HIV-1 Reverse Transcriptase in Complex with Nevirapine: Difference between revisions

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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 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.  
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.


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>  
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.  
== HIV-1 RT resistance mutations ==
Binding of DNA to the polymerase active site requires the primer grip to be near the active site in order for the interaction to be catalytically competent. Binding of nevirapine interferes with the primer grip, moving it away from the active site. A bound nonnucleoside inhibitor is surrounded on three sides: 1) β6-β10-β9 sheet, 2) β12-β13-β14 sheet, and 3) 100-105 loop of p66 + Glu138 loop of p51. Chemical changes in these motifs could lead to the facilitated entrance and exit of most nonnucleosides. In many cases, single amino acid mutations in the binding pocket can significantly decrease the antiviral potency of nevirapine. The mutation K103N confers resistance to a wide variety of nonnucleosides. In addition, loop mutations (E138K and K103N) can facilitate exit of nonnucleosides from the binding pocket. To combat this problem, researchers have developed second generation NNRTIs that are generally more effective against a range of drug resistant strains.  


== Conclusion ==
== 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.  
Analysis of the crystal structures of RT-DNA complexes in the presence and absence of nevirapine allows us to determine the effects of nonnucleosides on RT structure and function. Binding of nevirapine reveals several changes to the RT-DNA complex. It directly displaces the primer grip located in the palm subdomain, which causes the primer terminus to relocate, the thumb to lock in hyper-extension, decreased interaction between DNA and the polymerase domain, and distortion the dNTP binding site. As a result of the conformational changes nevirapine causes, the process of DNA synthesis by RT is essentially inhibited. Unfortunately, the high mutation rate caused by HIV-1 polymerase's low fidelity readily produces mutant strains that are resistant to NNRTIs. Understanding the precise mechanism of these compounds' inhibition is a key step in developing more effective drugs against HIV.  


== References ==
== References ==
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