HIV resistance to reverse transcriptase inhibitors

Precursors of Viral Proteases as Distinct Drug Targets

Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.

Advances in Nucleoside and Nucleotide Analogues in Tackling Human Immunodeficiency Virus and Hepatitis Virus Infections

Nucleoside and nucleotide analogues are structurally similar antimetabolites and are promising small-molecule chemotherapeutic agents against various infectious DNA and RNA viruses. To date, these analogues have not been documented in-depth as anti-human immunodeficiency virus (HIV) and anti-hepatitis virus agents, these are at various stages of testing ranging from pre-clinical, to those withdrawn from trials, or those that are approved as drugs. Hence, in this review, the importance of these analogues in tackling HIV and hepatitis virus infections is discussed with a focus on the viral genome and the mechanism of action of these analogues, both in a mutually exclusive manner and their role in HIV/hepatitis coinfection. This review encompasses nucleoside and nucleotide analogues from 1987 onwards, starting with the first nucleoside analogue, zidovudine, and going on to those in current clinical trials and even the drugs that have been withdrawn. This review also sheds light on the prospects of these nucleoside analogues in clinical trials as a treatment option for the COVID-19 pandemic.

Therapeutic potential of uracil and its derivatives in countering pathogenic and physiological disorders

Uracil is one of the most notable pharmacophores in medicinal chemistry as the pyrimidine nucleobase forms an integral part of many commercial drugs. Though the name uracil is usually associated with cancer drugs, there are many uracil-based compounds which can treat different diseases when they are employed. So far, there has been no in-depth review concerning uracil drugs in the market, or in the different stages of clinical trials, including those approved or discontinued. The current work focuses on the importance of uracil and its derivatives in treating different diseases. The use of uracil compounds in treating viral infections, cancer, diabetic, thyroid and autosomal recessive disorders are discussed in the review. The mechanism of action of each uracil drug with emphasis on their structure and properties are discussed in detail. The targeted action of these drugs on sites or on the different stages of a disorder/pathogenic life cycle are also discussed. This review encompasses uracil drugs approved as well as those in development from the 1950's onwards. The utility of uracil in drug discovery and its association with a wide range of diseases is brought forth within this review to demonstrate its potential to a wider audience.

Novel Isoxazolidine and γ-Lactam Analogues of Homonucleosides

Homonucleoside analogues cis-16 and trans-17 having a (5-methoxycarbonyl)isoxazolidine framework were synthesized via the 1,3-dipolar cycloaddition of nucleobase-derived nitrones with methyl acrylate. Hydrogenolysis of the isoxazolidines containing thymine, dihydrouracil, theophylline and adenine moieties efficiently led to the formation of the respective γ-lactam analogues. γ-Lactam analogues having 5-bromouracil and 5-chlorouracil fragments were synthesized by treatment of uracil-containing γ-lactams with NBS and NCS. Isoxazolidine and γ-lactam analogues of homonucleosides obtained herein were evaluated for activity against a broad range of DNA and RNA viruses. None of the compounds that were tested exhibited antiviral or cytotoxic activity at concentrations up to 100 µM. The cytostatic activities of all compounds toward nine cancerous cell lines was tested. γ-Lactams trans-15e (Cl-Ura) and cis-15h (Theo) appeared the most active toward pancreatic adenocarcinoma cells (Capan-1), showing IC50 values 21.5 and 18.2 µM, respectively. Isoxazolidine cis-15e (Cl-Ura) inhibited the proliferation of colorectal carcinoma (HCT-116).

Identification of potential agents for thymoma by integrated analyses of differentially expressed tumour-associated genes and molecular docking experiments

Thymoma, derived from the epithelial cells of the thymus, is a rare malignant tumour type. Following diagnosis with thymoma, patients generally undergo surgical treatment. However, patients with advanced-stage disease are only candidates for chemotherapy and have poor survival. Therefore, it is urgently required to explore effective chemotherapeutic agents for the treatment of thymoma. In the present study, a Bioinformatics analysis was performed to identify novel drugs for thymoma. Differentially expressed genes (DEGs) in thymoma were obtained by Gene Expression Profiling Interactive Analysis. Subsequently, these genes were processed by Connectivity Map analysis to identify suitable compounds. In addition, Metascape software was used to verify drug and target binding. Molecular docking technology was used to verify drug and target binding. Finally, absorption, distribution, metabolism and excretion parameters in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database were used for drug screening and for evaluation of the potential clinical value. In total, 2,447 DEGs, including 2,204 upregulated and 243 downregulated genes, were identified from 118 thymoma patients and 339 normal samples. The top 10 drugs displaying the most significant negative correlations were fulvestrant, hesperetin, zidovudine, hydrocortisone, rolitetracycline, ellipticine, sirolimus, quinisocaine, oestradiol (estradiol) and harmine. The predicted targets of these drugs were then confirmed. The score for the association between estrogen receptor 1 (ESR1) and fulvestrant was 0.99. According to the molecular docking analysis, the total scores for the interaction between ESR1 were 10.26, and those for the interaction between tamoxifen and ESR1 were 6.60. The oral bioavailability (%), drug-likeness and drug half-life for hesperetin were 70.31, 0.27 and 15.78, respectively; those for oestradiol were 53.56, 0.32 and 3.50, respectively; and those for harmine were 56.80, 0.13 and 5.04, respectively. In conclusion, several potential therapeutic drugs for thymoma were identified in the present study. The results suggested that the compounds, including fulvestrant, estradiol, hesperetin and ellipticine, represent the most likely drugs for the treatment of thymoma. Future studies should focus on testing these novel compounds in vitro and in vivo.

Torsional flexibility of undecorated catechol diether compound as potent NNRTI targeting HIV-1 reverse transcriptase

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.

Unusual Nucleophilic Addition of Grignard Reagents in the Synthesis of 4-Amino-pyrimidines

Pyrimidines have always received considerable attention because of their importance in synthesis and elucidation of biochemical roles, in particular that of vitamin B1. Herein, we describe a reaction pathway in a Grignard reagent-based synthesis of substituted pyrimidines. A general synthesis of α-keto-2-methyl-4-amino pyrimidines and their C6-substituted analogues from 4-amino-5-cyano-2-methylpyrimidine is reported. The presence of the nitrile substituent in the starting material also results in an unusual reaction pathway leading to C6-substituted 1,2-dihydropyrimidines. Grignard reagents that give normal pyrimidine products under standard reaction conditions can be switched to give dihydropyrimidines by holding the reaction at 0 °C before quenching.

Synthesis of novel 1,2,3-triazole based artemisinin derivatives and their antiproliferative activity

Novel artemisinin-1,2,3-triazole derivatives show significant antiproliferative activity, and induce apoptosis and ROS generation and arrest the cell cycle at the G2/M phase.

Recent progress in prodrug design strategies based on generally applicable modifications

The development of prodrugs has progressed with the aim of improving drug bioavailability by overcoming various barriers that reduce drug benefits in clinical use, such as stability, duration, water solubility, side effect profile, and taste. Many conventional drugs act as the precursors of an active agent in vivo; for example, the anti-HIV agent azidothymidine (AZT) is converted into its corresponding active triphosphate ester in the body, meaning that AZT is a prodrug in the broadest sense. However prodrug design is generally difficult owing to the lack of general versatility. Thus, these prodrugs, broadly defined, are often discovered by chance or trial-and-error. Recently, many prodrugs that could release the corresponding parent drugs with or without enzymatic action under physiological conditions have been reported. These prodrugs can be easily designed and synthesized because of their generally applicable modifications. This digest paper provides an overview of recent development in prodrug strategies for drugs with a carboxylic acid or hydroxyl/amino group on the basis of a generally applicable modification strategy, such as esterification, amidation, or benzylation.

Structural Features and Anti-Human Immunodeficiency Virus (HIV) Activity of the Isomers of 1-(2′,6′-Difluorophenyl)-1H,3H-Thiazolo[3,4-a]Benzimidazole, a Potent Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitor

The structural features, including the absolute configuration, of the enantiomers of 1-(2′,6′-difluorophenyl)-1 H,3 H-thiazolo[3,4- a]benzimidazole (TBZ; NSC 625487), the lead compound of a new class of human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase inhibitors (NNRTIs), are described. Diffractometric analysis revealed that TBZ, like other NNRTIs, assumes a butterfly-like conformation in which the phenyl ring at C1 is in an orthogonal orientation relative to the thiazolobenzimidazole system, and the 2′,6′-fluorine atoms form two intramolecular hydrogen bonds with H1 and one of the methylene protons at C3, respectively. The stereochemistry in solution, as confirmed by lanthanide shift reagent-assisted ‘H NMR, paralleled the situation present in the solid state. The in vitro anti-HIV activity of the two enantiomers was also evaluated and the results obtained showed that the R-(+) is more active than the S-(−) isomer in inhibiting HIV-1 replication. Resistance and cross-resistance to other NNRTIs as well as inhibitory effects on HIV-1 reverse transcriptase activity are also reported.

Synergistic Inhibition of Human Immunodeficiency Virus Type 1 Replication in Vitro by Two- and Three-Drug Combinations of Delavirdine, Lamivudine and Zidovudine

Delavirdine (DLV), a non-nucleoside human immunodeficiency virus type 1 (HIV-1) reverse transcriptase inhibitor, was evaluated in two- and three-drug combination regimens with lamivudine (3TC) and zidovudine (ZDV). The effect of continuous drug treatment on HIV-1JR-CSF replication in human peripheral blood mononuclear cells was measured by an ELISA for p24 core antigen. Drug synergy, estimated by the combination index method and the method of Pritchard & Shipman, was observed when DLV was combined with 3TC over a range of drug concentrations (DLV at 1, 3, 10, 30 and 100 nM; 3TC at 3, 10, 30, 100 and 300 nM). Two-drug combinations of ZDV and DLV at a 1: 3 ratio or ZDV and 3TC at a 1: 10 ratio were synergistic at greater than 75% inhibition levels. Three-drug combinations of ZDV, DLV and 3TC (ZDV at 0.3, 1, 3 and 10 nM; DLV at 1, 3, 10 and 30 nM; 3TC at 3, 10, 30 and 100 nM) at the ratio of 1: 3: 10 also yielded significant synergistic effects. None of the combinations studied showed significant additive or synergistic drug toxicity. These in vitro data suggest that DLV should be evaluated in two- and three-drug combinations with 3TC and ZDV in clinical trials.

Oxathiin Carboxanilide Derivatives: A Class of Non-Nucleoside HIV-1-Specific Reverse Transcriptase Inhibitors (NNRTIs) that are Active against Mutant HIV-1 Strains Resistant to other NNRTIs

The HIV-1-specific oxathiin carboxanilide derivative 1-methylethyl 2-chloro-5-[[(5,6-dihydro-2-methyl-1,4-oxathiin-3-yl)carbonyl]amino]benzoate (NSC 615985) (designated UC84) has potent activity against HIV-1(IIIB) (50% effective concentration: 0.015 μg ml−1). UC84 was found to select for a 138-Lys mutant virus strain in HIV-1-infected CEM cell cultures. When the 138-Lys mutation was introduced solely in the p51 subunit of the p51/p66 reverse transcriptase (RT) heterodimer by site-directed mutagenesis, the enzyme proved 10-fold more resistant to UC84 than when the amino acid mutation was introduced solely in the p66 subunit of the p51/p66 RT heterodimer. These data provided clear evidence for a structural and functional role of the p51 subunit in the sensitivity/resistance of the enzyme to UC84. UC84 also proved to be virtually inactive against mutant HIV-1 strains containing the 100-lle, 106-Ala, 138-Lys or 181-Cys mutation in their RT. However, minor structural changes in the molecule, such as replacement of the oxygen of the amide moiety by sulfur, or the isopropyl ester moiety by cyclopentyl or a secondary butyl, or the methyl group of the oxathiin part by ethyl, made the compound markedly more inhibitory to one or several HIV-1 mutant strains. For example, compound 131 (1-methylethyl 2-chloro-5-[[(5,6-dihydro-2-methyl-1,4-oxathiin-3-yl)thioxomethyl]amino]benzoate was only 2-fold more active than the parent compound UC84 against wild-type HIV-1, but 30- to 100-fold more inhibitory to HIV-1 mutant strains that contained the 100-11e, 106-A1a, 138-Lys or 181-Cys in their RT. These findings should be taken into account when selecting suitable drug candidates for the treatment of HIV-1 infections, particularly those that have developed resistance to other non-nucleoside RT inhibitors (NNRTIs).

2′-Fluoro-2′,3′-Dideoxyarabinosyladenine (F-ddA): Activity against Drug-Resistant Human Immunodeficiency Virus Strains and Clades A-E

2′-Fluoro-2′,3′-dideoxyarabinosyladenine (F-ddA), an anti-human immunodeficiency virus (HIV) drug currently in clinical trial, was compared with zidovudine (AZT), ddl and ddC for anti-HIV activity and potency in HIV-1 strains both sensitive and resistant to zidovudine, ddl and non-nucleoside reverse transcriptase inhibitors. A variety of host cell systems [MT-2, MT-4, phytohaemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMC)] was used. F-ddA was effective against each of the drug-resistant isolates, including the strain resistant to ddl, the other purine dideoxynucleoside evaluated in this study. The anti-HIV-1 activities of F-ddA and zidovudine were also determined against clades A-E in PHA-PBMCs. Although activities were similar, zidovudine was significantly more potent than F-ddA in the PHA-PBMC system.

Anti-HIV Activities of Anionic Metalloporphyrins and Related Compounds

Various water-soluble polysulphonated and polycarboxylated porphyrins and some of their metallated derivatives have been prepared and their antiviral properties against human immunodeficiency virus (HIV-1, HIV-2), simian immunodeficiency virus and other viruses are reported. Besides these polyanionic compounds, two new series of porphyrins were included and studied from the perspective of bio-availability modulation: (i) acefylsulphonamido derivatives endowed with weak acidity properties (deprotonation gives the corresponding anionic derivatives in a pH range 4.5-8.5) and (ii) compounds with the anionic charge transiently masked by esterification (acetoxymethyl- and pivaloyloxymethylesters). Among the more active compounds in inhibiting HIV-induced cytopathic effects, the sulphonated and carboxylated porphyrin complexes were found to interact directly with the HIV protein gp 120 and not with the CD4 cellular receptor.

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.

Electrochemical detection of azidothymidine on modified probes based on chitosan stabilised silver nanoparticles hybrid material

Silver nanoparticle stabilized by chitosan is synthesized for modification of sensing probe for AZT estimation in human plasma.

Amperometric sensing of anti-HIV drug zidovudine on Ag nanofilm-multiwalled carbon nanotubes modified glassy carbon electrode

The zidovudine (ZDV) is the first drug approved for the treatment of HIV virus infection. The detection and determination of this drug are very importance in human serum because of its undesirable effects. A new ZDV sensor was fabricated on the basis of nanocomposite of silver nanofilm (Ag-NF) and multiwalled carbon nanotubes (MWCNTs) immobilized on glassy carbon electrode (GCE). The modified electrodes were characterized by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), cyclic voltammetry (CV), and linear sweep voltammetry (LSV) techniques. Results showed that the electrodeposited silver has a nanofilm structure and further electrochemical studies showed that the prepared nanocomposite has high electrocatalytic activity and is appropriate for using in sensors. The amperometric technique under optimal conditions is used for the determination of ZDV ranging from 0.1 to 400ppm (0.37μM-1.5mM) with a low detection limit of 0.04ppm (0.15μM) (S/N=3) and good sensitivity. The prepared sensor possessed accurate and rapid response to ZDV and shows an average recovery of 98.6% in real samples.

Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition

BACKGROUND

LINE-1s (L1, Long Interspersed Element-1) are the most abundant autonomous non-LTR retrotransposons in the human genome and replicate by reverse transcription of an RNA intermediate. Full-length L1 encodes two open reading frames (ORF1, ORF2) and ORF2 has reverse transcriptase activity.

RESULTS

Here we expressed human L1 RT in E. coli and the purified protein displayed the same RT activity as that of ORF2p expressed in insect cells. We tested the effect of different reverse transcriptase inhibitors on L1 RT and found that all four tested nucleoside inhibitors efficiently inhibited L1 RT activity competitively. The Ki values of NRTIs were calculated (AZTTP, 16.4 ± 4.21 nM; d4TTP, 0.73 ± 0.22 nM; ddCTP, 0.72 ± 0.16 nM; 3TCTP, 12.9 ± 2.07 nM). L1 RT was less sensitive to non-nucleoside reverse transcriptase inhibitors, among these nevirapine had no effect, even at concentrations up to 500 μM. We also examined the effect of RT inhibitors on L1 retrotransposition efficiency in vivo using a cell-based retrotransposition assay. Similarly, all analog inhibitors decreased L1 retrotransposition frequency with different potencies whereas nevirapine had little or no effect on L1 retrotransposition. For comparison, we also tested the same inhibitors to highly purified RT of an LTR-retrotransposon (Ty1) and found it was less sensitive to NRTIs than L1 RT and has the same inhibition profile as L1 RT to NNRTIs.

CONCLUSIONS

These data indicate that bacterially expressed L1 RT is an active reverse transcriptase sensitive to nucleoside RT inhibitors but not to non-nucleoside inhibitors.

Docking study of HIV-1 reverse transcriptase with phytochemicals

Natural products are important sources of drug discovery. In this context groups of different set of phytochemicals were taken and docked into the different cavities of the Reverse transcriptase (PDB ID: 1REV) of Human immunodeficiency virus (HIV) and results were discussed. Natural compounds such as Curcumin, Geranin, Gallotannin, Tiliroside, Kaempferol-3-o-glucoside and Trachelogenin were found to very effective according to its binding energy and ligand efficiency score. Those compounds also were found to have no adverse effect as carcinogenicity and mutagenicity and favorable drug likeness score. Hence, considering the facts those compounds could use effectively for HIV-1 drug discovery.

Strategies for recognition of stem-loop RNA structures by synthetic ligands: application to the HIV-1 frameshift stimulatory sequence

Production of the Gag-Pol polyprotein in human immunodeficiency virus (HIV) requires a -1 ribosomal frameshift, which is directed by a highly conserved RNA stem-loop. Building on our discovery of a set of disulfide-containing peptides that bind this RNA, we describe medicinal chemistry efforts designed to begin to understand the structure-activity relationships and RNA sequence-selectivity relationships associated with these compounds. Additionally, we have prepared analogues incorporating an olefin or saturated hydrocarbon bioisostere of the disulfide moiety, as a first step toward enhancing biostability. The olefin-containing compounds exhibit affinity comparable to the lead disulfide and, importantly, have no discernible toxicity when incubated with human fibroblasts at concentrations up to 1 mM.

Development of resistance of human immunodeficiency virus (HIV) to anti-HIV agents: how to prevent the problem?

Of the multitude of reverse transcriptase inhibitors and protease inhibitors that have been pursued for the treatment of HIV infections, nine compounds (viz. zidovudine, didanosine, zalcitabine, stavudine, lamivudine, saquinavir, ritonavir, indinavir and nevirapine) have been approved and several others (i.e. adefovir dipivoxyl [bis(POM)-PMEA], PMPA, bis(POC)-PMPA, 1592U89, delavirdine, loviride, MKC-442, nelfinavir and VX-478) are under clinical development. All these compounds can select for mutations in the reverse transcriptase or protease that confer various degrees of resistance or diminished susceptibility to the compounds. Both the reverse transcriptase and protease are able to accumulate multiple mutations in their genome, thus engendering high-level resistance. To avoid drug resistance from emerging it is recommended to use from the beginning combinations of the different drugs at sufficiently high (that is maximal tolerated) doses. If installed as soon as possible after infection, when it has become evident that the virus is replicating, these drug combinations may achieve a pronounced and sustained virus suppression. This should be reflected by a dramatic reduction of viral load in both the plasma and lymphnodes. With the most effective drug combination regimens, the viral load may even fall under the threshold of detection, and this may clinically translate into an arrest or prevention of progression to AIDS.

Prioritizing Hits with Appropriate Trade-Offs Between HIV-1 Reverse Transcriptase Inhibitory Efficacy and MT4 Blood Cells Toxicity Through Desirability-Based Multiobjective Optimization and Ranking

Nonnucleoside reverse transcriptase (RT) inhibitors (NNRTIs) constitute a promising therapeutic option for AIDS. However, the emergence of virus-NNRTIs resistance was found to be a major problem in the field. Toward that goal, a "knock-out" strategy stands out between the several options to circumvent the problem. However the high drug or drug-drug concentrations often used generate additional safety concerns. The need for approaches able to early integrate drug- or lead-likeness, toxicity and bioavailability criteria in the drug discovery phase is an emergent issue. Given that, we propose a combined strategy based on desirability-based multiobjective optimization (MOOP) and ranking for the prioritization of HIV-1 NNRTIs hits with appropriate trade-offs between inhibitory efficacy over the HIV-1 RT and toxic effects over MT4 blood cells. Through the MOOP process, the theoretical levels of the predictive variables required to reach a desirable RT inhibitor candidate with the best possible compromise between efficacy and safety were found. This information is used as a pattern to rank the library of compounds according to a similarity-based structural criterion, providing a ranking quality of 64 %/71 %/73 % in training/validation/test set. A comparative study between the sequential, parallel and multiobjective virtual screening revealed that the multiobjective approach can outperform the other approaches. These results suggest that the identification of NNRTIs hits with appropriate trade-offs between potency and safety, rather than fully optimized hits solely based on potency, can facilitate the hit to lead transition and increase the likelihood of the candidate to evolve into a successful antiretroviral drug.

Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design

Allele-specific PCR based on subtype consensus sequences is a powerful technique for detecting low frequency drug resistant mutants in HIV-1 infected patients. However, this approach can be limited by genetic variation in the region complementary to the primers, leading to variability in allele detection. The goals of this study were to quantify this effect and then to improve assay performance.

Efficacy and resistance of recently developed non-nucleoside reverse transcriptase inhibitors for HIV-1

Since the introduction of the HAART, non-nucleoside reverse transcriptase inhibitors (NNRTIs) have played an essential role in treating HIV: their strong antiviral potency, good metabolic profile and low pill burden make them an ideal option in the design of an optimized triple drug regimen. Nonetheless, the currently approved NNRTIs (efavirenz and nevirapine) are weighed by peculiar toxicities, while a low genetic barrier and the development of cross-resistance significantly limits their use in cases of suboptimal adherence. Many drugs are in development and they are all designed with the aim to overcome resistance problems. In this review we present data on virological efficacy and resistance profiles of some of the most promising new molecules: some (such as rilpivirine) are close to being marketed, others are in Phase II trials (IDX899 and RDEA806), others again have just completed preclinical studies and are having their first clinical evaluations (RO-5028, UK-453061 and BILR-355 BS); etravirine is already approved by the US FDA, but it is still not licensed in Europe. Other new molecules (Merck MK-4965, GlaxoSmithKline GW678284 and a pyridazinone derivative by Roche), which are currently in early-development phases, are also briefly described.

Study of the Effects on DNA of Two Novel Nucleoside Derivatives Synthesized as Potential Anti-HIV Agents

The pursuit of antiviral active compounds against different classes of viruses, in particular HIV, HBV, and HTLV is an area of important and intense research. In the current study, two novel nucleoside derivatives belonging to a new class of isoxazolidine were successfully synthesized as potential anti-HIV agents by replacement of the furanose ring by a N,O-heterocyclic ring Both compounds were investigated for biological activity, namely, mutagenic and antimutagenic properties. Using Salmonella typhimurium strains TA97, TA100, and TA102, both compounds proved to be nonmutagenic, which may be considered an encouraging result to further elucidate other biological activities. Antimutagenic testing of the synthesized compounds revealed that they are active against the base-pair substitution mutagen sodium azide. However, they did not show any indication as antimutagenic agents against hydrogen peroxide and mitomycin C (oxidative mutagens) or against nitrophenylenediamine (a base-pair substitution and frameshift mutagen). Structure-activity relationship is also discussed. Testing these compounds as antiviral agents is highly recommended.

HIV-1-Resistant Strains during 8-Week on 8-Week off Intermittent Therapy and their Effect on CD4+ T-cell Counts and Antiviral Response

Background

We aimed here to study drug-associated HIV resistance mutations in peripheral blood mononuclear cells (PBMC) and plasma during intermittent therapy.

Methods

A substudy of 86 patients randomized to the intermittent treatment arm (8-week on/8-week off) of the ANRS 106 Window trial. HIV reverse transcriptase and protease genes were sequenced and resistance mutations identified according to the International AIDS Society list.

Results

Resistance mutations were detected in PBMC of 27/86 (31%) patients at baseline and 25/72 (35%) patients at week 96. Resistance mutations were detected in plasma of 28/86 (33%), 24/83 (29%) and 33/80 (41%) patients at weeks 8, 40 and 88, respectively. The detection of nucleoside reverse transcriptase inhibitor and protease inhibitor associated resistance mutations in plasma remained stable over time, but there was an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI)-associated resistance mutations in patients on an NNRTI-based regimen: 1/33 (3%) versus 7/26 patients (27%) at weeks 8 and 88, respectively ( P=0.02). The proportions of patients with plasma HIV RNA levels ≤400 copies/ml after 8 weeks of treatment at weeks 16, 48 and 96 in patients with drug-resistant and wild-type viruses were 93% versus 74% ( P=0.04), 96% versus 88% ( P=0.43) and 70% versus 84% ( P=0.13), respectively. Patients with drug-resistant virus had a lower CD4+ T-cell decrease from baseline at weeks 40 and 88 as compared to patients with wild-type virus ( P=0.05 and 0.002, respectively).

Conclusions

NNRTI-associated resistance mutations increased over time in plasma of patients who were given NNRTIs. Drug-associated HIV resistance mutations did not seem to impair short-term antiviral response and might be associated with reduced CD4+ T-cell loss during interruptions.

Structural basis for drug resistance mechanisms for non-nucleoside inhibitors of HIV reverse transcriptase

The selection of drug resistant virus is a significant obstacle to the continued successful treatment of HIV infection. Reverse transcriptase is the target for numerous approved anti-HIV drugs including both nucleoside inhibitor (NRTI) and non-nucleosides (NNRTI). The many available crystal structures of RT reveal that, generally, in relation to their binding sites NRTI resistance mutations are generally more distally positioned, whilst for NNRTIs mutations are clustered. Such clustering implies a direct stereochemical basis for NNRTI resistance mechanisms, which is indeed observed in many cases such as the loss of key ring stacking interactions with inhibitors via mutations at Tyr181 and Tyr188. However, there are also indirect resistance mechanisms observed, e.g. V108I (via perturbation of Tyr188 and Tyr181) and K103N (apo-enzyme stabilisation). The resistance mechanism can be NNRTI-dependent as is the case for K101E where either indirect (nevirapine) or direct effects (efavirenz) apply. Structural studies have contributed to the design of newer generation NNRTIs and identified a number of features which may contribute to their much improved resistance profiles. Such factors include reduced interactions with Tyr181, the presence of inhibitor/main-chain H-bonds and ability to undergo conformational flexing and rearrangement within the mutated drug site.

The structure-activity relationships of 2,4(1H,3H)-pyrimidinedione derivatives as potent HIV type 1 and type 2 inhibitors

Since the discovery of the 2,4 (1H,3H)-pyrimidinediones as potent non-nucleoside inhibitors of the HIV-1 reverse transcriptase (RT) this class of compounds has yielded a number of N-1 acyclic substituted pyrimidinediones with substantial antiviral activity, which is highly dependent upon their molecular fit into the binding pocket common to this inhibitory class. We have specifically examined the structure activity relationships of compounds with chemical modification made by substituting homocyclic rather than acyclic moieties at N-1 of the pyrimidinedione. Seventy-four compounds were synthesized and evaluated for antiviral activity against HIV-1 and HIV-2. The homocyclic modifications resulted in compounds with significant activity against both HIV-1 and HIV-2, suggesting these compounds represent a new class of non-nucleoside RT inhibitors. The structure-activity relationship (SAR) evaluations indicated that cyclopropyl, phenyl and 1- or 3-cyclopenten-1-yl substitutions at the N-1 of the pyrimidinedione, the addition of a methyl linker between the cyclic moiety and the N-1 and the addition of a benzoyl group at the C-6 of the pyrimidinedione had the greatest contribution to antiviral activity. Five pyrimidinedione analogues with therapeutic indexes (TIs) > 450,000 and a specific analogue (1-cyclopropylmethyl-5-isopropyl-6-(3,5-dimethylbenzoyl)-2,4(1H,3H)-pyrimidinedione), which exhibited a TI of > 2,000,000, were identified. None of the analogues were cytotoxic to target cells at the highest in vitro test concentration, which is the upper limit of compound solubility of the analogues in aqueous solution. Thus, we have identified a series of pyrimidinediones with substantially improved antiviral efficacy and range of action and with significantly reduced cellular cytotoxicity.

Phosphonated Carbocyclic 2‘-Oxa-3‘-azanucleosides as New Antiretroviral Agents

Phosphonated carbocyclic 2'-oxa-3'-azanucleosides have been synthesized and tested for their antiretroviral activity. The obtained results have shown that some of the compounds were as powerful as azydothymidine in inhibiting the reverse transcriptase activity of the human retrovirus T-cell leukemia/lymphotropic virus type 1 and in protecting human peripheral blood mononuclear cells against human retrovirus T-cell leukemia/lymphotropic virus type 1 transmission in vitro. These data indicate that phosphonated carbocyclic 2'-oxa-3'-azanucleosides possess the necessary requirements to efficiently counteract infections caused by human retroviruses.

Fluorescent HIV-1 Dimerization Initiation Site: design, properties, and use for ligand discovery

The HIV-1 Dimerization Initiation Site (DIS) is an intriguing, yet underutilized, viral RNA target for potential antiretroviral therapy. To study the recognition features of this target and to provide a quantitative, rapid, and real-time tool for the discovery of new binders, a fluorescence-based assay has been constructed. It relies on strategic incorporation of 2-aminopurine, an isosteric fluorescent adenosine analogue, into short hairpin RNA constructs. These oligomers self-associate to form a kissing loop that thermally rearranges into a more stable extended duplex, thereby mimicking the association and structural features of the native RNA sequence. We demonstrate the ability of two fluorescent DIS constructs, DIS272(2AP) and DIS273(2AP), to report the binding of known DIS binders via changes in their emission intensity. Binding of aminoglycosides such as paromomycin to DIS272(2AP) results in significant fluorescence enhancement, while ligand binding to DIS273(2AP) results in fluorescence quenching. These observations are rationalized by comparison to the sequence-analogous bacterial A-site, where the relative emission of the fluorescent probe is dependent on the placement of the flexible purine residues inside or outside the helical domain. Analysis of binding isotherms generated using DIS272(2AP) yields submicromolar EC50 values for paromomycin (0.5 +/- 0.2 microM) and neomycin B (0.6 +/- 0.2 microM). Other neomycin-family aminoglycosides are less potent binders with neamine, the core pharmacophore, displaying the lowest affinity of 21 +/- 1 microM. Screening of additional aminoglycosides and their derivatives led to the discovery of new, previously unreported, aminoglycoside binders of the HIV DIS RNA, among them butirosin A (5.5 +/- 0.6 microM) and apramycin (7.6 +/- 1.0 microM). A conformationally constrained neomycin B analogue displays a rather high affinity to the DIS (1.9 +/- 0.2 microM). Among a series of nucleobase aminoglycoside conjugates, only the uracil derivatives display a measurable affinity using this assay with EC50 values in the 2 microM range. In addition, similarity between the solution behavior of HIV-1 DIS and the bacterial decoding A-site has been observed, particularly with respect to the intra- and extra-helical residence of the conformationally flexible A residues within the bulge. Taken together, the observations reported here shed light on the solution behavior of this important RNA target and are likely to facilitate the design of new DIS selective ligands as potential antiretroviral agents.

Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy

BACKGROUND

Understanding the selection and decay of drug-resistant HIV-1 variants is important for designing optimal antiretroviral therapy.

OBJECTIVE

To develop a high-throughput, real-time reverse transcriptase (RT) polymerase chain reaction (PCR) assay to quantify non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant variants K103N (AAT or AAC alleles) at frequencies as low as 0.1%, and to apply this to monitor these variants before, during, and after NNRTI therapy.

METHODS

HIV-1 RNA in longitudinal plasma samples obtained from patients starting and stopping NNRTI therapy was converted to cDNA and the target sequence region amplified and quantified by real-time PCR. Approximately 10 copies/reaction provided a template for a second round of PCR using primers that discriminated between the mutant and wild-type alleles. Amplification specificity was confirmed by thermal denaturation analysis.

RESULTS

Frequencies of 103N similar to assay background (0.029%) were observed in longitudinal samples from 9 of 12 treatment-naive patients; three patients had transient increases in 103N frequency to a range of 0.21-0.48%, which was 7-16.5 times assay background. Analysis of longitudinal plasma samples from six NNRTI-experienced patients showed three patterns: persistence of 103N variants after stopping NNRTI therapy, codon switching of 103N between AAC and AAT during NNRTI therapy, and decay of 103N variants to below assay background after cessation of NNRTI therapy.

CONCLUSIONS

Allele-specific RT-PCR quantified the emergence and decay of drug-resistant variants in patients over a broad range of frequencies (0.1-100%). The rate of decay of K103N variants after stopping NNRTI therapy was highly variable.

Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method

Two-layered and three-layered ONIOM calculations were performed to compare the binding energies of 8-Cl TIBO inhibitor when bound into the human immunodeficiency virus reverse transcriptase binding pocket and a Y181C variant. Both consisted of 20 residues within a radius of 15 A. A combination of different methods [MP2/6-31G(d), B3LYP/6-31G(d,p), and PM3] were performed to take advantage of ONIOM's layering strategy analysis. The obtained results clearly indicate that the Y181C mutation reduces the binding affinity and stability of the inhibitor by approximately 8-9 kcal/mol as obtained from different combined MO:MO methods. Analyses regarding the energetic components of the interaction and deformation energies for 8-Cl TIBO inhibitor upon binding were also examined extensively. Additional calculations involving the interaction energies between 8-Cl TIBO with individual residues surrounding the binding pocket were performed at MP2/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory to gain more insight into the energetic differences of wild-type and Y181C mutant type at the atomistic level.

Convenient Synthesis of Nucleoside and Isonucleoside Analogues

[reaction: see text]. A very simple methodology to stereoselectively achieve tricyclic isonucleosides (nucleobase = thymine, uracil, and 5-fluoruracil) and 3'-C-branched nucleosides (nucleobase = theophylline) was performed by means of a DBU-mediated addition process using a readily available 2-bromo sugar. The mechanism for these transformations implies the loss of both substituents at C-2 and C-3 on the sugar moiety, and although it seems that DBU is probably involved, its involvement has not yet been ascertained. Cytosine did not react under these conditions.

Pharmacokinetics of the antiviral agent beta-L-3'-fluoro-2',3'-didehydro-2',3'-dideoxycytidine in rhesus monkeys

beta-L-3'-Fluoro-2',3'-didehydro-2',3'-dideoxycytidine (L-3'-Fd4C) is a potent and selective antiretroviral nucleoside with activity against lamivudine-resistant human immunodeficiency virus type 1 (HIV-1) and hepatitis B virus (HBV) in vitro. The pharmacokinetics of L-3'-Fd4C were characterized in three rhesus monkeys given single intravenous and oral doses. A two-compartment open model was fitted to the plasma and urine data. Plasma concentrations declined in a biexponential fashion with an average beta half-life of 12.45 h and central and steady-state volumes of distribution of 0.43 and 1.90 liters/kg, respectively. The average systemic and renal clearance values were 0.23 and 0.08 liters/kg, respectively, and the apparent mean terminal half-life of the oral dose was 12.5 h. The serum concentrations exceeded the 90% effective concentration value for lamivudine-resistant and wild-type HIV-1 after oral administrations. A large variation was observed in the oral bioavailability, which ranged from 15 to 31%. To determine whether the bioavailability may be improved by using a basic buffer solution, the oral dose was repeated to the same animals in a sodium bicarbonate solution. The bioavailability of L-3'-Fd4C administered with sodium bicarbonate was not significantly different from the bioavailability when the oral dose was administered in the absence of buffer (P = 0.49), suggesting that further development of this compound may warrant other approaches, such as development of a prodrug to improve its oral absorption.

Synthesis of Phosphonated Carbocyclic 2‘-Oxa-3‘-aza-nucleosides: Novel Inhibitors of Reverse Transcriptase

Phosphonated carbocyclic 2'-oxa-3'-aza-nucleosides have been synthesized in good yields by 1,3-dipolar cycloaddition methodology. The cytotoxicity and the reverse transcriptase inhibitory activity of the obtained compounds have been investigated. Phosphonated carbocyclic 2'-oxa-3'-aza-nucleosides, while showing low levels of cytotoxicity, exert a specific inhibitor activity on two different reverse transcriptases, which is comparable with that of AZT, opening new perspectives on their possible use as therapeutic agents, in anti-retroviral and anti-HBV chemotherapy.

Synthesis of 3‘-Fluoro-2‘,3‘-dideoxy-2‘,3‘-didehydro-4‘-ethynyl-d- and -l-furanosyl Nucleosides

An efficient procedure has been developed for the synthesis of 3'-fluoro-2',3'-dideoxy-2',3'-didehydro-4'-ethynyl D- and L-furanosyl nucleosides (1 and 2) starting from 2,3-O-isopropylidene-d-glyceraldehyde. The key intermediate 1-O-benzoyl-3E-fluoro-3,4-unsaturated-5,6-di(tert-butyldimethylsilyloxy)-2-hexanone 8 was obtained in nine steps with the overall yield of 22%. The alpha,beta-unsaturated ketone 8 was then treated with ethynylmagnesium bromide in a typical Grignard reaction procedure to afford the two intermediates 9 and 10, which after deprotection, oxidation, and acetylation gave the corresponding 4-ethynyl-substituted D- and L-sugar moieties 15 and 16, respectively. A series of D- and L-pyrimidine and purine nucleosides were prepared by the coupling of the sugar moieties with various silylprotected bases. The anomeric mixtures were obtained after condensation. After separation, the beta-isomers were further deprotected to yield the target nucleosides. All the newly synthesized 4'-substituted nucleosides were tested for their activities against HIV, among which the D-adenine derivative showed moderate anti-HIV activity (EC(50) = 25.1 microM) without significant cytotoxicity.

Novel 4'-substituted stavudine analog with improved anti-human immunodeficiency virus activity and decreased cytotoxicity

The antiviral drug 2',3'-didehydro-3'-deoxythymidine (D4T; also know as stavudine and Zerit), which is used against human immunodeficiency virus (HIV), causes delayed toxicity (peripheral neuropathy) in long-term use. After examining a series of 2',3'-didehydro-3'-deoxy-4'-substituted thymidine (4'-substituted D4T) analogs, 4'-ethynyl D4T was found to have a fivefold-better antiviral effect and to cause less cellular and mitochondrial toxicity than D4T. The antiviral activity of this compound can be reversed by dThd but not by dCyd. The compound acted synergistically with beta-L-2',3'-deoxy-3'-thiacytidine (also known as lamivudine) and beta-L-2',3'-dideoxy-2',3'-didehydro-5-fluorocytidine (also known as elvucitabine) and additively with 2',3'-dideoxyinosine (also known as didanosine and Videx) and 3'-azido-3'-deoxythymidine (also known as Retovir and zidovudine) against HIV. 4'-Ethynyl D4T is phosphorylated by purified human thymidine kinase 1 (TK-1) from CEM cells with a faster relative V(max) and a lower K(m) value than D4T. The efficiency of TK-1 in the phosphorylation of 4'-ethynyl D4T is fourfold better than that of D4T. While D4T is broken down by the catabolic enzyme thymidine phosphorylase, the level of breakdown of 4'-ethynyl D4T was below detection. Since 4'-ethynyl D4T has increased anti-HIV activity and decreased toxicity and interacts favorably with other currently used anti-HIV drugs, it should be considered for further development as an anti-HIV drug.

Crystal Structures of HIV-1 Reverse Transcriptases Mutated at Codons 100, 106 and 108 and Mechanisms of Resistance to Non-nucleoside Inhibitors

Leu100Ile, Val106Ala and Val108Ile are mutations in HIV-1 reverse transcriptase (RT) that are observed in the clinic and give rise to resistance to certain non-nucleoside inhibitors (NNRTIs) including the first-generation drug nevirapine. In order to investigate structural mechanisms of resistance for different NNRTI classes we have determined six crystal structures of mutant RT-inhibitor complexes. Val108 does not have direct contact with nevirapine in wild-type RT and in the RT(Val108Ile) complex the biggest change observed is at the distally positioned Tyr181 which is > 8 A from the mutation site. Thus in contrast to most NNRTI resistance mutations RT(Val108Ile) appears to act via an indirect mechanism which in this case is through alterations of the ring stacking interactions of the drug particularly with Tyr181. Shifts in side-chain and inhibitor positions compared to wild-type RT are observed in complexes of nevirapine and the second-generation NNRTI UC-781 with RT(Leu100Ile) and RT(Val106Ala), leading to perturbations in inhibitor contacts with Tyr181 and Tyr188. Such perturbations are likely to be a factor contributing to the greater loss of binding for nevirapine compared to UC-781 as, in the former case, a larger proportion of binding energy is derived from aromatic ring stacking of the inhibitor with the tyrosine side-chains. The differing resistance profiles of first and second generation NNRTIs for other drug resistance mutations in RT may also be in part due to this indirect mechanism.