Polyphenols as Potential Inhibitors of SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp)

An increasing number of studies have demonstrated the antiviral nature of polyphenols, and many polyphenols have been proposed to inhibit SARS-CoV or SARS-CoV-2. Our previous study revealed the inhibitory mechanisms of polyphenols against DNA polymerase α and HIV reverse transcriptase to show that polyphenols can block DNA elongation by competing with the incoming NTPs. Here we applied computational approaches to examine if some polyphenols can also inhibit RNA polymerase (RdRp) in SARS-CoV-2, and we identified some better candidates than remdesivir, the FDA-approved drug against RdRp, in terms of estimated binding affinities. The proposed compounds will be further examined to develop new treatments for COVID-19.

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 human immunodeficiency virus (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 (RT) enzyme. Here, we introduce a probabilistic predictive 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 (TFV-DP), emtricitabine triphosphate (FTC-TP), and azidothymidine triphosphate (AZT-TP) with agreement between experiment and theory. RESTRICT represents a new class of activity-based assays for therapeutic drug monitoring and precision dosing in HIV care and could be extended to other diseases treated with nucleotide analogs.

An Overview of the Cure of HIV/AIDS Harbal Therapy Containing Natural Antioxidant, Vitamins and Minerals

Purposes: The unprecedented and sequence through which an estimate of 25 million lives have gone to their early grave yard through Acquired Immune-deficiency Syndrome HIV/AIDS can never be quantified; since, when it was first describes in 1981. In 2017/2018 by (UNAIDS) it was estimated globally for about 36.9millions people were living with Human, Immunodeficiency Virus (HIV) so to say. Henceforth the progress made in the field of treatment in the form of Antiretroviral Therapy (ART) disease has not been fully ascertain for the cure of HIV/AIDS; except, perpetual clinical suppressions. Thus, the current challenges that man kinds faces with the used of perpetual intake of antiretroviral therapy (clinical suppression)/artificial vaccine is un-justifiable. However, search for HIV therapy have open a new chapter in the search for novel drugs from Kaduna Polytechnic procedure. This review focuses on vitamins, antioxidant, mineral and supplement as sources of in-hibitors or eradications for human immunodeficiency virus type-1 (HIV) reverse transcriptase. Objective: To assess whether vitamins, antioxidant, minerals supplement are effective and safe in eradicating mortality and morbidity among populace with HIV infection. Selection criteria: Randomized control trials were selected that compared the effect of vitamins (A, C, D, E, K,), antioxidant, minerals and supplement with regard to treatment measures in HIV infected persons. Methods: To prevent authors bias, based on a systematic search of literature; anti-HIV reverse transcriptase activity of some plant’s species like those of Eucalyptus leaves, Garlic fresh fruits, Baobab leaves, aloe vera, neem leaves, moringa leaves, bitter leaves etc. respectively. Thus, these medicinal plants contain an appreciable or above values antioxidant compound or photochemical like those of Phenolic, anthraquinone, tannin, falconoid, terpenoid, lignin, coumarins etc. respectively. Contrarywise, these phytochemical compounds have been exploited traditionally for the cure of many diseases as well as inhibition of viral replication/transcription. Further investigations have shared more light through which phytochemicals compounds inhibit virus replication either during the viral entry inside the host cell or during their replication. Originality: in view of the current investigation or to accelerate drug discovery and innovation, this review recommends the urgent need to tap into the enrich locally available endogenous knowledge of putative anti- HIV/AIDS, photochemical and their derivatives, (reverse pharmacology, determine pan assay, interferences compounds, microbial enzyme metabolites relationship and their mechanisms to treat virial diseases.

Anti-HIV reverse transcriptase plant polyphenolic natural products with in silico inhibitory properties on seven non-structural proteins vital in SARS-CoV-2 pathogenesis

Background Accessing COVID-19 vaccines is a challenge despite successful clinical trials. This burdens the COVID-19 treatment gap, thereby requiring accelerated discovery of anti-SARS-CoV-2 agents. This study explored the potential of anti-HIV reverse transcriptase (RT) phytochemicals as inhibitors of SARS-CoV-2 non-structural proteins (nsps) by targeting in silico key sites in the structures of SARS-CoV-2 nsps. One hundred four anti-HIV phytochemicals were subjected to molecular docking with nsp3, 5, 10, 12, 13, 15, and 16. Top compounds in complex with the nsps were investigated further through molecular dynamics. The drug-likeness and ADME (absorption, distribution, metabolism, and excretion) properties of the top compounds were also predicted using SwissADME. Their toxicity was likewise determined using OSIRIS Property Explorer. Results Among the top-scoring compounds, the polyphenolic functionalized natural products comprised of biflavones 1, 4, 11, 13, 14, 15; ellagitannin 9; and bisisoquinoline alkaloid 19 were multi-targeting and exhibited strongest binding affinities to at least two nsps (binding energy = − 7.7 to − 10.8 kcal/mol). The top ligands were stable in complex with their target nsps as determined by molecular dynamics. Several top-binding compounds were computationally druggable, showed good gastrointestinal absorptive property, and were also predicted to be non-toxic. Conclusions Twenty anti-HIV RT phytochemicals showed multi-targeting inhibitory potential against SARS-CoV-2 non-structural proteins 3, 5, 10, 12, 13, 15, and 16. Our results highlight the importance of polyhydroxylated aromatic substructures for effective attachment in the binding/catalytic sites of nsps involved in post-translational mechanism pathways. As such with the nsps playing vital roles in viral pathogenesis, our findings provide inspiration for the design and discovery of novel anti-COVID-19 drug prototypes.

Sensitive Detection of Site-wise Convergent Evolution in Large Protein Alignments with ConDor

Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and the changes observed at these different levels tend to be strongly correlated. Here we propose a simulation-based method to detect positions under convergent evolution in large protein alignments, without prior knowledge on the phenotype and environmental constraints. A phylogeny is inferred from the data and used in simulations to estimate the expected number of amino-acid changes in stable evolutionary constraints (null model) for each position. Similarly, we count the number of mutations towards the same amino acid in the data and test if they are occurring more often than expected. We applied our method to two real datasets: HIV reverse transcriptase and fish rhodopsin, and to HIV-like simulated data. On the latter, with known convergent events and substitution model, we detected on average two third of these events, with a low fraction of false positives. With HIV data, one knows that drug resistance mutations (DRMs) are convergent. Even without any knowledge of patient treatment status, we retrieved more than 70% of positions corresponding to known DRMs. On the rhodopsin dataset, four substitutions are supposed to be convergent, as they change the maximum wavelength absorption of the photoreceptor and occurred several times independently during evolution. We detected three of them. These results demonstrate the potential of the method to target specific mutations to be further studied experimentally or, for example, using a nonsynonymous/synonymous rate ratio approach. Our software named ConDor is available at http://condor.pasteur.cloud.

Exploring New Scaffolds for the Dual Inhibition of HIV-1 RT Polymerase and Ribonuclease Associated Functions

Current therapeutic protocols for the treatment of HIV infection consist of the combination of diverse anti-retroviral drugs in order to reduce the selection of resistant mutants and to allow for the use of lower doses of each single agent to reduce toxicity. However, avoiding drugs interactions and patient compliance are issues not fully accomplished so far. Pursuing on our investigation on potential anti HIV multi-target agents we have designed and synthesized a small library of biphenylhydrazo 4-arylthiazoles derivatives and evaluated to investigate the ability of the new derivatives to simultaneously inhibit both associated functions of HIV reverse transcriptase. All compounds were active towards the two functions, although at different concentrations. The substitution pattern on the biphenyl moiety appears relevant to determine the activity. In particular, compound 2-{3-[(2-{4-[4-(hydroxynitroso)phenyl]-1,3-thiazol-2-yl} hydrazin-1-ylidene) methyl]-4-methoxyphenyl} benzamide bromide (EMAC2063) was the most potent towards RNaseH (IC50 = 4.5 mM)- and RDDP (IC50 = 8.0 mM) HIV RT-associated functions.

Exploring the anti-HIV-1 reverse transcriptase, anti-inflammatory, anti-cancer activities and cytotoxicity of two fermented commercial herbal concoctions sold in Limpopo Province of South Africa

Background and objectives The use of herbal concoctions is very popular in South Africa, including Limpopo Province. The herbal concoctions are claimed to be capable of treating numerous illnesses such as ulcers, cancer, HIV/AIDS, diabetes, certain STDs, blood cleansing to mention but a few. The focus of this study was to evaluate the anti-HIV 1 reverse transcriptase, anti-inflammatory and anti-cancerous activities as well as cytotoxic effects of 2 fermented herbal concoctions used for the treatment of the related ailments in Limpopo province of South Africa. Method Two fermented herbal concoctions obtained from a herbalist in Polokwane were extracted with 80% acetone. The anti-HIV activity of the herbal concoctions was determined using the anti-HIV reverse transcriptase assay. The anti-cancer and cytotoxic effects of the herbal concoctions were evaluated using cancerous Human Colon (HT-29) cells and the normal human Hepatoma cells (C3A) respectively. Results Notable anti-HIV reverse transcriptase activity was observed from the 80% acetone fraction of herbal concoction 1 (IC50 38.031 μg/mL) which exhibited better activity than the positive control Lamivudine (IC50 40.90 μg/mL). There was variation in the anti-inflammation activity as determined by the sPL2, 15-LOX and COX enzyme assays. The only concerning matter was the high COX-1 activity in some of the extracts, which is not desirable due to the mucosal protection action of COX-1 enzyme. The herbal concoctions did not exhibit cytotoxic effects on normal human cells, however, toxicity against cancerous cells was observed. Conclusion The herbal concoctions displayed some considerable pharmacological effects against various ailments as claimed by the herbalist. More work to ascertain the toxicity of both concoctions against cancerous cells need to be followed as this could lead to the discovery of anticancer drugs.

Pilot evaluation of an enzymatic assay for rapid measurement of antiretroviral drug concentrations

Objective Maintaining adequate drug adherence is crucial to ensure the HIV prevention benefits of pre-exposure prophylaxis (PrEP). We developed an enzymatic assay for rapidly measuring tenofovir-diphosphate (TFV-DP) concentrations—a metabolite that indicates long-term PrEP adherence. Setting The study was conducted at the Madison HIV Clinic at Harborview Medical Center in Seattle. Methods We enrolled adults receiving standard oral PrEP, and individuals not receiving any antiretrovirals. We measured TFV-DP concentrations in diluted whole blood using our novel REverSe TRanscrIptase Chain Termination (RESTRICT) assay, based on inhibition of HIV reverse transcriptase (RT) enzyme. Blood samples were diluted in water, DNA templates, nucleotides, RT, and intercalating dye added, and results measured with a fluorescence reader—stronger fluorescence indicated higher RT activity. We compared RESTRICT assay results to TFV-DP concentrations from matched dried blood spot samples measured by liquid chromatography tandem mass spectrometry (LC–MS/MS) using ≥ 700 fmol/punch TFV-DP as a threshold for adequate adherence (≥ 4 doses/week). Results Among 18 adults enrolled, 4 of 7 participants receiving PrEP had TFV-DP levels ≥ 700 fmol/punch by LC–MS/MS. RESTRICT fluorescence correlated with LC–MS/MS measurements (r = − 0.845, p < 0.0001). Median fluorescence was 93.3 (95% confidence interval [CI] 90.9 to 114) for samples < 700 fmol/punch and 54.4 (CI 38.0 to 72.0) for samples ≥ 700 fmol/punch. When calibrated to an a priori defined threshold of 82.7, RESTRICT distinguished both groups with 100% sensitivity and 92.9% specificity. Conclusions This novel enzymatic assay for measuring HIV reverse transcriptase activity may be suitable for distinguishing TFV-DP concentrations in blood that correspond to protective PrEP adherence.