Delineation of the Molecular Mechanisms of Nucleoside Recognition by Cytidine Deaminase through Virtual Screening

Abstract

Cytidine deaminase (3.5.4.5, CDA), an enzyme of the pyrimidine salvage pathways, is responsible for the degradation and inactivation of several cytidine-based antitumoral drugs, such as cytarabine, gemcitabine, decitabine, and azacytidine. Thus, CDA inhibitors are highly sought after as compounds to be co-administered with said drugs in order to improve their effectiveness. Alternatively, the design of antitumoral drugs not susceptible to the action of CDA is also regarded as an attractive solution. Here, we describe a virtual screening for CDA ligands based on chemical similarity and molecular docking. The campaign led to identification of three novel inhibitors and one novel substrate, with a 19% hit rate, and allowed a significant extension of the structure-activity relationships, also in light of the compounds that resulted inactive. The most active compound identified through the screening was the inhibitor pseudoisocytidine, which has the potential to serve as a lead for highly stable compounds. The study also delineated the detrimental effect of 5-aza and 6-aza substitutions, the incompatibility of the presence of an amino group at the 3′-position, as well as the presence of very strict steric requirements around the 2′-arabino position and, even more, the N4-position. Importantly, these features can be exploited for the design of novel antineoplastic agents resistant to the action of CDA.

DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis

“…The substrate (CMP), product (UMP) and a K915A mutation do not have an effect on the overall high T m of OTP86 DYW , which is about 71–2 °C in each case ( Fig. 6a ) 47 . These results imply a limited accessibility of the active site due to steric inhibition, consistent with the structures and corroborated by mutants.…”

Pharmacogenomics of Gemcitabine Metabolism: Functional Analysis of Genetic Variants in Cytidine Deaminase and Deoxycytidine Kinase

“…The reason for the substrate dependency is unknown. It is possible that the Ala70Thr substitution may modify the interactions of Glu67 in the CDA active site with the C29-arabino position of substrates, around which strict steric requirements have been reported (Costanzi et al, 2011). Consequently, slight changes at the 29-sugar position from a hydroxyl group in Ara-C to fluorines in dFdC would result in differential reduction of CDA catalytic activity toward Ara-C and dFdC.…”

Gemcitabine diphosphate choline is a major metabolite linked to the Kennedy pathway in pancreatic cancer models in vivo

“…2′,2′-difluorodeoxyuridine (dFdU) has been considered to be the major inactive metabolite of dFdC; however, its triphosphorylated form dFdUTP may contribute to cytotoxicity ( Veltkamp et al , 2008 ). Metabolism-based approaches to improve dFdC efficacy are ultimately aimed at increasing the amount of dFdCTP and have thus far manipulated nodes in the drug's metabolic pathway likely to favour dFdCTP formation, such as reducing cytidine deaminase-mediated dFdU formation ( Beumer et al , 2008 ; Costanzi et al , 2011 ; Tibaldi et al , 2011 ). However, such approaches will be informed by knowledge of intra-tumoural metabolism of the drug that has been limited by the scarcity of tissue specimens from patients.…”