How A Small Molecule Targeting Two Oncogenes Triggers Synthetic Lethality in Leukaemia

Unlike many current leukaemia drugs that target only one pathway, a molecule designed by IACS researchers attacks two essential oncogenes at the same time, leaving cancer cells with no fallback options. As the molecule acts at the DNA-regulation level, it may also bypass some of the resistance mechanisms seen with protein-targeting inhibitors

Leukaemia cells that rely simultaneously on the oncogenes c-KIT and KRAS appear highly vulnerable to a triazolyl-indole small molecule that we designed and synthesised. By stabilising G-quadruplex DNA structures at the promoter regions of both genes, the compound suppresses their transcription and drives synthetic lethality — a strategy that selectively kills cancer cells while sparing healthy ones. The results were published recently in the Journal of Medicinal Chemistry.

Many leukemic subtypes maintain proliferation and survival through combined activation of c-KIT signalling and KRAS-driven pathways. While each oncogene can support malignant growth independently, cells co-dependent on both appear to operate on a narrow functional threshold: perturb one, and the other compensates; perturb both, and the cells collapse.

A triazolyl-indole derivative targets G-quadruplex structures

Based on earlier reports of anti-cancer properties of indoles and triazoles, we designed a family of triazolyl-indole derivatives with the goal of targeting G-quadruplex (G4) structures — four-stranded nucleic-acid conformations enriched in promoter regions of oncogenes. G-quadruplex structures are increasingly recognised as regulatory elements that can modulate transcription: stabilising them can silence gene expression. c-KIT and KRAS each contain G-rich promoter sequences capable of forming such structures. Stabilising these structures can prevent a gene from switching on, making them prime candidates for duplex disruption.

The molecular docking and molecular dynamics simulation studies were done alongside high-throughput biophysical studies to establish high affinity interaction of the Triazolyl-indole derivative with promoter G4 structures of oncogenic c-KIT and KRAS. We identified one derivative (TI12) with particularly strong G4-binding and gene-silencing activity.

Selective repression of c-KIT, KRAS

In laboratory (in vitro) tests, the hit molecule showed strong, dose-dependent effects on leukaemia cells. At 6.8 μM, the molecule sharply lowered the levels of c-KIT and KRAS, cutting off the signals that these cancer cells rely on. As both genes were silenced, the cells stopped dividing, accumulated damage, and moved rapidly toward death. The response was also quick — within 48 hours, treated cells showed reduced viability, increased DNA damage, and clear signs of apoptosis. Cells that were dependent on both oncogenes were the most vulnerable, revealing a strong synthetic-lethal effect. Normal, non-cancerous cells responded very differently. Even at similar or higher concentrations, they remained largely unaffected, highlighting the molecule’s high selectivity for cancer-specific vulnerabilities.

Cells with low or single-oncogene dependency were far less affected, providing a mechanistic rationale for the compound’s selectivity.

Unlike many current leukaemia drugs that target only one pathway, the molecule attacks two essential oncogenes at the same time, leaving cancer cells with no fallback options. Because the molecule acts at the DNA-regulation level rather than directly targeting proteins, it may also bypass some of the resistance mechanisms seen with protein-targeting inhibitors.

Targeted cytotoxicity

A central concern for any transcription-modulating therapy is toxicity to normal cells. We systematically evaluated the compound across non-malignant cell lines.

Across these models, viability remained largely unchanged, whereas leukaemia cells showed clear, dose-dependent cytotoxicity. This selective response underscores the reliance of cancer cells — but not healthy cells — on aberrantly heightened c-KIT and KRAS signalling.

The mechanism fits a broader principle in cancer biology: malignant cells often become addicted to specific oncogenic circuits they hijack for survival, creating therapeutic windows not present in normal tissues.

Mouse studies

In mouse studies, the molecule was tested in vivo by injecting it directly into human leukaemia tumours at two concentrations, twice weekly for 24 days. Tumour growth decreased by over 50% at the lower dose and more than 65% at the higher dose. Treated tumours also showed reduced c-KIT, KRAS, and Ki-67 levels. The mice maintained stable body weight with no major organ damage.

The study used intratumoural dosing in mice, not systemic dosing. Whether the hit molecule, TI12 can circulate through the bloodstream and reach tumours throughout the body remains to be tested. Its pharmacokinetic behaviour — how long it stays in the body and how it is metabolised — also needs detailed evaluation. Only one leukaemia model was studied; more models will be required to generalise the findings.

Achieving synthetic lethality

One of the most notable contributions of the study is the demonstration of a single-molecule synthetic-lethal strategy. Synthetic lethality typically involves pairwise genetic interactions — where mutation in one gene is tolerable, but combined perturbation is not. We demonstrated that pharmacological stabilisation of distinct G4 structures can simultaneously repress two independent oncogenes, driving a synthetic-lethal phenotype.

This shifts the framework from classical gene-gene interactions to structure-based dual oncogene suppression, broadening how synthetic lethality can be therapeutically engineered.

G-quadruplex therapeutics

Interest in G-quadruplex-targeting small molecules has grown rapidly, with several molecules undergoing preclinical evaluation. The present study extends that field in three important ways:

Dual-target transcriptional control: Most existing G4 ligands modulate one gene; here, two oncogenes with independent G4 motifs are repressed simultaneously.

Mechanistically rich design: The triazolyl-indole scaffold is engineered for specificity, reducing the nonspecific DNA binding seen in many earlier G4 ligands.

Synthetic lethality integration: Connecting G4 modulation to a synthetic-lethal outcome gives the strategy therapeutic coherence and translational relevance.

The work suggests a possible roadmap for next-generation leukaemia treatments. One could be precision targeting of transcriptional vulnerabilities rather than kinase inhibition alone. The other is by overcoming redundancy in which dual-oncogene repression may avoid compensatory signalling that often drives drug resistance. Finally, designing multi-target small molecules guided by structural motifs — not by random polypharmacology.

By integrating promoter G-quadruplex structural biology with rational small-molecule design, the study provides a blueprint for selectively disrupting oncogenic circuits in leukaemia. The dual suppression of c-KIT and KRAS illustrates how structurally informed ligands can uncover and exploit precise vulnerabilities in cancer cells.

If subsequent studies validate and extend these findings, triazolyl-indole scaffolds may offer a new entry point into synthetic-lethal drug discovery, with implications reaching well beyond leukaemia.

The future of cancer treatment

Our work highlights a new concept in cancer therapy: using one molecule to disable two vital cancer genes at once. Cancer cells that depend on both genes cannot survive when both switches are turned off together, making this a powerful “double-strike” strategy.

Unlike many cancer drugs that target proteins, the novel small molecule works at the level of DNA regulation. This opens possibilities for treating cancers that have become resistant to protein-targeting drugs or those that rely on multiple growth pathways at once.

The findings are early, but promising. Future studies will focus on systemic administration, optimisation of the molecule’s chemical stability, expanded animal testing (including patient-derived samples), and deeper exploration of potential resistance mechanisms. If future studies confirm safety and effectiveness, this approach could inspire a new class of medicines designed to cut off cancer’s lifelines at the source.