Monosaccharide-linked inhibitors of O-6-methylguanine-DNA methyltransferase (MGMT): Synthesis, molecular modeling, and structure-activity relationships

A series of potential inhibitors of the human DNA repair protein O-6-methyl guanine-DNA methyltransferase (MGMT) were synthesized, characterized in det ail by NMR, and tested for their ability to deplete MGMT activity in vitro. The new compounds, omega-[O-6-R-guan-9-yl]-(CH2)(n)-beta -d-glucosides wit h R = benzyl or 4-bromothenyl and omega = n = 2, 4, ... 12, were compared w ith the established inhibitors O-6 -benzylguanine (O-6-BG), 8-aza-O-6-benzy lguanine (8-aza-BG), and O-6-(4-bromothenyl)guanine (4-BTG), which exhibit in an in vitro assay IC50 values of 0.62, 0.038, and 0.009 muM, respectivel y. Potential advantages of the glucosides are improved water solubility and selective uptake in tumor cells. The 4-BTG glucosides with n = 2, 4, 6 sho w moderate inhibition with an IC50 of ca. 0.5 muM, while glucosides derived from BG and 8-aza-BG showed significantly poorer inhibition compared to th e parent compounds. The 4-BTG glucosides with n = 8, 10, 12 were effective inhibitors with IC50 values of ca. 0.03 muM. To understand this behavior, e xtensive molecular modeling studies were performed using the published crys tal structure of MGMT (PDB entry: 1QNT). The inhibitor molecules were docke d into the BG binding pocket, and molecular dynamics simulations with expli cit water molecules were carried out. Stabilization energies for the intera ctions of specific regions of the inhibitor and individual amino acid resid ues were calculated. The alkyl spacer is located in a cleft along helix 6 o f MGMT. With increasing spacer length there is increasing interaction with several amino acid residues which play an important role in the proposed nu cleotide flipping mechanism required for DNA repair.