Labelled animal toxins as selective molecular markers of ion channels: Applications in neurobiology and beyond

The scorpion toxin BeKm-1 blocks hERG cardiac potassium channels using an indispensable arginine residue

BeKm-1 is a peptide toxin from scorpion venom that blocks the pore of the potassium channel hERG (Kv11.1) in the human heart. Although individual protein structures have been resolved, the structure of the complex between hERG and BeKm-1 is unknown. Here, we used molecular dynamics and ensemble docking, guided by previous double-mutant cycle analysis data, to obtain an in silico model of the hERG-BeKm-1 complex. Adding to the previous mutagenesis study of BeKm-1, our model uncovers the key role of residue Arg20, which forms three interactions (a salt bridge and hydrogen bonds) with the channel vestibule simultaneously. Replacement of this residue even by lysine weakens the interactions significantly. In accordance, the recombinantly produced BeKm-1R20K mutant exhibited dramatically decreased activity on hERG. Our model may be useful for future drug design attempts.

Effect of animal venom toxins on the main links of the homeostasis of mammals (Review)

The human body is affected by environmental factors. The dynamic balance between the organism and its environment results from the influence of natural, anthropogenic and social aspects. The factors of exogenous origin determine development of adaptive changes. The present article summarises the mechanisms of animal venom toxins and homeostasis disruption in the body of mammals. The mechanisms underlying pathological changes are associated with shifts in biochemical reactions. Components of the immune, nervous and endocrine systems are key in the host defense and adaptation processes in response to venom by triggering signalling pathways (PI3kinase pathway, arachidonic acid cascade). Animal venom toxins initiate the development of inflammatory processes, the synthesis of pro-inflammatory mediators (cytokines), ROS, proteolytic enzymes, activate the migration of leukocytes and macrophages. Keratinocytes and endothelial cells act as protective barriers under the action of animal venom toxins on the body of mammals. In addition, the formation of pores in cell membranes, structural changes in cell ion channels are characteristic of the action of animal venom toxins.

Kalium 3.0 is a comprehensive depository of natural, artificial, and labeled polypeptides acting on potassium channels

Here, we introduce the third release of Kalium database (http://kaliumdb.org/), a manually curated comprehensive depository that accumulates data on polypeptide ligands of potassium channels. The major goal of this amplitudinous update is to summarize findings for natural polypeptide ligands of K+ channels, as well as data for the artificial derivatives of these substances obtained over the decades of exploration. We manually analyzed more than 700 original manuscripts and systematized the information on mutagenesis, production of radio- and fluorescently labeled derivatives, and the molecular pharmacology of K+ channel ligands. As a result, data on more than 1200 substances were processed and added enriching the database content fivefold. We also included the electrophysiological data obtained on the understudied and neglected K+ channels including the heteromeric and concatenated channels. We associated target channels in Kalium with corresponding entries in the official database of the International Union of Basic and Clinical Pharmacology. Kalium was supplemented with an adaptive Statistics page, where users are able to obtain actual data output. Several other improvements were introduced, such as a color code to distinguish the range of ligand activity concentrations and advanced tools for filtration and sorting. Kalium is a fully open-access database, crosslinked to other databases of interest. It can be utilized as a convenient resource containing ample up-to-date information about polypeptide ligands of K+ channels.

AgTx2-GFP, Fluorescent Blocker Targeting Pharmacologically Important Kv1.x (x = 1, 3, 6) Channels

The growing interest in potassium channels as pharmacological targets has stimulated the development of their fluorescent ligands (including genetically encoded peptide toxins fused with fluorescent proteins) for analytical and imaging applications. We report on the properties of agitoxin 2 C-terminally fused with enhanced GFP (AgTx2-GFP) as one of the most active genetically encoded fluorescent ligands of potassium voltage-gated K_v1.x (x = 1, 3, 6) channels. AgTx2-GFP possesses subnanomolar affinities for hybrid KcsA-K_v1.x (x = 3, 6) channels and a low nanomolar affinity to KcsA-K_v1.1 with moderate dependence on pH in the 7.0-8.0 range. Electrophysiological studies on oocytes showed a pore-blocking activity of AgTx2-GFP at low nanomolar concentrations for K_v1.x (x = 1, 3, 6) channels and at micromolar concentrations for K_v1.2. AgTx2-GFP bound to K_v1.3 at the membranes of mammalian cells with a dissociation constant of 3.4 ± 0.8 nM, providing fluorescent imaging of the channel membranous distribution, and this binding depended weakly on the channel state (open or closed). AgTx2-GFP can be used in combination with hybrid KcsA-K_v1.x (x = 1, 3, 6) channels on the membranes of E. coli spheroplasts or with K_v1.3 channels on the membranes of mammalian cells for the search and study of nonlabeled peptide pore blockers, including measurement of their affinity.

Combining mKate2-Kv1.3 Channel and Atto488-Hongotoxin for the Studies of Peptide Pore Blockers on Living Eukaryotic Cells

The voltage-gated potassium Kv1.3 channel is an essential component of vital cellular processes which is also involved in the pathogenesis of some autoimmune, neuroinflammatory and oncological diseases. Pore blockers of the Kv1.3 channel are considered as potential drugs and are used to study Kv1 channels' structure and functions. Screening and study of the blockers require the assessment of their ability to bind the channel. Expanding the variety of methods used for this, we report on the development of the fluorescent competitive binding assay for measuring affinities of pore blockers to Kv1.3 at the membrane of mammalian cells. The assay constituents are hongotoxin 1 conjugated with Atto488, fluorescent mKate2-tagged Kv1.3 channel, which was designed to improve membrane expression of the channel in mammalian cells, confocal microscopy, and a special protocol of image processing. The assay is implemented in the "mix and measure", format and allows the screening of Kv1.3 blockers, such as peptide toxins, that bind to the extracellular vestibule of the K⁺-conducting pore, and analyzing their affinity.

Characterising ion channel structure and dynamics using fluorescence spectroscopy techniques

Ion channels undergo major conformational changes that lead to channel opening and ion conductance. Deciphering these structure-function relationships is paramount to understanding channel physiology and pathophysiology. Cryo-electron microscopy, crystallography and computer modelling provide atomic-scale snapshots of channel conformations in non-cellular environments but lack dynamic information that can be linked to functional results. Biophysical techniques such as electrophysiology, on the other hand, provide functional data with no structural information of the processes involved. Fluorescence spectroscopy techniques help bridge this gap in simultaneously obtaining structure-function correlates. These include voltage-clamp fluorometry, Förster resonance energy transfer, ligand binding assays, single molecule fluorescence and their variations. These techniques can be employed to unearth several features of ion channel behaviour. For instance, they provide real time information on local and global rearrangements that are inherent to channel properties. They also lend insights in trafficking, expression, and assembly of ion channels on the membrane surface. These methods have the advantage that they can be carried out in either native or heterologous systems. In this review, we briefly explain the principles of fluorescence and how these have been translated to study ion channel function. We also report several recent advances in fluorescence spectroscopy that has helped address and improve our understanding of the biophysical behaviours of different ion channel families.

Apamin structure and pharmacology revisited

Apamin is often cited as one of the few substances selectively acting on small-conductance Ca²⁺-activated potassium channels (K_Ca2). However, published pharmacological and structural data remain controversial. Here, we investigated the molecular pharmacology of apamin by two-electrode voltage-clamp in Xenopus laevis oocytes and patch-clamp in HEK293, COS7, and CHO cells expressing the studied ion channels, as well as in isolated rat brain neurons. The microtitre broth dilution method was used for antimicrobial activity screening. The spatial structure of apamin in aqueous solution was determined by NMR spectroscopy. We tested apamin against 42 ion channels (K_Ca, K_V, Na_V, nAChR, ASIC, and others) and confirmed its unique selectivity to K_Ca2 channels. No antimicrobial activity was detected for apamin against Gram-positive or Gram-negative bacteria. The NMR solution structure of apamin was deposited in the Protein Data Bank. The results presented here demonstrate that apamin is a selective nanomolar or even subnanomolar-affinity K_Ca2 inhibitor with no significant effects on other molecular targets. The spatial structure as well as ample functional data provided here support the use of apamin as a K_Ca2-selective pharmacological tool and as a template for drug design.

Site-Specific Fluorescent Labeling of the Cysteine-Rich Toxin, DkTx, for TRPV1 Ion Channel Imaging and Membrane Binding Studies

Peptide toxins secreted by venomous animals bind to mammalian ion channel proteins and modulate their function. The high specificity of these toxins for their target ion channels enables them to serve as powerful tools for ion channel biology. Toxins labeled with fluorescent dyes are employed for the cellular imaging of channels and also for studying toxin-channel and toxin-membrane interactions. Several of these toxins are cysteine-rich, rendering the production of properly folded fluorescently labeled toxins technically challenging. Herein, we evaluate a variety of site-specific protein bioconjugation approaches for producing fluorescently labeled double-knot toxin (DkTx), a potent TRPV1 ion channel agonist that contains an uncommonly large number of cysteines (12 out of a total of 75 amino acids present in the protein). We find that popular cysteine-mediated bioconjugation approaches are unsuccessful as the introduction of a non-native cysteine residue for thiol modification leads to the formation of misfolded toxin species. Moreover, N-terminal aldehyde-mediated bioconjugation approaches are also not suitable as the resultant labeled toxin lacks activity. In contrast to these approaches, C-terminal bioconjugation of DkTx via the sortase bioconjugation technology yields functionally active fluorescently labeled DkTx. We employ this labeled toxin for imaging rat TRPV1 heterologously expressed in Xenopus laevis oocytes, as well as for performing membrane binding studies on giant unilamellar vesicles composed of different lipid compositions. Our studies set the stage for using fluorescent DkTx as a tool for TRPV1 biology and provide an informative blueprint for labeling cysteine-rich proteins.

Atto488-Agitoxin 2—A Fluorescent Ligand with Increased Selectivity for Kv1.3 Channel Binding Site

Fluorescently labeled peptide blockers of ion channels are useful probes in studying the localization and functioning of the channels and in the performance of a search for new channel ligands with bioengineering screening systems. Here, we report on the properties of Atto488-agitoxin 2 (A-AgTx2), a derivative of the Kv1 channel blocker agitoxin 2 (AgTx2), which was N-terminally labeled with Atto 488 fluorophore. The interactions of A-AgTx2 with the outer binding sites of the potassium voltage-gated Kv1.x (x = 1, 3, 6) channels were studied using bioengineered hybrid KcsA–Kv1.x (x = 1, 3, 6) channels. In contrast to AgTx2, A-AgTx2 was shown to lose affinity for the Kv1.1 and Kv1.6 binding sites but to preserve it for the Kv1.3 site. Thus, Atto488 introduces two new functionalities to AgTx2: fluorescence and the selective targeting of the Kv1.3 channel, which is known for its pharmacological significance. In the case of A-AgTx2, fluorescent labeling served as an alternative to site-directed mutagenesis in modulating the pharmacological profile of the channel blocker. Although the affinity of A-AgTx2 for the Kv1.3 binding site was decreased as compared to the unlabeled AgTx2, its dissociation constant value was within a low nanomolar range (4.0 nM). The properties of A-AgTx2 allow one to use it for the search and study of Kv1.3 channel blockers as well as to consider it for the imaging of the Kv1.3 channel in cells and tissues.

Snake Toxins Labeled by Green Fluorescent Protein or Its Synthetic Chromophore are New Probes for Nicotinic acetylcholine Receptors

Fluorescence can be exploited to monitor intermolecular interactions in real time and at a resolution up to a single molecule. It is a method of choice to study ligand-receptor interactions. However, at least one of the interacting molecules should possess good fluorescence characteristics, which can be achieved by the introduction of a fluorescent label. Gene constructs with green fluorescent protein (GFP) are widely used to follow the expression of the respective fusion proteins and monitor their function. Recently, a small synthetic analogue of GFP chromophore (p-HOBDI-BF₂) was successfully used for tagging DNA molecules, so we decided to test its applicability as a potential fluorescent label for proteins and peptides. This was done on α-cobratoxin (α-CbTx), a three-finger protein used as a molecular marker of muscle-type, neuronal α7 and α9/α10 nicotinic acetylcholine receptors (nAChRs), as well as on azemiopsin, a linear peptide neurotoxin selectively inhibiting muscle-type nAChRs. An activated N-hydroxysuccinimide ester of p-HOBDI-BF₂ was prepared and utilized for toxin labeling. For comparison we used a recombinant α-CbTx fused with a full-length GFP prepared by expression of a chimeric gene. The structure of modified toxins was confirmed by mass spectrometry and their activity was characterized by competition with iodinated α-bungarotoxin in radioligand assay with respective receptor preparations, as well as by thermophoresis. With the tested protein and peptide neurotoxins, introduction of the synthetic GFP chromophore induced considerably lower decrease in their affinity for the receptors as compared with full-length GFP attachment. The obtained fluorescent derivatives were used for nAChR visualization in tissue slices and cell cultures.

Chimeras of KcsA and Kv1 as a bioengineering tool to study voltage-gated potassium channels and their ligands

Chimeric potassium channels KcsA-Kv1, which are among the most intensively studied hybrid membrane proteins to date, were constructed by replacing a part of the pore domain of bacterial potassium channel KcsA (K channel of streptomyces A) with corresponding regions of the mammalian voltage-gated potassium channels belonging to the Kv1 subfamily. In this way, the pore blocker binding site of Kv1 channels was transferred to KcsA, opening up possibility to use the obtained hybrids as receptors of Kv1-channel pore blockers of different origin. In this review the recent progress in KcsA-Kv1 channel design and applications is discussed with a focus on the development of new assays for studying interactions of pore blockers with the channels. A summary of experimental data is presented demonstrating that hybrid channels reproduce the blocker-binding profiles of parental Kv1 channels. It is overviewed how the KcsA-Kv1 chimeras are used to get new insight into the structure of potassium channels, to determine molecular basis for high affinity and selectivity of binding of peptide blockers to Kv1 channels, as well as to identify new peptide ligands.

N-Terminal Tagging with GFP Enhances Selectivity of Agitoxin 2 to Kv1.3-Channel Binding Site

Recently developed fluorescent protein-scorpion toxin chimeras (FP-Tx) show blocking activities for potassium voltage-gated channels of Kv1 family and retain almost fully pharmacological profiles of the parental peptide toxins (Kuzmenkov et al., Sci Rep. 2016, 6, 33314). Here we report on N-terminally green fluorescent protein (GFP)-tagged agitoxin 2 (GFP-L2-AgTx2) with high affinity and selectivity for the binding site of Kv1.3 channel involved in the pathogenesis of various (primarily of autoimmune origin) diseases. The basis for this selectivity relates to N-terminal location of GFP, since transposition of GFP to the C-terminus of AgTx2 recovered specific interactions with the Kv1.1 and Kv1.6 binding sites. Competitive binding experiments revealed that the binding site of GFP-L2-AgTx2 overlaps that of charybdotoxin, kaliotoxin 1, and agitoxin 2, the known Kv1.3-channel pore blockers. GFP-L2-AgTx2 was demonstrated to be applicable as a fluorescent probe to search for Kv1.3 pore blockers among individual compounds and in complex mixtures, to measure blocker affinities, and to visualize Kv1.3 distribution at the plasma membrane of Kv1.3-expressing HEK293 cells. Our studies show that definite combinations of fluorescent proteins and peptide blockers can result in considerable modulation of the natural blocker-channel binding profile yielding selective fluorescent ligands of certain channels.

Scorpion toxin MeuNaTxα-1 sensitizes primary nociceptors by selective modulation of voltage-gated sodium channels

Venoms are a rich source of highly specific toxins, which allow the identification of novel therapeutic targets. We have now applied high content screening (HCS) microscopy to identify toxins that modulate pain sensitization signaling in primary sensory neurons of rat and elucidated the underlying mechanism. A set of venoms and fractions thereof were analyzed for their ability to activate type II protein kinase A (PKA-II) and extracellular signal-regulated kinases (ERK1/2). We identified MeuNaTxα-1, a sodium channel-selective scorpion α-toxin from Mesobuthus eupeus, which affected both PKA-II and ERK1/2. Recombinant MeuNaTxα-1 showed identical activity to the native toxin on mammalian voltage-gated sodium channels expressed in Xenopus laevis oocytes and induced thermal hyperalgesia in adult mice. The effect of MeuNaTxα-1 on sensory neurons was dose-dependent and tetrodotoxin-sensitive. Application of inhibitors and toxin mutants with altered sodium channel selectivity demonstrated that signaling activation in sensory neurons depends on Na_V 1.2 isoform. Accordingly, the toxin was more potent in neurons from newborn rats, where Na_V 1.2 is expressed at a higher level. Our results demonstrate that HCS microscopy-based monitoring of intracellular signaling is a novel and powerful tool to identify and characterize venoms and their toxins affecting sensory neurons.

Optical Imaging in Brainsmatics

When neuroscience’s focus moves from molecular and cellular level to systems level, information technology mixes in and cultivates a new branch neuroinformatics. Especially under the investments of brain initiatives all around the world, brain atlases and connectomics are identified as the substructure to understand the brain. We think it is time to call for a potential interdisciplinary subject, brainsmatics, referring to brain-wide spatial informatics science and emphasizing on precise positioning information affiliated to brain-wide connectome, genome, proteome, transcriptome, metabolome, etc. Brainsmatics methodology includes tracing, surveying, visualizing, and analyzing brain-wide spatial information. Among all imaging techniques, optical imaging is the most appropriate solution to achieve whole-brain connectome in consistent single-neuron resolution. This review aims to introduce contributions of optical imaging to brainsmatics studies, especially the major strategies applied in tracing and surveying processes. After discussions on the state-of-the-art technology, the development objectives of optical imaging in brainsmatics field are suggested. We call for a global contribution to the brainsmatics field from all related communities such as neuroscientists, biologists, engineers, programmers, chemists, mathematicians, physicists, clinicians, pharmacists, etc. As the leading approach, optical imaging will, in turn, benefit from the prosperous development of brainsmatics.

Versatile spider venom peptides and their medical and agricultural applications

Spiders have been evolving complex and diverse repertoires of peptides in their venoms with vast pharmacological activities for more than 300 million years. Spiders use their venoms for prey capture and defense, hence they contain peptides that target both prey (mainly arthropods) and predators (other arthropods or vertebrates). This includes peptides that potently and selectively modulate a range of targets such as ion channels, receptors and signaling pathways involved in physiological processes. The contribution of these targets in particular disease pathophysiologies makes spider venoms a valuable source of peptides with potential therapeutic use. In addition, peptides with insecticidal activities, used for prey capture, can be exploited for the development of novel bioinsecticides for agricultural use. Although we have already reviewed potential applications of spider venom peptides as therapeutics (in 2010) and as bioinsecticides (in 2012), a considerable number of research articles on both topics have been published since, warranting an updated review. Here we explore the most recent research on the use of spider venom peptides for both medical and agricultural applications.