Antiviral therapy: nucleotide and nucleoside analogs

Activities and metabolomics of Cordyceps gunnii under different culture conditions

Many active metabolites have been identified from various species of the fungal genus Cordyceps. A predominant species of this genus is Cordyceps gunnii, but there are limited reports on the active ingredients from this species. This study aimed to conduct activity assays and metabolome analysis on extracts of C. gunnii obtained under different culture conditions. Five different solid media were selected to culture the mycelium of C. gunnii and the metabolites were extracted with organic solvents; concurrently, the wild stroma and host complexes of C. gunnii were extracted by ethyl acetate. Extracts were subsequently assayed for various biological activities and were analyzed by untargeted metabolomics. There were significant differences in the activities and metabolites of C. gunnii extracts from different culture conditions and from wild stroma and host complexes. The extracts of stroma and host complexes and mycelia cultured on WGA medium for 21 days exhibited similar effective inhibitory activity against five cell lines. A total of 51 metabolites were annotated and included various structural types. The literatures indicate that most of the identified compounds have a variety of different biological activities. These findings provide the basis for further systematic excavation of C. gunnii and improved utilization of this fungal species.

High throughput screening identifies inhibitors for parvovirus B19 infection of human erythroid progenitor cells

Parvovirus B19 (B19V) infection can cause hematological disorders and fetal hydrops during pregnancy. Currently, no antivirals or vaccines are available for the treatment or the prevention of B19V infection. To identify novel small-molecule antivirals against B19V replication, we developed a high throughput screening assay, which is based on an in vitro nicking assay using recombinant N-terminal 1-176 amino acids of the viral large nonstructural protein (NS1N) and a fluorescently labeled DNA probe (OriQ) that spans the nicking site of the viral DNA replication origin. We collectively screened 17,040 compounds and identified 2,178 (12.78%) hits that possess >10% inhibition of the NS1 nicking activity, among which 84 hits were confirmed to inhibit nicking in a dose-dependent manner. Using ex vivo expanded primary human erythroid progenitor cells (EPCs) infected by B19V, we validated 24 compounds demonstrated >50% in vivo inhibition of B19V infection at 10 μM, which can be categorized into 7 structure scaffolds. Based on the therapeutic index [half maximal cytotoxic concentration (CC₅₀)/half maximal effective concentration (EC₅₀)] in EPCs, the top 4 compounds were chosen to examine their inhibitions of B19V infection in EPCs at two times of the 90% maximal effective concentration (EC₉₀). A purine derivative (P7), demonstrated an antiviral effect (EC₅₀=1.46 μM) without prominent cytotoxicity (CC₅₀=71.8 μM) in EPCs, exhibited 92% inhibition of B19V infection in EPCs at 3.32 μM, which can be used as the lead compound in future studies for the treatment of B19V infection caused hematological disorders. Importance B19V encodes a large non-structural protein NS1. Its N-terminal domain (NS1N) consisting of 1-176 amino acids binds to viral DNA and serves as an endonuclease to nick the viral DNA replication origins, which is a pivotal step in rolling hairpin-dependent B19V DNA replication. For high throughput screening (HTS) of anti-B19V antivirals, we miniaturized a fluorescence-based in vitro nicking assay, which employs a fluorophore-labeled probe spanning the trs and the NS1N protein, into a 384-well plate format. The HTS assay showed a high reliability and capability in screening 17,040 compounds. Based on the therapeutic index [half maximal cytotoxic concentration (CC₅₀)/half maximal effective concentration (EC₅₀)] in EPCs, a purine derivative demonstrated an antiviral effect of 92% inhibition of B19V infection in EPCs at 3.32 μM (two times EC₉₀). Our study demonstrated a robust HTS assay for screening antivirals against B19V infection.

Development of a Simple In Vitro Assay To Identify and Evaluate Nucleotide Analogs against SARS-CoV-2 RNA-Dependent RNA Polymerase

Nucleotide analogs targeting viral RNA polymerase have been proved to be an effective strategy for antiviral treatment and are promising antiviral drugs to combat the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. In this study, we developed a robust in vitro nonradioactive primer extension assay to quantitatively evaluate the efficiency of incorporation of nucleotide analogs by SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Our results show that many nucleotide analogs can be incorporated into RNA by SARS-CoV-2 RdRp and that the incorporation of some of them leads to chain termination. The discrimination values of nucleotide analogs over those of natural nucleotides were measured to evaluate the incorporation efficiency of nucleotide analog by SARS-CoV-2 RdRp. In agreement with the data published in the literature, we found that the incorporation efficiency of remdesivir-TP is higher than that of ATP and incorporation of remdesivir-TP caused delayed chain termination, which can be overcome by higher concentrations of the next nucleotide to be incorporated. Our data also showed that the delayed chain termination pattern caused by remdesivir-TP incorporation is different for different template sequences. Multiple incorporations of remdesivir-TP caused chain termination under our assay conditions. Incorporation of sofosbuvir-TP is very low, suggesting that sofosbuvir may not be very effective in treating SARS-CoV-2 infection. As a comparison, 2'-C-methyl-GTP can be incorporated into RNA efficiently, and the derivative of 2'-C-methyl-GTP may have therapeutic application in treating SARS-CoV-2 infection. This report provides a simple screening method that should be useful for evaluating nucleotide-based drugs targeting SARS-CoV-2 RdRp and for studying the mechanism of action of selected nucleotide analogs.

Complex genetic encoding of the hepatitis B virus on-drug persistence

Tenofovir disoproxil fumarate (TDF) is one of the nucleotide analogs capable of inhibiting the reverse transcriptase (RT) activity of HIV and hepatitis B virus (HBV). There is no known HBV resistance to TDF. However, detectable variation in duration of HBV persistence in patients on TDF therapy suggests the existence of genetic mechanisms of on-drug persistence that reduce TDF efficacy for some HBV strains without affording actual resistance. Here, the whole genome of intra-host HBV variants (N = 1,288) was sequenced from patients with rapid (RR, N = 5) and slow response (SR, N = 5) to TDF. Association of HBV genomic and protein polymorphic sites to RR and SR was assessed using phylogenetic analysis and Bayesian network methods. We show that, in difference to resistance to nucleotide analogs, which is mainly associated with few specific mutations in RT, the HBV on-TDF persistence is defined by genetic variations across the entire HBV genome. Analysis of the inferred 3D-structures indicates no difference in affinity of TDF binding by RT encoded by intra-host HBV variants that rapidly decline or persist in presence of TDF. This finding suggests that effectiveness of TDF recognition and binding does not contribute significantly to on-drug persistence. Differences in patterns of genetic associations to TDF response between HBV genotypes B and C and lack of a single pattern of mutations among intra-host variants sensitive to TDF indicate a complex genetic encoding of the trait. We hypothesize that there are many genetic mechanisms of on-drug persistence, which are differentially available to HBV strains. These pervasive mechanisms are insufficient to prevent viral inhibition completely but may contribute significantly to robustness of actual resistance. On-drug persistence may reduce the overall effectiveness of therapy and should be considered for development of more potent drugs.

Efficient Biocatalytic Synthesis of Dihalogenated Purine Nucleoside Analogues Applying Thermodynamic Calculations

The enzymatic synthesis of nucleoside analogues has been shown to be a sustainable and efficient alternative to chemical synthesis routes. In this study, dihalogenated nucleoside analogues were produced by thermostable nucleoside phosphorylases in transglycosylation reactions using uridine or thymidine as sugar donors. Prior to the enzymatic process, ideal maximum product yields were calculated after the determination of equilibrium constants through monitoring the equilibrium conversion in analytical-scale reactions. Equilibrium constants for dihalogenated nucleosides were comparable to known purine nucleosides, ranging between 0.071 and 0.081. To achieve 90% product yield in the enzymatic process, an approximately five-fold excess of sugar donor was needed. Nucleoside analogues were purified by semi-preparative HPLC, and yields of purified product were approximately 50% for all target compounds. To evaluate the impact of halogen atoms in positions 2 and 6 on the antiproliferative activity in leukemic cell lines, the cytotoxic potential of dihalogenated nucleoside analogues was studied in the leukemic cell line HL-60. Interestingly, the inhibition of HL-60 cells with dihalogenated nucleoside analogues was substantially lower than with monohalogenated cladribine, which is known to show high antiproliferative activity. Taken together, we demonstrate that thermodynamic calculations and small-scale experiments can be used to produce nucleoside analogues with high yields and purity on larger scales. The procedure can be used for the generation of new libraries of nucleoside analogues for screening experiments or to replace the chemical synthesis routes of marketed nucleoside drugs by enzymatic processes.

Identification of Structural and Molecular Features Involved in the Transport of 3'-Deoxy-Nucleoside Analogs by Human Equilibrative Nucleoside Transporter 3

Combination antiretroviral drug treatments depend on 3'-deoxy-nucleoside analogs such as 3'-azido-3'-deoxythymidine (AZT) and 2'3'-dideoxyinosine (DDI). Despite being effective in inhibiting human immunodeficiency virus replication, these drugs produce a range of toxicities, including myopathy, pancreatitis, neuropathy, and lactic acidosis, that are generally considered as sequelae to mitochondrial damage. Although cell surface-localized nucleoside transporters, such as human equilibrative nucleoside transporter 2 (hENT2) and human concentrative nucleoside transporter 1 (hCNT1), are known to increase the carrier-mediated uptake of 3'-deoxy-nucleoside analogs into cells, another ubiquitously expressed intracellular nucleoside transporter (namely, hENT3) has been implicated in the mitochondrial transport of 3'-deoxy-nucleoside analogs. Using site-directed mutagenesis, generation of chimeric hENTs, and 3H-permeant flux measurements in mutant/chimeric RNA-injected Xenopus oocytes, here we identified the molecular determinants of hENT3 that dictate membrane translocation of 3'-deoxy-nucleoside analogs. Our findings demonstrated that whereas hENT1 had no significant transport activity toward 3'-deoxy-nucleoside analogs, hENT3 was capable of transporting 3'-deoxy-nucleoside analogs similar to hENT2. Transport analyses of hENT3-hENT1 chimeric constructs demonstrated that the N-terminal half of hENT3 is primarily responsible for the hENT3-3'-deoxy-nucleoside analog interaction. In addition, mutagenic studies identified that 225D and 231L in the N-terminal half of hENT3 partially contribute to the ability of hENT3 to transport AZT and DDI. The identification of the transporter segment and amino acid residues that are important in hENT3 transport of 3'-deoxy-nucleoside analogs may present a possible mechanism for overcoming the adverse toxicities associated with 3'-deoxy-nucleoside analog treatment and may guide rational development of novel nucleoside analogs.

Effects of BMS-986094, a Guanosine Nucleotide Analogue, on Mitochondrial DNA Synthesis and Function

BMS-986094, the prodrug of a guanosine nucleotide analogue (2'-C-methylguanosine), was withdrawn from clinical trials due to serious safety issues. Nonclinical investigative studies were conducted as a follow up to evaluate the potential for BMS-986094-related mitochondrial-toxicity. In vitro, BMS-986094 was applied to human hepatoma cells (HepG2 and Huh-7) or cardiomyocytes (hiPSCM) up to 19 days to assess mitochondrial DNA content and specific gene expression. There were no mitochondrial DNA changes at concentrations ≤10 µM. Transcriptional effects, such as reductions in Huh-7 MT-ND1 and MT-ND5 mRNA content and hiPSCM MT-ND1, MT-COXII, and POLRMT protein expression levels, occurred only at cytotoxic concentrations (≥10 µM) suggesting these transcriptional effects were a consequence of the observed toxicity. Additionally, BMS-986094 has a selective weak affinity for inhibition of RNA polymerases as opposed to DNA polymerases. In vivo, BMS-986094 was given orally to cynomolgus monkeys for 3 weeks or 1 month at doses of 15 or 30 mg/kg/day. Samples of heart and kidney were collected for assessment of mitochondrial respiration, mitochondrial DNA content, and levels of high energy substrates. Although pronounced cardiac and renal toxicities were observed in some monkeys at 30 mg/kg/day treated for 3-4 weeks, there were no changes in mitochondrial DNA content or ATP/GTP levels. Collectively, these data suggest that BMS-986094 is not a direct mitochondrial toxicant.

Clinical study on prevention of HBV re-infection by entecavir after liver transplantation

PURPOSE

This aims to evaluate the effects of lamivudine (LAM) and entecavir (ETV) in preventing hepatitis B virus (HBV) re-infection after liver transplantation (LT).

METHODS

A retrospective matched case-control method was used in this study. From June 2005 to May 2007, the patients who received LAM (100 mg qd) or ETV (0.5 mg qd) were chosen. The LAM and ETV groups were matched using a 3:1 ratio based on the factors, such as age, gender, LAM or ETV antiviral duration, primary disease, and HBV DNA levels at the initiation of antiviral therapy. Data on serum HBV markers, HBV DNA, and cumulative recurrence were collected.

RESULTS

Two hundred and fifty-two patients were enrolled. The average duration of follow-up was 38.5 and 41.2 months (LAM and ETV groups) (p>0.05). Duration of pre-operative antiviral therapy was 30.3 and 25.8 d (LAM and ETV groups) (p>0.05). The HBV DNA level decreased from 3.89×10(6) to 5.31×10(5) copies/mL before LT in the LAM group, and decreased from 8.74×10(6) to 5.49×10(4) copies/mL in the ETV group (p<0.05). Eighteen patients in LAM group developed HBV re-infection and 0 in ETV group.

CONCLUSION

ETV is superior to LAM for preventing HBV re-infection following LT.

Artificial recombinant cell-penetrating peptides interfere with envelopment of hepatitis B virus nucleocapsid and viral production

Hepatitis B virus (HBV) is a major human infectious pathogen, with over 300 million chronically infected patients worldwide. Current therapeutics for chronic HBV infection have shown only limited success. The plasma membrane represents an impermeable barrier for development of most macromolecular antiviral agents. To develop new anti-HBV macromolecules that can cross the membrane barrier, we designed a series of artificial recombinant peptides including cell penetrating sequence oligoarginine R7 and several nucleocapsid binding subunits (NBS). The anti-HBV function of these peptides was evaluated in a HBV DNA replicative cell line HepG2.2.15. Our results showed that the synthetic recombinant cell penetrating peptides retained the activity of cell penetrating in the living cells. HBV DNA in culture medium markedly decreased in cells treated with cell penetrating peptides bearing NBS for three days. Intracellular HBcAg and HBV DNA replicative intermediates increased by 2-3 fold. In conclusion, the synthetic recombinant cell penetrating peptides bearing NBS can efficiently enter into the cells; block nucleocapsid assembly and inhibit HBV release. Cell penetrating subunit presents a high efficiency tool to deliver synthetic antiviral peptides into cells.

Prevalence of lamivudine-resistant hepatitis B virus strains in patients with acute hepatitis B virus infection

AIM: To investigate the prevalence of lamivudine-resistant hepatitis B virus (HBV) strains (YIDD/YVDD variants) in patients with acute HBV infection (AHB).

METHODS: A total of 321 patients with HBV infection (HBV DNA ≥ 1.0 × 10⁷ copies/L) were included in the study, of which 100 had AHB and underwent no treatment, and 221 had chronic HBV infection (CHB) and were treated with lamivudine (100 mg/d). Serum specimens were taken from these patients and used to identify wild-type and YMDD motif mutant HBV strains by fluorescent hybridization biprobe-based polymerase chain reaction (PCR) and melting curve assay (FH-PCR-MC).

RESULTS: Only wild-type HBV was detected in patients with AHB (YMDD, 100%). Both wild-type and YMDD motif mutant HBV strains were detected in patients with CHB. The YMDD mutation rate in CHB patients was 63.4%. Of all YMDD mutations detected, YIDD variant accounted for 52.1%, YVDD variant 37.9%, and the mixed type (YIDD + YVDD) 10.0%. The YMDD mutation rates in CHB patients treated with lamivudine for < 1 year, 1-2 years, 2-3 years, 3-4 years and > 4 years were 45%, 66%, 77%, 75% and 40%, respectively. There was a significant difference in the YMDD mutation rate between the two groups of patients (χ² = 112.3, P = 0.00).

CONCLUSION: Lamivudine-resistant HBV strains are not detected in patients with acute HBV infection.

Recurrent viral liver disease (hepatitis B and C) after liver transplantation

Hepatitis C represents more than 35% of liver transplant candidates worldwide. Meanwhile, hepatitis B continues to be an important cause of end-stage liver disease and hepatocellular carcinoma in Asia and Africa. Recurrent viral liver disease is a significant event after liver transplantation and continues to be one of the main causes of graft dysfunction and loss in the middle and long-term follow-up. Mechanisms of liver reinfection and disease recurrence vary between these two viruses and pre-emptive as well as the therapeutic approaches are different. Hepatitis B patients can be managed with immune globulin immediately after liver transplant and various agents such as nucleotide and nucleoside analogues can be associated. As a result, disease recurrence has been delayed or prevented in these patients. Individuals transplanted for hepatitis C are known to have universal reinfection and a high rate of disease recurrence has been reported in the literature. Strategies to treat hepatitis C recurrence are limited to the use of pegylated interferon and ribavirin when disease is demonstrated histologically and biochemically, although other strategies have been described with limited or no success. We herein review the mechanisms of disease recurrence and the current as well as the future therapeutic approaches to prevent and to treat these diseases.

Targets of emerging therapies for viral hepatitis B and C

Viral hepatitis B and C, structurally two completely different viruses, commonly infect human hepatocytes and cause similar clinical manifestations. Since their discovery, IFN has been a pillar in the treatment. However, because of the different natures of the viruses, therapeutic approaches diverge and new treatment targets are tailored specifically for each virus. Herein, the authors analyse therapeutic approaches for hepatitis B virus (HBV) and hepatitis C virus (HCV) and focus on emerging concepts that are under clinical evaluation. In particular, promising viral inhibitors for HBV and HCV are reviewed and the current status of research for gene therapy for HCV is described. Immune therapy is a fast-moving field with fascinating results which include therapeutic vaccines and toll-like receptor agonists that could improve tomorrow's treatment approaches.

Correlation of hepatitis B virus YMDD mutations with the polymorphism of HLA alleles in patients with chronic hepatitis B virus infection

AIM: To investigate the relationship between HBV YMDD mutations and the polymorphism of human leukocyte antigen (HLA) alleles in patients with chronic hepatitis B virus (HBV) infection.

METHODS: Fluorescent hybridization biprobe PCR and melting curve assay (FH-PCR-MC) was used to determine HBV YMDD mutations in serum specimens from 142 patients with chronic HBV infection. HLA-A, B, and DRB1 alleles in peripheral blood mononuclear cells (PBMCs) were detected by polymerase chain reaction-sequence specific primer (PCR-SSP). The PBMCs were collected from 56 of the 142 patients.

RESULTS: YMDD mutations occurred in 56.3% of the 142 patients who received lumivudine treatment. The frequencies of HLA-B*58 and DRB1*03 alleles were significantly lower in YMDD mutation group in comparison with those in YMDD wild group (0.013 vs 0.094, P = 0.036; 0.000 vs 0.063, P = 0.024). The frequency of HLA-A*30 allele was markedly higher in YIDD group than that in YVDD group (0.158 vs 0.024, P = 0.034), while the frequency of HLA-A*33 allele was lower in YIDD group ( 0.119vs 0.000, P = 0.028).

CONCLUSION: YMDD mutation is associated with the polymorphism of HLA alleles in patients with chronic hepatitis B. Individuals with HLA-B*58 and DRB1*03 alleles may have resistance to YMDD mutation. Patients with HLA-A*30 allele may have a susceptibility to YIDD mutation, and those with HLA-A*33 allele are susceptible to YVDD mutation.

Emerging therapeutics for chronic hepatitis B

Hepatitis B is a global health problem. Patients with chronic hepatitis B (CHB) carry a significant risk to eventually develop cirrhotic liver disease. Recent therapeutic advances against CHB offer excellent potential for long-term suppression of hepatitis B virus (HBV) replication during antiviral therapy, and occasionally a durable remission off medication. Selection of appropriate patients for antiviral therapy depends on identification of HBV replication and an elevated alanine aminotransferase level or histologic liver injury. Pegylated interferon alpha offers potent immunomodulatory and antiviral activity with the potential for durability, but also with adverse effects and significant cost. The nucleoside or nucleotide analogs, lamivudine, adefovir, and entecavir, suppress HBV replication and are extremely well-tolerated, but long-term or even lifelong therapy is required. Most experience has been gained with lamivudine, but viral resistance occurs frequently. Newer analogs appear to be relatively free of this problem. Approaches using a combination of agents have promise, but have yet to be proven superior to individual drugs alone.

Managing hepatitis B coinfection in HIV-infected patients

Since viral hepatitis is one of the most common causes of morbidity and mortality in HIV, it is critical to recognize and treat these patients appropriately. Hepatitis B infection is particularly difficult to manage as it changes with shifts in immune status. Inactive infection may flare up with restoration of CD4 cell count. In addition, many drugs used to treat HIV are also active against hepatitis B. Thus, patients may require therapy for both diseases or only for hepatitis B. The practicing physician must be aware of which drug to use with antiretrovirals and which can be used for hepatitis B alone. Current therapies for HIV that have hepatitis B activity include lamivudine, emtricitabine, and tenofovir. Therapies for hepatitis B without HIV activity are adefovir and entecavir. The major advances in the past year include emerging data on epidemiology, occult infection, genotypes, and newer therapies. Long-term management of hepatitis B includes monitoring for hepatocellular carcinoma. Two recent consensus conferences have provided excellent reviews of management of coinfection .

Evaluation of fluorescent hybridization biprobe PCR and melting curve assay

AIM: To evaluate a fluorescent hybridization biprobe PCR and melting curve assay for detection of (hepatitis B virus) YMDD mutation associated with lamivudine therapy.

METHODS: HBV DNA and YMDD mutations in the 217 clinical serum specimens from patients with chronic HBV infection who were treated with lamivudine (100 mg/d) were detected by the fluorescence quantitative polymerase chain reaction (PCR) using TaqMan probe (FT-PCR) and the fluorescent hybridization biprobe PCR and melting curve assay (FH-PCR-MC), respectively. Seventy-eight positive sera were then genotyped by nested PCR with six pairs of HBV genotype-specific primes (A to F), and the cloned DNA fragments derived from conventional PCR of HBV YMDD of 30 positive sera were sequenced.

RESULTS: Among 217 samples, 75.6%(164/217) were HBV DNA positive, and 67.7% (147/217) were HBV YMDD positive, including YMDD 44.9%(66/147), YIDD 22.5%(33/147),YVDD 17.7%(26/147),YI/VDD 10.9%(16/147), and others 4.0%(6/147). In HBV DNA≥10⁷copies/L, all the positive and mutant rates of YMDD have no significant difference in different HBV DNA levels. Among 78 genotype samples (genotype C 89.8%, B 8.9% and D 1.3%), the positive and mutant rates of YMDD were 100%(78/78) and 58.97%(46/78) respectively. One genotype D was YIDD/YVDD. The mutant rates of YMDD in genotype B and C were 71.4% and 55.7% respectively, but have no marked difference (P >0.5). Using the results by DNA sequencing as reference standard, the relative specificity, sensitivity and over-all accordance of FH-PCR-MC were 96.3% (26/27), 100% (3/3) and 96.7% (29/30) respectively. The results of YMDD typing by FH-PCR-MC were confirmed by the sequencing of clones.

CONCLUSION: The fluorescent hybridization biprobe PCR and melting curve assay kit in detection of HBV YMDD mutation has high sensitivity and specificity. It is a convenient and rapid test kit, and may be used in YMDD genotyping.

A Practical Approach to Management of Chronic Hepatitis B

Chronic hepatitis B (CHB) is one of the important public health problems worldwide. Major advances have been made in the treatment of CHB during the past several years. This article systemically reviews advances in the application of HBV DNA quantitation and three approved drugs for HBV treatment, and presents an updated and practical clinical approach to managing CHB. Highly sensitive PCR-based quantitation of HBV DNA makes it possible to precisely determine pre-treatment HBV load and monitor HBV DNA response during treatment. HBV DNA level, HBeAg status, degree of hepatic histological activity and fibrosis, and serum transaminases are the most important parameters in determining indication, regimen, and duration of HBV treatment. Although interferon alfa-2b, lamivudine, and adefovir are all approved as initial HBV treatment, understanding the advantages and advantages of each agent is important in choosing the best treatment for each individual patient with CHB.