Reaction Mechanism and Metal Selectivity of Human SAMHD1 Elucidated by QM/MM Calculations

2'-Deoxynucleoside-5'-triphosphate triphosphohydrolases (dNTPases) constitute a crucial enzyme family that plays a pivotal role in antiviral innate immunity. Among these enzymes, human SAMHD1 has emerged as a dNTPase with distinct catalytic properties and active-site architecture. This metalloenzyme regulates cellular dNTP concentration through its ability to hydrolyze all four canonical dNTPs into their corresponding 2'-deoxynucleosides and inorganic triphosphates, a reaction requiring coordinated iron and magnesium ions for enzymatic activity. In the present work, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations are employed to investigate the mechanistic details of dATP hydrolysis mediated by two metal ions. Starting from the resolved crystal structure, Model-1, containing a Fe²⁺ in the active site, was constructed. Our calculations demonstrate that SAMHD1 employs a bridging hydroxide anion OH^- to attack the Pα site of dNTP, triggering the cleavage of the Pα-O5' bond via a trigonal-bipyramidal transition state. Simultaneously, His215 donates a proton to O5' of the leaving group, leading to the formation of 2'-deoxyadenosine and triphosphate ion. It is further demonstrated that the native Fe²⁺-Mg²⁺ bimetallic center help catalyze this hydrolysis reaction with a barrier of 13.4 kcal/mol, while the substitution from Fe²⁺ to Fe³⁺ abolishes the catalytic activity of SAMHD1. The comparison between different QM/MM models highlight the high affinity of SAMHD1 for Fe²⁺ relative to Mn²⁺ and Mg²⁺ at one of the bimetallic sites. In addition, the metal ion swapping between Fe²⁺ and Mg²⁺ from their crystallographic positions is shown to elevate the energy of the reactant state, underscoring the critical influence of the metal coordination geometry on catalytic activity. These computational insights not only expand the understanding of how SAMHD1 wisely modulates catalytic reactivity and metal selectivity by binding suitable metal ions but also provide a valuable foundation for guiding the design of drugs for antiviral therapies.