How does influenza virus a escape from amantadine?

Effects of Cholesterol on the Partitioning of a Drug Molecule in Lipid Bilayers

Drug molecules either bind to membrane-bound targets or permeate through cell membranes to reach intracellular targets, and hence, their membrane partition and permeation are of great importance. Here, we studied the effects of cholesterol on the partition of amantadine, an antiflu drug molecule, into 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayers using molecular dynamics simulations. The membrane partition of amantadine is sensitive to the cholesterol mole fraction (x_chol). In the absence of cholesterol, amantadine is stably bound in membranes, but at x_chol = 32%, it can escape to the aqueous phase, in agreement with recent experiments. The reduced membrane partition of amantadine at a high cholesterol content is mainly due to the perturbation of the bilayer structure and dynamics. Surrounding lipids stabilize amantadine by having their tails wrapped around the drug molecule, and this ability is compromised when cholesterol is present to increase the order in lipid tails. The atomic details on interactions with lipids and perturbations by cholesterol revealed here provide insight into membrane partition and delivery of drug molecules to their targets.

Resistance-Mutation (N31) Effects on Drug Orientation and Channel Hydration in Amantadine-Bound Influenza A M2

The mechanism of amantadine binding to the S31 variant of the M2 protein of Influenza A is well understood, but the reasons behind N31 M2 amantadine insensitivity remain under investigation. Many molecular dynamics studies have evaluated the influence of amantadine position within the channel pore on its ability to inhibit proton conductance in M2, but little is known about the influence of amantadine rotational orientation. Replica-exchange umbrella sampling, steered, and classic molecular dynamics simulations were performed on amantadine in the solid-state NMR structure of S31 M2 and an N31 M2 homologue, both in the homotetramer configuration, to explore the effects of the position and tilt angle of amantadine on inhibition of the M2 channel. Steered simulations show that amantadine rotates with the amine toward the bulk water as it passes into the hydrophobic entryway lined by Val27 side chains. Results from all simulation types performed indicate that amantadine has a strong, specific orientation with the amine turned inward toward the central cavity in the S31 M2 pore but has variable orientation and a strong propensity to remain outward pointing in N31 M2. Free energy profiles from umbrella sampling, measured relative to bulk water, show amantadine binds more strongly to the S31 M2 pore by 8 kcal/mol in comparison to amantadine in the N31 pore, suggesting that it can escape more readily from the N31 channel through the Val27 secondary gate, whereas it is captured by the S31 channel in the same region. Lower water density and distribution near amantadine in S31 M2 reveal that the drug inhibits proton conductance in S31 M2 because of its inward-pointing configuration, whereas in N31 M2, amantadine forms hydrogen bonds with an N31 side chain and does not widely occlude water occupancy in any configuration. Both amantadine's weaker binding to and weaker water occlusion in N31 M2 might contribute to its inefficacy as an inhibitor of the mutant protein.

Why bound amantadine fails to inhibit proton conductance according to simulations of the drug-resistant influenza A M2 (S31N)

The mechanisms responsible for drug resistance in the Asn31 variant of the M2 protein of influenza A are not well understood. Molecular dynamics simulations were performed on wild-type (Ser31) and S31N influenza A M2 in the homotetramer configuration. After evaluation of 13 published M2 structures, a solid-state NMR structure with amantadine bound was selected for simulations, an S31N mutant structure was developed and equilibrated, and the native and mutant structures were used to determine the binding behavior of amantadine and the dynamics of water in the two channels. Amantadine is stable in the plugging region of wild-type M2, with the adamantane in contact with the Val27 side chains, while amantadine in S31N M2 has more variable movement and orientation, and spontaneously moves lower into the central cavity of the channel. Free energy profiles from umbrella sampling support this observation. In this configuration, water surrounds the drug and can easily transport protons past it, so the drug binds without blocking proton transport in the S31N M2 channel.

Preliminary success in the characterization and management of a sudden breakout of a novel H7N9 influenza A virus

Influenza has always been one of the major threats to human health. The Spanish influenza in 1918, the pandemic influenza A/H1N1 in 2009, and the avian influenza A/H5N1 have brought about great disasters or losses to mankind. More recently, a novel avian influenza A/H7N9 broke out in China and until December 2, 2013, it had caused 139 cases of infection, including 45 deaths. Its risk and pandemic potential attract worldwide attention. In this article, we summarize epidemiology, virology characteristics, clinical symptoms, diagnosis methods, clinical treatment and preventive measures about the avian influenza A/H7N9 virus infection to provide a reference for a possible next wave of flu outbreak.

Exploring the proton conductance and drug resistance of BM2 channel through molecular dynamics simulations and free energy calculations at different pH conditions

BM2 channel plays an important role in the replication of influenza virus B. However, few studies attempt to investigate the mechanism of the proton conductance in BM2 channel, as well as the drug resistance of the BM2 channel. The first experimental structure of the BM2 protein channel has recently been solved, enabling us to theoretically study BM2 systems with different protonation states of histidine. By performing molecular dynamics simulations on the BM2 systems with different protonation states of four His19 residues, we provided our understanding of the structure, dynamics, and drug resistance of the BM2 channel. In general, the results of our study and other investigations both have demonstrated that whether the BM2 channel adopts an open or a closed form depends on the protonation state of His19. Meanwhile, we discovered that a drug (amantadine) was unable to enter into the center of the BM2 channel even at a low pH condition probably due to the number of hydrophilic residues of the BM2 channel. Finally, potentials of mean force (PMF) calculations were performed for the drug binding BM2 channel, energetically explaining why the BM2 channel exhibited drug resistance to two inhibitors of the AM2 channel, amantadine and rimantadine.

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

The M2 channel protein on the influenza A virus membrane has become the main target of the anti-flu drugs amantadine and rimantadine. The structure of the M2 channel proteins of the H3N2 (PDB code 2RLF) and 2009-H1N1 (Genbank accession number GQ385383) viruses may help researchers to solve the drug-resistant problem of these two adamantane-based drugs and develop more powerful new drugs against influenza A virus. In the present study, we searched for new M2 channel inhibitors through a combination of different computational methodologies, including virtual screening with docking and pharmacophore modeling. Virtual screening was performed to calculate the free energies of binding between receptor M2 channel proteins and 200 new designed ligands. After that, pharmacophore analysis was used to identify the important M2 protein-inhibitor interactions and common features of top binding compounds with M2 channel proteins. Finally, the two most potential compounds were determined as novel leads to inhibit M2 channel proteins in both H3N2 and 2009-H1N1 influenza A virus.

Toward an evolutionary containment of evolving pathogen-receptors by using an ensemble of multiple mutant ligands: from the viewpoint of fitness landscape in sequence space

It is known that even if a ligand peptide is designed to bind to a target receptor on the surface of a pathogen such as viruses, bacteria or cancer cells, it is likely that some receptors are subject to random mutation and thus the ligand has a reduced ability to bind to these receptors. This issue is known as drug-resistant or escape mutants. In this paper, we present an idea to inhibit the evolving receptors by using an ensemble of all possible single- or double-point mutant sequences of the ligand peptide. Several mutant ligands in the ensemble are expected to bind to the mutant receptors, and then the ensemble may create a defensive wall surrounding the target receptors in receptor-sequence space. We examined the effectiveness of this "evolutionary containment" of the evolving receptors through eight peptide-protein complex systems, which were retrieved from the Protein Data Bank (PDB). As a result, we obtained a suggestion that the original (or parent) ligand sequence should be designed to have as high fitness as possible but to be not local optima, in order to maximize the rate of the evolutionary containment. This may be a strategy of the drug-design against evolving pathogens.

Structural and dynamic mechanisms for the function and inhibition of the M2 proton channel from influenza A virus

The M2 proton channel from influenza A virus, a prototype for a class of viral ion channels known as viroporins, conducts protons along a chain of water molecules and ionizable sidechains, including His37. Recent studies highlight a delicate interplay between protein folding, proton binding, and proton conduction through the channel. Drugs inhibit proton conduction by binding to an aqueous cavity adjacent to M2's proton-selective filter, thereby blocking access of proton to the filter, and altering the energetic landscape of the channel and the energetics of proton-binding to His37.