Design and Development of Small-Molecule Drugs Targeting Enzymes Utilizing Two-Metal-Ion Catalytic Mechanisms

The active sites of numerous metalloproteins feature two metal ion cofactors-either identical or distinct-that are positioned in close proximity, typically around 3.8 Å apart. This two-metal-ion catalytic mechanism (TCM) endows these enzymes with a remarkable catalytic efficiency. Enzymes employing TCM play vital biological roles in both humans and pathogenic organisms, with some identified as validated therapeutic targets. Various rational drug design approaches, including nucleoside analogs, prodrugs, metal-binding group design, bioisosteres, pharmacophore modeling, scaffold hopping, tautomerism, and structure-based drug design, have been successfully applied to several enzymes with TCMs, thus yielding the development and approval of many small-molecule drugs for the treatment of several diseases, including certain catastrophic illnesses, such as hepatitis C infection, coronavirus disease 2019, and acquired immune deficiency syndrome. Additionally, drug repurposing has proven to be a critical strategy in the development of therapeutics targeting TCM enzymes. This article reviews the significant achievements in design and development of small-molecule drugs targeting several enzymes with TCMs, including RNA-dependent RNA polymerase, HIV-1 integrase, influenza virus cap-dependent endonuclease, and phosphodiesterase, hoping to offer valuable insights and guidance to facilitate future drug discovery efforts focused on these enzymes and related molecular targets.