The HIV-1 reverse transcription (RT) process as target for RT inhibitors

Deciphering the enigmas of non-nucleoside reverse transcriptase inhibitors (NNRTIs): A medicinal chemistry expedition towards combating HIV drug resistance

The pivotal involvement of reverse transcriptase activity in the pathogenesis of the progressive HIV virus has stimulated gradual advancements in drug discovery initiatives spanning three decades. Consequently, nonnucleoside reverse transcriptase inhibitors (NNRTIs) have emerged as a preeminent category of therapeutic agents for HIV management. Academic institutions and pharmaceutical companies have developed numerous NNRTIs, an essential component of antiretroviral therapy. Six NNRTIs have received Food and Drug Administration approval and are widely used in clinical practice, significantly improving the quality of HIV patients. However, the rapid emergence of drug resistance has limited the effectiveness of these medications, underscoring the necessity for perpetual research and development of novel therapeutic alternatives. To supplement the existing literatures on NNRTIs, a comprehensive review has been compiled to synthesize this extensive dataset into a comprehensible format for the medicinal chemistry community. In this review, a thorough investigation and meticulous analysis were conducted on the progressions achieved in NNRTIs within the past 8 years (2016-2023), and the experiences and insights gained in the development of inhibitors with varying chemical structures were also summarized. The provision of a crucial point of reference for the development of wide-ranging anti-HIV medications is anticipated.

Synthesis, in vitro Anti-HIV-1RT evaluation, molecular modeling, DFT and acute oral toxicity studies of some benzotriazole derivatives

This study synthesized and evaluated a series of benzotriazole derivatives denoted 3(a-j) and 6(a-j) for their anti-HIV-1 RT activities compared to the standard drug efavirenz. Notably, compound 3 h, followed closely by 6 h, exhibited significant anti-HIV-1 RT efficacy relative to the standard drug. In vivo oral toxicity studies were conducted for the most active compound 3 h, confirming its nontoxic nature to ascertain the safety profile. By employing molecular docking techniques, we explored the potential interactions between the synthesized compounds (ligands) and a target biomolecule (protein)(PDB ID 1RT2) at the molecular level. We undertook the molecular dynamics study of 3 h, the most active compound, within the active binding pocket of the cocrystallized structure of HIV-1 RT (PDB ID 1RT2). We aimed to learn more about how biomolecular systems behave, interact, and change at the atomic or molecular level over time. Finally, the DFT-derived HOMO and LUMO orbitals, as well as analysis of the molecular electrostatic potential map, aid in discerning the reactivity characteristics of our molecule.

Current insights and molecular docking studies of HIV-1 reverse transcriptase inhibitors

Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS), a lethal disease that is prevalent worldwide. According to the Joint United Nations Programme on HIV/AIDS (UNAIDS) data, 38.4 million people worldwide were living with HIV in 2021. Viral reverse transcriptase (RT) is an excellent target for drug intervention. Nucleoside reverse transcriptase inhibitors (NRTIs) were the first class of approved antiretroviral drugs. Later, a new type of non-nucleoside reverse transcriptase inhibitors (NNRTIs) were approved as anti-HIV drugs. Zidovudine, didanosine, and stavudine are FDA-approved NRTIs, while nevirapine, efavirenz, and delavirdine are FDA-approved NNRTIs. Several agents are in clinical trials, including apricitabine, racivir, elvucitabine, doravirine, dapivirine, and elsulfavirine. This review addresses HIV-1 structure, replication cycle, reverse transcription, and HIV drug targets. This study focuses on NRTIs and NNRTIs, their binding sites, mechanisms of action, FDA-approved drugs and drugs in clinical trials, their resistance and adverse effects, their molecular docking studies, and highly active antiretroviral therapy (HAART).

Integrase inhibitors: current protagonists in antiretroviral therapy

Since HIV was identified as the etiological agent of AIDS, there have been significant advances in antiretroviral therapy (ART) that has reduced morbidity/mortality. Still, the viral genome's high mutation rate, suboptimal ART regimens, incomplete adherence to therapy and poor control of the viral load generate variants resistant to multiple drugs. Licensing over 30 anti-HIV drugs worldwide, including integrase inhibitors, has marked a milestone since they are potent and well-tolerated drugs. In addition, they favor a faster recovery of CD4+ T cells. They also increase the diversity profile of the gut microbiota and reduce inflammatory markers. All of these highlight the importance of including them in different ART regimens.

Druggability modification strategies of the diarylpyrimidine-type non-nucleoside reverse transcriptase inhibitors

Drug discovery of human immunodeficiency virus (HIV) is a hot field in medicinal chemistry community for many years. The diarylpyrimidines (DAPYs) are the second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting reverse transcriptase, playing a great irreplaceable role in HIV transcriptional therapy. However, fast-growing drug-resistant mutations as nonnegligible challenge are still unpredictably appeared in the clinical practice, leading to deactivate or reduce the existing drugs. In the last 20 years, more and more novel DAPY derivatives have developed with the purpose to counter the mutants. Nevertheless, most of them have dissatisfactory pharmacokinetics (PK) or poor antiviral activity toward resistant mutant strains. In this article, we will analyze the NNRTI derivatives with promising druggability, and summarize a series of druggability modification strategies to improve the antiviral activity, reduce toxicity and improve the PK properties in recent years. The prospects of DAPYs and the directions for future efforts will be discussed.

Synthesis of Biologically Active Molecules through Multicomponent Reactions

Focusing on the literature progress since 2002, the present review explores the highly significant role that multicomponent reactions (MCRs) have played as a very important tool for expedite synthesis of a vast number of organic molecules, but also, highlights the fact that many of such molecules are biologically active or at least have been submitted to any biological screen. The selected papers covered in this review must meet two mandatory requirements: (1) the reported products should be obtained via a multicomponent reaction; (2) the reported products should be biologically actives or at least tested for any biological property. Given the diversity of synthetic approaches utilized in MCRs, the highly diverse nature of the biological activities evaluated for the synthesized compounds, and considering their huge structural variability, much of the reported data are organized into concise schemes and tables to facilitate comparison, and to underscore the key points of this review.

The Effects of Statistical Multiplicity of Infection on Virus Quantification and Infectivity Assays

Many biological assays are employed in virology to quantify parameters of interest. Two such classes of assays, virus quantification assays (VQAs) and infectivity assays (IAs), aim to estimate the number of viruses present in a solution and the ability of a viral strain to successfully infect a host cell, respectively. VQAs operate at extremely dilute concentrations, and results can be subject to stochastic variability in virus-cell interactions. At the other extreme, high viral-particle concentrations are used in IAs, resulting in large numbers of viruses infecting each cell, enough for measurable change in total transcription activity. Furthermore, host cells can be infected at any concentration regime by multiple particles, resulting in a statistical multiplicity of infection and yielding potentially significant variability in the assay signal and parameter estimates. We develop probabilistic models for statistical multiplicity of infection at low and high viral-particle-concentration limits and apply them to the plaque (VQA), endpoint dilution (VQA), and luciferase reporter (IA) assays. A web-based tool implementing our models and analysis is also developed and presented. We test our proposed new methods for inferring experimental parameters from data using numerical simulations and show improvement on existing procedures in all limits.

Microwave-Assisted Expeditious Synthesis of 2-Alkyl-2-(N-arylsulfonylindol-3-yl)-3-N-acyl-5-aryl-1,3,4-oxadiazolines Catalyzed by HgCl₂ under Solvent-Free Conditions as Potential Anti-HIV-1 Agents

A series of 2-alkyl-2-(N-arylsulfonylindol-3-yl)-3-N-acyl-5-aryl-1,3,4-oxadiazolines were expeditious prepared under microwave-assisted, catalyzed by HgCl₂ and solvent-free conditions. This method has the advantage of low catalyst loading and recovering catalyst, ease reaction and repaid reaction times, easy separation products and excellent yields, and more conducive to the large-scale synthesis products. Furthermore, compounds 3s, 3y, 3a', 3b', 3f', 3i', 3q', and 3r' exhibited more potent anti-HIV-1 activity with EC50 values of 3.35, 6.12, 3.63, 9.54, 1.79, 0.51, 3.00, and 4.01 μg/mL, and TI values of 32.66, >32.68, 31.22, 13.94, 24.27, 39.59, 26.01, and 24.51, respectively. Especially compound 3i' displayed the highest anti-HIV-1 activity with TI values of 39.59.

Synthesis, docking, ADMET prediction, cytotoxicity and antimicrobial activity of oxathiadiazole derivatives

A series of molecules bearing oxathiadiazole, a five membered heterocyclic ring has been designed, synthesized and screened for antimicrobial activity. Molecules, 1a, 1b, 1d, 3a-b and 4a-b were found to be highly active (MIC value upto 1.5 μg/mL) against different human pathogens, namely S. aureus, B. cerus, P. aeruginosa and E. coli. Some of the compounds, 1a, 1b and 1d have also shown the antifungal activity (MIC value upto 6.2 μg/mL) against Candida albicans, Candida glubrate and Candida crusei. During in vitro cytotoxicity study, the oxathiadiazole derivatives showed less toxicity than the reference used against PBM, CEM and Vero (African green monkey kidney) cell lines. Docking studies suggested that all designed ligands interacted well within active site of PDF enzyme (PDB ID: 1G2A). Oxathiadiazole ring of all ligands formed H-bond with amino acid Leu91 at a distance ranging between 2.5-2.8 Å and also exhibited π - + and π - π interactions with amino acid residues Arg97 and His132, respectively. In silico ADMET evaluations of compounds showed more than 90% intestinal absorption for all compounds except 4b (87.45%), which too was greater than the reference drugs sulfamethoxazole (76.46%) and chloramphenicol (69.94%). TOPKAT results also supported the lower cytotoxicity of all compounds.

Combining New Non-Nucleoside Reverse Transcriptase Inhibitors (RTIs) with AZT Results in Strong Synergism against Multi-RTI-Resistant HIV-1 Strains

Reverse transcriptase inhibitors (RTIs), including nucleoside RTIs (NRTIs) and non-nucleoside RTIs (NNRTIs), are critical antiretroviral drugs for the treatment of human immunodeficiency virus (HIV) infection. Emergence of multi-RTI resistance calls for the development of more potent therapeutics or regimens against RTI-resistant strains. Here, we demonstrated that combining azidothymidine (AZT) with a new NNRTIs under development, diarylpyridine (DAPA)-2e, diarylanilin (DAAN)-14h, or DAAN-15h, resulted in strong synergism against infection by divergent HIV-1 strains, including those resistant to NRTIs and NNRTIs, suggesting the potential for developing these novel NNRTIs as salvage therapy for HIV/acquired immune deficiency syndrome (AIDS) patients.

Aptamers in HIV research diagnosis and therapy

Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.

Discovery of novel diarylpyrimidines as potent HIV-1 NNRTIs by investigating the chemical space of a less explored “hydrophobic channel”

We described the identification of novel HIV-1 NNRTIs via exploration of the chemical space of a seldom explored “hydrophobic channel”.

In silico studies of diarylpyridine derivatives as novel HIV-1 NNRTIs using docking-based 3D-QSAR, molecular dynamics, and pharmacophore modeling approaches

A series of novel diarylpyridine derivatives has recently been identified as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs), and most of them exhibited potent activities against HIV-1 strains, with EC₅₀ values in the low nanomolar range. However, the three-dimensional quantitative structure–activity relationships (3D-QSARs) and pharmacophore characteristics of these compounds remain to be studied. In the present study, forty-two diarylpyridine derivatives were firstly docked into HIV-1 reverse transcriptase, and molecular dynamics (10 ns) simulations were further performed to validate the reliability of the docking results, which indicated that residues Lys101, Tyr181, Tyr188, Phe227, and Trp229 might play important roles in binding with these diarylpyridines. The “U”-shaped docking conformations of all compounds were then used to construct 3D-QSAR and pharmacophore models. The satisfactory statistical parameters of CoMFA (q_loo² = 0.665, r_ncv² = 0.989, r_pred² = 0.962, etc.) and CoMSIA (q_loo² = 0.727, r_ncv² = 0.988, r_pred² = 0.912, etc.) models demonstrated that both constructed models had excellent predictability, and their contour maps gave insights into the structural requirements of the diarylpyridines for the anti-HIV-1 activity. A docking-conformation-based pharmacophore model, containing three hydrophobic centers, three hydrogen-bond acceptors, and three hydrogen-bond donors, was also established. The observations in this study might provide important information for the rational design and development of novel HIV-1 NNRTIs.

Computational modeling approaches were successfully applied to a series of diarylpyridine derivatives as novel HIV-1 NNRTIs.

Dual-target inhibitor screening against thrombin and factor Xa simultaneously by mass spectrometry

An accurate, rapid, and cost-effective methodology for enzyme assay is highly demanded to screen the effect of compounds on target at the molecular level. Thrombin (EC 3.4.21.5) and factor Xa (FXa, EC 3.4.21.6) have been identified as the critical targets for the development of potential drugs with anticoagulant activity. In this study, a rapid, sensitive and accurate assay based on UHPLC-MS/MS method has been developed for inhibitor screening against thrombin and factor Xa simultaneously. For thrombin and factor Xa, the Michaelis-Menten constants (K_m) were calculated to be 6.14 and 57.27 μM, respectively. The inhibition constants (K_i) for two known inhibitors, argatroban and rivaroxaban, were determined to be 16.23 and 0.41 nM, respectively. The assay was further validated through the determination of a high Z' factor value of 0.89. Finally, the developed assay was applied to screen a chemical library against two enzymes. Three hit compounds belonging to a class of sulfated polysaccharides were identified and their targets of inhibition action were further evaluated. The results indicated that the dual-target assay by UHPLC-MS/MS analysis could be used as a reliable method for screening anticoagulant agents.

ANN QSAR workflow for predicting the inhibition of HIV-1 reverse transcriptase by pyridinone non-nucleoside derivatives

Aim: Pyridinone derivatives have high potency against non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant human immunodeficiency virus type-1 strains. Quantitative structure–activity relationship (QSAR) studies on a series of pyridinone derivatives acting as NNRTIs are very important in designing the next generation of NNRTIs. Methodology & results: The QSAR models were developed using linear (single and forward stepwise) and combined nonlinear artificial neural network (ANN) approaches. ANN provided QSAR model with highly correlating values of 0.963, 0.964, 0.920 and 0.917, corresponding to the biological activity pIC50 of the training, validation, testing and all samples, respectively. Conclusion: The nonlinear ANN-QSAR model based on the topological polarizability, geometrical steric, hydrophobicity and substituted benzene functional group indices might be able to help for designing novel pyridinone NNRTIs.

Identification of cytochrome P450s involved in the metabolism of 6-benzyl-1-benzyloxymethyl-5-iodouracil (W-1) using human recombinant enzymes and rat liver microsomes in vitro

1. The aim of this study was to identify the hepatic metabolic enzymes, which involved in the biotransformation of 6-benzyl-1-benzyloxymethyl-5-iodouracil (W-1), a novel non-nucleoside reverse transcriptase inhibitor (NNRTI) in rat and human in vitro. 2. The parent drug of W-1 was incubated with rat liver microsomes (RLMs) or recombinant CYPs (CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, and CYP3A5, respectively) in the presence or absence of nicotinamide adeninedinucleotide phosphate (NADPH)-regenerating system. The metabolites of W-1 were analyzed with liquid chromatography-ion trap-time of flight-mass spectrometry (LC-IT-TOF-MS). 3. The parent drug of W-1 was metabolized in a NADPH-dependent manner in RLMs. The kinetic parameters of prototype W-1 including K_m, V_max, and CL_int were 2.3 μM, 3.3 nmol/min/mg protein, and 1.4 mL/min/mg protein, respectively. Two metabolites M1 and M2 were observed in shorter retention times (2.988 and 3.188 min) with a higher molecular ion at m/z 463.0160 (both M1 and M2) than that of the W-1 parent drug (6.158 min with m/z 447.0218). The CYP selective inhibition and recombinant enzymes also showed that two hydroxyl metabolites M1 and M2 are mainly mediated by CYP2C19 and CYP3A4. 4. The identification of CYPs involved in W-1 biotransformation is important to understand and minimize, if possible, the potential of drug-drug interactions.

Quantifying the Sensitivity of HIV-1 Viral Entry to Receptor and Coreceptor Expression

Infection by many viruses begins with fusion of viral and cellular lipid membranes, followed by entry of viral contents into the target cell and ultimately, after many biochemical steps, integration of viral DNA into that of the host cell. The early steps of membrane fusion and viral capsid entry are mediated by adsorption to the cell surface, and receptor and coreceptor binding. HIV-1 specifically targets CD4+ helper T-cells of the human immune system and binds to the receptor CD4 and coreceptor CCR5 before fusion is initiated. Previous experiments have been performed using a cell line (293-Affinofile) in which the expressions of CD4 and CCR5 concentration were independently controlled. After exposure to HIV-1 of various strains, the resulting infectivity was measured through the fraction of infected cells. To design and evaluate the effectiveness of drug therapies that target the inhibition of the entry processes, an accurate functional relationship between the CD4/CCR5 concentrations and infectivity is desired in order to more quantitatively analyze experimental data. We propose three kinetic models describing the possible mechanistic processes involved in HIV entry and fit their predictions to infectivity measurements, contrasting and comparing different outcomes. Our approach allows interpretation of the clustering of infectivity of different strains of HIV-1 in the space of mechanistic kinetic parameters. Our model fitting also allows inference of nontrivial stoichiometries of receptor and coreceptor binding and provides a framework through which to quantitatively investigate the effectiveness of fusion inhibitors and neutralizing antibodies.

Structure-Activity Relationship Studies on a Novel Family of Specific HIV-1 Reverse Transcriptase Inhibitors

We have previously reported the discovery and preliminary structure-activity relationships of a new class of specific HIV-1 reverse transcriptase (RT) inhibitors whose prototype compound is the 1-[2′,5′-bis- O-( tert-butyldimethylsilyl)-β-D-ribofuranosyl]-3- N-[(carboxy) methyl]-thymine. In an attempt to increase the inhibitory efficacy against HIV-1 RT of this new class of nucleosides, and to further explore the structural features required for anti-HIV-1 activity, different types of modifications have been carried out on the prototype compound. These include substitution of the tert-butyldimethylsilyl groups by other liphophilic groups, replacement of the carboxy group at the N-3 position of the nucleobase by other functional groups, change in the length of the spacer between the thymine and the carboxylic acid residue and substitution of the thymine moiety by other pyrimidine (uracil, 5-ethyluracil) or purine (hypoxanthine) nucleobases. In addition, the most salient structural features of this new class of HIV-1-specific nucleosides have been incorporated into classical HIV RT nucleoside inhibitors such as ddI, AZT, d4T. Our studies demonstrate that both the carboxymethyl moiety at the nucleobase and tert-butyldimethylsilyl groups at the sugar are important structural components since deletion of either of them is detrimental to the antiviral activity.

Design, synthesis and anti-HIV evaluation of novel diarylpyridine derivatives targeting the entrance channel of NNRTI binding pocket

The development of novel NNRTIs with activity against variants of HIV-1RT is crucial for overcoming treatment failure. In the present study, a series of novel 6-substituted diarylpyridine derivatives targeting the entrance channel of the NNIBP of RT were designed through a molecular hybridization strategy. Encouragingly, these new diarylpyridine derivatives were found to be active against wild-type (WT) HIV-1 with an EC50 values ranging from 0.035 μM to 1.99 μM. Nearly half of them exhibited more potent inhibitory activities in cellular assays than the control drug nevirapine (NVP). Notably, three most promising compounds If (EC50 = 35 nM), Ia (EC50 = 43 nM) and IIa (EC50 = 41 nM) showed high potency against WT and were comparable to the reference drug delavirdine (DLV) (EC50 = 33 nM). Moreover, compounds Ib, IIb and IIh displayed effective activity against the most common clinically observed single and double-mutated HIV-1 strains in micromolar concentrations. In particular, the inhibition of IIb against the K103N mutation (EC50 = 49 nM), which confers resistance to a wide variety of NNRTIs, was about 140 times more effective than NVP (EC50 = 6.78 μM), 50 times more than DLV (EC50 = 2.48 μM) and about 3 times more than EFV (EC50 = 0.12 μM), indicating that the newly designed compounds have great potential to be further developed as new anti-HIV-1 agents. Preliminary structure-activity relationships (SARs) and molecular modeling of the new diarylpyridine derivatives were discussed in detail.

SJP-L-5, a novel small-molecule compound, inhibits HIV-1 infection by blocking viral DNA nuclear entry

Background

Small-molecule compounds that inhibit human immunodeficiency virus type 1 (HIV-1) infection can be used not only as drug candidates, but also as reagents to dissect the life cycle of the virus. Thus, it is desirable to have an arsenal of such compounds that inhibit HIV-1 infection by various mechanisms. Until now, only a few small-molecule compounds that inhibit nuclear entry of viral DNA have been documented.

Results

We identified a novel, small-molecule compound, SJP-L-5, that inhibits HIV-1 infection. SJP-L-5 is a nitrogen-containing, biphenyl compound whose synthesis was based on the dibenzocyclooctadiene lignan gomisin M2, an anti-HIV bioactive compound isolated from Schisandra micrantha A. C. Smith. SJP-L-5 displayed relatively low cytotoxicity (50 % cytoxicity concentrations were greater than 200 μg/ml) and high antiviral activity against a variety of HIV strains (50 % effective concentrations (EC₅₀)) of HIV-1 laboratory-adapted strains ranged from 0.16–0.97 μg/ml; EC₅₀s of primary isolates ranged from 1.96–5.33 μg/ml). Analyses of the viral DNA synthesis indicated that SJP-L-5 specifically blocks the entry of the HIV-1 pre-integration complex (PIC) into the nucleus. Further results implicated that SJP-L-5 inhibits the disassembly of HIV-1 particulate capsid in the cytoplasm of the infected cells.

Conclusions

SJP-L-5 is a novel small-molecule compound that inhibits HIV-1 nuclear entry by blocking the disassembly of the viral core.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0605-3) contains supplementary material, which is available to authorized users.

Theoretical investigation of the interactions in binding pocket of Reverse Transcriptase

Interactions in proteins have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. In this work we adopt an approach to study these interactions accounting for as many as possible explicit solvent molecules and without the need of a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, and which combined with the MD paradigm results in an ultra accelerated QCMD method for protein–ligand interaction evaluations. We have applied our newly developed method to the Nevirapine (NVP)–Reverse Transcriptase (RT) system. We show how the proposed method leads us to new findings. The advanced QCMD was applied to a system of RT with NVP and it has led to the knowledge of specific groups and atoms that interact with surrounding amino acids of RT and help in drug binding. The information derived from this calculation may be used in designing drugs for NVP resistant virus strains that have binding capability like NVP.

In-silico Studies Show Potent Inhibition of HIV-1 Reverse Transcriptase Activity by a Herbal Drug

Acquired immunodeficiency syndrome (AIDS) is a life threatening disease of the human immune system caused by human immunodeficiency virus (HIV). Effective inhibition of reverse transcriptase activity is a prominent, clinically viable approach for the treatment of AIDS. Few non-nucleoside reverse transcriptase inhibitors (NNRTIs) have been approved by the United States Food and Drug Administration (US FDA) as drugs for AIDS. In order to enhance therapeutic options against AIDS we examined novel herbal compounds of 4-thiazolidinone and its derivatives that are known to have remarkable antiviral potency. Our molecular docking and simulation experiments have identified one such herbal molecule known as (5E)-3-(2-aminoethyl)-5-benzylidene-1, 3-thiazolidine-2,4-dione that may bind HIV-1RT with high affinity to cause noncompetitive inhibition. Results are also compared with other US FDA approved drugs. Long de novo simulations and docking study suggest that the ligand (5E)-3-(2-aminoethyl)-5-benzylidene-1, 3-thiazolidine-2,4-dione (CID: 1656714) has strong binding interactions with Asp113, Asp110, Asp185 and Asp186 amino acids, all of which belong to one or the other catalytic pockets of HIV-1RT. It is expected that these interactions could be critical in the inhibitory activity of the HIV-1RT. Therefore, this study provides an evidence for consideration of (5E)-3-(2-aminoethyl)-5-benzylidene-1, 3-thiazolidine-2,4-dione as a valuable natural molecule in the treatment and prevention of HIV-associated disorders.

Halolactones are potent HIV-1 non-nucleoside reverse transcriptase inhibitors

Halolactones with an isobenzofuran-1(3H)-one core structure have been developed as efficient non-nucleoside reverse transcriptase inhibitors (NNRTIs). The best compound 13a showed excellent potency against WT HIV-1 with a low EC₅₀ value of 0.45 μM.

Current perspectives on HIV-1 antiretroviral drug resistance

Current advancements in antiretroviral therapy (ART) have turned HIV-1 infection into a chronic and manageable disease. However, treatment is only effective until HIV-1 develops resistance against the administered drugs. The most recent antiretroviral drugs have become superior at delaying the evolution of acquired drug resistance. In this review, the viral fitness and its correlation to HIV-1 mutation rates and drug resistance are discussed while emphasizing the concept of lethal mutagenesis as an alternative therapy. The development of resistance to the different classes of approved drugs and the importance of monitoring antiretroviral drug resistance are also summarized briefly.

Identification of HIV-1 reverse transcriptase inhibitors using a scintillation proximity assay

The human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) converts the viral single-stranded RNA into double-stranded DNA. The inhibition of reverse transcription in the viral life cycle has proven its efficacy as a clinically relevant antiviral target, but the appearance of resistance mutations remains a major cause of treatment failure and stresses the continuous need for new antiviral compounds. In this chapter, we describe an HIV-1 RT scintillation proximity assay (SPA) to identify inhibitors of the RT. The assay uses an RNA/DNA (poly(rA)/oligo(dT)) template/primer bound to SPA beads, which contain scintillant. Reverse transcriptase extends the primer by incorporating [(3)H]dTTP and dTTP, which results in light production by the scintillant in the bead. Compounds that inhibit reverse transcriptase will prevent the incorporation of tritiated dTTP resulting in a reduction of emitted light compared to the untreated controls.

In vitro and in vivo activities of AIC292, a novel HIV-1 nonnucleoside reverse transcriptase inhibitor

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are important and frequently used elements of highly active antiretroviral therapy (HAART) for the treatment of human immunodeficiency virus type 1 (HIV-1) infection. However, the development of drug resistance, as well as the side effects of existing drugs, defines a medical need for novel NNRTIs with excellent tolerability, improved activity against NNRTI-resistant viruses, and a low barrier to resistance. Within the chemical class of diarylpyrazole-[imidazolidinone]-carboxamides, AIC292 was identified as a promising novel HIV-1 NNRTI and has successfully completed single-dose clinical phase I studies. Here, we report on the antiviral activity of AIC292, evaluated in vitro against wild-type and NNRTI-resistant HIV-1 isolates and in vivo using an engineered mouse xenograft model. AIC292 inhibited wild-type HIV-1 laboratory strains at low nanomolar concentrations, was well tolerated in different cell lines, and showed excellent selectivity in a lead profiling screen. In addition, activity of AIC292 could be demonstrated against a broad panel of wild-type HIV-1 group M and group O clinical isolates. AIC292 also retained activity against viruses harboring NNRTI resistance-associated mutations (RAMs), including the most prevalent variants, K103N, Y181C, and G190A. Interestingly, viruses bearing the L100I RAM were hypersusceptible to AIC292. Two-drug combination assays showed no antagonistic interactions between AIC292 and representative marketed HIV drugs with regard to antiviral activity. Furthermore, AIC292 displayed potent antiviral in vivo efficacy in a mouse xenograft model when applied once daily. Taken together, these data show that AIC292 represents a molecule with the antiviral properties of a novel NNRTI for the treatment of HIV-1 infection.

N1,N3-disubstituted uracils as nonnucleoside inhibitors of HIV-1 reverse transcriptase

A series of phenyloxyethyl and cinnamyl derivatives of substituted uracils were synthesized and found to exhibit potent activity against HIV-RT and HIV replication in cell culture. In general, the cinnamyl derivatives proved superior to the phenyloxyethyl derivatives, however 1-[2-(4-methylphenoxy)ethyl]-3-(3,5-dimethylbenzyl)uracil (19) exhibited the highest activity (EC(50)=0.27 μM) thus confirming that the 3-benzyluracil fragment in the NNRTI structure can be regarded as a functional analogue of the benzophenone pharmacophore typically found in NNRTIs.

Molecular docking of (5E)-3-(2-aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione on HIV-1 reverse transcriptase: novel drug acting on enzyme

The study of Human immunodeficiency virus (HIV) in humans and animal models in last 31 years suggested that it is a causative agent of AIDS. This causes serious pandemic public health concern globally. It was reported that the HIV-1 reverse transcriptase (RT) played a critical role in the life cycle of HIV. Therefore, inhibition of HIV-1RT enzyme is one of the major and potential targets in the treatment of AIDS. The enzyme (HIV-1RT) was successfully targeted by non nucleotide reverse transcriptase inhibitors (NNRTIs). But frequent application of NNRTIs led drug resistance mutation on HIV infections. Therefore, there is a need to search new NNRTIs with appropriate pharmacophores. For the purpose, a virtually screened 3D model of unliganded HIV-1RT (1DLO) was explored. The unliganded HIV-1RT (1DLO) was docked with 4-thiazolidinone and its derivatives (ChemBank Database) by using AutoDock4. The best seven docking solutions complex were selected and analyzed by Ligplot. The analysis showed that derivative (5E)-3-(2- aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione (CID 3087795) has maximum potential against unliganded HIV-1RT (1DLO). The analysis was done on the basis of scoring and binding ability. The derivative (5E)-3-(2- aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione (CID 3087795) indicated minimum energy score and highest number of interactions with active site residue and could be a promising inhibitor for HIV-1 RT as Drug target.

Conformation depends on 4D-QSAR analysis using EC-GA method: pharmacophore identification and bioactivity prediction of TIBOs as non-nucleoside reverse transcriptase inhibitors

The electron conformational and genetic algorithm methods (EC-GA) were integrated for the identification of the pharmacophore group and predicting the anti HIV-1 activity of tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepinone (TIBO) derivatives. To reveal the pharmacophore group, each conformation of all compounds was arranged by electron conformational matrices of congruity. Multiple comparisons of these matrices, within given tolerances for high active and low active TIBO derivatives, allow the identification of the pharmacophore group that refers to the electron conformational submatrix of activity. The effects of conformations, internal and external validation were investigated by four different models based on an ensemble of conformers and a single conformer, both with and without a test set. Model 1 using an ensemble of conformers for the training (39 compounds) and test sets (13 compounds), obtained by the optimum seven parameters, gave satisfactory results (R²(training) = 0.878, R²(test)= 0.910, q² = 0.840, q²(ext1) = 0.926 and q²(ext2) = 0.900).

Study on the structure and vibrational spectra of efavirenz conformers using DFT: comparison to experimental data

Efavirenz, (S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3,1-benzoxazin-2-one, is an anti HIV agent belonging to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. A systematic quantum chemical study of the possible conformations, their relative stabilities and vibrational spectra of efavirenz has been reported. Structural and spectral characteristics of efavirenz have been studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for potential energy curve, optimized geometries and vibrational spectra have been carried out using 6-311++G(d,p) basis sets and B3LYP functionals. Based on these results, we have discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of efavirenz. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The infrared and the Raman spectra of the molecule based on DFT calculations show reasonable agreement with the experimental results. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule.