Polymerases have a structurally highly conserved negatively charged amino acid motif that is strictly required for Mg 2+ cation-dependent catalytic incorporation of (d)NTP nucleotides into nucleic acids. Based on these characteristics, a nucleoside monophosphonate scaffold, α-carboxy nucleoside phosphonate (α-CNP), was designed that is recognized by a variety of polymerases. Kinetic, biochemical, and crystallographic studies with HIV-1 reverse transcriptase revealed that α-CNPs mimic the dNTP binding through a carboxylate oxygen, two phosphonate oxygens, and base-pairing with the template. In particular, the carboxyl oxygen of the α-CNP acts as the potential equivalent of the α-phosphate oxygen of dNTPs and two oxygens of the phosphonate group of the α-CNP chelate Mg 2+ , mimicking the chelation by the β-and γ-phosphate oxygens of dNTPs. α-CNPs (i) do not require metabolic activation (phosphorylation), (ii) bind directly to the substrate-binding site, (iii) chelate one of the two active site Mg 2+ ions, and (iv) reversibly inhibit the polymerase catalytic activity without being incorporated into nucleic acids. In addition, α-CNPs were also found to selectively interact with regulatory (i.e., allosteric) Mg 2+ -dNTP-binding sites of nucleos(t)ide-metabolizing enzymes susceptible to metabolic regulation. α-CNPs represent an entirely novel and broad technological platform for the development of specific substrate active-or regulatory-site inhibitors with therapeutic potential. The polymerization of nucleotides by Escherichia coli DNA polymerase I represents a general model for catalytic action of nucleic acid polymerases (SI Appendix, Fig. S1) (1, 2). According to this model, there is a universal role for the Mg 2+ cation to interact with three phosphate oxygens of dNTP. The highly conserved consensus motifs in every polymerase active site consist of either aspartate or glutamate residues that chelate Mg 2+ through three additional coordination bonds during polymerization (2, 3). The crucial role of the metal cofactor and structurally conserved active site architecture in polymerases has also been demonstrated by validating Mg 2+ as a target for the design of antiviral drugs, not only against HIV RT but also, among others, against HIV integrase, HIV ribonuclease H (RNase H), and influenza-encoded endonuclease (4, 5). Hence, it should be feasible to design a universal but simplified (d)NTP mimic that binds efficiently to a wide variety of DNA/RNA polymerases.It was hypothesized that a universal nucleoside triphosphate mimic should contain three major indispensable entities: (i) a nucleobase part (i.e., to achieve optimal Watson-Crick basepairing with the template overhang), (ii) a replacement of the triphosphate moiety that should enable efficient Mg 2+ -directed coordination, and (iii) a variable linker between the nucleobase and the modified triphosphate to mimic the pentose entity present in natural (d)NTPs. For the triphosphate part, we chose an α-carboxy phosphonate entity that is chemically stable in physiolog...

Here we report on the expression, purification and characterization of recombinant ebola virus RNA-dependent RNA polymerase (EBOV RdRp). Active protein complexes composed of the large L protein and viral protein VP35 were isolated from insect cells and analyzed using a short primer/template substrate that allowed benchmarking against related enzymes. RNA synthesis by multiprotein complexes of EBOV, influenza B, respiratory syncytial virus (RSV) and monomeric enzymes of hepatitis C and Zika (ZIKV) viruses required a 5′-phosporylated primer. The minimum length of the primer varied between two and three nucleotides in this system. The EBOV enzyme utilizes Mg2+ as a co-factor and the D742A substitution provides an active site mutant that likely affects binding of the catalytic metal ions. Selectivity measurements with nucleotide analogues translate our assay into quantitative terms and facilitate drug discovery efforts. The related EBOV and RSV enzymes are not able to efficiently discriminate against ara-cytidine-5′-triphosphate. We demonstrate that this compound acts like a non-obligate chain-terminator.

Background:The RNase H activity of HIV-1 reverse transcriptase (RT) is an under-explored target. Results: GSK5750 is a novel RNase H active site inhibitor that displays slow dissociation kinetics. Conclusion: Tight binding may compensate for the inability of active site inhibitors to access the RT-substrate complex. Significance: The GSK5750 scaffold may lead to the development of clinically relevant RNase H inhibitors.

Domain II of the nonstructural protein 5 (NS5A) of the hepatitis C virus (HCV) is involved in intermolecular interactions with the viral RNA genome, the RNA-dependent RNA polymerase NS5B, and the host factor cyclophilin A (CypA). However, domain II of NS5A (NS5A) is largely disordered, which makes it difficult to characterize the protein-protein or protein-nucleic acid interfaces. Here we utilized a mass spectrometry-based protein footprinting approach in attempts to characterize regions forming contacts between NS5A and its binding partners. In particular, we compared surface topologies of lysine and arginine residues in the context of free and bound NS5A. These experiments have led to the identification of an RNA binding motif (RSRKFPR) in an arginine-rich region of NS5A. Furthermore, we show that K308 is indispensable for both RNA and NS5B binding, whereas W316, further downstream, is essential for protein-protein interactions with CypA and NS5B. Most importantly, NS5A binding to NS5B involves a region associated with RNA binding within NS5B. This interaction down-regulated RNA synthesis by NS5B, suggesting that NS5A modulates the activity of NS5B and potentially regulates HCV replication.

Background:The 4-chlorophenylhydrazone of mesoxalic acid (CPHM) is a known inhibitor of HIV-1 reverse transcriptase (RT). Results: We demonstrate that CPHM traps the pre-translocational conformation of the RT-DNA complex. Conclusion:The data validate this complex as a possible drug target. Significance: This work can therefore contribute to the development of novel classes of antiretroviral agents.