HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors Research Articles

Recent Advances in the Discovery and Development of Novel HIV-1 NNRTI Platforms: 2006-2008 Update

Currently, the long-term usage of non-nucleoside reverse transcriptase inhibitors (NNRTIs) in HIVAIDS patients eventually leads to the development of drug resistance and severe side effect. Therefore, it is imperative to look for the novel NNRTIs with potent and broad spectrum anti-mutant activity that are also safe and have excellent pharmacokinetic profiles. In this article, newly emerging NNRTIs scaffolds in recent three years, together with the underlying strategies for developing new generation HIV-1 NNRTIs with improved resilience to current drug resistant mutants, are reviewed and analysed.

Non-nucleoside reverse transcriptase inhibitor efavirenz increases monolayer permeability of human coronary artery endothelial cells

Highly active antiretroviral therapy (HAART) is often associated with endothelial dysfunction and cardiovascular complications. In this study, we determined whether HIV non-nucleoside reverse transcriptase inhibitor efavirenz (EFV) could increase endothelial permeability. Human coronary artery endothelial cells (HCAECs) were treated with EFV (1, 5 and 10 μg/ml) and endothelial permeability was determined by a transwell system with a fluorescence-labeled dextran tracer. HCAECs treated with EFV showed a significant increase of endothelial permeability in a concentration-dependent manner. With real time PCR analysis, EFV significantly reduced the mRNA levels of tight junction proteins claudin-1, occludin, zonula occluden-1 and junctional adhesion molecule-1 compared with controls ( P < 0.05). Protein levels of these tight junction molecules were also reduced substantially in the EFV-treated cells by western blot and flow cytometry analyses. In addition, EFV also increased superoxide anion production with dihydroethidium and cellular glutathione assays, while it decreased mitochondrial membrane potential with JC-staining. Antioxidants (ginkgolide B and MnTBAP) effectively blocked EFV-induced endothelial permeability and mitochondrial dysfunction. Furthermore, EFV increased the phosphorylation of MAPK JNK and IκBα, thereby increasing NFκB translocation to the nucleus. Chemical JNK inhibitor and dominant negative mutant JNK and IκBα adenoviruses effectively blocked the effects of EFV on HCAECs. Thus, EFV increases endothelial permeability which may be due to the decrease of tight junction proteins and the increase of superoxide anion. JNK and NFκB activation may be directly involved in the signal transduction pathway of EFV action in HCAECs.

Discovery of diarylpyridine derivatives as novel non-nucleoside HIV-1 reverse transcriptase inhibitors

Two series ( 4 and 5) of diarylpyridine derivatives were designed, synthesized, and evaluated for anti-HIV-1 activity. The most promising compound, 5e, inhibited HIV-1 IIIB, NL4-3, and RTMDR1 with low nanomolar EC 50 values and selectivity indexes of >10,000. The results of this study indicate that diarylpyridine can be used as a novel scaffold to derive a new class of potent NNRTIs, active against both wild-type and drug-resistant HIV-1 strains.

1,2,3-Selenadiazole thioacetanilides: Synthesis and anti-HIV activity evaluation

The development of new HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) offers the possibility of generating novel structures of increased potency. Based on the bioisosteric principle, novel series of 1,2,3-selenadiazole thioacetanilide derivatives were designed, and synthesized using an original synthetic route, structurally confirmed by spectral analysis, and evaluated for their anti-HIV activity in MT-4 cells. The results showed that only compound 7f possessed potent activity against HIV-1 replication (EC 50 = 2.45 μM) similar to the prototype series of sulfanyltriazoles. None of the compounds were active against HIV-2 replication.

Metabolic bone disease in HIV infection

HIV mainly replicates in CD4þ T lymphocytes andmonocyte/macrophages causing severe immunologicalimpairment. In addition to the immune system, HIVinfection affects tissues and organs such as kidney, liver,the central nervous system, heart and bone showing acomplex pathogenesis [1].The advent and widespread use of highly activeantiretroviral therapy (HAART) in the last two decadeshasled toa markedimprovementinthe treatmentofHIVdisease even though viral infection cannot be eradicatedbecause HAART does not completely eliminate the viralreservoirs [2]. HAART has dramatically changed thecourseofHIVinfection froma fatalinfectiontoachronicand relatively manageable disease. The increased lifeexpectancyofHIVpatientsandtheeffectsofHAARThavechanged the management of HIV infection. Nowadaysmedical treatment is no longer focused solely on HIVinfection, opportunistic diseases and monitoring immunederangement, but also includes the control of metabolic,cardiovascular, liver, bone and kidney complications. Inparticular, bone alterations have been observed in thecourse of HIV disease representing a pivotal clinicalprobleminthemanagementofHIVpatientsespeciallyforapossible development of bone fractures [3]. The majorbonelesionsdetectableinHIVpatientsarerelatedtobonedemineralization (osteopenia/osteoporosis and osteoma-lacia) and osteonecrosis ([4] for a review).This report will discuss the pathogenesis, diagnosis andtreatment of major bone complications represented bybone demineralization diseases during HIV infection andHAART treatment.

Synthesis and anti-HIV activity evaluation of 2-(4-(naphthalen-2-yl)-1,2,3-thiadiazol-5-ylthio)- N-acetamides as novel non-nucleoside HIV-1 reverse transcriptase inhibitors

A series of 2-(4-(naphthalen-2-yl)-1,2,3-thiadiazol-5-ylthio)acetamide (TTA) derivatives were synthesized and evaluated as potent inhibitors of HIV-1. Among the newly disclosed TTAs, compounds 7f, 7g and 7c were the most potent inhibitors of HIV-1 replication of the series (EC 50 = 0.17 ± 0.02, 0.36 ± 0.19 and 0.39 ± 0.05 μM, respectively), coupled with a reasonable selectivity index (SI > 1452, >845, and >774, respectively). They possess improved or similar HIV-1 inhibitory activity compared with NVP (EC 50 = 0.208 μM) and DLV (EC 50 = 0.320 μM). The preliminary structure–activity relationships among the newly synthesized congeners are discussed briefly and rationalized by docking studies.

Sulfanyltriazole/tetrazoles: A Promising Class of HIV-1 NNRTIs

There is an urgent need for the design and development of new and safer drugs for the treatment of human immunodeficiency virus (HIV) infection, specifically active against drug-resistant viral strains. Recently, sulfanyltriazole/tetrazole derivatives were reported as potent HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), with low nanomolar intrinsic activity against RT and submicromolar antiviral activity in HIV infected cells. In this review, the structural modifications, SAR analysis and docking studies of sulfanyltriazole/tetrazoles HIV-1 NNRTIs are discussed, and other interesting NNRTIs with the same or similar pharmacophore as the sulfanyltriazole/tetrazole derivatives are also presented and analyzed for their in SAR.

New Pyridinone Derivatives as Potent HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors

Several 5-ethyl-6-methyl-4-cycloalkyloxy-pyridin-2(1H)-ones were synthesized and evaluated for their anti HIV-1 activities against wild-type virus and clinically relevant mutant strains. A racemic mixture (10) with methyl substituents at positions 3 and 5 of the cyclohexyloxy moiety had potent antiviral activity against wild-type HIV-1. Subsequent stereoselective synthesis of a stereoisomer displaying both methyl groups in equatorial position was found to have the best EC(50). Further modulations focused on position 3 of the pyridinone ring improved the antiviral activity against mutant viral strains. Compounds bearing a 3-ethyl (22) or 3-isopropyl group (23) had the highest activity against wild-type HIV-1 and displayed low-nanomolar potency against several clinically relevant mutant strains.

Crystal structures of HIV-1 nonnucleoside reverse transcriptase inhibitors: N-benzyl-4-methyl-benzimidazoles

HIV-1 nonnucleoside reverse transcriptase inhibitors are potentially specific and effective drugs in AIDS therapy. The presence of two aromatic systems with an angled orientation in the molecule of the inhibitor is crucial for interactions with HIV-1 RT. The inhibitor drives like a wedge into the cluster of aromatic residues of RT HIV-1 and restrains the enzyme in a conformation that blocks the chemical step of nucleotide incorporation. Structural studies provide useful information for designing new, more active inhibitors. The crystal structures of four NNRTIs are presented here. The investigated compounds are derivatives of N-benzyl-4-methyl-benzimidazole with various aliphatic and aromatic substituents at carbon 2 positions and a 2,6-dihalogeno-substituted N-benzyl moiety. Structural data reported here show that the conformation of the investigated compounds is relatively rigid. Such feature is important for the nonnucleoside inhibitor binding to HIV-1 reverse transcriptase.

Synthesis and biological evaluation of novel 2-arylalkylthio-4-amino-6-benzyl pyrimidines as potent HIV-1 non-nucleoside reverse transcriptase inhibitors

Novel 2-aryalkylthio-4-amino-6-benzylpyrimidines ( 3a– i), which can be considered as S-DABO and TMC-125 analogue hybrid molecules, have been designed and synthesized as inhibitors of HIV-1 RT. The results clearly indicated that the changes at the N 3/C 4 position of pyrimidine ring could affect the hydrogen bonds strength and number between N 3/C 4 and the Lys101 residue which are indispensable for anti-HIV-1 RT activity. The biological activity results are also in accordance with the docking study.

Discovery of Wild-Type and Y181C Mutant Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors Using Virtual Screening with Multiple Protein Structures

To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercially available compounds. Two of the structures are for WT-virus with different conformations of Tyr181, while the third structure incorporates the Y181C modification. Eventually nine compounds were purchased and assayed. Three of the compounds show low-micromolar antiviral activity toward either or both the wild-type and Y181C HIV-1 strains. The study illustrates a viable protocol to seek anti-HIV agents with enhanced resistance profiles.

Metabolic Activation of Nevirapine in Human Liver Microsomes: Dehydrogenation and Inactivation of Cytochrome P450 3A4

Nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, has been associated with incidences of skin rash and hepatotoxicity in patients. Although the mechanism of idiosyncratic hepatotoxicity remains unknown, it is proposed that metabolic activation of nevirapine and subsequent covalently binding of reactive metabolites to cellular proteins play a causative role. Studies were initiated to determine whether nevirapine undergoes cytochrome P450 (P450)-mediated bioactivation in human liver microsomes to electrophilic intermediates. Liquid chromatography-tandem mass spectrometry analysis of incubations containing nevirapine and NADPH-supplemented microsomes in the presence of glutathione (GSH) revealed the formation of a GSH conjugate derived from the addition of the sulfydryl nucleophile to nevirapine. No other GSH conjugates were detected, including conjugates of oxidized metabolites of nevirapine. These findings are consistent with a bioactivation sequence involving initial P450-catalyzed dehydrogenation of the aromatic nucleus with a 4-methyl group in nevirapine to an electrophilic quinone methide intermediate, which is subsequently attacked by glutathione yielding the sulfydryl conjugate. Formation of the nevirapine GSH conjugate was primarily catalyzed by heterologously expressed recombinant CYP3A4 and, to a lesser extent, CYP2D6, CYP2C19, and CYP2A6. In addition, the quinone methide reactive metabolite was a mechanism-based inactivator of CYP3A4, with inactivation parameters K(I) = 31 microM and k(inact) = 0.029 min(-1), respectively. It is proposed that formation of the quinone methide intermediate may represent a rate-limiting step in the initiation of nevirapine-mediated hepatotoxicity.

Selective kinetics of HIV-1 non-nucleoside reverse transcriptase inhibitor drug resistanace-associated mutations in AIDS patients receiving highly active anti-retrovirul therapy

Objective To elucidate the molecular evolutional characteristics of HIV-1 non-nucleoside reverse transcriptase inhibitor (NNRTI) drug resistance-associated mutations in AIDS patients receiving highly active antiretroviral therapy (HAART).Methods Four AIDS patients receiving HAART with good adherence within a HlV-1 drug resistance cohort from a rural region in central China were selected,who possessed susceptible virus at the beginning of treatment and gradually came to produce resistance to NNRTIs during the process of antiretroviral therapy (ART),reverse transcriptase (RT) genes from each patient's peripheral blood samples (from 3 to 30 months after withdrawal) were cloned and sequenced in succession.Results To sequenced total 855 clones and obtained the HIV-1 NNRTI drug resistance-asseciated mutations patterns of the four patients: (1)G190A often appeared with F227 L and had the tendency of accumulating P236V during the process of treatmenL (2)Y188C always presented alone and sometimes it concured with P236V.(3) YI81C frequently concured with VI79D or KIO3N and the combination varies from patient to patient.(4)K103N often combined with Y181C or M230L Conclusions The molecular evolutional characteristics of HIV-1 NNRTI drug resistance-asseciated mutations in the 4 AIDS patients are summarized.They showed different pathways on HIV-1 NNRTI drug resistance-associated mutations and those mutations detected early tend to be predominant strains. Key words: Acquired immunodeficiency syndrome; Reverse transcriptase inhibitors; Drug resistance; Mutation; Evolution,molecular

Screening for NNRTIs with Slow Dissociation and High Affinity for a Panel of HIV-1 RT Variants

A lead optimization library consisting of 800 HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs) was screened in parallel against 4 clinically relevant variants of HIV-1 RT (Wt, L100I, Y181C, and K103N) using a surface plasmon resonance-based biosensor. The aim was to identify inhibitors suitable in specific topical microbicides efficient for preventing the transmission of a range of clinically significant strains of HIV-1. The authors hypothesized that such compounds should have high affinity and slow dissociation rates for multiple variants of the target. To efficiently analyze the large amount of real-time data (sensorgrams) that were generated in the screening, they initially used signals from 3 selected time points to identify compounds with high affinity and slow dissociation for the complete panel of enzyme variants. Hits were confirmed by visually inspecting the complete sensorgrams. Two structurally unrelated compounds fulfilled the hit criteria, but only 1 compound was found to (a) compete with a known NNRTI for binding to the NNRTI site, (b) inhibit HIV-1 RT activity, and (c) inhibit HIV-1 replication in cell culture, for all 4 enzyme variants. This novel screening methodology offers high-resolution real-time kinetic data for multiple targets in parallel. It is expected to have broad applicability for the discovery of compounds with defined kinetic profiles, crucial for optimal therapeutic effects.

Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations

Human immunodeficiency virus-1 reverse transcriptase (RT) inhibition is a major focus of current anti-AIDS drug discovery and development programs, comprising 17 of the 31 Food and Drug Administration-approved compounds. The emergence of the non-nucleoside RT inhibitor (NNRTI) class of compounds provides a highly specific and structurally diverse set of drugs, which act noncompetitively to perturb normal RT function. Despite a relatively rich set of crystallographic data of RT in various states, details of the allosteric modulation of RT dynamics by NNRTIs are lacking. Capturing this inhibitory mechanism could fuel the design of more effective inhibitors at the NNRTI site and also drive the identification of novel allosteric sites. To address this, we have performed multicopy molecular dynamics (MD) simulations of RT in the presence and absence of the NNRTI nevirapine (cumulative total simulation time, 360 ns). By comparing the collective motions of the MD and crystallographic structures, we demonstrate that the chief effect of NNRTIs is to constrain a key rigid-body motion between the “fingers” and “thumb” subdomains of the p66 subunit. We show that the NNRTI binding pocket (NNIBP) is proximal to the hinge points for this essential motion, and NNRTIs therefore act as “molecular wedges,” sterically blocking the full range of motion. To explain how this impaired movement might result in the experimentally observed loss of polymerase activity, we show that the motion influences the geometry of key catalytic residues on opposite faces of the NNIBP. From a methodological point of view, our results suggest that the multicopy MD simulation approach is very useful when studying proteins that perform such large conformational changes.

Bridge water mediates nevirapine binding to wild type and Y181C HIV-1 reverse transcriptase—Evidence from molecular dynamics simulations and MM-PBSA calculations

The important role of the bridge water molecule in the binding of HIV-1 reverse transcriptase (RT) inhibitor complex was elucidated by molecular dynamics (MD) simulations using an MM-PBSA approach. Binding free energies and thermodynamic property differences for nevirapine bound to wild type and Y181C HIV-1 reverse transcriptase were investigated, and the results were compared with available experimental data. MD simulations over 3 ns revealed that the bridge water formed three characteristic hydrogen bonds to nevirapine and two residues, His235 and Leu234, in the binding pocket. The energetic derived model, which was determined from the consecutive addition of a water molecule, confirmed that only the contribution from the bridge water was essential in the binding configuration. Including this bridge water in the MM-PBSA calculations reoriented the binding energies from −32.20 to −37.65 kcal/mol and −28.07 to −29.82 kcal/mol in the wild type and Y181C HIV-1 RT, respectively. From the attractive interactions via the bridge water, His235 and Leu234 became major contributions. We found that the bridge water is the key in stabilizing the bound complex; however, in the Y181C RT complex this bridge water showed weaker hydrogen bond formation, lack of attractive force to nevirapine and lack of binding efficiency, leading to the failure of nevirapine against the Y181C HIV-1 RT. Moreover, the dynamics of Val179, Tyr181Cys, Gly190 and Leu234 in the binding pocket showed additional attractive energetic contributions in helping nevirapine binding. These findings that the presence of a water molecule in the hydrophobic binding site plays an important role are a step towards a quantitative understanding of the character of bridge water in enzyme-inhibitor binding. This can be helpful in developing designs for novel non-nucleoside HIV-1 RT inhibitors active against the mutant enzyme.

Receptor- and ligand-based 3D-QSAR study for a series of non-nucleoside HIV-1 reverse transcriptase inhibitors

Molecular modeling of a series of HIV reverse transcriptase (RT) non-nucleoside inhibitors (2-amino-6-arylsulfonylbenzonitriles and their thio and sulfinyl congeners) was carried out by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) approaches. Docking simulations were employed to position the inhibitors into RT active site to determine the most probable binding mode and most reliable conformations. The study was conducted using a complex receptor-based and ligand-based alignment procedure and different alignment modes were studied to obtain highly reliable and predictive CoMFA and CoMSIA models with cross-validated q 2 value of 0.723 and 0.760, respectively. Furthermore, the CoMFA and CoMSIA contour maps with the 3D structure of the target (the binding site of RT) inlaid were obtained to better understand the interaction between the RT protein and the inhibitors and the structural requirements for inhibitory activity against HIV-1. We show that for 2-amino-6-arylsulfonylbenzonitriles inhibitors to have appreciable inhibitory activity, bulky and hydrophobic groups in 3- and 5-position of the B ring are required. Moreover, H-bond donor groups in 2-position of the A ring to build up H-bonding with the Lys101 residue of the RT protein are also favorable to activity.

Specific Targeting of Highly Conserved Residues in the HIV-1 Reverse Transcriptase Primer Grip Region. 2. Stereoselective Interaction to Overcome the Effects of Drug Resistant Mutations

Starting from the prototypic compound 4, we describe new, potent, and broad-spectrum pyrrolobenzo(pyrido)oxazepinones antivirals. A biochemical and enzymological investigation was performed for defining their mechanism of inhibition at either recombinant HIV-1 RT wild type and non-nucleoside reverse transcriptase inhibitors (NNRTIs)-resistant mutants. For the novel compounds (S)-(+)-5 and (S)-(-)-7, a clear-cut stereoselective mechanism of enzyme inhibition was found. Molecular modeling studies were performed for revealing the underpinnings of this behavior.

Acylthiocarbamates as non-nucleoside HIV-1 reverse transcriptase inhibitors: docking studies and ligand-based CoMFA and CoMSIA analyses

Acylthiocarbamates (ATCs) have been identified as a class of potent non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors. A computational strategy based on molecular docking studies followed by comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was used to identify the most important features impacting ATC antiretroviral activity. The CoMSIA model proved to be the more predictive, with r(2)(ncv) = 0.89, r(cv)(2) = 0.38, standard error of estimate (SEE) = 0.494, F = 84, and r(2)(pred) = 0.81. The results of these studies will be useful in designing new ATCs with improved potency, also against clinically relevant resistant mutants.

Quantification of HIV protease inhibitors and non-nucleoside reverse transcriptase inhibitors in peripheral blood mononuclear cell lysate using liquid chromatography coupled with tandem mass spectrometry

For pharmacokinetic monitoring, measurement of antiretroviral agents in plasma is the gold standard. However, human immunodeficiency virus protease inhibitors (PIs) or non-nucleoside reverse transcriptase inhibitors (NNRTIs) exert their action within the infected cell. Cell-associated concentrations may therefore more adequately reflect therapy outcome. Therefore, for the quantification of nine PIs (amprenavir, atazanavir, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir and tipranavir), 1 active PI metabolite (nelfinavir M8) and 2 NNRTIs (efavirenz and nevirapine) in lysate of peripheral blood mononuclear cells (PBMCs) an assay was developed and validated, using liquid chromatography coupled with tandem mass spectrometry. Analytes were extracted from a PBMC pellet by means of a one-step extraction with 50% methanol containing the internal standards D6-indinavir, D5-saquinavir, 13C6-efavirenz and dibenzepine. Chromatographic separation was performed on a reversed phase C18 column (150 mm × 2.0 mm, particle size 5 μm) with a quick stepwise gradient using an acetate buffer (pH 5) and methanol, at a flow rate of 0.25 mL/min. The analytical run time was 10 min. The triple quadrupole mass spectrometer was operated in the positive ion-mode and multiple reaction monitoring was used for drug quantification. The method was validated over a range of 1–500 ng/mL in PBMC lysate for all analytes. The method was proven to be specific, accurate, precise and robust. The mean precision and accuracy was less than ±12% at all concentration levels. Using the developed assay and a previously developed assay for these analytes in plasma, the relationship between plasma and intracellular pharmacokinetics and their relationship with therapy outcome can now be determined.