Identification of a small molecule inhibitor of BLM helicase


BLM helicase is a member of the RecQ helicase family of ATP-dependent proteins that separate the two strands of duplex DNA, allowing DNA replication and repair processes to proceed. Mutations in this protein result in Bloom’s syndrome (BS), characterised by genomic instability, particularly an increased frequency of sister chromatid exchanges (SCEs), and a predisposition to cancer development, amongst other clinical features. Patients often develop leukaemia’s and lymphoma’s although most types of cancer have been observed in this group. BLM has also been demonstrated to be involved in a process known as Alternative Lengthening of the Telomeres (ALT). This is a homologous recombination-mediated mechanism by which new telomeric DNA is synthesised from an existing DNA template. The finer details of this pathway are unknown but it is known that depletion of BLM by siRNA in ALT+ cells results in telomere shortening.

Telomeres are ‘caps’ at the ends of the chromosomes and consist of repetitive DNA sequence and proteins. They function to protect the chromosome end from degradation or association with other chromosomes. The length of the telomere shortens with each cell division, resulting in replicative  senescence when a critical telomere length is reached. Telomeres are maintained in cancer cells either by up regulation of Telomerase, an enzyme that adds telomeric repeats, or via the use of the ALT pathway, enabling cells to proliferate aberrantly. Approximately 10% of all tumours rely on the ALT pathway for their continued growth and 66% of Osteosarcoma tumours are ALT+. Repression of ALT in ALT+ immortal cell lines results in senescence and cell death, making inhibition of this pathway an attractive therapeutic target.

Nguyen et al., recently described the identification of a novel small molecule BLM inhibitor. The group developed a high-throughput screening assay using a labelled partly duplex DNA substrate. Quenching of the substrate was lost upon separation of the two strands, resulting in increased fluorescence with increasing BLM helicase activity. Hits from this primary screen were then confirmed in a helicase gel assay. Medicinal chemistry optimisation of a hit compound resulted in a lead molecule termed ML216 which inhibited BLM with an IC50 value of 3µM. They went on to show that ML216 affects the DNA binding activity of BLM . Further, the group demonstrated that ML216 inhibited the proliferation of cells transfected with BLM, but not the isogenic BLM negative control cells. Treatment with ML216 also sensitised the BLM+ cells to the replication inhibitor, aphidicolin but with no sensitising effect on the BLM negative controls.  A further important observation was that treatment of cells with ML216 increased the frequency of SCE’s observed, but only in the BLM expressing cells. The group also observed that ML216 could inhibit WRN, a related DNA helicase, in in vitro gel assays. However, they found no inhibitory effects on WRN in the cell-based assays conducted, indicating that the primary target of this compound in human cells is BLM. There is currently no available crystal structure of BLM for further analysis of ML216 binding.sw3sw4

 

The identification of this novel small molecule could now enable studies of the effects of BLM helicase inhibition in ALT+ tumour cells and potentially uncover a new treatment strategy for ALT+ tumours.

 

 

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