Effect of stacking interactions on charge transfer states in photoswitches interacting with ion channels

The activity of ion channels can be reversibly photo-controlled via the binding of molecular photoswitches, often based on an azobenzene scaffold. Those azobenzene derivatives interact with aromatic residues of the protein via stacking interactions. In the present work, the effect of face-to-face and t-shaped stacking interactions on the excited state electronic structure of azobenzene and p-diaminoazobenzene integrated into the Na V1.4 channel is computationally investigated. The formation of a charge transfer state, caused by electron transfer from the protein to the photoswitches, is observed. This state is strongly red shifted when the interaction takes place in a face-to-face orientation and electron donating groups are present on the aromatic ring of the amino acids. The low-energy charge transfer state can interfere with the photoisomerization process after excitation to the bright state by leading to the formation of radical species. </p

Membrane permeation of psychedelic tryptamines by dynamic simulations

Renewed scientific interest in psychedelic compounds represents one of the most promising avenues for addressing the current burden of mental health disorders. Classic psychedelics are a group of compounds that exhibit structural similarities to the naturally occurring neurotransmitter serotonin (5-HT). Acting on the 5-HT type 2A receptors (HT2ARs), psychedelics induce enduring neurophysiological changes that parallel their therapeutic psychological and behavioral effects. Recent preclinical evidence suggests that the ability of psychedelics to exert their action is determined by their ability to permeate the neuronal membrane to target a pool of intracellular 5-HT2ARs. In this computational study, we employ classical molecular dynamics simulations and umbrella sampling techniques to investigate the permeation behavior of 12 selected tryptamines and to characterize the interactions that drive the process. We aim at elucidating the impact of N-alkylation, indole ring substitution and positional modifications, and protonation on their membrane permeability. Dimethylation of the primary amine group and the introduction of a methoxy group at position 5 exhibited an increase in permeability. Moreover, there is a significant influence of positional substitutions on the indole groups, and the protonation of the molecules substantially increases the energy barrier at the center of the bilayer, making the compounds highly impermeable. All the information extracted from the trends predicted by the simulations can be applied in future drug design projects to develop psychedelics with enhanced activityPID2020-117806GA-I0

Binding of azobenzene and p-diaminoazobenzene to the human voltage-gated sodium channel Nav1.4

The activity of voltage-gated ion channels can be controlled by the binding of photoswitches inside their internal cavity and subsequent light irradiation. We investigated the binding of azobenzene and p-diaminoazobenzene to the human Nav1.4 channel in the inactivated state by means of Gaussian accelerated molecular dynamics simulations and free-energy computations. Three stable binding pockets were identified for each of the two photoswitches. In all the cases, the binding is controlled by the balance between the favorable hydrophobic interactions of the ligands with the nonpolar residues of the protein and the unfavorable polar solvation energy. In addition, electrostatic interactions between the ligand and the polar aminoacids are also relevant for p-diaminoazobenzene due to the presence of the amino groups on the benzene moieties. These groups participate in hydrogen bonding in the most favorable binding pocket and in long-range electrostatic interactions in the other pockets. The thermodinamically preferred binding sites found for both photoswitches are close to the selectivity filter of the channel. Therefore, it is very likely that the binding of these ligands will induce alterations in the ion conduction through the channel

Next-generation sequencing and metagenomic analysis advances plant virus diagnosis and discovery

The advent of next generation sequencing (NGS) technologies dramatically advanced our ability to comprehensively investigate diseases of unknown etiology and expedited the entire process of virus discovery, identification, viral genome sequencing and, subsequently, the development of routine assays for new viral pathogens. Unlike traditional techniques, these novel approaches require no preliminary knowledge of the suspected virus(es). Currently, the RNA-Seq approach has been widely used to identify new viruses in infected plants, by analyzing virus-derived small interfering RNA populations, single- and double-stranded RNA (dsRNA) molecules extracted from infected plants. The method generates sequence in an unbiased fashion, likely allowing to detect all viruses that are present in a sample. We applied the Illumina NGS, coupled with metagenomic analysis, to generate large sequence dataset in different woody crops affected by diseases of unknown origin or infected with uncharacterized viruses or new strains. This approach allowed the identification of five novel viral species and, in addition, the sequencing of the whole genome of several viruses and viroids infecting Citrus spp., Prunus spp., grapes, fig, hazelnut, olive, persimmon and mulberry. Combined analysis of the datasets generated by using either siRNA fractions and dsRNA templates, enhanced the characterization of the whole virus-derived sequences in the infected tissues. Furthermore, profiling small RNAs from virus-infected plants led to a better understanding of host-plant response to virus and viroid infections in perennial plants. A general bioinformatic pipeline and an experimental validation strategy were developed and its application illustrated

MoBioTools: a toolkit to setup quantum mechanics/molecular mechanics calculations

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch caseSpanish Ministry of Science and Innovation; MCIN/AEI, Grant/Award Numbers: PID2020-117806GA-I00, PID2019-110091GB-I00; María de Maeztu, Grant/Award Number: CEX2018-000805-M; Comunidad de Madrid, Grant/Award Number: 2018-T1/BMD-10261; Xunta de Galicia, Grant/Award Number: GRC2019/24; the European Social Fund; Spanish Ministry of Education and Vocational Training, Grant/Award Number: FPU19/02292; Universidade de Vigo, Grant/Award Number: PREUVIGO-21; Universidad Autonoma de Madri

Light-Induced Control of Voltage Gated Ion Channels

Voltage gated ion channels are transmembrane proteins responsible for the generation and propagation of action potentials in excitable cells. They are key targets in receptor pharmacology, since the simple actions of opening and closing their pore with different kinetics or conductivity have been associated with a large number of channelopaties. Crystal structures of ion channels became available only in the last decades and, in combination with mutagenesis data, allowed the identification of drugs able to modulate ion conduction. However, most of the traditional modulators are not selective and present adverse side effects. Photopharmacology is establishing a new approach to overcome the problem of selectivity often present in voltage gated ion channels due to highly conserved binding regions among channels of the same subfamily. In this review, we describe the central pore region of Voltage gated sodium and potassium channels from a structural and pharmacological perspective, characterizing the binding mode of natural toxins and synthetic compounds able to physically occlude ion conduction. In addition, a bridge is created between classical pharmacology and photopharmacology, describing the approaches aimed to control the activity of voltage gated ion channels by photosensitive drugs