Journal of Enzyme Inhibition and Medicinal Chemistry, 2010; 25(2): 250-265 Abstract Recently, the three-dimensional structure of the active site of human DNA polymerase α (pol α) was proposed based on the application of molecular modeling methods and molecular dynamic simulations. The modeled structure of the enzyme was used for docking selective inhibitors (nucleotide analogs and the non-nucleoside inhibitor aphidicolin) in its active site in order to design new drugs for actinic keratosis and squamous cell carcinoma (SCC). The resulting complexes explained the geometrical and physicochemical interactions of the inhibitors with the amino acid residues involved in binding to the catalytic site, and offered insight into the experimentally derived binding data. The proposed structures were synthesized and tested in vitro for their influence on human keratinocytes and relevant tumor cell lines. Effects were compared to aphidicolin which inhibits pol α in a non-competitive manner, as well as to diclofenac and 5-fluorouracil, both approved for therapy of actinic keratosis. Here we describe three new nucleoside analogs inhibiting keratinocyte proliferation by inhibiting DNA synthesis and inducing apoptosis and necrosis. Thus, the combination of modeling studies and in vitro tests should allow the derivation of new drug candidates for the therapy of skin tumors, given that the agents are not relevant substrates of nucleotide transporters expressed by skin cancer cells. Kinases for nucleoside activation were detected, too, corresponding with the observed effects of nucleoside analogs.
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Keywords: Human DNA polymerase; polymerase inhibitors; keratinocytes; molecular dynamic simulations; nucleoside analogs; kinases; nucleoside transportersAbbreviations: 5-FU, 5-fluorouracil; annexin V-FITC, rh annexin V labeled with fluorescein isothiocyanate; ara-G (nelarabine), 2-amino-9--d-arabinofuranosyl-6-methoxy-9H-purine; ATCC, American Type Culture Collection; dCK, deoxycytidine kinase; dGK, deoxyguanosine kinase; DMEM, Dulbecco's modified Eagle's medium; DMSO, dimethylsulfoxide; dNTP, deoxynucleoside triphosphate; EDTA, ethylene diamine tetraacetic acid; FCS, fetal calf serum; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; HaCaT, spontaneously transformed human keratinocyte cell line; hENT-1, human equilibrative nucleoside transporter; KBM, keratinocyte basal medium; KGM, keratinocyte growth medium; MCF-7, human breast adenocarcinoma cell line; MRP, multidrug resistance protein; MTT, methylthiazolyldiphenyltetrazolium bromide; NHK, normal human keratinocytes; NRU, neutral red uptake; PBS, phosphate buffered saline, pH 7.4; PI, propidium iodide; RPMI, Roosevelt Park Memorial Institute; RT-PCR, reverse transcriptase polymerase chain reaction; SCC, squamous cell carcinoma; TK-1, thymidine kinase; TPace, thymidine phosphorylase; TP, triphosphate