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The development of effective antiretroviral inhibitors (HIV-1 Reverse Transcriptase) and glucosamine-6-phosphate (GlcN6P) agents represent a significant challenge for combating viral infections and related diseases. In this study, we employed a multidisciplinary approach to design and evaluate a series of novel triazole analogs as potential candidates for anti-retroviral and glucosamine-6-phosphate agents. Using molecular docking, we explored the binding interactions between the RSA3 analog and the target proteins implicated in viral replication and glucosamine metabolism. Density functional theory (DFT) employing the 6-311++G(d,p) basis set was utilized for computational analysis, with a subsequent examination of the electronic parameters. The HOMO and LUMO orbitals as well as the molecular electrostatic potential map were investigated using DFT to characterize the reactivity of our molecule. Molecular dynamics simulations were performed to investigate the stability and dynamic behavior of the ligand-protein complex (RSA3) over time (300 ns). Furthermore, we employed MM-GBSA calculations of the compound RSA3 (molecular mechanics generalized band surface area) to estimate the binding free energies (−71.30 ± 7.26 kcal/mol and −67.86 ± 7.09 kcal/mol, respectively) and identified the most promising compounds with high affinity for the target proteins. Additionally, predictive absorption, distribution, metabolism, excretion and toxicity (ADMET) studies of compound RSA3 were conducted to assess its drug-like properties and potential safety profiles of the selected compound. Our results revealed that RSA3 has favorable binding interactions, is a stable complex and has significant binding affinity for target proteins. Moreover, predictive ADMET studies indicated that RSA3 possesses desirable drug-like properties, suggesting its potential for further investigation as an anti-retroviral agent and glucosamine-6-phosphate agent. Overall, this integrative computational approach combining molecular docking, DFT analysis, dynamics simulations, MM-GBSA and predictive ADMET studies provides valuable insights into the design and evaluation of novel triazole analogs with potential therapeutic applications, highlighting the importance of rational drug design strategies in the field of antiretroviral and glucosamine research. [ABSTRACT FROM AUTHOR]

Feline immunodeficiency virus (FIV) is a common infection found in domesticated and wild cats worldwide. Despite the wealth of therapeutic understanding of the disease in humans, considerably less information exists regarding the treatment of the disease in felines. Current treatment relies on drugs developed for the related human immunodeficiency virus (HIV) and includes compounds of the popular non‐nucleotide reverse transcriptase (NNRTI) class. This is despite FIV‐RT being only 67% similar to HIV‐1 RT at the enzyme level, increasing to 88% for the allosteric pocket targeted by NNRTIs. The goal of this project was to try to quantify how well the more extensive pharmacological knowledge available for human disease translates to felines. To this end we screened known NNRTIs and 10 diverse pyrimidine analogs identified virtually. We use this chemo‐centric probe approach to (a) assess the similarity between the two related RT targets based on the observed experimental inhibition values, (b) try to identify more potent inhibitors at FIV, and (c) gain a better appreciation of the structure–activity relationships (SAR). We found the correlation between IC50s at the two targets to be strong (r2 = 0.87) and identified compound 1 as the most potent inhibitor of FIV with IC50 of 0.030 μM ± 0.009. This compared to FIV IC50 values of 0.22 ± 0.17 μM, 0.040 ± 0.010 μM and >160 μM for known anti HIV‐1 RT drugs Efavirenz, Rilpivirine, and Nevirapine, respectively. This knowledge, along with an understanding of the structural origin that give rise to any differences could improve the way HIV drugs are repurposed for FIV. [ABSTRACT FROM AUTHOR]

In this study, a novel series of diarylpyrimidine derivatives with Fsp3‐enriched spirocycles were designed and synthesized to further explore the chemical space of the hydrophobic channel of the NNRTI‐binding pocket. The biological evaluation results showed that most of the compounds displayed effective inhibitory potency against the HIV‐1 wild‐type strain, with EC50 values ranging from micromolar to submicromolar levels. Among them, TT6 turned out to be the most effective inhibitor with an EC50 value of 0.17 μM, demonstrating up to 47 times more active than that of reference drug 3TC (EC50 = 8.01 μM). More encouragingly, TT6 was found to potently inhibit the HIV‐1 mutant strain K103N with an EC50 value of 0.69 μM, being about 6‐fold more potent than 3TC (EC50 = 3.68 μM) and NVP (EC50 = 4.62 μM). Furthermore, TT6 exhibited the most potent inhibitory activity toward HIV‐1 reverse transcriptase with an IC50 value of 0.33 μM. Additionally, molecular simulation studies were conducted to investigate the binding modes between TT6 and NNRTI‐binding pocket, which may provide valuable clues for the follow‐up structural optimizations. [ABSTRACT FROM AUTHOR]

Introduction: The worldwide distribution of herpes simplex virus type 1 (HSV-1) allied to the emergence of resistant strains makes necessary and urgent the search and development of new substances capable of preventing and treating HSV-1 infections. Studies demonstrate synergy between genital herpes and human immunodeficiency virus type 1 (HIV-1), which represents a major concern for global public health. Objective: The objective of this study was to evaluate the activity of crude extracts and isolated substances from C. fluminensis in the in vitro replication of the HSV-1 virus and HIV-1-RT activity. Methods: This study evaluated the activity of extracts and isolated compounds from Clusia fluminensis Planch. & Triana against HSV-1 using Vero cells in culture and against HIV-1 using a recombinant reverse transcriptase enzyme (HIV -1 RT). The percentage of inhibition against HSV-1 was determined from viral lysis plaque reduction assay, and the anti-HIV-1-RT test was performed by a fluorimetric assay. It was also evaluated the cytotoxic activity of the samples using MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide]. Results: The crude extracts showed high percentage of inhibition against HSV-1, reaching 81.4 to 100.0% inhibition in non-cytotoxic concentration (50 μg/mL). The isolated compounds, lanosterol and clusianone, demonstrated 100% inhibition in non-cytotoxic concentration (50 μg/mL). We also examined the effects of the extracts and isolates on the activity of the HIV-1-RT. Among the crude extracts, only the methanolic extract of leaves and methanolic extract of stems showed inhibitory activity against HIV-1-RT. Regarding the isolated compounds, lanosterol showed a moderate activity. Conclusion: Our data demonstrate that extracts and isolates compounds Clusia fluminensis Planch. & Triana have promising antiviral activity inhibiting HSV-1 replication and HIV-1 by inhibiting the anti-RT activity.

The human immunodeficiency virus type-1 Reverse Transcriptase (HIV-1 RT) plays a pivotal role in essential viral replication and is the main target for antiviral therapy. The anti-HIV-1 RT drugs address resistance-associated mutations. This research focused on isolating the potential specific DNA aptamers against K103N/Y181C double mutant HIV-1 RT. Five DNA aptamers showed low IC50 values against both the KY-mutant HIV-1 RT and wildtype (WT) HIV-1 RT. The kinetic binding affinity forms surface plasmon resonance of both KY-mutant and WT HIV-1 RTs in the range of 0.06–2 µM and 0.15–2 µM, respectively. Among these aptamers, the KY44 aptamer was chosen to study the interaction of HIV-1 RTs-DNA aptamer complex by NMR experiments. The NMR results indicate that the aptamer could interact with both WT and KY-mutant HIV-1 RT at the NNRTI drug binding pocket by inducing a chemical shift at methionine residues. Furthermore, KY44 could inhibit pseudo-HIV particle infection in HEK293 cells with nearly 80% inhibition and showed low cytotoxicity on HEK293 cells. These together indicated that the KY44 aptamer could be a potential inhibitor of both WT and KY-mutant HIV-RT. [ABSTRACT FROM AUTHOR]

In this study, a novel series of diarylpyrimidine derivatives with Fsp 3 -enriched spirocycles were designed and synthesized to further explore the chemical space of the hydrophobic channel of the NNRTI-binding pocket. The biological evaluation results showed that most of the compounds displayed effective inhibitory potency against the HIV-1 wild-type strain, with EC 50 values ranging from micromolar to submicromolar levels. Among them, TT6 turned out to be the most effective inhibitor with an EC 50 value of 0.17 μM, demonstrating up to 47 times more active than that of reference drug 3TC (EC 50  = 8.01 μM). More encouragingly, TT6 was found to potently inhibit the HIV-1 mutant strain K103N with an EC 50 value of 0.69 μM, being about 6-fold more potent than 3TC (EC 50  = 3.68 μM) and NVP (EC 50  = 4.62 μM). Furthermore, TT6 exhibited the most potent inhibitory activity toward HIV-1 reverse transcriptase with an IC 50 value of 0.33 μM. Additionally, molecular simulation studies were conducted to investigate the binding modes between TT6 and NNRTI-binding pocket, which may provide valuable clues for the follow-up structural optimizations., (© 2024 John Wiley & Sons Ltd.)

Abstract Conformational adaptation of non-nucleoside reverse transcriptase inhibitor (NNRTI) via torsional flexibility is found to be very significant for targeting human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) mutants. Catechol diether derivative including flexible torsions is new potent NNRTI with picomolar activity. Moreover, this derivative also reveals the good solubility, low toxicity and potent inhibition for HIV-1 mutants. In this study, torsional flexibility of an undecorated catechol diether compound in the binding pocket of wild type and mutants (Y181C and K103N/Y181C) HIV-1 RT is investigated by using QM/MM calculations. From the results, the uracil ring is found to exhibit more flexibility in the NNIBP. On the contrary, potential energy surfaces show that high energy is encountered by changing of the corresponding torsion of the cyanovinyl aryl ring indicating the limitation for torsional flexibility. For pointing out the key interaction for the binding, the residual interaction energies are performed by means of QM calculations. Important attractive interactions through hydrogen bonds between the inhibitor and K102, K/N103, V106, and Y188 are observed. The catechol ring is proposed to be modified in order to strengthen interactions with surrounding amino acids. The results may help for the designing of new potent NNRTIs. Graphical abstract Image 1 Highlights • Conformational adaptation of NNRTI via torsional flexibility is very significant for targeting HIV-1 RT mutants. • Torsional flexibility of an undecorated catechol diether in the binding pocket is investigated by using QM/MM calculations. • The catechol ring is suggested to modify in order to gain more interactions with the surrounding amino acids. [ABSTRACT FROM AUTHOR]

Human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT) plays a key in the life cycle of HIV-1. It is considered to be one of the promising targets for treating HIV/AIDS which contains two drug binding sites, a substrate binding site, and an allosteric site. Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a class of RT inhibitors that bind to allosteric sites on HIV-1 RT in a non-competitive manner and thereby disrupting the conformation of RT. Hence, they can act as potent inhibitors against HIV-1 RT. In present study, the key structural requirements for enhancing HIV-1 RT inhibitory activity were explored from combined docking and three-dimensional quantitative structure activity relationship (3D QSAR) protocols. Initially, multiple-receptor conformation docking (MRCD) was performed using a series of diaryl pyridine and pyrimidine derivatives into the active site of ten X-ray crystal structures and one NMR-resolved conformation of HIV-1 RT. Later, the dock poses obtained from docking were clustered and 3D QSAR models were developed using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) methods. Finally, a robust model was established using cross-validation techniques and the robustness of the model was confirmed through high accuracy of q2loo of 0.843 and 0.682, r2ncv of 0.977 and 0.949, and r2pred of 0.702 and 0.690, respectively, for CoMFA and CoMSIA. Based on the outcome of the results, new pyrimidine derivatives having potential inhibitory against HIV-1 RT were designed. [ABSTRACT FROM AUTHOR]

Reverse transcriptase (RT) is responsible for replicating the HIV-1 genome and is a validated therapeutic target for the treatment of HIV infections. During each cycle of the RT-catalyzed DNA polymerization process, inorganic pyrophosphate is released as the by-product of nucleotide incorporation. Small molecules were identified that act as bioisosteres of pyrophosphate and can selectively freeze the catalytic cycle of HIV-1 RT at the pre-translocated stage of the DNA- or RNA-template-primer-enzyme complex. [ABSTRACT FROM AUTHOR]

Objective: This research was conducted to screen inhibition of HIV-1 reverse transcriptase activity of selected Indonesia medicinal plants and to isolate HIV-1 reverse transcriptase inhibitor from Erythrina variegata leaves. Method: Screening inhibition of HIV-1 RT activity of selected Indonesia medicinal plants and isolated compounds were performed using HIV-1 RT colorimetric assay. The isolation of HIV-1 reverse transcriptase inhibitor was conducted using chromatography technique. The isolated compound was determined based on the data of UV, IR spectrophotometry, MS, 1D and 2D NMR spectroscopy. Results: Beside that, in vitro study of the leaves methanolic extract exhibited inhibition against HIV-1 RT activity with percent inhibition of 97.64% at concentration of 5 mg/mL. Ethyl acetate fraction from the extract showed the strongest HIV-1 RT inbitory activity with IC50 of 429.28 μg/mL. Isolation the HIV-1 RT inhibitor from the fraction give compound 1. Conclusion: Erythrina variegata leave extract exhibited potent inhibition on HIV-1 RT activity. The isolated compound from the leaves was determined as apigenin-7-O-β-D-glucopyranoside and demonstrated HIV-1 RT inhibitory activity with the IC50 value of 100.59 μg/mL. [ABSTRACT FROM AUTHOR]

HIV-1 reverse transcriptase (RT) in the cytoplasm of HIV-infected cells efficiently inserts the non-canonical dUTP into the proviral DNA, and extends the dU-terminated DNA. The misincorporation of dUTP leads to mutagenesis, and uracils can down-regulate viral gene expression. However, uracilation might also protect HIV DNA from auto-integration in the cytoplasm. Tumor suppressor p53 protein, exhibiting inherent 3′→5′ exonuclease activity, provides a potential host-derived repair mechanism during HIV reverse transcription for the misincorporation of various wrong nucleotides, leading to both base-base mismatches and incorporated non-canonical ribonucleotides. Since the presence of proofreading activity is essential for DNA synthesis accuracy, we elucidated the potential involvement of cytoplasmic p53 in the U-editing activities during insertion of dUTP into DNA by recombinant HIV-1 RT (using isogenic p53-proficient and -deficient HCT116 cells). The biochemical data show that p53 in cytoplasm can participate through the intermolecular pathway in a dU-damage-associated repair mechanism by its ability to remove preformed 3′-terminal dUs, thus preventing further extension of 3′ dU-terminated primer during DNA synthesis by HIV-1 RT. The specific depletion of p53 from cytoplasmic lysates of repair-proficient p53-harboring cells reduced this negative effect. Accordingly, the increased abundance of p53 in nutlin-treated cells correlates with enhanced error-correction functions, namely, removal of incorporated uracil. The data substantiate the significance of p53 as a potential proofreader for removal of non-canonical dUTP from HIV DNA, thus preventing the consequences of dUTP misincorporation in cell-type specific infectivity of HIV. [ABSTRACT FROM AUTHOR]

The traditional drug design strategy centrally focuses on optimizing binding affinity with the receptor target and evaluates pharmacokinetic properties at a later stage which causes high rate of attrition in clinical trials. Alternatively, parallel screening allows evaluation of these properties and affinity simultaneously. In a case study to identify leads from natural compounds with experimental HIV-1 reverse transcriptase (RT) inhibition, we integrated various computational approaches including Caco-2 cell permeability QSAR model with applicability domain (AD) to recognize drug-like natural compounds, molecular docking to study HIV-1 RT interactions and shape similarity analysis with known crystal inhibitors having characteristic butterfly-like model. Further, the lipophilic properties of the compounds refined from the process with best scores were examined using lipophilic ligand efficiency (LLE) index. Seven natural compound hits viz. baicalien, (+)-calanolide A, mniopetal F, fagaronine chloride, 3,5,8-trihydroxy-4-quinolone methyl ether derivative, nitidine chloride and palmatine, were prioritized based on LLE score which demonstrated Caco-2 well absorption labeling, encompassment in AD structural coverage, better receptor affinity, shape adaptation and permissible Alog P value. We showed that this integrative approach is successful in lead exploration of natural compounds targeted against HIV-1 RT enzyme. [ABSTRACT FROM AUTHOR]

The therapeutic effectiveness of the catechol diether analogs against both the wild-type and drug-resistant reverse transcriptase (RT) mutants of HIV strains are investigated by performing molecular docking and hybrid ONIOM calculations. The docking protocol has been used to predict the binding modes of the non-nucleoside inhibitors inside the active site cavity of the viral enzymes. For each enzyme-inhibitor adduct, the predicted docked poses are assessed by employing different scoring function based programs. However, the docking protocol fails to explain satisfactorily the antiviral activities of the drug molecules. Two-layered ONIOM calculations have been carried out to compute the relative binding affinities of the catechol diether derivatives to the binding pockets of RT variants. The binding efficacies of the inhibitors are significantly suppressed by the Y181C and K103N mutations, as revealed by the computed interaction energies at the ONIOM [B3LYP/6-31G(d,p):PM6] level of theory. Deformation energies for each bound ligand conformer are also estimated. The nature of interactions between the drug molecules and the active site residues are analyzed from the reduced density gradient (RDG) isosurfaces. The simulated ECD spectra support the conformational adaption upon inhibitor binding in the binding pockets of HIV strains. [ABSTRACT FROM AUTHOR]

Based on an established common pharmacophore of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNTTIs), a series of quinolin-2-one derivatives were synthesized and assayed for their in vitro activities against HIV-1 reverse transcriptase (RT) for the first time. Some of the tested compounds were active against HIV-1 RT. Compounds 4a2 and 4d2 showed inhibitory activities with IC50 values of 0.21 and 0.15 mM, respectively, with a mode of interaction with RT residues of the allosteric pocket similar to that of efavirenz.

Based on the molecular modeling analysis against Y181CHIV-1 RT, dipyridodiazepinone derivatives containing an unsubstituted lactamnitrogen and 2-chloro-8-arylthiomethyl were synthesized via an efficientroute. Some of them were evaluated for their antiviral activity against HIV-1RT subtype E and were found to exhibit virustatic activity comparable to some clinically usedtherapeutic agents.

The synthesis and characterization of novel acyclic and cyclic pyridone-based nucleosides and nucleotides is described. In total, seven nucleosides and four nucleotides were synthesized. None of the tested nucleosides showed inhibitory properties against Klenow exo- polymerase and M.MuLV and HIV-1 reverse transcriptases. The nucleotides containing 4-chloro- and 4-bromo-2-pyridone as a nucleobase were accepted by the Klenow fragment, but at the expense of fidelity and extension efficiency. [ABSTRACT FROM AUTHOR]

Through a structure-based molecular hybridization and bioisosterism approach, a series of novel 2-(pyridin-3-yloxy)acetamide derivatives were designed, synthesized, and evaluated for their anti- HIV activities in MT-4 cell cultures. Biological results showed that three compounds ( Ia, Ih, and Ij) exhibited moderate inhibitory activities against wild-type (wt) HIV-1 strain (IIIB) with EC50 values ranging from 8.18 μ m to 41.52 μ m. Among them, Ij was the most active analogue possessing an EC50 value of 8.18 μ m. To further confirm the binding target, four compounds were selected to implement an HIV-1 RT inhibitory assay. In addition, preliminary structure-activity relationship ( SAR) analysis and some predicted physicochemical properties of three active compounds Ia, Ih, and Ij were discussed in detail. Molecular docking studies were also carried out to investigate the binding modes of Ij and the lead compound GW678248 in the binding pocket of RT, which provided beneficial information for further rational design of non-nucleoside reverse transcriptase inhibitors. [ABSTRACT FROM AUTHOR]

Background: Acquired Immune Deficiency Syndrome (AIDS) is the advanced stage of infection caused by Human Immunodeficiency Virus (HIV). HIV/AIDS had a great impact on society, both as an illness and as a source of discrimination. Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) are structurally diverse group of compounds which binds to Reverse Transcriptase (RT) enzyme of HIV. Like other anti-HIV drugs, long-term clinical effectiveness of approved NNRTIs has been hampered due to the rapid development of drug resistance. So, there is an urgent need to discover the NNRTIs, which can be effective against the drug sensitive as well as drug resistant strains of HIV-1 RT. Results: Two series of novel thirty, 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline analogues (5a-o) and (8a-o) were designed and synthesized as inhibitor of HIV-1 reverse transcriptase. All the synthesized compounds were characterized by infrared spectroscopy, proton nuclear magnetic resonance spectroscopy, mass spectroscopy and evaluated for in-vitro RT inhibitory activity. Among the tested compounds, eighteen compounds exhibited more than 50 % inhibition at tested 100 μM concentration, in which two compounds 8h and 8l showed promising inhibition (74.82 and 72.58 %) respectively. The preliminary structure-activity relationship (SAR) of the test compounds and docking studies of the two significantly active compounds 8h and 8l were performed to examine their putative binding with HIV-RT. Predicted physiochemical parameters of the synthesized compounds were within the acceptable range of drugable properties. Conclusion: The results obtained from this investigation revealed that, the synthesized compounds (5a-o) and (8a-o) showed moderate to promising HIV-1 RT inhibition activity. The overall SAR studies can help in identification of further lead as well as in designing of newer potential inhibitor of HIV-1 RT. [ABSTRACT FROM AUTHOR]

Through a structure-guided core-refining approach, a series of novel imidazo[1,2- a ]pyrazine derivatives were designed, synthesized and evaluated as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Biological results of antiviral assay in MT-4 cell cultures showed that 12 target compounds displayed moderate activities against wild-type (wt) HIV-1 strain (III B ) with EC 50 values ranging from 0.26 μM to 19 μM. Among them, 4a and 5a were found to be the two most active analogues possessing EC 50 values of 0.26 μM and 0.32 μM respectively, comparable to delavirdine (DLV, EC 50 = 0.54 μM) and nevirapine (NVP, EC 50 = 0.31 μM) in a cell-based assay. Additionally, 9 compounds showed RT inhibitory activity superior to that of NVP. Moreover, some predicted drug-like properties of representative compounds 4a and 5a , as well as the structure-activity relationship (SAR) analysis were discussed in detail. The binding mode of compound 4a was investigated by molecular simulation studies. [ABSTRACT FROM AUTHOR]

In our arduous efforts to develop new potent HIV-1 non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs), novel piperidine-linked [1,2,4]triazolo[1,5- a ]pyrimidine derivatives were designed, synthesized and evaluated for their antiviral activities in MT-4 cell cultures. Biological results showed that all of the title compounds displayed moderate to excellent activities against wild-type (wt) HIV-1 strain (III B ) with EC 50 values ranging from 8.1 nM to 2284 nM in a cell-based assay. Among them, the most promising analog 7d possessed an EC 50 value of 8.1 nM against wt HIV-1, which was much more potent than the reference drugs DDI, 3 TC, NVP and DLV. Additionally, 7d demonstrated weak activity against the double mutant HIV-1 strain (K103N + Y181C), and was more efficient than NVP in a RT inhibition assay. Besides, some measured and calculated physicochemical properties of 7d , like log P and water solubility, as well as the structure–activity relationships (SARs) analysis have been discussed in detail. Furthermore, the binding mode of the active compound 7d was rationalized by molecular simulation studies. [ABSTRACT FROM AUTHOR]

A novel series of uracil derivatives with a 3,5-dimethylbenzyl group at the C-6 position were synthesized and evaluated as non-nucleoside HIV-1 reverse transcriptase inhibitors. Purity of the compounds has been confirmed by TLC. Structures of these compounds were established on the basis of elemental analyses and spectral studies. Some of the tested compounds showed moderate to potent activities against wildtype HIV-1, and N-1 alkylated derivatives were highly active. [ABSTRACT FROM AUTHOR]

Non-nucleoside reverse transcriptase inhibitors have a definitive role and most commonly used in treatment of HIV-1 infection. A new series of 4-ethylidene/substituted-benzylidene-1-(4-hydroxy/chloro-6-methylpyrimidin-2-yl)-2-ethyl/phenyl-1H-imidazol-5(4H)-one were designed, synthesized, and evaluated for HIV-1 reverse transcriptase (RT) inhibitory activity. The results of in-vitro HIV-1 RT assay showed that some of the new compounds, such as 4c, 4d, 4e, 5a, and 5e effectively inhibit HIV-1 RT activity. 1-(4-Chloro-6-methylpyrimidin-2-yl)-4-(furan-2-ylmethylene)-2-methyl-1H-imidazol-5(4H)-one ( 5e) exerted most potent in-vitro HIV-1 RT inhibitory activity, among the group of compounds. Molecular docking studies were carried out to explore the binding affinity of imidazole-5-one analogs in active site of HIV-1 RT enzyme. [ABSTRACT FROM AUTHOR]

Abstract: A ZnO-mediated one-pot solvent-free protocol for the regioselective C-arylsulfonylation of indoles is described and some novel derivatives were tested on wild type and non-nucleoside inhibitor resistant K103N and Y181C HIV-1 reverse transcriptases (RTs). [Copyright &y& Elsevier]

Abstract: A novel series of uracil derivatives with a 3,5-dimethylbenzyl group at the N 3-position were synthesized and evaluated as non-nucleoside HIV-1 reverse transcriptase inhibitors. Some of these compounds showed good-to-moderate activity with EC50 values in the submicromolar range. Among them, compound 10c showed significant potency against HIV-1 activity with an EC50 value of 0.03μM and a high selectivity index of 2863. Preliminary structure–activity relationships and molecular modeling analyses were used to explore the major interactions between HIV-1 reverse transcriptase and the potent inhibitor 10c, which may serve as an important lead for further optimization. [Copyright &y& Elsevier]

CoMFA and CoMSIA based 3D-QSAR of HIV-1 RT wild and mutant (K103, Y181C, and Y188L) inhibitory activities of 4-benzyl/benzoyl pyridin-2-ones followed by protein informatics of corresponding non-nucleoside inhibitors' binding pockets from pdbs 2BAN, 3MED, 1JKH, and 2YNF were analysed to discover consensus features of the compounds for broad-spectrum activity. The CoMFA/CoMSIA models indicated that compounds with groups which lend steric-cum-electropositive fields in the vicinity of C5, hydrophobic field in the vicinity of C3 of pyridone region and steric field in aryl region produce broad-spectrum anti-HIV-1 RT activity. Also, a linker rendering electronegative field between pyridone and aryl moieties is common requirement for the activities. The protein informatics showed considerable alteration in residues 181 and 188 characteristics on mutation. Also, mutants' isoelectric points shifted in acidic direction. The study offered fresh avenues for broad-spectrum anti-HIV-1 agents through designing new molecules seeded with groups satisfying common molecular fields and concerns of mutating residues. [ABSTRACT FROM AUTHOR]

MK-4965, 3-{5-[(6-Amino-1H-pyrazolo[3,4-b]pyridine-3-yl)methoxy]-2-chlorophenoxy}-5-chloro-benzonitrile, is a novel non-nucleoside reverse transcriptase inhibitor (NNRTI) revealing high levels of potency against wild-type (WT) the human immunodeficiency virus type-1 (HIV-1) and some important mutants. The divide-and-conquer (DC) based Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) calculations were performed for the binding modes of MK-4965 in the reverse transcriptase (RT) of the WT HIV-1 and a mutant Y181C, 181 tyrosine mutated by cysteine. The binding pockets of MK-4965 consisting of 19 residues are selected for the study. Numerical assessments confirmed the efficiency and accuracy of the DC-MP2 method in comparison with the conventional MP2 one. Subsystem interaction energies obtained by the DC-MP2 calculations clarified the key parts of the binding between MK-4965 and HIV-1: hydrogen bonding with 102 lysine, which is apart from mutated 181 residue. The present information can give a helpful guide for the future inhibitor design. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract: Pre-steady state kinetic analysis was utilized for biochemical evaluation of a series of cyclobutyl adenosine nucleotide analogs with HIV-1 RTWT. The phosphonyl-diphosphate form of the cyclobutyl nucleotide, 5, was the most efficiently incorporated of the series. Nucleotide 5 was fourfold more efficiently incorporated than the FDA approved TFV-DP by RTWT. The kinetics of incorporation for 5 using the drug resistant mutant enzyme K65R was also determined. Compound 5 was threefold more efficiently incorporated compared to TFV-DP with RTK65R. These results demonstrate cyclobutyl adenosine analogs can act as substrates for incorporation by HIV-1 RT and be a potential scaffold for HIV inhibitors. [Copyright &y& Elsevier]

Abstract: Calophyllum species are sources of calanolides, which inhibit human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). The hexane extract of the leaves from C. brasiliense collected in Soconusco, State of Chiapas, Mexico, analyzed by HPLC showed to contain apetalic acid, calanolides B, and C. It showed potent anti-HIV-1 RT inhibition (IC50 =20.2μg/ml), but was not toxic in mice (LD50 =1.99g/kg). The histological study of the mice treated at the highest dose revealed no alteration on hepatocytes, and an increase in the number of spleen megakaryocytes. These results suggest this extract is suitable to continue studies for developing a phytodrug against HIV-1. [Copyright &y& Elsevier]

Three-dimensional Quantitative Structure Activity Relationship (3D-QSAR) has been derived for a set of HEPT derivatives of HIV-1 reverse transcriptase (RT) using Comparative Molecular Field Analysis (CoMFA). The CoMFA models have been developed using two different alignment procedures such as common substructure and bioactive conformation. The CoMFA model I is derived from a common substructure procedure that includes steric and electrostatic fields with the cross-validated q2 and the non-cross-validated r2 value of 0.86 and 0.97, respectively. The same for the CoMFA model II that is derived based on the bioactive conformation are 0.19 and 0.77, respectively. It is evident from the results that the common substructure-based alignment model has good statistical significance when compared with that of bioactive conformation for the selected systems in this study. The docking study revealed that the conformational flexibility observed at the R3 position favors different orientations of the substitution at the active site of HIV-1 RT and thereby leads to inconsistency in the CoMFA alignment based on bioactive conformation. [ABSTRACT FROM AUTHOR]

The interactions between ligands and the surrounding binding site depend on the different contributions of individual amino acids. The determination of these particular interaction energies is sensitive to the model used, i.e., which part of the amino acids is taken into account and which terminating procedure is applied. In this study, the subtle interaction between individual residues from the HIV-1 reverse transcriptase allosteric binding site and an inhibitor, isopropyl ( S)-2-ethyl-7-fluoro-3,4-dihydro-3-oxoquinoxalin-1(2 H)-carboxylate (GW420867X), was investigated by using high-level quantum chemical calculations (MP2, M06-2X, and B3LYP) with the following basis sets: 6-31G(d), 6-31G(d,p), 6-311G(d), and 6-311G(d,p). The results obtained indicate that the interaction between the inhibitor and Lys101 is the most important one for the binding. We have calculated this interaction using various models to evaluate the effect of neighboring residues. Electrostatic interactions induced by the terminating substituents were also studied using natural population analysis. The results show that even systems where the amide bond is cut and capped with hydrogen atoms can be used as reliable models for estimating the individual interaction energies. Furthermore, the interaction energies of GW420867X in wild-type and Lys101Glu mutant are also investigated to explain the loss of GW420867X's activity in the Lys101Glu mutant. Graphical Abstract: [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Nucleoside triphosphate mimetics, which are substrates for polymerases, can be used in the enzymatic synthesis of nucleic acids. Alternatively, they might also become reversible or irreversible enzyme inhibitors. In order to analyze the effects of 5'-phosphoramidate modification of deoxynucleotide in DNA synthesis, 3-phosphono-L-Ala-dNMP (N = A, T, or G) were evaluated as substrates of HIV-1 RT, Vent (exo-), and Therminator polymerase, respectively. The DNA-dependent DNA polymerase activity is significantly higher for Vent exo- polymerase than for HIV-1 RT, which is reflected by the capacity of Vent exo- polymerase to efficiently synthesize DNA without stalling effects. In addition, Vent (exo-) polymerase proved to be more accurate than Therminator polymerase, based on Watson-Crick base-pairing. The optimal yield (88%-97%) of full-length elongation can be obtained in 60 minutes by Vent (exo-) polymerase at 0.025 U/μL, with the phosphoramidate analogues as substrates. These data led us to conclude that the optimal pyrophosphate mimetic for the enzyme-catalyzed synthesis of DNA is polymerase dependent. [ABSTRACT FROM AUTHOR]

Abstract: Phyllanthus species has long been used in folk medicine in many countries as antimicrobials and/or antioxidants. Eighty percent methanol extracts obtained from seven Phyllanthus sp. were evaluated for antibacterial activity using the broth micro-dilution assay, anti-HIV-1 reverse transcriptase (RT) activity using the HIV-RT assay, antiradical scavenging effects and phenolic contents using the DPPH assay and Folin–Ciocalteau colorimetric method, respectively. Best antibacterial activity as indicated by the minimum inhibitory concentration (MIC) values was obtained by Phyllanthus amarus against Staphylococcus aureus (Gram-positive) with a MIC value of 17.7μg/ml. Phyllanthus myrtifolius and Phyllanthus urinaria inhibited growth of Pseudomonas stutzeri (Gram-negative) with MIC values of 78μg/ml and 117μg/ml, respectively. A strong inhibition of HIV-RT was obtained by Phyllanthus pulcher (IC50 5.9μg/ml) followed by P. urinaria and P. myrtifolius (IC50 of 10.4 and 12.7μg/ml, respectively). A remarkable DPPH scavenging effect was observed with P. myrtifolius, Phyllanthus reticulatus and P. urinaria (IC50 of 10.2, 10.8 and 17.4μg/ml, respectively). Highest total phenolic contents were recorded for P. myrtifolius and P. urinaria (207 and 205mg/GAE/g respectively). With the exception of P. amarus, Phyllantus debilis and P. pulcher, total phenolic contents correlated with DPPH radical scavenging activity. Our findings support the uses of the Phyllanthus species in traditional medicine. The interesting biological activities obtained by P. myrtifolius, P. urinaria and P. pulcher need to be further investigated to isolate active agents and to study their mechanism of action. [ABSTRACT FROM AUTHOR]

Abstract: A probable NRTI molecule, viz. 3′-N,N-dimethylamino-2′,3′-dideoxythymidine (4) and its 5′-O-carboxyl ester prodrugs – 5′-(N-α-BOC-l-phenylalanyl)-3′-N,N-dimethylamino-2′,3′-dideoxythymidine (5), 5′-l-phenylalanyl-3′-N,N-dimethylamino-2′,3′-dideoxythymidine (6) and 5′-decanoyl-3′-N,N-dimethylamino-2′,3′-dideoxythymidine (7) have been synthesized and screened against HIV, HSV-1 and 2, parainfluenza-3, vesicular stomatitis and several other viruses. The compound 6 showed good antiviral activity with EC50 value 0.03μM (SI=8) against VSV in Hela and HEL cell lines. However, the lead compound 4 and its derivatives 5, 6 and 7 showed no remarkable activity against HIV-1 and other viruses. Molecular docking studies with HIV-1 RT using DS 2.5 and pymol softwares have shown marked differences in the interaction patterns between the lead compound 4 and AZT. [ABSTRACT FROM AUTHOR]

Abstract: A series of novel S-DABO analogues (4a1–5a12) have been synthesized by an efficient method and evaluated as inhibitors of human immunodeficiency virus type-1 (HIV-1). The biological testing results clearly indicated that the substitution of halogen at the C5 position of pyrimidine ring could increase the anti-HIV-1 RT activity. The most active compounds showed activity in the low micromole range with IC50 values (IC50 0.18–3.03μM) comparable to nevirapine (IC50 4.12μM). The docking showed that a new halogen bond was formed between halogen and carbonyl of TYR188 in the HIV-I RT. [Copyright &y& Elsevier]

Abstract: Roche COBAS Amplicor monitor version 1.5 assay is considered gold standard for viral load monitoring in Botswana. Due to its demand for elaborate infrastructure, viral load testing has been confined to the national HIV reference laboratories. Cavidi ExaVir Load version 2 assay was considered as a potential alternative to decentralize viral load testing to the rural/remote hospital laboratories and thus increase access to therapy. This study compared the performance of ExaVir Load v2 assay at a district hospital laboratory in Serowe and COBAS Amplicor monitor v1.5 assay at the Botswana Harvard HIV Reference Laboratory using quality assessment samples and plasma from HIV-positive individuals. ExaVir Load v2 and COBAS Amplicor monitor v1.5 assays had very good agreement; Kappa statistic 0.951. The COBAS Amplicor monitor v1.5 and ExaVir Load v2 assays detected HIV-1 RNA in 84 and 86 samples but did not detect HIV-1 RNA in 221 and 219 samples, respectively. The two assays detected HIV-1 RNA concordantly in 82 samples and were strongly correlated (r =0.8554, P <0.0001). ExaVir Load v2 assay provided a simple and reliable alternative viral load system that is adaptable to district hospital laboratories. The cost per test is less than RT-PCR. The ExaVir Load v2 systems have since been placed in four more district and primary hospital laboratories. [Copyright &y& Elsevier]

Abstract: For the activity values against HIV-1 RT wild-type and mutant strains (L100I, Y181C and Y188N) of 34 diarylpyrimidines (DAPYs) taken from literature, multiple linear regression analysis and the crossvalidation of Leave-One-Out method are carried out against the activity values with the hydrophobicity index log P, the modified steric parameter L Y, the Muliken charge of nitrogen atom on the right wing N C and the indicator index I for the substituents R3′ and R1 on the left wing, and four good QSAR models are established: R =0.8211(N =34), R =0.8599 (N =33), R =0.8711(N =30) and R =0.9079 (N =29) for the cases of wild type, and mutant strain forms L100I, Y181C and Y188N, respectively. Additionally, the results indicate that log P plays a vital role in the prediction of the activity of DAPYs, and the cyano group on the left wing is important for inhibiting the mutant forms L100I and Y188N. [Copyright &y& Elsevier]

Delvardine and its structural derivatives are important non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs). In this work, 15 delvardine analogues were studied. A free energy-of-binding (FEB) expression was developed in the form of an optimized linear combination of van der Waal (vdW), electrostatic, solvation and solvent-accessible surface area (SASA) energy terms. The solvation energy terms estimated by generalized born/surface area (GB/SA) play an important role in predicting the binding affinity of delvardine analogues. Out of 15 derivatives, substitution of CH 3 with H at the Y and R positions, as well as substitution of SO 2 CH 3 with only CH 2 at the Z position in S2, S8 and S12 analogues, were found to be the most potent (glide score = -7.60², -8.06 and -7.44; pIC50 = 7.28, 7.37 and 7.64) in comparison with the template delvardine (which is used currently as the drug candidate). All the three analogues also passed the absorption, distribution, metabolism and excretion (ADME) screening and Lipinski's rule of 5, and have the potential to be used for second-generation drug development. The work demonstrates that dock molecular mechanics-generalized born/surface area (MM-GB/SA-ADME) is a promising approach to predict the binding activity of ligands to the receptor and further screen for a successful candidate drug in a computer-aided rational drug design. [ABSTRACT FROM AUTHOR]

Abstract: We have investigated the structure and dynamics of the HIV-1 reverse transcriptase (HIV-RT) active site, by modelling the active conformation of the HIV-1 RT/DNA/deoxythymidine triphosphate (dTTP) ternary complex. This has included molecular dynamics simulations with the CHARMM27 force field, and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three different ternary systems were studied to investigate the effects of different protonation states of the dTTP substrate (a deprotonated and two different mono-protonated triphosphate forms of dTTP at the active site), and the effects of different possible protonation state of potentially catalytic aspartate residues (Asp185 and Asp186) were tested. Several potentially important hydrogen-bonding interactions with amino acids and bound water molecules in the deoxyribonucleoside triphosphate (dNTP) binding pocket were examined. The model of the deprotonated form of the dTTP substrate with the two aspartates in their charged (basic) form seemed to be the most stable and its orientation was in good agreement with X-ray crystallographic structure. In addition, two different semiempirical (AM1/CHARMM and PM3/CHARMM) QM/MM methods were tested for the HIV-RT system, in structural optimizations. Both methods provided conformations of the triphosphate moiety in either fully deprotonated or mono-protonated forms, which agreed well with the experimental structure of dTTP. The only significant difference between the AM1/CHARMM and PM3/CHARMM minimized structures is that the PM3/CHARMM Pα–O3′ optimized distance (important for nucleotide addition) is longer by 0.66Å in the deprotonated system but shorter by 0.37Å in the mono-protonated triphosphate system as compared with those obtained from AM1/CHARMM minimized structure. The obtained results suggest that both of these QM/MM methods, and the stochastic boundary molecular dynamics approach applied in this work, can give reasonable results for modelling the catalytically active complex of this important enzyme. The results provide insight into the structure and interactions of the active site of this important enzyme, with implications for its mechanism, which may be useful in inhibitor design. [Copyright &y& Elsevier]

Abstract: A series of 2-(2,6-dihalophenyl)-3-(substituted pyrimidinyl)-1,3-thiazolidin-4-ones were designed on the prediction of quantitative structure–activity relationship (QSAR) studies, synthesized, and evaluated as HIV-1 reverse transcriptase inhibitors. Our attempts in correlating the identified molecular surface features related properties for modeling the HIV-1 RT inhibitory activity resulted in some statistically significant QSAR models with good predictive ability. The results showed that compounds 4m and 4n were highly active in inhibiting HIV-1 replication with EC50 values in the range of 22–28nM in MT-4 as well as in CEM cells with selectivity indexes of >10,000. The derived models collectively suggest that the compounds should be compact without bulky substitution on its peripheries for better HIV-1 RT inhibitory activity. These models also indicate a preference for hydrophobic compounds to obtain good HIV-1 RT inhibitory activity. [Copyright &y& Elsevier]

Abstract: Surface plasmon resonance (SPR) biosensor technique was applied to analyze the human immunodeficiency virus 1 reverse transcriptase (HIV-1 RT) binding to DNA template–primer (T–P) duplexes. The kinetics including the initial binding and the subsequent conformation change of the protein–DNA complex in the absence and presence of various chemicals were determined. The effects of three nucleoside-based reverse transcriptase inhibitors (NRTIs) and three non-nucleoside-based reverse transcriptase inhibitors (NNRTIs) on the RT–DNA interaction were analyzed based on the conformation change model. Efavirenz (EFV) slightly affected the binding kinetics of the RT–DNA interaction and the binding affinity (K A =2.99×108 M−1) is lower than that in the absence of the inhibitor (K A =5.61×108 M−1). Nevirapine (NVP) induced RT to bind tightly to DNA duplexes followed by a conformation change step. The action of an unsaturated fatty acid, nervonic acid (NA) was similar to NVP. The dideoxynucleosides, whether complementary (‘correct’) or non-complementary (‘incorrect’) to the bases of 3′-end of template–primer DNA, showed no effect on the binding of RT to DNA. However, the initial association and dissociation rates for the RT–DNA interaction are greater in the presence of ‘correct’ dideoxynucleosides than that of in the presence ‘incorrect’ ones, indicating slight preference of RT to ‘correct’ bases. The azido group of AZT (3′-azido-3′-deoxythymidine) enhanced the dissociation of RT from DNA in the initial binding step, where the absence of which resulted in a 34-fold increase in the overall binding affinity (K A =1.94×1010 M−1). [Copyright &y& Elsevier]

Nevirapine (Viramune®) belongs to the first generation of non-nucleoside reverse transcriptase inhibitors (NNRTIs). Its efficiency is limited by drug resistant mutations, such as K103N and Y181C, so, the aim of this work was to design novel nevirapine analogues insensitive to the K103N and Y181C HIV-1 RT. 360 Nevirapine derivatives were designed using a combinatorial library design approach and these compounds were docked into the binding pocket of mutant HIV-1 RT enzyme structures, using the GOLD program. 124 Compounds having a GoldScore higher than that of nevirapine (55.00 and 52.00 for K103N and Y181C mutants, respectively) were first retrieved and submitted to a topological analysis with the SILVER program. Consequently, 31 compounds presenting a significant percentage of the surfaces buried upon binding (>80%) and exhibiting hydrogen bonds to either N103 or C181 residues of the HIV-RT were selected. To ensure that these compounds had hydrogen bonding interaction to either N103 or C181 residues, their interaction energies were estimated by quantum chemical calculations (QCCs). Finally, QCCs represent an alternative method for performing post docking procedure. [ABSTRACT FROM AUTHOR]

Emtricitabine (FTC) and lamivudine (3TC) are deoxycytidine analogues with potent and selective inhibition of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) replication. The K65R mutation in the HIV reverse transcriptase (RT) confers reduced susceptibility to 3TC, ddC, ddI, abacavir, and tenofovir in vitro. The Q151M mutation confers reduced susceptibility to many of the approved anti-HIV nucleoside analogues with the exception of 3TC and tenofovir. The double mutation K65R/Q151M has been shown to be more resistant to many NRTIs than either of the single mutations alone. In this study, we measured the antiviral activity of FTC and 3TC against HIV-1 containing K65R, Q151M, and K65R/Q151M mutations. We also studied the steady-state kinetic properties for the inhibition of dCTP incorporation by FTC 5′-triphosphate (TP) and 3TC-TP. In addition, we measured the incorporation of dCTP, FTC-TP, and 3TC-TP into a random sequence DNA/DNA primer/template by the HIV-1 RTs using pre-steady-state kinetic analysis. Finally, we studied the incorporation of these deoxycytidine analogues into a HIV-1 genomic DNA/DNA primer/template by K65R HIV-1 RT to address certain concerns associated with DNA sequence specificity. Overall, this study demonstrated that K65R and K65R/Q151M related drug resistance to FTC and 3TC was mainly due to a significant decrease in the rate of incorporation. There was little to no effect on the binding affinities of the mutant HIV-1 RTs for the deoxycytidine analogues. The Q151M mutation remained sensitive to both FTC and 3TC in both cell culture and enzymatic assays. At a molecular level, FTC-TP was incorporated at least as efficiently as 3TC-TP for all of the HIV-1 RT and primer/templates tested. [ABSTRACT FROM AUTHOR]

3'-Azido-3',5'-dideoxythymidine 5'-phosphonate and 3',5'-dideoxy-5'-difluoromethylenethymidine 5'-phosphonate were prepared by multistep syntheses. The nucleoside 5'-phosphonates were converted to their triphosphates and triphosphate mimics (P3Ms) containing ß,?-difluoromethylene, ß,?-dichloromethylene, or ß,?-imodo by condensation with pyrophosphate or pyrophosphate mimics, respectively. Inhibition of HIV-1 reverse transcriptase by the nucleoside P3Ms is briefly discussed. [ABSTRACT FROM AUTHOR]

HIV-1 RT catalyses the reverse transcription of viral genetic material (RNA) into double-stranded DNA, and is an important target of antiviral therapy in the treatment of AIDS. Better understanding of the structure, mechanism and functional role of residues involved in the resistance of HIV-1 RT against nucleoside-analog drugs may assist in the development of improved inhibitors, and also in understanding the effects of genetic variation on RT specificity and activity. In this study, firstly, molecular dynamics simulations (with CHARMM27) have been used to investigate binding interactions at the active site and the conformational behavior of the enzyme, then, mechanisms of deprotonation and DNA polymerization reactions have been modelled by the QM/MM method. A combined quantum mechanical and molecular mechanical (QM/MM) method (AM1/CHARMM) has been used to study the triphosphate substrate and the active site of HIV-1 reverse transcriptase complex structure, a virally-encoded enzyme. Free energy profiles for the reaction are also calculated. The obtained results provide important insight into the mechanistic activity of HIV-1 RT. [ABSTRACT FROM AUTHOR]

The antiviral effect of the CH2Cl2/MeOH-soluble fraction from the alga Dictyota menstrualis on HIV-1 replication was evaluated in vitro. The antiretroviral activity was attributed to two diterpenes: (6R)-6-hydroxydichotoma-3,14-diene-1,17-dial, named Da-1, and (6R)-6-acetoxi-dichotoma-3,14-diene-1,17-dial, named AcDa-1. Da-1 or AcDa-1 were added to the culture medium of HIV-1-infected PM-1 cells at different times post-infection or during virus adsorption/penetration. The results indicated that the compounds affected an early step of the virus replicative cycle. Virus binding and entry into the host cells were evaluated in the presence of each diterpene, but no inhibitory effect was observed. To evaluate provirus DNA synthesis/integration into the host genome, the viral protease coding sequence was amplified from total cellular DNA. Proviral DNA was not detected in infected cells incubated with the diterpenes. To investigate the effect of the diterpenes on the reverse transcription of the viral genomic RNA, the recombinant HIV-1 reverse transcriptase (RT) was assayed in vitro in the presence of each diterpene. Da-1 and AcDa-1 inhibited the RNA-dependent DNA-polymerase activity of HIV-1 RT in a dose-dependent manner. Taken together, our results demonstrate that both diterpenes inhibit HIV-1 RT and consequently virus replication. [Copyright &y& Elsevier]

The tumor suppressor protein p53 displays 3'?5'exonuclease activity and can provide a proofreading function for DNA polymerases. Reverse transcriptase (RT) of human immunodeficiency virus (HIV)-1 is responsible for the conversion of the viral genomic ssRNA into the proviral DNA in the cytoplasm. The relatively low fidelity of HIV-1 RT was implicated as a dominant factor contributing to the genetic variability of the virus. The lack of intrinsic 3'?5'exonuclease activity, the formation of 3'-mispaired DNA and the subsequent extension of this DNA were shown to be determinants for the low fidelity of HIV-1 RT. It was of interest to analyse whether the cytoplasmic proteins may affect the accuracy of DNA synthesis by RT. We investigated the fidelity of DNA synthesis by HIV-1 RT with and without exonucleolytic proofreading provided by cytoplasmic fraction of LCC2 cells expressing high level of wild-type functional p53. Two basic features related to fidelity of DNA synthesis were studied: the misinsertion and mispair extension. The misincorporation of noncomplementary deoxynucleotides into nascent DNA and subsequent mispair extension by HIV-1 RT were substantially decreased in the presence of cytoplasmic fraction of LCC2 cells with both RNA/DNA and DNA/DNA template-primers with the same target sequence. The mispair extension frequencies obtained with the HIV-1 RT in the presence of cytoplasmic fraction of LCC2 cells were significantly lower (about 2.8-15-fold) than those detected with the purified enzyme. In addition, the productive interaction between polymerization (by HIV-1 RT) and exonuclease (by p53 in cytoplasm) activities was observed; p53 preferentially hydrolyses mispaired 3'-termini, permitting subsequent extension of the correctly paired 3'-terminus by HIV-1 RT. The data suggest that p53 in cytoplasm may affect the accuracy of DNA replication and the mutation spectra of HIV-1 RT by acting as an external proofreader. Furthermore, the decrease in error-prone DNA synthesis with RT in the presence of external exonuclease, provided by cytoplasmic p53, may partially account for lower mutation rate of HIV-1 observed in vivo.Oncogene (2004) 23, 6890-6899. doi:10.1038/sj.onc.1207846 Published online 2 August 2004 [ABSTRACT FROM AUTHOR]

The high affinity of a given nucleic acid for a protein ligand can be used to isolate specific inhibitors of enzymes involved in pathological situations. The latter property is the basis of the SELEX (systematic evolution of ligands by exponential enrichment) technique. Recently, several potent nucleic acids inhibitors of HIV-1 replication have been isolated using the SELEX approach. However, phosphodiester oligodeoxynucleotides (PO-ODNs) were not used as antiviral agents because of their sensitivity to nucleases. Our goal in this work was to explore the possibility of selecting, from a fully substituted phosphorothioate library, oligonucleotides having both a strong affinity for HIV-1 reverse transcriptase (RT) and nuclease resistance. HIV-1 RT initiates in vivo reverse transcription from the 3′ end of a host tRNALys. Although phosphorothioate ODNs (PS-ODNs) have been claimed to bind unspecifically to proteins, we have shown previously that an ODN corresponding to the acceptor stem of tRNALys was able to inhibit specifically HIV-1 replication in HIV-1 infected cells, without showing cytotoxicity up to 10 µm. As the SELEX strategy requires ‘in vitro’ transcription and reverse transcription of the selected DNA, we have assayed the available PS precursors as a model system by using PS-dNTPs and rNTPs. We have also developed an experimental procedure to optimize the incorporation of four PS-dNTPs during the PCR step of the SELEX approach. In the course of this work, we have showed that the PS-dGTP is a strong inhibitor of thermostable DNA polymerases as well as of HIV-1 RT. [ABSTRACT FROM AUTHOR]