HIV-1 Reverse Transcriptase in Complex with Nevirapine: Difference between revisions
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== NNRTIs: Anti-retroviral Drugs == | == NNRTIs: Anti-retroviral Drugs == | ||
RT is a prime target for anti-HIV drugs because of its essential role in the viral life cycle. A wide variety of drugs have been developed to target this enzyme in order to decrease the infectivity of HIV and slow the progression of this chronic disease. Of the 26 anti-retroviral drugs approved by the FDA to treat individuals infected with HIV, 13 target the viral polymerase of RT.<ref>U.S.F.&D. Administration. http://www.fda.gov/ForConsumers/byAudience/ForPatientAdvocates/HIVandAIDSActivities/ucm118915.htm</ref> One class of drugs, called non-nucleoside reverse transcriptase inhibitors (NNRTIs), contain compounds that bind noncompetitively to a hydrophobic pocket near the polymerase active site. NNRTIs are a group of small hydrophobic compounds with diverse structures that allosterically inhibit HIV-1 but not HIV-2 RT.<ref>PMID: 1298242</ref> | RT is a prime target for anti-HIV drugs because of its essential role in the viral life cycle. A wide variety of drugs have been developed to target this enzyme in order to decrease the infectivity of HIV and slow the progression of this chronic disease. Of the 26 anti-retroviral drugs approved by the FDA to treat individuals infected with HIV, 13 target the viral polymerase of RT.<ref>U.S.F.&D. Administration. http://www.fda.gov/ForConsumers/byAudience/ForPatientAdvocates/HIVandAIDSActivities/ucm118915.htm</ref> One class of drugs, called non-nucleoside reverse transcriptase inhibitors (NNRTIs), contain compounds that bind noncompetitively to a hydrophobic pocket near the polymerase active site. NNRTIs are a group of small hydrophobic compounds with diverse structures that allosterically inhibit HIV-1 but not HIV-2 RT.<ref>PMID: 1298242</ref> Recent pre-steady kinetics studies suggest that the conformational state and not the chemical step leading to nucleotide incorporation is blocked by a NNRTI, favoring the "primer grip distortion" model.<ref>PMID:9000632</ref> Binding of these compounds allosterically inhibit RT, causing its distortion and incompetent binding to dNTP. | ||
== The NNRTI Binding Pocket == | == The NNRTI Binding Pocket == | ||
Although nonnucleoside RT inhibitors are structurally diverse compounds, they all bind RT in the same location - the NNRTI hydrophobic binding pocket. The pocket is located in the palm domain of the p66 subunit between the β6-β10-β9 and β12-β13-β14 sheets approximately 10 angstroms from the three catalytic asp residues that make up the polymerase active site.<ref>PMID:1377403</ref> The NNRTI BP is mostly hydrophobic in nature with considerable aromatic residues (Y181, Y188, F227, W229, and Y232), but also contains several hydrophilic residues (K101, K103, S105, D192, and E224 of the p66 subunit and E138 of the β7-β8 loop of the p51 subunit). NNRTIs most likely access the binding pocket at the p66/p51 heterodimer interface surrounded by residues L100, K101, K103, V179, and Y181 of the p66 subunit and E138 of the p51 subunit.<ref>PMID:8805568</ref> Actually, in the absence of ligand, the side chains of Y181 and Y188 point into the core, so the binding pocket doesn't exist in the free enzyme. The binding of NNRTI to HIV RT causes these side chains to shift away and make room for the ligand to enter the binding pocket.<ref>PMID:8805568</ref> | Although nonnucleoside RT inhibitors are structurally diverse compounds, they all bind RT in the same location - the NNRTI hydrophobic binding pocket. The pocket is located in the palm domain of the p66 subunit between the β6-β10-β9 and β12-β13-β14 sheets approximately 10 angstroms from the three catalytic asp residues that make up the polymerase active site.<ref>PMID:1377403</ref> The NNRTI BP is mostly hydrophobic in nature with considerable aromatic residues (Y181, Y188, F227, W229, and Y232), but also contains several hydrophilic residues (K101, K103, S105, D192, and E224 of the p66 subunit and E138 of the β7-β8 loop of the p51 subunit). NNRTIs most likely access the binding pocket at the p66/p51 heterodimer interface surrounded by residues L100, K101, K103, V179, and Y181 of the p66 subunit and E138 of the p51 subunit.<ref>PMID:8805568</ref> Actually, in the absence of ligand, the side chains of Y181 and Y188 point into the core, so the binding pocket doesn't exist in the free enzyme. The binding of NNRTI to HIV RT causes these side chains to shift away and make room for the ligand to enter the binding pocket.<ref>PMID:8805568</ref> | ||
Nevirapine is a first generation NNRTI, which binds RT in a butterfly-like conformation. Several factors stabilize its interaction with RT's hydrophobic pocket, and the conformational changes it causes in RT essentially inhibits DNA synthesis. Unfortunately, single amino acid mutations in the binding pocket can significantly decrease the antiviral potency of this drug. This is true of the first generation NNRTIs, but new second generation NNRTIs are more effective against a range of drug resistant strains. | == Effects of nevirapine binding on RT-DNA complex == | ||
Nevirapine is a first generation NNRTI, which binds RT in a butterfly-like conformation. When DNA binds RT, the polymerase is stabilized by the presence of incoming dNTPs and is said to be in a polymerase-competent state. This is the only way the DNA-RT complex can bind dNTP and incorporate nucleotide. However, nevirapine has a destabilizing effect resulting from decreased interaction of key regions of the polymerase active site with nucleic acid. As previously mentioned, nevirapine leads to opening of the NNRTI binding pocket as a result of switching of the Tyr181 and Tyr188 rotamer conformations and shearing of the β12-β13-β14 sheet away from the β6-β10-β9 sheet. The β6-β10-β9 sheet contains the polymerase "catalytic triad" and the β12-β13-β14 sheet contains the "primer grip" that positions the primer strand for polymerization. Nevirapine binding causes the primer grip to shift by 4 angstroms, lifting the terminus of the DNA primer away from the P site, and diminishing interactions of the primer terminus with the conserved catalytic Y183MDD motif. Therefore, the first effect of nevirapine is loosening of the "primer grip." | |||
The second significant conformational change wrought by nevirapine is on the finger subdomain. The nevirapine-tertiary structure deforms the β3-β4 motif, which usually base pairs with the first template overhang, and interacts with incoming dNTPs that will be incorporated during polymerization. As a result of changes to the β3-β4 motif, parts of the fingers are shifted by 5-7 angstroms into regions that would normally accommodate the template overhang in catalytically-competent RT-DNA molecules. This puts the finger subdomain in an open or semi-open conformation. | |||
The crystal structure of nevirapine in solution with RT and DNA showed that the primer grip distortions locked the thumb in a hyper-extended position, resulting in diminished interactions between DNA and the polymerase domain. The flexible fingers, altered template-primer, and shifted template-overhang all reduce the productive binding of dNTPs. It appears that the flexibility of the fingers allow dNTP to still bind the RT-DNA-nevirapine complex at the polymerase active site, however, in a polymerase incompetent mode. The exact mechanism of how dNTPs are able to bind in such a nonproductive manner is yet to be uncovered. The dNTPs may enter the N site and bind in multiple orientations, or they may bind in an ordered yet non-productive fashion once the nucleic acid duplex has slid past the polymerase active site.<ref>PMID:19008444</ref> | |||
Third, the nevirapine-ternary structure extends the conformation of the thumb subdomain making it rigid. This is due to restricted inward movement of the thumb by the displaced β12-β13-β14 sheet. | |||
== Conclusion == | |||
Several factors stabilize its interaction with RT's hydrophobic pocket, and the conformational changes it causes in RT essentially inhibits DNA synthesis. Unfortunately, single amino acid mutations in the binding pocket can significantly decrease the antiviral potency of this drug. This is true of the first generation NNRTIs, but new second generation NNRTIs are more effective against a range of drug resistant strains. | |||
== References == | == References == | ||
