Non-nucleoside reverse-transcriptase inhibitors (NNRTIs), also known as "non-nucleosides" or "non-nukes" for short, attach themselves to reverse transcriptase and prevent the enzyme from converting RNA to DNA. In turn, HIV's genetic material cannot be incorporated into the healthy genetic material of the cell, and prevents the cell from producing new virus.
Reverse transcriptase (RT) inhibitors targeting DNA polymerase function are categorized into two groups: NRTIs and NNRTIs. Inhibition of RT via NNRTI binding has been proposed to employ a number of possible mechanisms. One of the early models suggested that NNRTI binding caused restrictions on movements of the relative domains important for catalytic transitions of the enzyme, otherwise known as ‘molecular arthritis’. However, determination of multiple structures in complex with NNRTIs, where subdomain orientations have been shown to differ, suggested that relative movement of catalytically important domains is still feasible even in the presence of NNRTI. Another inhibition mechanism proposes that NNRTI binding resulted in repositioning of the three-stranded-sheet of p66 that contained key catalytic residues Asp110, Asp185, and Asp186, therefore, forcing RT into a trapped, inactive conformation. Another mechanism suggested by Das et al., proposed that the significant repositioning of the “primer grip” that accompanies NNRTI binding may interfere with catalysis owing to inappropriate positioning of the primer terminus for catalysis. A more detailed evaluation based on crystallographic structures suggested a distortion of key catalytic residue orientations in such fashion that binding of divalent cations Mn2+/Mg2+ was inhibited and was proposed to weaken ability of the enzyme to bind dNTPs. A contrary result was obtained in kinetic studies of NNRTI binding to RT where association between the subunits was not affected by the inhibitor binding, and suggested that metal coordination was not involved in the inhibitory mechanism. Though a large number of plausible mechanisms had been proposed, presence of conflicting information continues to put under question our understanding of the NNRTI inhibitory mechanisms, therefore leaving the need for further investigation.
Mechanisms of NNRTI Resistance
The NNRTI binding pocket is located largely in the p66 subunit of RT and does not naturally exist in the unliganded enzyme. The NNRTI binding pocket is present in the palm subdomain of p66 between the β6-β10-β9 and β6-β13-β14 sheets. Residues forming the NNRTI binding pocket include the following in the p66 subunit: 95, 100, 101 and 103 (beta 5-6 loop), 106 and 108 (beta 6 loop), 179, 181, 188, 190 (beta 9-10 hairpin), 227, 229, 234, and 236 (beta 12-13 hairpin) and 318 (beta 15). Some residues from p51, such as 138, contribute to the NNRTI binding pocket as well. The NNRTI binding pocket is only 10 A away from the polymerase active site. In the DNA-bound or unliganded RT structures, the hydrophobic pocket is filled with the side chains of Tyrl81 and Tyr 188, which point away from the polymerase active site. When NNRTIs bind RT, the two side chains rotate away from the hydrophobic pocket and point toward the polymerase active site. This creates space to allow the inhibitor to bind. Although NNRTIs have diverse chemical structures, they adopt a similar configuration, when binding to the NNRTI pocket, assuming a “butterfly” configuration. The binding is stabilized primarily by hydrophobic interactions, and the complementarity between pocket and inhibitor is accomplished through induced conformational changes in each.
Mutations conferring NNRTI resistance generally affect interactions between the inhibitor and the enzyme. NNRTI resistance mutations can inhibit drug binding through at least three mechanisms: they can prevent inhibitor entry into the NNRTI binding pocket, they can disrupt specific contacts between the inhibitor and residue(s) lining the NNRTI binding pocket, or they can have more global effects on the conformation or size of the NNRTI binding pocket. A given mutation may affect binding of NNRTIs through more than one mechanism. Below, we will summarize what is known about the mechanisms of resistance of both commonly and uncommonly occurring NNRTI-resistance mutations.
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Frenkel, Y. (2009). The roles of structural variability and amphiphilicity of TMC278/rilpivirine in mechanisms of HIV drug resistance avoidance and enhanced oral bioavailability. Rutgers The State University of New Jersey-New Brunswick.