most notable findings was the steep structure-activity relationship associated with methyl substitution on the benzamide ring. Although the analogues differ only by the position of a single methyl group, these minor changes were able to alter the kinase selectivity. Among the series, compound 5 was the most informative example: despite retaining the antiproliferative activity, particularly in the colony formation assay, it showed a narrower kinase target spectrum than ponatinib. DSF analyses showed that strong interactions with B-Raf, Flt1, and STK10 were largely preserved, whereas several kinases targeted by ponatinib, including FGFR1 and SLK, both associated with cardiovascular toxicity, were no longer significantly engaged. These findings illustrate that subtle steric modifications can reshape kinase recognition rather than simply attenuating potency.
Rather than presenting a new therapeutic candidate, this study provides elegant proof of concept that kinase selectivity can be intentionally engineered through minimal structural modifications. By demonstrating that a single methyl substituent can markedly remodel the interaction profile of a clinically established multikinase inhibitor, the authors highlight an important principle in medicinal chemistry: optimizing a drug is not only about maximizing potency, but also about controlling polypharmacology.
๐ Read the full article here: https://buff.ly/4meFCZ4
