Substrates and Inhibitors of SAMHD1

• Published in: PloS one 2017-01, Vol.12 (1), p.e0169052-e0169052
• Main Authors: Hollenbaugh, Joseph A, Shelton, Jadd, Tao, Sijia, Amiralaei, Sheida, Liu, Peng, Lu, Xiao, Goetze, Russell W, Zhou, Longhu, Nettles, James H, Schinazi, Raymond F, Kim, Baek
• Format: Article
• Language: English
• Subjects: Acquired immune deficiency syndrome; AIDS; Analogs; Animals; Arabinofuranosylcytosine Triphosphate; Arabinose; Biology and Life Sciences; Carbohydrates - chemistry; Catalysis; Cellular proteins; Chickens; Computational biology; Computer applications; Deoxyribonucleic acid; DNA; DNA polymerase; Docks; Enzyme Inhibitors - pharmacology; Health aspects; Hepatitis; HIV; Human immunodeficiency virus; Humans; Hydrolysis; Infections; Influence; Kinases; Laboratories; Macrophages - drug effects; Macrophages - metabolism; Medicine; Medicine and Health Sciences; Methods; Models, Molecular; Monocytes - cytology; Monomeric GTP-Binding Proteins - antagonists & inhibitors; Monomeric GTP-Binding Proteins - metabolism; Mutation; Nucleoside analogs; Nucleosides; Nucleotides; Nucleotides - metabolism; Pediatrics; Pharmacological research; Pharmacology; Phosphorylation; Physical Sciences; Protein Multimerization - drug effects; Proteins; Research and Analysis Methods; Ribonucleotide reductase; SAM Domain and HD Domain-Containing Protein 1; Structure-activity relationships (Pharmacology); Substrate inhibition; Substrate specificity; Substrate Specificity - drug effects; Substrates; Sugar; Viral infections
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0169052

SAMHD1 hydrolyzes 2'-deoxynucleoside-5'-triphosphates (dNTPs) into 2'-deoxynucleosides and inorganic triphosphate products. In this paper, we evaluated the impact of 2' sugar moiety substitution for different nucleotides on being substrates for SAMHD1 and mechanisms of actions for the results. We found that dNTPs ((2'R)-2'-H) are only permissive in the catalytic site of SAMHD1 due to L150 exclusion of (2'R)-2'-F and (2'R)-2'-OH nucleotides. However, arabinose ((2'S)-2'-OH) nucleoside-5'-triphosphates analogs are permissive to bind in the catalytic site and be hydrolyzed by SAMHD1. Moreover, when the (2'S)-2' sugar moiety is increased to a (2'S)-2'-methyl as with the SMDU-TP analog, we detect inhibition of SAMHD1's dNTPase activity. Our computational modeling suggests that (2'S)-2'-methyl sugar moiety clashing with the Y374 of SAMHD1. We speculate that SMDU-TP mechanism of action requires that the analog first docks in the catalytic pocket of SAMHD1 but prevents the A351-V378 helix conformational change from being completed, which is needed before hydrolysis can occur. Collectively we have identified stereoselective 2' substitutions that reveal nucleotide substrate specificity for SAMHD1, and a novel inhibitory mechanism for the dNTPase activity of SAMHD1. Importantly, our data is beneficial for understanding if FDA-approved antiviral and anticancer nucleosides are hydrolyzed by SAMHD1 in vivo.