HIV-1 Reverse Transcriptase Enzyme Research Articles

In Silico Study of Bioactive Compounds in Herba Sambiloto (Andrographis paniculata Burm. F. Nees) as HIV-1 Reverse Transcriptase Inhibitor

A medicinal plant known as sambiloto (Andrographis paniculata Burm. F. Nees) contains certain active compounds that potentially are anti-HIV. However, it is not yet known which compounds are involved in inhibiting HIV activity. This study aimed to identify potentially active compounds from the sambiloto plant that could inhibit the HIV-1 reverse transcriptase enzyme using the in-silico method. In silico methods that will be carried out are internal validation, molecular docking, ADMET prediction, and molecular dynamics. The molecular docking results showed that the five best compounds have potential as anti-HIV drugs compared to efavirenz with the rerank score -152.119 until -125.177 kcal/mol. In contrast, the rerank score of the comparison ligand is -94.7639 kcal/mol. The ADMET prediction showed that the selected compounds have a good pharmacokinetics profile and are nontoxic. The molecular dynamic results showed that deoxy-11,12-didehydroandrographiside and andropraphiside are stable and have potential as anti-HIV drugs with average RMSD values of 1.88 and 2.02 Å while the comparison ligand is 1.67 Å.

A case report on tenofovir induced osteoporosis

The antiretroviral drug tenofovir, is a nucleotide analogue which is used in the treatment of HIV and hepatitis B infections. This drug works by inhibiting the HIV reverse transcriptase enzyme and prevent the synthesis of viral DNA. It is administered as a single 300 mg tablet once daily. This drug is mostly used in the combination with lamivudine, dolutegravir (TLD regimen). Although there has been success in the use of tenofovir in treating HIV infection, there have been some adverse effects associated with it. Multiple studies have implicated tenofovir associated bone loss and renal failure. In order to treat the adverse effects which are caused due to tenofovir, an alternate drug should be administered.

Building a ML-based QSAR model for predicting the bioactivity of therapeutically active drug class with imidazole scaffold

Human immunodeficiency virus, a retrovirus, causes AIDS, a chronic immune system disease. HIV interferes with the ability of our body to combat disease and infection by weakening our immune system. An essential enzyme necessary for HIV replication is reverse transcriptase (RT). RT inhibitors (RTIs) are a class of antiretroviral drugs that target HIV's RT enzyme, blocking its ability to convert viral RNA into DNA. The RT-1 enzyme has been found to be inhibited by imidazole. It attaches to the RT-1 enzyme's active site and prevents it from performing its usual activity. As a result, viral replication is inhibited, which can eventually aid in slowing the course of HIV and other retroviral diseases. A computational tool allows researchers to simulate and analyze the drug's behaviour in a virtual environment, providing valuable insights into its pharmacological properties, efficacy, and safety. QSAR modelling uses machine learning methods to create predictive models from datasets of chemical substances and the accompanying biological activity. Here, a comparative analysis of the model performances by four different algorithms for the Imidazole scaffold are reported. The algorithms of Support Vector Regression (SVR), Random Forest Regression (RFR), Decision Tree Regression (DTR) and Hist Gradient Boosting Regression (HGBR) have given promising results with the R2 value of 0.905, 0.993, 0.688 and 0.921 respectively for the train sets and for the test set 0.843, 0.977, 0.567 and 0.880. The best performed RFR model have been validated using developed RFR codes for randomly selected compounds and it shows the error percentage of about 0.151% only. From the R2 values, it is observed that the RFR and HGBR models show a better fit with the variables compared to the other models thereby making them the potential models for predicting the activity of novel anti-viral compounds.

7,8-Dihydroxy Efavirenz Is Not as Effective in CYP46A1 Activation In Vivo as Efavirenz or Its 8,14-Dihydroxy Metabolite.

High dose (S)-efavirenz (EFV) inhibits the HIV reverse transcriptase enzyme and is used to lower HIV load. Low-dose EFV allosterically activates CYP46A1, the key enzyme for cholesterol elimination from the brain, and is investigated as a potential treatment for Alzheimer's disease. Simultaneously, we evaluate EFV dihydroxymetabolites for in vivo brain effects to compare with those of (S)-EFV. We have already tested (rac)-8,14dihydroxy EFV on 5XFAD mice, a model of Alzheimer's disease. Herein, we treated 5XFAD mice with (rac)-7,8dihydroxy EFV. In both sexes, the treatment modestly activated CYP46A1 in the brain and increased brain content of acetyl-CoA and acetylcholine. Male mice also showed a decrease in the brain levels of insoluble amyloid β40 peptides. However, the treatment had no effect on animal performance in different memory tasks. Thus, the overall brain effects of (rac)-7,8dihydroxy EFV were weaker than those of EFV and (rac)-8,14dihydroxy EFV and did not lead to cognitive improvements as were seen in treatments with EFV and (rac)-8,14dihydroxy EFV. An in vitro study assessing CYP46A1 activation in co-incubations with EFV and (rac)-7,8dihydroxy EFV or (rac)-8,14dihydroxy EFV was carried out and provided insight into the compound doses and ratios that could be used for in vivo co-treatments with EFV and its dihydroxymetabolite.

Elucidating the sensing properties of thiophene amended organosilane for detection of chromium(III) ion and its potential activity against HIV-1 RT via computational approach

This work describes the synthesis of thiophene based Schiff bases in which we incorporate the triazole allied organosilanes. This thiophene amended organosilanes showed good selectivity towards Cr 3+ ion. Further molecular docking study was done towards HIV-1 RT which showed the good binding energy between the protein and ligand(compound 4a). • Thiophene based organosilanes have been synthesized. • Absorption spectra were obtained to study the sensing property towards various metal ions. • Limit of detection, association constant and binding stoichiometry was calculated using linear calibration curve, B-H plot and job’s plot method respectively. • DFT calculations were carried out to optimize the geometry and generate FMO. • Molecular docking study was done with HIV-1 RT protein giving good binding energy. Thiophene modified organosilanes were synthesized by two manageable steps. Firstly, thiophene based Schiffbases (3a-3c) were synthesized by the simple condensation reaction further triazole allied organosilanes (4a-4c) were incorporated via Click chemistry and then characterized by various spectral techniques. The sensing property of synthesized compound 4a was studied using absorption studies. Among various metal ions compound 4a showed the recognisable behaviour towards trivalent form of chromium ion. The limit of detection and association constant were estimated to be 0.34 x 10 -7 M and 4.4 x 10 5 M -1 respectively.The selectivity of sensor 4a was unaltered in the presence of other metal ions. Job’s variation method was opted for calculating binding stoichiometry which showed 1:1 binding ratio. Binding mechanism was clarified by 1 HNMR spectroscopy. Further compound 4a and complex 4a-Cr 3+ were explored using density functional theory. Molecular docking study was carried out with HIV-1 RT and it showed the inhibitory activity towards reverse transcriptase by blocking the active site of enzyme. The lowest binding energy was found to be -6.91kcal/mol indicating effective association between ligand and protein. Hence compound 4a may act as a good potent inhibitor against HIV-1 reverse transcriptase enzyme.

Inhibitory effect against reverse transcriptase of HIV-1 of the extract of selected medicinal plants

HIV is a virus that multiplies inside of your body and impairs your defences. This makes it more difficult to fend against common illnesses and bacteria. The study's goals included preparing a crude extract from specific medicinal herbs and determining its ability to inhibit HIV-I reverse transcriptase in vitro. This study aimed to conduct an ethnobotanical survey of the healing plants used by Telangana state's indigenous people. Five distinct medicinal plant parts were chosen from a variety of plants, and the % yield was measured after sequential maceration with the five different solvents n-hexane, chloroform, ethyl acetate, acetone, and methanol. Using the RetroSys kit, the HIV reverse transcriptase enzyme inhibition was carried out on crude extracts. Withania somnifera demonstrated excellent inhibitory activity with a range of 40.5 percent to 72.5 percent from a concentration of 0.62 mg/ml to 10 mg/ml, which is close to nevirapine, the control, at 75.3 percent and an effective IC50 value of 1.40 mg/ml used as a lead molecule. HIV-RT inhibition for the aforementioned plants was determined with a range of 32.5 to 72.8 percent.

REverSe TRanscrIptase chain termination (RESTRICT) for selective measurement of nucleotide analogs used in HIV care and prevention.

Sufficient drug concentrations are required for efficacy of antiretroviral drugs used in HIV care and prevention. Measurement of nucleotide analogs, included in most HIV medication regimens, enables monitoring of short- and long-term adherence and the risk of treatment failure. The REverSe TRanscrIptase Chain Termination (RESTRICT) assay rapidly infers the concentration of intracellular nucleotide analogs based on the inhibition of DNA synthesis by HIV reverse transcriptase enzyme. Here, we introduce a probabilistic model for RESTRICT and demonstrate selective measurement of multiple nucleotide analogs using DNA templates designed according to the chemical structure of each drug. We measure clinically relevant concentrations of tenofovir diphosphate, emtricitabine triphosphate, lamivudine triphosphate, and azidothymidine triphosphate with agreement between experiment and theory. RESTRICT represents a new class of activity-based assays for therapeutic drug monitoring in HIV care and could be extended to other diseases treated with nucleotide analogs.

Molecular Docking Study of HIV-1 Antiretroviral Candidate via Reverse Transcriptase Inhibitor from Zingiber officinale var. Roscoe

HIV-1 is a member of the Retrovirus and the virus causes AIDS in humans. AIDS affects the dynamics of the immune system leading to fatal opportunistic infections. Reverse transcriptase plays an important role as a functional enzyme in the viral replication process, the enzyme works to carry out the transcription process of ssRNA into cDNA and then initiates the viral integration process of the genome into the nucleus. Currently many use of HIV-1 NNRTIs, the nevirapine type, with a molecular mechanism that can bind to the active site of the HIV-1 reverse transcriptase enzyme to inhibit its activation. A new problem arises because the reverse transcriptase in HIV-1 undergoes a cross mutation and causes nevirapine resistance. Previous research using an in vitro approach showed the ability to inhibit the process of replication, attachment, and internalization of the virus shown by Zingiber officinale var. Roscoe, then another ability is that these herbal plants can trigger cell stimulation for interferon-β secretion. This study aims to screen the chemical compounds of Zingiber officinale var Roscoe for the discovery of new antiretrovirals through computational study. Zingiber officinale var. Roscoe is predicted to act as an antiretroviral agent through with a mechanism of HIV-1 reverse transcriptase activity inhibition at Pro95, Tyr181, Val179, Leu100, Tyr188, Val106, Leu234, Phe227, Tyr318, Asn103, Gly99 residues, β-sitosterol is predicted to act as a drug-like molecule, the antiretroviral potential of Zingiber officinale var. Roscoe must undergo further analysis to provide strong scientific evidence.

Synthesis, virtual screening and computational approach of a quinoxaline derivative as potent anti-HIV agent targeting the reverse transcriptase enzyme

Infection by the human immunodeficiency virus still represents a continuous serious concern and a global threat to human health. Due to the appearance of multi-resistant virus strains and the serious adverse side effects of the antiretroviral therapy administered, there is an urgent need for the development of new treatment agents that are more active, less toxic, and with increased tolerability to mutations. Quinoxaline derivatives are a class of heterocyclic compounds with a wide range of organic and remedial applications. In addition, they are known to significantly inhibit HIV reverse transcriptase (RT) and HIV replication in cell cultures. For these reasons, we are investigating the synthesis and computational studies of quinoxaline derivatives with a focus on their effects on the HIV RT enzyme, and we present here the structure of one such molecule, methyl 2-[(2E)-3-oxo-1,2,3,4-tetrahydroquinoalin-2-ylidene] acetate, which was confirmed by X-ray diffraction studies. In the crystal, N—H···O and C—H···O hydrogen bonds form ribbons whose mean planes are inclined to (111) by 25.69(8)°. The ribbons are formed into stacks by C—H···π(ring) interactions and π-stacking interactions between carbonyl groups. The Hirshfeld surface map allows us to understand the nature of interactions in the contribution to crystal packing. A density functional theory (DFT) calculation was performed to optimize the geometrical parameters and then they were compared with the solid-state phase. The molecular electrostatic potential map displays reactive sites on the surface, which are responsible for intermolecular interaction in the chemical species. Computational molecular docking, in addition to molecular dynamics simulations and MMGB/PBSA binding energy techniques, was used to assess the affinity of the molecule for the HIV reverse transcriptase enzyme. The new quinoxaline derivative is more powerful in terms of binding affinity and binding conformation stability with the HIV reverse transcriptase enzyme, which suggests the molecule is a good candidate for further biological optimization. Communicated by Ramaswamy H. Sarma

In Silico Adme and Toxicity Studies of Derivative Phthalimide Compounds as Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitor

Phthalimide derivate compounds was reported as a new class of nonnucleoside reverse tranckriptase inhibitors. The aim of this research is to determine the prediction of absorption, distribution, metabolism, and excretion (ADME) as well as the toxicity test of phthalimide-derived compounds which have the best potential as HIV-1 reverse transcriptase enzyme inhibitors. This study used an in silico approach to predict oral bioavailability and toxicity. The prediction of the ADME in this study using SwissADME which is run online where thirty-three phthalimide derivate compounds have molecular weight, hydrogen donor and acceptor bond, and log P ​​that meet the criteria of Lipinski Rules. Prediction of toxicity ​​in this study using in silico method with Toxtree v1.60 and it is known that phthalimide derivate compounds are not carcinogenic and mutagenic.

HIV Drug Resistance Mutations

ART resistance, according to WHO, is the presence of one or more mutations in HIV that reduces the ability of certain drugs or drug groups to inhibit viral replication. According to the 2019 HIV Drug Resistance Report issued by the WHO, the prevalence of Antiretroviral Therapy (ART) drug resistance is 3%-29%. The prevalence of HIV drug resistance varies by country. In developed countries, the prevalence ranges from 6.6% to 11%. There are two types of resistance to ART: primary and secondary resistance. Primary resistance reflects the acquisition of drug-resistant strains in individuals who have recently been infected and have not received therapy. Secondary resistance occurs after treatment with ART. Resistance to antiretroviral therapy, mainly NRTIs, NNRTIs, and protease inhibitors, is caused by continuous inhibition of the HIV reverse transcriptase enzyme. World Health Organization (WHO) has recommended two NRTIs plus Lopinavir or Atazanavir as a second-line regimen for individuals who have failed treatment with efavirenz or dolutegravir; two NRTIs plus Darunavir and Lopinavir plus Raltegravir are recommended as an alternative due to cost constraints and the fact that Darunavir is unstable in moderately hot conditions.

HIV-1 Reverse Transcriptase Inhibition by Major Compounds in a Kenyan Multi-Herbal Composition (CareVid™): In Vitro and In Silico Contrast.

CareVid is a multi-herbal product used in southwest Kenya as an immune booster and health tonic and has been anecdotally described as improving the condition of HIV-positive patients. The product is made up of roots, barks and whole plant of 14 African medicinal plants: Acacia nilotica (L.) Willd. ex Delile (currently, Vachelia nilotica (L.) P.J.H Hurter & Mabb.), Adenia gummifera (Harv.) Harms, Anthocleista grandiflora Gilg, Asparagus africanus Lam., Bersama abyssinica Fresen., Clematis hirsuta Guill. & Perr., Croton macrostachyus Hochst. ex Delile, Clutia robusta Pax (accepted as Clutia kilimandscharica Engl.), Dovyalis abyssinica (A. Rich.) Warb, Ekebergia capensis Sparm., Periploca linearifolia Quart.-Dill. & A. Rich., Plantago palmata Hook.f., Prunus africana Hook.f. Kalkman and Rhamnus prinoides L’Her. The objective of this study was to determine the major chemical constituents of CareVid solvent extracts and screen them for in vitro and in silico activity against the HIV-1 reverse transcriptase enzyme. To achieve this, CareVid was separately extracted using CH2Cl2, MeOH, 80% EtOH in H2O, cold H2O, hot H2O and acidified H2O (pH 1.5–3.5). The extracts were analysed using HPLC–MS equipped with UV diode array detection. HIV-1 reverse transcriptase inhibition was performed in vitro and compared to in silico HIV-1 reverse transcriptase inhibition, with the latter carried out using MOE software, placing the docking on the hydrophobic pocket in the subdomain of p66, the NNRTI pocket. The MeOH and 80% EtOH extracts showed strong in vitro HIV-1 reverse transcriptase inhibition, with an EC50 of 7 μg·mL−1. The major components were identified as sucrose, citric acid, ellagic acid, catechin 3-hexoside, epicatechin 3-hexoside, procyanidin B, hesperetin O-rutinoside, pellitorine, mangiferin, isomangiferin, 4-O-coumaroulquinic acid, ellagic acid, ellagic acid O-pentoside, crotepoxide, oleuropein, magnoflorine, tremulacin and an isomer of dammarane tetrol. Ellagic acid and procyanidin B inhibited the HIV-1 reverse transcription process at 15 and 3.2 µg/mL−1, respectively. Docking studies did not agree with in vitro results because the best scoring ligand was crotepoxide (ΔG = −8.55 kcal/mol), followed by magnoflorine (ΔG = −8.39 kcal/mol). This study showed that CareVid has contrasting in vitro and in silico activity against HIV-1 reverse transcriptase. However, the strongest in vitro inhibitors were ellagic acid and procyanidin B.

Design, antihuman immunodeficiency activity and molecular docking studies of synthesized 2-aryl and 2-pyrimidinyl pyrrolidines.

A series of thirty-one new compounds were synthesized and evaluated for their anti-HIV-1 and cytotoxicity activity. Of these, twelve were found to be inhibitors of HIV replications in primary human lymphocytes with median effective concentration (EC50) values < 20µM. However, most of the compounds demonstrated cytotoxicity in different cells. Our structure activity relationship study identified different patterns. In the series of 2-aryl pyrrolidines, comparing the activity of the compounds containing 2-aryl substituents we observed that compounds 1c, 1f-j, 2f,g with benzyloxyphenyl and isopropoxy groups were more potent. Compounds 1g-j, 2f,g, in which the 1-aryl moiety contained a methyl group in 3,5- or 4-positions also showed high activity. In the series of compounds containing the amide, aminomethyl and nitrile groups we observed an increase in activity with C(O)NH2 < CH2NH2 < CN. In the series of 2-pyrimidinyl pyrrolidines, the best results were demonstrated with derivatives 5e and 5f, in which the presence of a benzyl fragment in 1st and aniline fragment in 6th positions of pyrimidine ring we observed an increase in anti-HIV activity. Molecular docking studies of synthesized compounds with HIV-1 reverse transcriptase enzyme were performed. Binding energies of ligands were estimated, and the interacting amino acids of HIV-1 reverse transcriptase protein were shown. Based on corroborative results of the molecular docking studies and in vitro experiments, we suggest that three groups of synthesized ligands (1c, 1f-i), (2f,g), (5e,f, 7) are of high interest for further research on new drugs against HIV. General structure of synthesized 2-aryl and 2-pyrimidinyl pyrrolidines.

Design, synthesis and biological evaluation of quinoxaline compounds as anti-HIV agents targeting reverse transcriptase enzyme

Infection by human immunodeficiency virus still represents a continuous serious concern and a global threat to human health. Due to appearance of multi-resistant virus strains and the serious adverse side effects of the antiretroviral therapy administered, there is an urgent need for the development of new treatment agents, more active, less toxic and with increased tolerability to mutations. Quinoxaline derivatives are an emergent class of heterocyclic compounds with a wide spectrum of biological activities and therapeutic applications. These types of compounds have also shown high potency in the inhibition of HIV reverse transcriptase and HIV replication in cell culture. For these reasons we propose, in this work, the design, synthesis and biological evaluation of quinoxaline derivatives targeting HIV reverse transcriptase enzyme. For this, we first carried out a structure-based development of target-specific compound virtual chemical library of quinoxaline derivatives. The rational construction of the virtual chemical library was based on previously assigned pharmacophore features. This library was processed by a virtual screening protocol employing molecular docking and 3D-QSAR. Twenty-five quinoxaline compounds were selected for synthesis in the basis of their docking and 3D-QSAR scores and chemical synthetic simplicity. They were evaluated as inhibitors of the recombinant wild-type reverse transcriptase enzyme. Finally, the anti-HIV activity and cytotoxicity of the synthesized quinoxaline compounds with highest reverse transcriptase inhibitory capabilities was evaluated. This simple screening strategy led to the discovery of two selective and potent quinoxaline reverse transcriptase inhibitors with high selectivity index.

Synthesis, molecular docking and biological evaluation of 2-(thiophen-2-yl)-1H-indoles as potent HIV-1 non-nucleoside reverse transcriptase inhibitors.

New 2-(thiophen-2-yl)-1H-indole derivatives bearing hydrophobic substituents at the 3-position were designed, synthesized and evaluated for their inhibition of HIV-1 reverse transcriptase (RT) enzyme. Dialkylphosphites (2a-c) or trialkylphosphites (3a-c) were reacted with 2-(thiophen-2-yl)-1H-indole-3-carbaldehyde (1) yielding the corresponding α-hydroxyphosphonate adducts (7a-7c). The reaction of compound 1 with the ylidenetriphenylphosphoranes (4a-4c) proceeds via Wittig mechanism giving the corresponding ethylenes (E, 8a-c). Compounds 8b,c were equally obtained upon reacting aldehyde 1 with the appropriate dialkylphosphonates 5a,b under the Horner-Wittig reaction conditions. On the other hand, the reaction of aldehyde 1 with diethyl cyanomethylene phosphonate (5c) yielded a mixture of the E-ethylene 10 and the cyanovinyl phosphonate 11. The thioaldehyde 12 was obtained upon refluxing aldehyde 1 with the Lawesson's reagent (LR, 6a) or with the Japanese reagent (JR, 6b) in dry toluene. Upon evaluation of HIV-1 Reverse Transcriptase enzyme inhibition, compound 8b (IC50=2.93nM) exhibited the superior HIV-1 RT inhibition and its potency was about 3-folds that of Efavirenz (IC50=6.03nM). Also, compounds 9a (IC50=4.09nM) and 12 (IC50=3.54nM) showed significantly higher inhibition potency. Moreover, compounds 7b (IC50=7.48nM), and 8a (IC50=4.55nM) showed potency not significantly different from that of Efavirenz. Molecular docking experiments on these potent compounds was in accordance with the in vitro data and confirmed binding of these compounds to the enzyme through ring-stacking and hydrogen bond interactions. According to these results, the new molecules would serve as potent HIV-1 NNRTIs inhibitors.

Molecular docking, design, synthesis and biological evaluation of novel 2,3-aryl-thiazolidin-4-ones as potent NNRTIs

ABSTRACTNonnucleoside reverse transcriptase inhibitors (NNRTIs) remain the most promising anti-AIDS agents that target the HIV-1 reverse transcriptase enzyme (RT). However, the efficiency of approved NNRTI drugs has decreased by the appearance of drug-resistant viruses and side effects upon long-term usage. Thus, there is an urgent need for developing new, potent NNRTIs with broad spectrum against HIV-1 virus and with improved properties. In this study, a series of thiazolidinone derivatives was designed based on a butterfly mimicking scaffold consisting of a substituted benzothiazolyl moiety connected with a substituted phenyl ring via a thiazolidinone moiety. The most promising derivatives were selected using molecular docking analysis and PASS prediction program, synthesized and evaluated for HIV-1 RT inhibition. Five out of fifteen tested compounds exhibited good inhibitory action. It was observed that the presence of Cl or CN substituents at the position 6 of the benzothiazole ring in combination with two fluoro atoms at the ortho-positions or a hydrogen acceptor substituent at the 4-position of the phenyl ring are favourable for the HIV RT inhibitory activity.

Synthesis, characterization: Spectral and theoretical, molecular docking and in vitro studies of copper complexes with HIV RT enzyme

Millions of people are living with human immunodeficiency virus type 1 (HIV-1), which causes AIDS or AIDS- related complex. HIV-1 reverse transcriptase (RT) is one of the key viral targets for HIV-1 inhibition. In the present work, new Cu(II) heterocyclic Schiff base complexes as HIV-1 reverse transcriptase inhibitors have been synthesized. Complexes were characterized by NMR, FTIR, Mass, UV-Vis, EPR spectra, TGA, magnetic moment and elemental analyses. DFT based molecular orbital energy calculations of the synthesized copper complexes have been studied, in which the complexes were theoretically optimized. Geometrical structures of the complexes were found to be square pyramidal and square planar. To test the reverse transcriptase inhibition activity of the ligands and their Cu(Il) complexes, HIV-1 RT kit assay was used. Nevirapine was used as reference drug. Results showed that the newly synthesized copper complexes effectively inhibited HIV-1 replication. Thiophene copper complexes were found to exhibit higher anti-HIV activity than pyrrole copper complexes. Molecular docking was also used to identify the interaction between Cu(II) complexes with the active site of the RT enzyme (with PDB ID: 1S1U). The cytotoxicity of these copper complexes has been evaluated by MTT assay against normal 3T3L1 cells and results show that the synthesized copper complexes [Cu(T2)2], [Cu(P2)2] and [Cu(P3)2] are non toxic in nature.

Biological evaluation of molecules of the azaBINOL class as antiviral agents: Inhibition of HIV-1 RNase H activity by 7-isopropoxy-8-(naphth-1-yl)quinoline

Inspired by bioactive biaryl-containing natural products found in plants and the marine environment, a series of synthetic compounds belonging to the azaBINOL chiral ligand family was evaluated for antiviral activity against HIV-1. Testing of 39 unique azaBINOLs and two BINOLs in a single-round infectivity assay resulted in the identification of three promising antiviral compounds, including 7-isopropoxy-8-(naphth-1-yl)quinoline (azaBINOL B#24), which exhibited low-micromolar activity without associated cytotoxicity. The active compounds and several close structural analogues were further tested against three different HIV-1 envelope pseudotyped viruses as well as in a full-virus replication system (EASY-HIT). The in vitro studies indicated that azaBINOL B#24 acts on early stages of viral replication before viral assembly and budding. Next we explored B#24’s activity against HIV-1 reverse transcriptase (RT) and individually tested for polymerase and RNase H activity. The azaBINOL B#24 inhibits RNase H activity and binds directly to the HIV-1 RT enzyme. Additionally, we observe additive inhibitory activity against pseudotyped viruses when B#24 is dosed in competition with the clinically used non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz. When tested against a multi-drug resistant HIV-1 isolate with drug resistance associated mutations in regions encoding for HIV-1 RT and protease, B#24 only exhibits a 5.1-fold net decrease in IC50 value, while efavirenz’ activity decreases by 7.6-fold. These results indicate that azaBINOL B#24 is a potentially viable, novel lead for the development of new HIV-1 RNase H inhibitors. Furthermore, this study demonstrates that the survey of libraries of synthetic compounds, designed purely with the goal of facilitating chemical synthesis in mind, may yield unexpected and selective drug leads for the development of new antiviral agents.

Parallel screening of drug-like natural compounds using Caco-2 cell permeability QSAR model with applicability domain, lipophilic ligand efficiency index and shape property: A case study of HIV-1 reverse transcriptase inhibitors

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 AlogP value. We showed that this integrative approach is successful in lead exploration of natural compounds targeted against HIV-1 RT enzyme.

The small-molecule 3G11 inhibits HIV-1 reverse transcription.

The small-molecule 6-(tert-butyl)-4-phenyl-4-(trifluoromethyl)-1H,3H-1,3,5-triazin-2-one (3G11) inhibits HIV-1 replication in the human T cell line MT-2. Here, we showed that 3G11 specifically and potently blocks HIV-1 infection. By contrast, 3G11 did not block other retroviruses such as HIV-2, simian immunodeficiency virus (SIVmac ), bovine immunodeficiency virus, feline immunodeficiency virus, equine infectious anemia virus, N-tropic murine leukemia virus, B-tropic murine leukemia virus, and Moloney murine leukemia virus. Analysis of DNA metabolism by real-time PCR revealed that 3G11 blocks the formation of HIV-1 late reverse transcripts during infection prior to the first-strand transfer step. In agreement, an in vitro assay revealed that 3G11 blocks the enzymatic activity of HIV-1 reverse transcriptase as strong as nevirapine. Docking of 3G11 to the HIV-1 reverse transcriptase enzyme suggested a direct interaction between residue L100 and 3G11. In agreement, an HIV-1 virus bearing the reverse transcriptase change L100I renders HIV-1 resistant to 3G11, which suggested that the reverse transcriptase enzyme is the viral determinant for HIV-1 sensitivity to 3G11. Although NMR experiments revealed that 3G11 binds to the HIV-1 capsid, functional experiments suggested that capsid is not the viral determinant for sensitivity to 3G11. Overall, we described a novel non-nucleoside reverse transcription inhibitor that blocks HIV-1 infection.