Discovery of potential M2 channel inhibitors based on the amantadine scaffold via virtual screening and pharmacophore modeling

Compounds based on Adamantyl-substituted Amino Acids and Peptides as Potential Antiviral Drugs Acting as Viroporin Inhibitors

The discussion has revolved around the derivatives of amino acids and peptides containing carbocycles and their potential antiviral activity in vitro against influenza A, hepatitis C viruses, and coronavirus. Studies conducted on cell cultures reveal that aminoadamantane amino acid derivatives exhibit the capacity to hinder the replication of viruses containing viroporins. Furthermore, certain compounds demonstrate potent virucidal activity with respect to influenza A/H5N1 and hepatitis C virus particles. A conceptual framework for viroporin inhibitors has been introduced, incorporating carbocyclic motifs as membranotropic carriers in the structure, alongside a functional segment comprised of amino acids and peptides. These components correspond to the interaction with the inner surface of the channel's pore or another target protein.

Aloe vera and its Components Inhibit Influenza A Virus-Induced Autophagy and Replication

Aloe vera ethanol extract (AVE) reportedly has significant anti-influenza virus activity, but its underlying mechanisms of action and constituents have not yet been completely elucidated. Previously, we have confirmed that AVE treatment significantly reduces the viral replication of green fluorescent protein-labeled influenza A virus in Madin-Darby canine kidney (MDCK) cells. In addition, post-treatment with AVE inhibited viral matrix protein 1 (M1), matrix protein 2 (M2), and hemagglutinin (HA) mRNA synthesis and viral protein (M1, M2, and HA) expressions. In this study, we demonstrated that AVE inhibited autophagy induced by influenza A virus in MDCK cells and also identified quercetin, catechin hydrate, and kaempferol as the active antiviral components of AVE. We also found that post-treatment with quercetin, catechin hydrate, and kaempferol markedly inhibited M2 viral mRNA synthesis and M2 protein expression. A docking simulation suggested that the binding affinity of quercetin, catechin hydrate, and kaempferol for the M2 protein may be higher than that of known M2 protein inhibitors. Thus, the inhibition of autophagy induced by influenza virus may explain the antiviral activity of AVE against H1N1 or H3N2. Aloe vera extract and its constituents may, therefore, be potentially useful for the development of anti-influenza agents.

On the role of water density fluctuations in the inhibition of a proton channel

Hv1 is a transmembrane four-helix bundle that transports protons in a voltage-controlled manner. Its crucial role in many pathological conditions, including cancer and ischemic brain damage, makes Hv1 a promising drug target. Starting from the recently solved crystal structure of Hv1, we used structural modeling and molecular dynamics simulations to characterize the channel's most relevant conformations along the activation cycle. We then performed computational docking of known Hv1 inhibitors, 2-guanidinobenzimidazole (2GBI) and analogs. Although salt-bridge patterns and electrostatic potential profiles are well-defined and distinctive features of activated versus nonactivated states, the water distribution along the channel lumen is dynamic and reflects a conformational heterogeneity inherent to each state. In fact, pore waters assemble into intermittent hydrogen-bonded clusters that are replaced by the inhibitor moieties upon ligand binding. The entropic gain resulting from releasing these conformationally restrained waters to the bulk solvent is likely a major contributor to the binding free energy. Accordingly, we mapped the water density fluctuations inside the pore of the channel and identified the regions of maximum fluctuation within putative binding sites. Two sites appear as outstanding: One is the already known binding pocket of 2GBI, which is accessible to ligands from the intracellular side; the other is a site located at the exit of the proton permeation pathway. Our analysis of the waters confined in the hydrophobic cavities of Hv1 suggests a general strategy for drug discovery that can be applied to any ion channel.

Investigation of the free energy profiles of amantadine and rimantadine in the AM2 binding pocket

The purpose of this work was to study the mechanism of drug resistance of M2 channel proteins by analyzing the interactions between the drugs amantadine and rimantadine and M2 channel proteins (including the wild type and the three mutants V27A, S31N, and G34A) and the drug binding pathways, by use of a computational approach. Our results showed that multiple drug-binding sites were present in the M2 channel, and the trajectory of the drugs through the M2 channel was determined. A novel method was developed to investigate of free energy profiles of the ligand-protein complexes. Our work provides a new explanation of the large amount of experimental data on drug efficacy.

Discovery of Potential, Non-Toxic Influenza Virus Inhibitor by Computational Techniques

Influenza infection continues to be a major problem in many parts of the world. Rimantadine is a first-line drug used to treat the influenza infection by targeting M2 proton channel. However, S31N mutation in M2 proton channel diminishes the efficiency of rimantadine and creates resistance. To address this issue, the present study was aimed to screen the effective lead candidate against drug resistance strain of influenza from DrugBank database. Initially, the lead molecules were filtered using Lipinski rule of five and the drug likeliness property. Subsequently, the data reduction was carried out by employing molecular docking study. Finally, molecular dynamics simulations techniques were performed to validate the lead compound. Most importantly, the -p LD50 of the screened lead molecule was calculated using CORAL software to estimate the Rat oral toxicity. Accordingly, memantine may possibly become a promising lead compound of rimantadine-resistant influenza virus strain.

The inhibitory effect of iridoid glycoside extracted from Fructus Gardeniae on intracellular acidification and extracellular Ca2+ influx induced by influenza A virus

Influenza is a serious public health problem that causes severe illnesses and deaths for higher risk populations. Iridoid glycoside is one of the main active components from Fructus Gardeniae with antivirus and anti-inflammatory characteristics. The present study was designed to investigate the inhibitory effect of iridoid glycoside extracted from Fructus Gardeniae (IGE) on influenza and explore the potential mechanism of the action. In vitro, IGE exhibited highest activity against influenza virus A/FM1/47 induced visible cytopathic effect (CPE), with half maximal inhibitory concentration and therapeutic index values of 3.15 mg/mL and 11.37, respectively, and the replication of influenza virus A/FM1/47 was inhibited markedly by IGE at the concentrations of 25, 12.5 and 6.25 mg/mL. In vivo, treatment of mice with IGE decreased pulmonary index, viral titers and M2 protein expression in a dose-dependent manner. IGE increased the declining pHi induced by influenza virus significantly at the concentrations of 25 and 12.5 mg/mL 0.5 or 1 h post-infection, respectively. IGE treatment inhibited elevation of [Ca2+]i significantly at the concentrations of 25 and 12.5 mg/mL 0.5, 1 or 24 h post-infection, respectively. In addition, IGE reduced the rate of early-apoptotic cells at the concentrations of 25, 12.5 and 6.25 mg/mL, but showed no apparent effect on the rate of late-apoptotic cells. Our study demonstrates that IGE possesses antiviral activity against influenza A virus, and the antiviral action might be related to the inhibition of intracellular acidification and Ca2+ influx during fusion and uncoating of influenza replication cycle.

Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications

The discovery of new drugs that selectively block or modulate ion channels has great potential to provide new treatments for a host of conditions. One promising avenue revolves around modifying or mimicking certain naturally occurring ion channel modulator toxins. This strategy appears to offer the prospect of designing drugs that are both potent and specific. The use of computational modeling is crucial to this endeavor, as it has the potential to provide lower cost alternatives for exploring the effects of new compounds on ion channels. In addition, computational modeling can provide structural information and theoretical understanding that is not easily derivable from experimental results. In this review, we look at the theory and computational methods that are applicable to the study of ion channel modulators. The first section provides an introduction to various theoretical concepts, including force-fields and the statistical mechanics of binding. We then look at various computational techniques available to the researcher, including molecular dynamics, brownian dynamics, and molecular docking systems. The latter section of the review explores applications of these techniques, concentrating on pore blocker and gating modifier toxins of potassium and sodium channels. After first discussing the structural features of these channels, and their modes of block, we provide an in-depth review of past computational work that has been carried out. Finally, we discuss prospects for future developments in the field.