Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding

Synthesis, biological evaluation and molecular modeling studies of N6-benzyladenosine analogues as potential anti-toxoplasma agents

“…This domain movement is complex, and apparently involves further tuning of the protein structure when substrates bind into the active-site of the enzyme. As a result, our initial modeling attempts of utilizing the apo form (1LIO.pdb) [23] of the enzyme were far less successful than subsequent analysis with the T. gondii adenosine kinaseadenosine complex (1LII.pdb) [23]. The crystal coordinates of the reported enzyme:substrate complex is missing the following residues:1-10, 239-240, 255-269, 359-363.…”

“…Previous structure-activity relationship studies [17,18] and X-ray structural reports [23,24] revealed the molecular criteria for ligand binding to the adenosine binding site of T. gondii adenosine kinase. Recent structural studies of adenosine kinase complex with N 6 -dimethyladenosine and 6-methylmercaptopurine riboside [29] showed the intermediateconformation between closed (catalytic-conformation) and open lid domain (apo-conformation), and revealed the conformational steps for catalysis.…”

“…Recent structural studies of adenosine kinase complex with N 6 -dimethyladenosine and 6-methylmercaptopurine riboside [29] showed the intermediateconformation between closed (catalytic-conformation) and open lid domain (apo-conformation), and revealed the conformational steps for catalysis. The molecular recognition analysis from the detailed study of the reported crystal structures of enzyme-ligand complexes [23] and structure-activity relationships analysis [17,18] indicate that the following factors play important roles in ligand binding into the adenosine binding pocket: (a) 2′-OH and 3′-OH are crucial for the binding because they form four strong H-bond with nearby residues, which accounts for a strong electrostatic interaction and conformational determinant for the ribose moiety as shown in Fig. 2a; (b) Active-site map analysis clearly showed the presence of a large hydrophobic regions around the N 6 and N 7 positions of adenine as shown in Fig.…”

“…Specifically, the activity of adenosine kinase (EC.2.7.1.20), the enzyme responsible for the salvage of adenosine in this parasite, is 10-fold higher than those of other enzymes in the purine salvage pathways, and hence contributes more significantly to the salvage of purines in T. gondii than any other enzyme of the purine salvage pathways [12][13][14][15][16]. Secondly, structure-activity relationships [17,18], comparative enzymatic [18][19][20], metabolic [19][20][21], molecular [22], and X-ray structural studies [23][24][25] have demonstrated that there are sufficient differences between the active sites and substrate specificities of human and T. gondii adenosine kinases that can be exploited to design specific "subversive substrates" for the T. gondii enzyme [12,13].…”

“…1b. The adenosine binding pocket is composed of the ribose binding hydrophilic region (Asp24, Gly69, and Asn73), the purine binding region [23], and an additional hydrophobic region [18]. The purine motif of adenosine is surrounded by some of the hydrophobic residues such as Tyr169 and Ile22, that forms aromatic stacking by π-πand C-H-π interaction (Fig.…”