Structure of Essential RNA Regulatory Elements in the West Nile Virus 3'-Terminal Stem Loop.

Flaviviruses, such as West Nile and Dengue Virus, pose a significant and growing threat to global health. Central to the flavivirus life cycle are highly structured 5'- and 3'-untranslated regions (UTRs), which harbor conserved cis-acting RNA elements critical for viral replication and host adaptation. Despite their essential roles, detailed molecular insights into these RNA elements have been limited.

Drug-Like Small Molecules That Inhibit Expression of the Oncogenic MicroRNA-21.

We report the discovery of drug-like small molecules that bind specifically to the precursor of the oncogenic and pro-inflammatory microRNA-21 with mid-nanomolar affinity. The small molecules target a local structure at the Dicer cleavage site and induce distinctive structural changes in the RNA, which correlate with specific inhibition of miRNA processing. Structurally conservative single nucleotide substitutions eliminate the conformational change induced by the small molecules, which is also not observed in other miRNA precursors.

CRISPR/Cas9: a tool to eradicate HIV-1.

The development of antiretroviral therapy (ART) has been effective in suppressing HIV replication. However, severe drug toxicities due to the therapy and its failure in targeting the integrated proviral genome have led to the introduction of a new paradigm of gene-based therapies. With its effective inhibition and high precision, clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein-9 nuclease (Cas9) or CRISPR/Cas9 has emerged as an effective genome editing tool in the last decade.

Preferential solvation of carbohydrates in water-trifluoroethanol mixtures: a solvent detected heteronuclear NMR approach.

The present study aims to establish a simple approach involving multi-field multinuclear longitudinal relaxation (R1) analysis of the solvents to decipher solute-solvent interactions during the solvation of model carbohydrates in aqueous trifluoroethanol (TFE) co-solvent systems (TFE:D2O). The behavior of D2O and TFE is monitored around β-CD (β-cyclodextrin) and glucose through R1D (2H) and R1F (19F), respectively. Correlation times (τc) are estimated for D2O and TFE for various % (v/v) compositions of TFE:D2O mixtures.

Solution-state NMR evaluation of molecular interaction between monoaromatic carboxylic acids and dissolved humic acid.

Understanding the nature of interactions between the aromatic organic pollutants with dissolved humic acid (HA) is fundamental for the prediction of their environmental fate and subsequent development of efficient remediation methods. The present study employs solution-state H/F NMR methods to investigate the non-covalent interaction between aqueous peat humic acid (Aldrich HA) and monoaromatic carboxylic acids (CA), viz., 2, 6 diflourobenzoic acid (DFBA) and its non-fluorinated analog, benzoic acid (BA).

Assessment of the Role of 2,2,2-Trifluoroethanol Solvent Dynamics in Inducing Conformational Transitions in Melittin: An Approach with Solvent F Low-Field NMR Relaxation and Overhauser Dynamic Nuclear Polarization Studies.

2,2,2-Trifluoroethanol (TFE) is one of the fluoroalcohols that have been known to induce and stabilize an open helical structure in many proteins and peptides. The current study has benchmarked low-field F NMR relaxation and F Overhauser dynamic nuclear polarization (ODNP) by providing a brief account of TFE solvent dynamics in a model melittin (MLT, an antimicrobial peptide) solution with a TFE-DO cosolvent mixture at pH 7.4.

Mitochondrial dysfunctions in HIV infection and antiviral drug treatment.

: With the introduction of highly active anti-retroviral therapy (HAART), treatment of HIV infection has improved radically, shifting the concept of HIV disease from a highly mortal epidemic to a chronic illness which needs systematic management. However, HAART does not target the integrated proviral DNA. Hence, prolonged use of antiviral drugs is needed for sustaining life.

Endoplasmic reticulum stress leads to mitochondria-mediated apoptosis in cells treated with anti-HIV protease inhibitor ritonavir.

Background And Aims: Endoplasmic reticulum (ER) stress is a growing concern for drug-induced toxicity which causes several side effects. Ritonavir, a potent HIV protease inhibitor, induces both ER and mitochondrial stress; however, the missing link between ER stress and mitochondrial damage has been unknown. In the present study, we have studied the sequential events that occur during ritonavir-induced cell cytotoxicity and elucidate the link between ER stress and mitochondrial damage.

Expression of Duplex shRNAs through a Lentiviral Vector against Cellular and Viral Genes Inflicts Sustained Inhibition of Hepatitis C Virus Replication.

Background: The RNAi-based transient therapeutic approach has been well explored for its potential against the hepatitis V virus (HCV). However, to achieve a sustained virological response, a consistent presence of siRNA is needed and it can be achieved by constitutively expressing shRNAs. In this context, the lentiviral vector has emerged as an attractive tool for shRNA delivery against HCV.

Binding Interaction of Organofluorine-Serum Albumin: A Comparative Ligand-Detected F NMR Analysis.

In the present study, we attempt to characterize fluorinated ligand-serum albumin interaction in solution by a set of one-dimensional F ligand-based experiments. In this regard, a model system diflunisal (DFL)-human serum albumin (HSA) has been chosen to benchmark the utility of F relaxation and diffusion-based experiments in deciphering ligand-protein interactions. Further, we extend the application of a similar set of F experiments to unravel the molecular interaction in an unexplored system of 2,6-difluorobenzoic acid (DFBA)-bovine serum albumin (BSA).

Novel Uridine Glycoconjugates, Derivatives of 4-Aminophenyl 1-Thioglycosides, as Potential Antiviral Compounds.

A novel series of uridine glycoconjugates, derivatives of 4-aminophenyl 1-thioglycosides, was designed and synthesized. All compounds were evaluated in vitro for their antiviral activity against hepatitis C virus (HCV) and classical swine fever virus (CSFV), two important human and animal viral pathogens for which new or improved therapeutic options are needed. The antiviral activity of all synthesized compounds was confirmed using pseudo-plaque reduction assays in which a significant arrest of CSFV and HCV growth was observed in the presence of these compounds.

Role of biofilm morphology, matrix content and surface hydrophobicity in the biofilm-forming capacity of various species.

The present study aimed to evaluate the role of biofilm morphology, matrix content and surface hydrophobicity in the biofilm-forming capacity of and non- (NAC) spp. Biofilm formation was determined by microtitre plate assay and bright-field and scanning electron microscopy. The matrix carbohydrates, proteins and e-DNA were quantified by phenol-sulfuric acid, bicinchoninic acid and UV spectroscopy, respectively.

Novel thioglycosyl analogs of glycosyltransferase substrates as antiviral compounds against classical swine fever virus and hepatitis C virus.

Hepatitis C virus (HCV) and classical swine fever virus (CSFV) are important pathogens for which new therapeutic approaches are in high demand. Herein, we report the synthesis of newly designed thioglycosyl analogs of glycosyltransferase substrates which were evaluated using cell-based assays for cytotoxicity and antiviral activity against both viruses. The antiviral activity of synthesized compounds against CSFV and HCV was confirmed using pseudo-plaque reduction assays where a significant arrest of viral growth was observed in the presence of selected compounds.

Solvent-dependent binding interactions of the organophosphate pesticide, chlorpyrifos (CPF), and its metabolite, 3,5,6-trichloro-2-pyridinol (TCPy), with Bovine Serum Albumin (BSA): A comparative fluorescence quenching analysis.

Analysis of the interaction of pesticides and their metabolites with the cellular proteins has drawn considerable attention in past several years to understand the effect of pesticides on environment and mankind. In this study, we have investigated the binding interaction of Bovine Serum Albumin (BSA) with a widely used organophosphorous insecticide chlorpyrifos (CPF), and its stable metabolite, 3,5,6-trichloro-2-pyridinol (TCPy) to provide a comparative analysis of the two molecules by employing various spectroscopic techniques viz., UV-vis absorption, Circular Dichroism (CD), and Fluorescence spectroscopy.

Anti-HCV Activity from Semi-purified Methanolic Root Extracts of Valeriana wallichii.

Hepatitis C virus (HCV) is a serious global health problem affecting approximately 130-150 million individuals. Presently available direct-acting anti-HCV drugs have higher barriers to resistance and also improved success rate; however, cost concerns limit their utilization, especially in developing countries like India. Therefore, development of additional agents to combat HCV infection is needed.

Depolarization of mitochondrial membrane potential is the initial event in non-nucleoside reverse transcriptase inhibitor efavirenz induced cytotoxicity.

Efavirenz is a non-nucleoside reverse transcriptase inhibitor (NNRTI) and an active constituent of the highly active antiretroviral therapy regime. It has significantly contributed in control and management of human immunodeficiency virus propagation. However, EFV administration has also led to severe adverse effects, several reports highlighted the role of EFV in mitochondrial dysfunction and toxicity but the molecular mechanism has been poorly understood.

Combinations of siRNAs against La Autoantigen with NS5B or hVAP-A Have Additive Effect on Inhibition of HCV Replication.

Hepatitis C virus is major cause of chronic liver diseases such as chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Presently available direct-acting antiviral drugs have improved success rate; however, high cost limits their utilization, especially in developing countries like India. In the present study, we evaluated anti-HCV potential of several siRNAs targeted against the HCV RNA-dependent RNA polymerase NS5B and cellular factors, La autoantigen, PSMA7, and human VAMP-associated protein to intercept different steps of viral life cycle.

P-Cl bond-induced lactamization of 2(2'-hydroxyl)phenyloxazoline to form a cyclic phosphinite, 3-(2-chloroethyl)-2-phenyl-2H-benzo[e][1,3,2]oxaza-phosphinin-4(3H)-one: synthesis, structural studies and transition metal complexes.

The equimolar reaction between 2(2'-hydroxy)phenyloxazoline (1) and PPhCl2 in the presence of triethylamine afforded an unexpected cyclic product, phenyl-benzo-oxazaphosphininone (2), instead of a simple phosphinite derivative A. A similar reaction between 1 and PPhCl2 in 2 : 1 ratio also yielded the same product 2, but with one equivalent of 2(2'-hydroxy)phenyloxazoline (1) left unreacted. The formation of the cyclic product 2 is due to the P-Cl bond induced oxazoline ring opening followed by the formation of a six-membered γ-lactam type product, 3-(2-chloroethyl)-2-phenyl-2H-benzo[e][1,3,2]oxazaphosphinin-4(3H)-one (2 also referred to as L).

Prospects for antisense peptide nucleic acid (PNA) therapies for HIV.

Since the discovery and synthesis of a novel DNA mimic, peptide nucleic acid (PNA) in 1991, PNAs have attracted tremendous interest and have shown great promise as potential antisense drugs. They have been used extensively as tools for specific modulation of gene expression by targeting translation or transcription processes. This review discusses the present and future therapeutic potential of this class of compound as anti-HIV-1 drugs.

Pharmacokinetic analysis of polyamide nucleic-acid-cell penetrating peptide conjugates targeted against HIV-1 transactivation response element.

We have demonstrated that polyamide nucleic acids complementary to the transactivation response (TAR) element of HIV-1 LTR inhibit HIV-1 production when transfected in HIV-1 infected cells. We have further shown that anti-TAR PNA (PNA(TAR)) conjugated with cell-penetrating peptide (CPP) is rapidly taken up by cells and exhibits strong antiviral and anti-HIV-1 virucidal activities. Here, we pharmacokinetically analyzed (125)I-labeled PNA(TAR) conjugated with two CPPs: a 16-mer penetratin derived from antennapedia and a 13-mer Tat peptide derived from HIV-1 Tat.

Single acute-dose and repeat-doses toxicity of anti-HIV-1 PNA TAR-penetratin conjugate after intraperitoneal administration to mice.

Polyamide (peptide) nucleic acids conjugated with membrane-penetrating peptide are potential antisense therapeutic agents because of their unique chemical properties, high target specificity, and efficient cellular uptake. However, studies of their potential toxicity in animal models are lacking. In this study, we evaluated the toxicity of the response of Balb/C mice to anti-HIV-1 PNA TAR-penetratin conjugate targeted against the transactivation response (TAR) element of HIV-1 LTR.

Mechanism of RNA cleavage catalyzed by sequence specific polyamide nucleic acid-neamine conjugate.

In earlier studies, we found that a conjugate of neamine-polyamide nucleic acid targeting transactivation response element of HIV-1 RNA genome (HIV-1 TAR) displayed anti-HIV-1 activity and sequence-specific cleavage of the target RNA in vitro. Here we show that both the position of conjugation of polyamide nucleic acid (PNA) on neamine and the length of the spacer are critical parameters for conferring cleavage activity to the conjugate. The conjugation of PNA via a spacer incorporating 11 atoms to the 5-position of ring I of the neamine core conferred sequence-specific RNA cleavage activity on the conjugate, while conjugation to the 4'-position of ring II abolished this activity.

Anti HIV-1 virucidal activity of polyamide nucleic acid-membrane transducing peptide conjugates targeted to primer binding site of HIV-1 genome.

We have shown that polyamide nucleic acids (PNAs) targeted to the PBS (PNA(PBS)) and A-loop (PNA(A-loop)) sequences, when transfected into cells, inhibit HIV-1 replication by blocking the initiation of reverse transcription via destabilizing tRNA(3)(Lys) primer from the viral genome. Here we demonstrate that both PNA(PBS) and PNA(A-loop) conjugated with the membrane-transducing peptide (MTD) vectors penetratin and Tat are rapidly taken up by cells and inhibit HIV-1 replication. Moreover, MTD peptide conjugates of PNA(PBS) and PNA(A-loop) displayed potent virucidal activity against HIV-1.

Identification of cellular factors associated with the 3'-nontranslated region of the hepatitis C virus genome.

Chronic infection by hepatitis C virus (HCV) is the leading cause of severe hepatitis that often develops into liver cirrhosis and hepatocellular carcinoma. The molecular mechanisms underlying HCV replication and pathogenesis are poorly understood. Similarly, the role(s) of host factors in the replication of HCV remains largely undefined.