Structure, evolution, and inhibitor interaction of S‐adenosyl‐L‐homocysteine hydrolase from Plasmodium falciparum

S‐adenosylhomocysteine hydrolase (SAHH) is a key regulator of S‐adenosylmethionine–dependent methylation reactions and an interesting pharmacologic target. We cloned the SAHH gene from Plasmodium falciparum (PfSAHH), with an amino acid sequence agreeing with that of the PlasmoDB genomic database. Even though the expressed recombinant enzyme, PfSAHH, could use 3‐deaza‐adenosine (DZA) as an alternative substrate in contrast to the human SAHH, it has a unique inability to substitute 3‐deaza‐(±)aristeromycin (DZAri) for adenosine. Among the analogs of DZA, including neplanocin A, DZAri was the most potent inhibitor of the PfSAHH enzyme activity, with a Ki of about 150 nM, whether Ado or DZA was used as a substrate. When the same DZA analogs were tested for their antimalarial activity, they also inhibited the in vitro growth of P. falciparum parasites potently. Homology‐modeling analysis revealed that a single substitution (Thr60‐Cys59) between the human and malarial PfSAHH, in an otherwise similar SAH‐binding pocket, might account for the differential interactions with the nucleoside analogs. This subtle difference in the active site may be exploited in the development of novel drugs that selectively inhibit PfSAHH. We performed a comprehensive phylogenetic analysis of the SAHH superfamily and inferred that SAHH evolved in the common ancestor of Archaea and Eukaryota, and was subsequently horizontally transferred to Bacteria. Additionally, an analysis of the unusual and uncharacterized AHCYL1 family of the SAHH paralogs extant only in animals reveals striking divergence of its SAH‐binding pocket and the loss of key conserved residues, thus suggesting an evolution of novel function(s). Proteins 2003;52:624–632. © 2003 Wiley‐Liss, Inc.