Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of trypanosomatidae via structure-based drug design

Article abstract of DOI:10.1021/jm000472o

In our continuation of the structure-based design of anti-trypanosomatid drugs, parasiteselective adenosine analogues were identified as low micromolar inhibitors of glyceraldehyde3-phosphate dehydrogenase (GAPDH). Crystal structures of Trypanosoma brucei, Trypanosoma cruzi, Leishmania mexicana, and human GAPDH's provided details of how the adenosyl moiety of NAD⁺ interacts with the proteins, and this facilitated the understanding of the relative affinities of a series of adenosine analogues for the various GAPDH's. From exploration of modifications of the naphthalenemethyl and benzamide substituents of a lead compound, N⁶-(1-naphthalenemethyl)-2′-deoxy-2′- (3-methoxybenzamido)adenosine (6e), N⁶-(substituted-naphthalenemethyl)-2′-deoxy-2′- (substituted-benzamido)adenosine analogues were investigated. N⁶(1 -Naphthalenemethyl)-2′-deoxy-2′-(3,5-dimethoxybenzamido)adenosine (6m), N⁶- [1-(3-hydroxynaphthalene)methyl]-2′-deoxy-2′- (3,5-dimethoxybenzamido)adenosine (7m), N⁶-[1-(3-methoxynaphthalene)methyl]-2′-deoxy-2′- (3,5-dimethoxybenzamido)adenosine (9m), N⁶-(2-naphthalenemethyl)-2′-deoxy-2′1- (3-methoxybenzamido)adenosine (11e), and N⁶-(2-naphthalenemethyl)-2′deoxy-2′- (3,5-dimethoxybenzamido)adenosine (11m) demonstrated a 2- to 3-fold improvement over 6e and a 7100- to 25000-fold improvement over the adenosine template. IC₅₀'S of these compounds were in the range 2-12 μM for T. brucei, T. cruzi, and L. mexicana GAPDH's, and these compounds did not inhibit mammalian GAPDH when tested at their solubility limit. To explore more thoroughly the structure- activity relationships of this class of compounds, a library of 240 N⁶-(substituted)-2′-deoxy-2′-(amido)adenosine analogues was generated using parallel solution-phase synthesis with N⁶ and C2′ substituents chosen on the basis of computational docking scores. This resulted in the identification of 40 additional compounds that inhibit parasite GAPDH's in the low micromolar range. We also explored adenosine analogues containing 5′-amido substituents and found that 2′,5′-dideoxy-2′-(3,5-dimethoxybenzamido)-5′- (diphenylacetamido)adenosine (49) displays an IC₅₀ of 60-100 μM against the three parasite GAPDH's.