Mechanistic cross-talk between DNA/RNA polymerase enzyme kinetics and nucleotide substrate availability in cells: Implications for polymerase inhibitor discovery

• Type of Material: Article
• Authors: Si'Ana A. Coggins, Emory University; Bijan Mahboubi, Emory University; Raymond Schinazi, Emory University; Baek Kim, Emory University
• Language: English
• Date: 2020-09-25
• Publisher: American Society for Biochemistry and Molecular Biology
• Publication Version: Final Published Version
• Copyright Statement: © 2020 Coggins et al.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1074/jbc.REV120.013746
• Title of Journal or Parent Work: Journal of Biological Chemistry
• Volume: 295
• Issue: 39
• Start Page: 13432
• End Page: 13443
• Grant/Funding Information: This work was supported by National Institutes of Health Grant AI136581 (to B. K.), AI150451 (to B. K.), and MH116695 (to R. F. S.).
• Keywords: Selective inhibition; dNTP; DNA-Polymerase; Life Sciences & Biomedicine; Steady-state kinetics; enzyme kinetics; rNTP; Immunodeficiency virus type 1; enzyme inhibitor; nucleoside; HIV-1 reverse transcriptase; DNA polymerase; De-novo mutations; Crystal structure; RNA polymerase; Dependent rma polynase; Ribonucleotide reductase; nucleotide metabolism; Science & Technology; Human cytomegalovirus; Biochemistry & Molecular Biology; inhibitors
• Research Categories: Biology, Genetics; Biology, Molecular; Health Sciences, Human Development; Chemistry, Biochemistry

Abstract

Enzyme kinetic analysis reveals a dynamic relationship between enzymes and their substrates. Overall enzyme activity can be controlled by both protein expression and various cellular regulatory systems. Interestingly, the availability and concentrations of intracellular substrates can constantly change, depending on conditions and cell types. Here, we review previously reported enzyme kinetic parameters of cellular and viral DNA and RNA polymerases with respect to cellular levels of their nucleotide substrates. This broad perspective exposes a remarkable co-evolution scenario of DNA polymerase enzyme kinetics with dNTP levels that can vastly change, depending on cell proliferation profiles. Similarly, RNA polymerases display much higher Km values than DNA polymerases, possibly due to millimolar range rNTP concentrations found in cells (compared with micromolar range dNTP levels). Polymerases are commonly targeted by nucleotide analog inhibitors for the treatments of various human diseases, such as cancers and viral pathogens. Because these inhibitors compete against natural cellular nucleotides, the efficacy of each inhibitor can be affected by varying cellular nucleotide levels in their target cells. Overall, both kinetic discrepancy between DNA and RNA polymerases and cellular concentration discrepancy between dNTPs and rNTPs present pharmacological and mechanistic considerations for therapeutic discovery.