Are potent inhibitors of the reverse transcriptase of HIV effective?
Numerous potent inhibitors of RT have been described including all of the drugs that have been currently licensed for the treatment of AIDS, but their efficacy has been limited by the emergence of drug-resistant HI … The reverse transcriptase of HIV is a key target for the antiviral treatment of AIDS.
What are HIV-1 reverse transcriptase stable complexes?
Stable complexes formed by HIV-1 reverse transcriptase at distinct positions on the primer-template controlled by binding deoxynucleoside triphosphates or foscarnet. J Mol Biol. 2007;369:41–54.
What are nukes used to treat HIV?
Nucleoside Reverse Transcriptase Inhibitors (NRTIs or nukes) Treatment. The first group of antiretroviral drugs is the nucleoside reverse transcriptase (pronounced "trans-krip-tase") inhibitors (NRTIs). NRTIs were the first type of drug available to treat HIV.
What are nucleoside reverse transcriptase inhibitors?
Nucleoside Reverse Transcriptase Inhibitors (NRTIs or nukes) NRTIs were the first type of drug available to treat HIV. They are effective, powerful, and important medications for treating HIV when combined with other drugs. They are better known as nucleoside analogues or "nukes.". When the HIV virus enters a healthy cell,...
Which drug is inhibiting viral reverse transcriptase?
Nucleoside analogue reverse transcriptase inhibitors including didanosine (ddI), lamivudine (3TC), stavudine (d4T), zalcitabine (ddC), and zidovudine (ZDV, formerly AZT) are used to treat human immunodeficiency virus (HIV) infection.
What inhibits reverse transcriptase?
Reverse-transcriptase inhibitors (RTIs) are a class of antiretroviral drugs used to treat HIV infection or AIDS, and in some cases hepatitis B. RTIs inhibit activity of reverse transcriptase, a viral DNA polymerase that is required for replication of HIV and other retroviruses.
How does AZT stop reverse transcriptase?
After being activated by phosphorylation in vivo, AZT inhibits HIV replication by blocking a critical HIV enzyme called reverse transcriptase. This enzyme uses the virus's RNA genome as a template to build a DNA version that can be inserted into the host's genome.
Which HIV medication is a nucleoside reverse transcriptase inhibitor?
Available NRTIs zidovudine (Retrovir) lamivudine (Epivir) abacavir sulfate (Ziagen) emtricitabine (Emtriva)
Which medication is classified as a non nucleoside reverse transcriptase inhibitor?
Abstract. The non-nucleoside reverse transcriptase inhibitors (NNRTIs) directly inhibit the HIV-1 reverse transcriptase (RT) by binding in a reversible and non-competitive manner to the enzyme. The currently available NNRTIs are nevirapine, delavirdine, and efavirenz; other compounds are under evaluation.
What type of inhibitor is AZT?
AZT is an analog of the thymidine deoxynucleoside and is a member of the class called the nucleoside-analog reverse transcriptase inhibitors. AZT and other members of this class function by inhibiting the HIV reverse transcriptase. This halts the life cycle of the virus and slows the progression of AIDS.
What feature of AZT makes it an effective inhibitor of reverse transcriptase?
This is because the active compound of AZT, known as zidovudine 5-triphosphate, has a high affinity (attraction) for an enzyme called reverse transcriptase, which is used by retroviruses such as HIV to replicate viral single-stranded RNA (ribonucleic acid) into proviral double-stranded DNA (deoxyribonucleic acid).
What is the antiviral drug ribavirin?
Ribavirin is used with an interferon medication such as peginterferon alfa-2a [Pegasys] or peginterferon alpha-2b [PEG-Intron]) to treat hepatitis C in people who have not been treated with an interferon before. Ribavirin is in a class of antiviral medications called nucleoside analogues.
Is ritonavir a reverse transcriptase inhibitor?
Ritonavir/saquinavir plus one nucleoside reverse transcriptase inhibitor (NRTI) versus indinavir plus two NRTIs in protease inhibitor-naive HIV-1-infected adults (IRIS study)
What is the drug that blocks reverse transcriptase?
The animation illustrates how the drug azidothymidine, or AZT (also known as zidovudine or Retrovir), blocks the function of reverse transcriptase. AZT is a small molecule that is structurally similar to the nucleotide base thymidine.
What is AZT used for?
Description. This animation shows how a medication called AZT, which is a reverse transcriptase inhibitor, can be used to treat HIV/AIDS. In order to complete its life cycle, HIV uses an enzyme called reverse transcriptase to convert its viral RNA to DNA.
How does HIV RT work?
The reaction begins with the binding of RT to the nucleic acid substrate, which results in a conformational change in the position of the p66 thumb, from a “closed” to an “open” conformation. Like many other DNA polymerases, RT requires both a primer and a template. In most sequence contexts, RT preferentially binds a double-stranded nucleic acid so that the 3’ end of the primer strand is bound at the priming site (P site), adjacent to the polymerase active site (6, 25–27). The initial step in nucleotide incorporation is the binding of the incoming dNTP at the nucleotide binding site (N site) to form a ternary complex (21). The rate-limiting step in the polymerization reaction is a conformational change in which a portion of the p66 fingers subdomain closes down on the incoming dNTP, which helps to precisely align the 3’-OH of the primer, the α-phosphate of the dNTP, and the polymerase active site (21, 28, 29). The chemical step that follows leads to the formation of a phosphodiester bond between the newly incorporated nucleoside and the primer with the concomitant generation of pyrophosphate. The fingers open to allow the pyrophosphate to leave the active site. In processive DNA synthesis, the nucleic acid substrate must translocate relative to RT to free the nucleotide-binding site so that RT can bind the next incoming dNTP.
What is the function of RT in HIV?
The HIV-1 virion contains, in addition to the viral proteins, two copies of a single-stranded RNA genome. RT has two enzymatic activities, a DNA polymerase that can copy either a DNA or an RNA template, and an RNase H that cleaves RNA only if the RNA is part of an RNA/DNA duplex. The two enzymatic functions of RT, polymerase and RNase H, cooperate to convert the RNA into a double-stranded linear DNA. This conversion takes place in the cytoplasm of the infected cell; after DNA synthesis has been completed, the resulting linear double-stranded viral DNA is translocated to the nucleus where the viral DNA is inserted into the host genome by IN. This inserted DNA copy, called a provirus, is the source of both viral genomic and viral messenger RNAs, which are generated by the host DNA-dependent RNA polymerase. Although other viral proteins (notably the nucleic acid chaperone nucleocapsid, and perhaps IN) and probably some cellular factors, help RT carry out the reactions that converts the viral RNA into DNA, RT contains all the necessary enzymatic activities for the conversion.
What is the nucleic acid binding cleft?
The nucleic-acid binding cleft is formed primarily by the p66 fingers, palm, thumb, connection, and RNase H subdomains of p66. The connection and thumb subdomains of p51 form the floor of the binding cleft (Figure 2). The binding cleft is configured so that the nucleic acid contacts both the polymerase and the RNase H active sites; these are located about 17–18 base pairs apart on the nucleic acid substrate. The αH and αI helices of the p66 thumb help to properly position the nucleic acid through interactions that involve both the primer and template strands. The DNA “primer grip”, a highly conserved structural motif (7) that consists of the p66 β12-β13 hairpin in HIV-1 RT (6) helps position the 3’-OH end of the primer strand at the polymerase active site. Mutational studies have shown that changes in the DNA primer grip alter nucleic acid binding and may affect both polymerase and RNase H activities of RT (8–16).
What is the RT of HIV?
RT of HIV-1 is an asymmetric heterodimer composed of two related subunits, p66 and p51. Both subunits derive, by cleavage by the viral protease (PR), from a Gag-Pol polyprotein that is synthesized from unspliced viral RNA (3, 4). p66 and p51 share a common amino terminus; p66 is 560 amino acids in length, p51 is 440 amino acids long. As has been discussed briefly, both of the enzymatic functions of RT, the DNA polymerase and RNase H, are essential for the copying of the single stranded RNA genome found in virions into the double-stranded DNA that is inserted into the host genome by IN (for a review of the retroviral life cycle, and an overview of reverse transcription, see Coffin, Hughes and Varmus, Retroviruses, 1997 (1)) . The larger subunit of the RT heterodimer, p66, contains the active sites for both of the enzymatic activities of RT (polymerase and RNase H); the smaller subunit plays a structural role (Figure 2). Important structural features of RT were elucidated by the first crystallographic studies (5, 6). p66 is composed of two spatially distinct domains, polymerase and RNase H. The polymerase domain is composed of four subdomains: fingers (residues 1–85 and 118–155), palm (residues 86–117 and 156–236), thumb (237–318), and connection (319–426) (5,6). p51 folds into the same four subdomains as the polymerase domain of p66 (fingers, palm, thumb, and connection); however the positions of the subdomains relative to each other are different in p66 and p51 (see Figure 2).
What color are the fingers of HIV-1?
The fingers, palm, thumb, connection, and RNase H subdomains of the p66 subunit are shown in blue, red, green, yellow, and orange, respectively. The p51 subunit is shown in dark brown. The template and primer DNA strands are shown in light and dark gray, respectively.
How does HIV-1 evolve?
The rapid replication of HIV-1 and the errors made during viral replication, cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. In the absence of an effective vaccine, drugs are the only useful treatment. Anti-HIV drugs work; so far drug therapy has saved more than three million years of life. Unfortunately, HIV-1 develops resistance to all of the available drugs. Although a number of useful anti-HIV drugs have been approved for use in patients, the problems associated with drug toxicity and the development of resistance means that the search for new drugs is an ongoing process. The three viral enzymes, reverse transcriptase (RT), integrase (IN), and protease (PR) are all good drug targets. Two distinct types of RT inhibitors, both of which block the polymerase activity of RT, have been approved to treat HIV-1 infections, nucleoside analogs (NRTIs) and nonnucleosides (NNRTIs), and there are promising leads for compounds that either block the RNase H activity or block the polymerase in other ways. A better understanding of the structure and function(s) of RT and of the mechanism(s) of inhibition can be used to generate better drugs; in particular drugs that are effective against the current drug-resistant strains of HIV-1.
What is the end product of reverse transcription?
As has already been mentioned, the end product of reverse transcription process is the substrate for IN. As such, the ends of the linear viral DNA need to be relatively precise. As is shown in Figure 1, it is the RNase H cleavages that generate and remove the PPT primer that define the U3 end of the linear viral DNA, and it is the removal of the tRNA primer that defines the U5 end. Although RNase H has no mechanism that allows it to recognize specific sequences, it carries out these particular cleavage reactions with absolute specificity; and the ends of the linear viral DNA genome are defined to the exact nucleotide.
What is the role of reverse transcription in HIV?
The essential role of reverse transcription in the HIV life cycle is illustrated by the fact that half of the ~30 FDA-approved drugs for HIV treatment target HIV-1 reverse transcriptase (RT). Even though more than 160 structures of RT deposited in the Protein Data Bank (PDB) have revealed the molecular architecture of RT in great detail, some key states of RT function and inhibition remain still unknown. Recent structures of RT initiation complexes, RT poised for RNA hydrolysis, and RT with approved drugs and investigational compounds have provided a deeper understanding of RT function and inhibition, suggesting novel avenues for targeting this central enzyme of HIV.
What is RT in HIV?
HIV-1 reverse transcriptase (RT) is central to HAART and in pre-exposure prophylaxis. Standard therapies include at least two RT inhibitors, and often three [1]. RT is a characteristic enzyme in all retroviruses, with polymerase and RNase H activities, and is essential for HIV replication. Figure 1shows the overall arrangement ...
What is the RNase H domain?
The RNase H domain hydrolyzes the vRNA in different stages of reverse transcription (Figure 2a) [9]. Several RT/RNA/DNA structures were available, with the substrate interacting either with the polymerase or the RNase H active site. However, all had the scissile phosphate distance >4 Å, that is, not poised for efficient catalysis. In 2018, the Yang laboratory reported the first structure of RT in complex with a RNA/DNA substrate poised for catalysis (Figure 2f) [10••]. They found that previous failures were due to unfavorable sequences for RNase H cleavage: 2 residues located 4 bp upstream of the cleavage site, and especially when position −4 has a rA-dT pair, block the unwinding needed for proper positioning of the substrate for catalysis.
What is the resolution of RT-RNHI?
RT-RNHI structure at 1.8 Å resolution in a crystal form that has two complexes in the asymmetric unit and where the RNHI shows two different conformations, with one being compatible with RNA/DNA binding that could facilitate achieving inhibition in vivo.
Is RT a heterodimer?
RT initially exists as homodimer and undergoes maturation, leading to a heterodimer with a sole RNase H domain (reviewed in Ref. [13]). Maturation starts with the transition of monomeric RT from a compact (p51-like) to an extended (p66-like) conformation. Next, dimerization yields a p66/p66’ homodimer in which just p66’ (but not p66) will unfold and become exposed, allowing cleavage by protease, finishing RT maturation. The unfolding step remains controversial. London and colleagues have solved the structure of an isolated RNase H domain-swapped dimer [14•] (it captures a partially unfolded monomer stabilized by the second monomer), that points to instability of the Y427 binding pocket as the trigger of RNase H unfolding. Electron paramagnetic resonance and modeling experiments by the Clore laboratory also support the unfolding of a single RNase H domain and the existence of an asymmetric homodimer [15•]. The Ishima laboratory (in collaboration with Sarafianos, Parniak and Sluis-Cremer laboratories) has also shown that tRNA (packaged in HIV-1 virions) may enhance maturation by interacting with the homodimer and promoting conformational asymmetry [16•]. According to their NMR data, though, the unfolding may not occur just with p66/p66’ alone, requiring presence of either nucleic acid or protease [17•]. Our laboratory in collaboration with that of Dmitry Lyumkis (Salk) has recently solved a structure of the HIV-1 Pol polyprotein precursor by cryo-EM, revealing a dimeric organization in which the RT dimer is very similar in structure to the mature p66/p51 heterodimer (Harrison et al.,unpublished), with many fascinating implications about RT maturation and assembly, as well as protease activation during virion morphogenesis.
Does tRNA help RT maturation?
004 Refs. [16] and [17] show the tRNA has a role in RT maturation, mainly by introducing conformational asymmetry that may facilitate the digestion of just one RNase H domain in the p66/p66’ homodimer.
Is HIV research vigorous?
Research efforts for HIV inhibitor/drug discovery and development, remain very numerous and vigorous [18]. Given the large number of papers on the topic in the review period, we will address those works comprising or based on structures.