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

In our continuation of the structure-based design of anti-trypanosomatid dr ugs, parasite-selective adenosine analogues were identified as low micromol ar inhibitors of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Crystal structures of Trypanosoma brucei, Trypanosoma cruzi, Leishmania mexicana, a nd human GAPDH's provided details of how the adenosyl moiety of NAD(+) inte racts with the proteins, and this facilitated the understanding of the rela tive affinities of a series of adenosine analogues for the various GAPDH's. From exploration of modifications of the naphthalenemethyl and benzamide s ubstituents of a lead compound, N-6(1-naphthalenemethyl)-2'-deoxy-2'-(3-met hoxybenzamido) adenosine (6e), N-6-(substituted-naphthalenemethyl)-2'-deoxy -2'-(substituted-benzamido)adenosine analogues were investigated. N-6(1-Nap hthalenemethyl)-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (6m), N-6-[1- (3-hydroxynaphthalene)methyl] -2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosin e (7m), N-6-[1-(3-methoxynaphthalene)methyl]-2'-deoxy-2'-(3,5-dimethoxybenz amido (9m), N-6-(2-naphthalenemethyl)-2'-deoxy-2'-(3-methoxybenzamido)adeno sine (11e), and N-6-(2-naphthalenemethyl)-2'deoxy-2'-(3,5-dimethoxybenzamid o)adenosine (11m) demonstrated a 2- to 3-fold improvement over se and a 710 0- to 25000-fold improvement over the adenosine template. IC(50)s of these compounds were in the range 2-12 muM for T. brucei, T. cruzi, and L. mexica na GAPDH's, and these compounds did not inhibit mammalian GAPDH when tested at their solubility limit. To explore more thoroughly the structure-activi ty relationships of this class of compounds, a library of 240 N-6-(substitu ted)-2'-deoxy-2'-(amido)aden analogues was generated using parallel solutio n-phase synthesis with N-6 and C2' substituents chosen on the basis of comp utational docking scores. This resulted in the identification of 40 additio nal compounds that inhibit parasite GAPDH's in the low micromolar range. We also explored adenosine analogues containing 5'-amido substituents and fou nd that 2',5'-dideoxy-2'-(3,5-dimethoxybenzamido)-5'-(diphenylacetamido)ade nosine (49) displays an IC50 of 60-100 muM against the three parasite GAPDH 's.