title: Algorithmic modeling quantifies the complementary contribution of metabolic inhibitions to gemcitabine efficacy.
abstract: Gemcitabine (2,2-difluorodeoxycytidine, dFdC) is a prodrug widely used for treating various carcinomas. Gemcitabine exerts its clinical effect by depleting the deoxyribonucleotide pools, and incorporating its triphosphate metabolite (dFdC-TP) into DNA, thereby inhibiting DNA synthesis. This process blocks the cell cycle in the early S phase, eventually resulting in apoptosis. The incorporation of gemcitabine into DNA takes place in competition with the natural nucleoside dCTP. The mechanisms of indirect competition between these cascades for common resources are given with the race for DNA incorporation; in clinical studies dedicated to singling out mechanisms of resistance, ribonucleotide reductase (RR) and deoxycytidine kinase (dCK) and human equilibrative nucleoside transporter1 (hENT1) have been associated to efficacy of gemcitabine with respect to their roles in the synthesis cascades of dFdC-TP and dCTP. However, the direct competition, which manifests itself in terms of inhibitions between these cascades, remains to be quantified. We propose an algorithmic model of gemcitabine mechanism of action, verified with respect to independent experimental data. We performed in silico experiments in different virtual conditions, otherwise difficult in vivo, to evaluate the contribution of the inhibitory mechanisms to gemcitabine efficacy. In agreement with the experimental data, our model indicates that the inhibitions due to the association of dCTP with dCK and the association of gemcitabine diphosphate metabolite (dFdC-DP) with RR play a key role in adjusting the efficacy. While the former tunes the catalysis of the rate-limiting first phosphorylation of dFdC, the latter is responsible for depletion of dCTP pools, thereby contributing to gemcitabine efficacy with a dependency on nucleoside transport efficiency. Our simulations predict the existence of a continuum of non-efficacy to high-efficacy regimes, where the levels of dFdC-TP and dCTP are coupled in a complementary manner, which can explain the resistance to this drug in some patients.
authors.affiliation: The Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto (Trento), Italy. ozan@cosbi.eu
authors.forename: Ozan
authors.initials: O
authors.lastname: Kahramanoğullari
authors.forename: Gianluca
authors.initials: G
authors.lastname: Fantaccini
authors.forename: Paola
authors.initials: P
authors.lastname: Lecca
authors.forename: Daniele
authors.initials: D
authors.lastname: Morpurgo
authors.forename: Corrado
authors.initials: C
authors.lastname: Priami
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004247:DNA / Q000096:biosynthesis*; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000627:therapeutic use; D003842:Deoxycytidine Kinase / Q000378:metabolism; D003845:Deoxycytosine Nucleotides / Q000378:metabolism; D033721:Equilibrative Nucleoside Transporter 1 / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008962:Models, Theoretical; D009369:Neoplasms / Q000188:drug therapy*; D012264:Ribonucleotide Reductases / Q000378:metabolism; D000093542:Gemcitabine
chemical_list: D003845:Deoxycytosine Nucleotides; D033721:Equilibrative Nucleoside Transporter 1; C438649:SLC29A1 protein, human; D003841:Deoxycytidine; C024107:2'-deoxycytidine 5'-triphosphate; D004247:DNA; D012264:Ribonucleotide Reductases; D003842:Deoxycytidine Kinase; D000093542:Gemcitabine