User:Katie.toperzer/RNA-dependent RNA polymerase

Drug Therapies
RdRPs can be used as drug targets for viral pathogens as their function is not necessary for eukaryotic survival. By inhibiting RNA-dependent RNA polymerase function, new RNAs cannot be replicated from an RNA template strand, however, DNA-dependent RNA polymerase will remain functional.

There are currently antiviral drugs against Hepatitis C and COVID-19 that specifically target RdRP. These include Sofosbuvir and Ribavirin against Hepatitis C and Remdesivir, the only FDA approved drug against COVID-19.

GS-441524 triphosphate, is a substrate for RdRP, but not mammalian polymerases. It results in premature chain termination and inhibition of viral replication. GS-441524 triphosphate is the biologically active form of the phosphate pro-drug, Remdesivir. Remdesivir is classified as a nucleotide analog in which it works to inhibit the function of RdRP by covalently binding to and interrupting termination of the nascent RNA through early or delayed termination or preventing further elongation of the RNA polynucleotide. This early termination leads to nonfunctional RNA that will be degraded through normal cellular processes.

Replication process
RdRP differs from RNA polymerase as it works to catalyze the synthesis of an RNA strand complementary to a given RNA template, rather than using a DNA template. The RNA replication process is a four-step mechanism, as described.


 * 1) Nucleotide triphosphate (NTP) binding - initially, the RdRP presents with a vacant active site in which an NTP binds, in which the NTP binds. Correct NTP binding causes the RdRP to undergo a conformational change.
 * 2) Active site closure - the conformational change initiated by the correct NTP binding, results in the restriction of active site access and produces a catalytically competent state.
 * 3) Phosphodiester bond formation - two Mg2+ ions are present in the catalytically active state and arrange themselves in such a way around the RNA primer that the substrate NTP is able to undergo a phosphatidyl transfer and form a phosphodiester bond with the existing nucleotide chain . With the use of these Mg2+ ions, the active site is no longer has the catalytically stable and the RdRP complex changes to an open conformation.
 * 4) Translocation - once the active site is open, the RNA strand is able to move through the RdRP protein complex and bind a new NTP and continue chain elongation, unless otherwise specified by the template.

RNA synthesis can be performed by means of a primer-independent (de novo) or a primer-dependent mechanism that utilizes a viral protein genome-linked (VPg) primer. The de novo initiation consists in the addition of a nucleoside triphosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product. Termination of the nascent RNA chain produced by RdRP is not completely known, however, it has been shown that RdRP termination is sequence-independent.

One major drawback of RNA-dependent RNA polymerase replication is the immense error rate during transcription. RdRPs are known to have a lack of fidelity on the order of 104 nucleotides, which is thought to be a direct result of its insufficient proofreading abilities. This high rate of variation is favored in viral genomes as it allows for the pathogen to overcome defenses developed by hosts trying to avoid infection allowing for evolutionary growth.

RNA interference
The use of RNA-dependent RNA polymerase plays a major role in RNA interference in eukaryotes, a process used to silence gene expression via small interfering RNAs (siRNAs) binding to mRNA rendering them inactive. Eukaryotic RdRP becomes active in the presence of dsRNA, however, RdRP is only present in a select subset of eukaryotes, including C. elegans and P. tetraurelia. This presence of dsRNA triggers the activation of RdRP and RNAi processes by priming the initiation of RNA transcription through the introduction of siRNAs into the system. In C. elegans, siRNAs are integrated into the RNA-induced silencing complex, RISC, which works alongside mRNAs targeted for interference to recruit more RdRPs to synthesize more secondary siRNAs and repress gene expression.