Pocket Of Reverse Transcriptase Research Articles

Design and in silico screening of analogs of rilpivirine as novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) for antiretroviral therapy

Part of the retroviral genus, the human immunodeficiency virus (HIV) relies on the host’s cellular machinery for replication. The viral genetic material is composed of ribonucleic acid (RNA) which, upon delivery into the host’s cells, is reverse transcribed into deoxyribonucleic acid (DNA) by the viral enzyme reverse transcriptase (RT). This is then used for the production of new viral components, thus allowing for further replication and spread of HIV. Because this virus selectively targets CD4+ T cells, the infection inevitably leads to weakening of the host’s immune system, which can then lead to acquired immunodeficiency syndrome (AIDS). One treatment for HIV is non-nucleoside reverse transcriptase inhibitors (NNRTIs), which are allosteric inhibitors of RT that disable the enzyme’s activity and thus viral replication. Previous NNRTIs approved for clinical use by the United States Food and Drug Association (FDA) include etravirine, doravirine, and rilpivirine. However, resistance to these drugs through mutations in RT necessitates the continued development of NNRTIs. Here, the structure of rilpivirine, a relatively recently FDA approved NNRTI, was used to design a library of analogs that were then evaluated in silico via high-throughput virtual screening (HTVS). From this, several structures were identified as potential next-generation NNRTIs with comparable predicted binding affinities to the allosteric binding pocket in RT as rilpivirine.

Molecular Modeling of Quinoline-Based Compounds as Potential Dual Inhibitors of Reverse Transcriptase and Integrase of HIV

As follow-up of our past publication [1], we propose that quinolones (as part of the pyridinone family) are capable to increase the number of interactions with HIV reverse transcriptase (RT) or integrase (IN) by adding a halogen in position C-8 of aromatic portion of the quinolones. This addition could help with the activity of dual inhibitors of RT and IN. In this work, we add a chlorine atom with the rationale to identify in the docking simulations a halogen interaction with the oxygen in the near aminoacids in the binding pockets of RT and IN enzymes. Our docking studies started with RT and 320 structures. Later, we took 73 structures with good results in docking with RT. The structures that we choose contain ester or acids groups in C-3 due the structural similarity with groups in charge to interact with the Mg++ ions in Elvitegravir. In conclusion, we obtained 14 structures that could occupy the allosteric pocket of RT and could inhibit the catalytic activity of IN, for this reason could be dual inhibitors. A major perspective of this work is the synthesis and testing of the potential dual inhibitors designed.

Structure-based evaluation of non-nucleoside inhibitors with improved potency and solubility that target HIV reverse transcriptase variants.

The development of novel non-nucleoside inhibitors (NNRTIs) with activity against variants of HIV reverse transcriptase (RT) is crucial for overcoming treatment failure. The NNRTIs bind in an allosteric pocket in RT ∼10 Å away from the active site. Earlier analogues of the catechol diether compound series have picomolar activity against HIV strains with wild-type RT but lose potency against variants with single Y181C and double K103N/Y181C mutations. As guided by structure-based and computational studies, removal of the 5-Cl substitution of compound 1 on the catechol aryl ring system led to a new analogue compound 2 that maintains greater potency against Y181C and K103N/Y181C variants and better solubility (510 μg/mL). Crystal structures were determined for wild-type, Y181C, and K103N/Y181C RT in complex with both compounds 1 and 2 to understand the structural basis for these findings. Comparison of the structures reveals that the Y181C mutation destabilizes the binding mode of compound 1 and disrupts the interactions with residues in the pocket. Compound 2 maintains the same conformation in wild-type and mutant structures, in addition to several interactions with the NNRTI binding pocket. Comparison of the six crystal structures will assist in the understanding of compound binding modes and future optimization of the catechol diether series.

Potent Nonnucleoside Reverse Transcriptase Inhibitors Target HIV-1 Gag-Pol

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) target HIV-1 reverse transcriptase (RT) by binding to a pocket in RT that is close to, but distinct, from the DNA polymerase active site and prevent the synthesis of viral cDNA. NNRTIs, in particular, those that are potent inhibitors of RT polymerase activity, can also act as chemical enhancers of the enzyme's inter-subunit interactions. However, the consequences of this chemical enhancement effect on HIV-1 replication are not understood. Here, we show that the potent NNRTIs efavirenz, TMC120, and TMC125, but not nevirapine or delavirdine, inhibit the late stages of HIV-1 replication. These potent NNRTIs enhanced the intracellular processing of Gag and Gag-Pol polyproteins, and this was associated with a decrease in viral particle production from HIV-1-transfected cells. The increased polyprotein processing is consistent with premature activation of the HIV-1 protease by NNRTI-enhanced Gag-Pol multimerization through the embedded RT sequence. These findings support the view that Gag-Pol multimerization is an important step in viral assembly and demonstrate that regulation of Gag-Pol/Gag-Pol interactions is a novel target for small molecule inhibitors of HIV-1 production. Furthermore, these drugs can serve as useful probes to further understand processes involved in HIV-1 particle assembly and maturation.

Structure and mechanism of action of nonnucleoside inhibitors of HIV-1 reverse transcriptase: strategies to combat drug resistance

In the past few years, drug research has focused on three HIV-1 enzymes, reverse transcriptase (RT), protease, and integrase. In the case of RT, a number of potent inhibitors have been discovered. These can be classified into two distinct groups, nucleoside analogs and nonnucleoside inhibitors; however, mutations in RT have allowed the virus to develop resistance to all of the known drugs. In order to better understand the interactions between amino acid residues in the protein and nonnucleoside inhibitors, a computer model of the nonnucleoside inhibitor binding pocket of RT has been developed, using a subset of amino acid residues surrounding the pocket. The results of molecular mechanics minimizations of three RT/nonnucleoside inhibitor complexes showed that the resultant total energies of complexation (binding energies) correlated with EC 50 values if and only if the calculations were carried out using coordinates from the cognate complex while allowing for adjustments of the protein relative to the inhibitor. If a model was constructed using only the crystal data of one particular RT/inhibitor complex (RT/8-Cl TIBO), the calculations did not correctly order the other inhibitors. The difficulty in devising such a “generic” model nonnucleoside binding site in HIV-1 RT is likely due to the inherent flexibility of the enzyme. A comparison of the structure(s) of HIV-1 RT in complexes with different nonnucleoside inhibitors shows that the enzyme readily adapts to the shape of each inhibitor upon complexation. In contrast to the side-chain residues of HIV protease, the amino acid residues surrounding the binding pocket in RT adopt geometries that are unique to each bound inhibitor, adopting positions that make tight van der Waals contacts. Accompanying these changes at the site where the inhibitor binds are alterations in the geometry of the nearby polymerase active site. These changes can be conveniently monitored by measuring the increase in the distance between residue G231 in the RT primer grip region and aspartyl residues (D110, D185, and D186) in the polymerase active site. The magnitude of the change in this distance correlates inversely with inhibitor EC 50, suggesting a possible mechanism of action of the drugs. Calculations using a site where various amino acids residues were changed to simulate mutations in RT that induce resistance to the nonnucleoside inhibitors revealed that a combination of less favorable inhibitor–protein interactions and slight geometry changes in the polymerase active site are responsible for the decreased effectiveness of the inhibitors against mutant RTs. The modeling results are discussed with regard to both the mechanism of inhibition as well as application of these insights to strategies for the design of better nonnucleoside inhibitors.