Structural insight into ligand interactions of thymidylate synthase from white spot syndrome virus

Abstract

White spot syndrome virus (WSSV) is one of the deadliest crustacean pathogens, causing huge economic loss in global shrimp industry. WSSV encodes a thymidylate synthase (wTS) that is essential for DNA replication and viral proliferation, serving as a promising drug target against WSSV infections. To aid drug design, we solved wTS structures in complex with dUMP and dUMP/raltitrexed, at 2.28 Å and 1.43 Å resolutions, respectively. wTS forms a homodimer and each ligand-binding cavity is contributed by both monomers. In wTS-dUMP binary structure, the protein adopts an open conformation, with dUMP bound to the cavity through extensive hydrogen bonds and salt bridges. In wTS-dUMP-raltitrexed ternary structure, the protein exhibits a closed conformation; the TS inhibitor raltitrexed contacts intensively with the protein and dUMP via hydrogen bonding and hydrophobic interactions, resulting in the covalent bond formation between dUMP and the catalytic cysteine. Pairwise comparison of the structures of wTS and shrimp TS shows that they share similarity in the dUMP bound forms but differ significantly in the dUMP/raltitrexed bound forms: wTS presents a more tightly closed conformation than shrimp TS, showing more interactions with raltitrexed. As the ligand binding residues are conserved between the two proteins, the observed structural differences are supposed to originate from the variations in other vicinity residues. In sum, the comparative structural study on the homologous viral and host proteins would boost the opportunity to design wTS-specific inhibitors against WSSV infections.