Transcriptomic evaluation of a potent trifluoromethyl phenyl acetamide derivative for its anticancer effect

Cancer is a global health crisis, ranking as one of the leading causes of mortality worldwide. Its persistent increase in incidence is driven by the intricate nature of tumor biology, rapid mutations, drug resistance, and limited efficacy of many current treatment options. These challenges highlight the need for mechanistically defined small-molecule therapeutics that selectively target tumor vulnerabilities while sparing normal tissues. Fluorinated scaffolds are of translational interest due to their ability to enhance metabolic stability, bioavailability, and drug-like properties. In this study, we synthesized and characterized a focused library of s-trifluoromethyl phenyl acetamide derivatives (N3-N6 and V1-V8) via a series of chemical reactions. The structural integrity of these compounds was verified through a combination of analytical techniques, including melting point determination, Proton Nuclear Magnetic Resonance ( 1 H NMR), Carbon-13 Nuclear Magnetic Resonance ( 13 C NMR), and Infrared (IR) spectroscopy. The s-trifluoromethyl phenyl acetamide scaffold is of particular interest in medicinal chemistry due to its favorable pharmacological properties, including enhanced stability, lipophilicity, and metabolic resistance. These compounds were evaluated for anticancer activity across a broad panel of human and murine cancer models, including colorectal cancer (HT-29, MC38, CT26and COLO 205), hepatic (C3a and PLC/PRF5), pancreatic (Suit-2, MiaPaca2, As-PC1 and Panc 02.03), breast (MDA-MB-468, MDA-MB-231, BT20, MCF7, 4T1, 4T1 paclitaxel resistant, JIMT-1, ZR-75-1, E0771, T47D, and HCC1806) and ovarian (OVCAR-5) cell lines. Normal mammary epithelial cells (MCF10A) were included to assess therapeutic selectivity & toxicity of the lead compound. Based on the SRB assay the 12 compounds exhibited variable but significant cytotoxic effects in various cancer cell lines. Lead compound V2 showed the highest potency across multiple tumor types while exhibiting reduced toxicity toward normal epithelial cells. To elucidate the mechanism of action underlying V2 activity, RNA-sequencing was performed on BT20 cells treated with V2 at IC 50 compared to untreated control group. Results revealed significant transcriptional reprogramming, with 420 genes upregulated and 336 genes downregulated following treatment with V2. Gene ontology (GO) enrichment, V2 initiated an integrated-stress-response (ISR)-like programme that rapidly lowers global protein synthesis while allowing selective translation of stress-response mRNAs. In addition, V2 treatment affected the proteasome machinery in BT20 cells. This dual disruption of protein synthesis and degradation represents a previously underexplored vulnerability in aggressive breast cancer models, including BT20 cells. Further experiments are in progress to validate the effects of V2 on RNA-binding proteins, translation factors and to identify the target and establish the mechanism in breast cancer.