EUK4010 has been identified to exhibit an inhibitory effect on β-amyloid (Aβ)1−42-induced loss of neuronal cell viability. Further studies demonstrated that EUK4010 attenuated the Aβ1−42-induced degeneration in both cultured rat hippocampal neurons and human neuroblastoma cells, as demonstrated by typical morphological changes, cell viability and the chip-based flow cytometric assay. Gene expression analysis using DNA microarray showed that the senescence marker calcium-binding protein, regucalcin (Rgn), GABA-A receptor pi subunit (Gabrp), the huntingtin binding protein, optineurin (Optn) and a semaphorin family plexin A3 similar protein (Plex-similar) changed their expression levels significantly in cultured neurons after Aβ1−42 treatment. In this report, we have undertaken a chemical genetic approach to study the molecular basis of Aβ1−42 effects on the neuronal degeneration. Our results demonstrate that EUK4010 completely blocked the Aβ1−42-induced up-regulation of GABA-A receptor pi subunit and the semaphorin family plexin A3 similar protein, and partially attenuated the down-regulation of senescence marker calcium-binding protein, regucalcin. These observations suggest that EUK4010 may prevent or reduce the Aβ toxicity by regulating the expression of genes involved in the Aβ induced neuronal degeneration. These genes may represent a promising target for the therapeutic drug development for Alzheimer's disease (AD) and other neurological disorders. Furthermore, EUK4010 and its analogues could potentially be developed as neuronal protective agents for the treatment of these diseases.