ABSTRACT

INTRODUCTION

Ion channels are proteins forming a pore that allows the flow of ions across membranes. Ion channels are voltage or ligand gated. Some of these proteins help nerve cells to transmit pain signals to the central nervous system and are therefore promising targets for the development of pain therapeutics.

Transient receptor potential channels (TRPs) are a family of 28 human cellular ion channels, varying in homology to each other but all with six transmembrane regions in common, and are nonselectively permeable to cations. There are seven subfamilies that can be divided into two groups. Group 1 includes TRPC, TRPV, TRPA, TRPM, TRPN, and group 2 comprises TRPP and TRPML (1). Compounds perceived as hot stimulate the vanilloid receptor (TRPV). At the same time, this receptor plays a crucial role in pain mediation and is therefore an interesting drug target. Known pungent chemicals with high receptor affinity such as capsaicin or resiniferatoxin were lead structures in drug development toward desensitization (2). Recent research focuses on novel analgesic mechanisms like positive allosteric modulation (3) and broad-spectrum TRP antagonists (4).

The mechanism of cold-induced analgesia was unclear until the discovery of TRPM8. This receptor is also known as the cold or menthol receptor (5). It is activated by cold temperatures and cooling agents, such as menthol or icilin, allowing the entry of Na+ and Ca2+ to the cell (6). Two modulating mechanisms are generally discussed. Whereas antagonists physically block the receptor for cold and menthol, agonists activate TRPM8 and generate a cooling sensation. Selective ligands could be used as a new generation of analgesic drugs in neuropathic pain (7,8).

TRPA1 plays a key role in chemical sensing in the inflammatory pain pathway. Many small molecules, including ingredients like wasabi, horseradish, garlic and mustard oil, can activate the channel. Recently, it has been shown that desensitizing TRPA1 could help in the treatment of neuropathic pain (9,10).

The human Ether-à-go-go Related Gene (hERG) channel or KCNH2 is a voltage-gated potassium channel. It has been the focus of pharmaceutical research for years because the inhibition of hERG potassium channels by drugs can lead to cardiac arrhythmia (11). In 2010, Stary and colleagues published a homology model (12) and a group from Canada investigated structural mechanisms of state-dependent drug binding (13). The different binding sites for ions and compounds are defined and the International Conference of Harmonization set up guidelines for drug development. Therefore, new screening methods for the prediction of drug liability to the hERG channel have been developed (14).

Voltage-gated sodium channels are activated through action potential firing. They represent the target for local anesthetic agents. It is challenging to find selective inhibitors of sodium channels in the pain pathway. Genotyping of families suffering from congenital indifference to pain identified mutations in gene coding for Nav1.7 channels (15). A lot of research is performed to find specific blockers to the treatment of pain and epilepsy (16).

There are some complementary resources on ion channels. Multiple analysis for voltage-gated potassium channels from different species is compiled in the voltage-gated potassium channel database VKCDB (17). Protein–protein interactions (PPIs) are the focus of the TRIP database (18): Shin and colleagues manually curated 653 PPIs for mammalian TRP channels. MoleOnline 2.0 (19) is a web server that provides interactive channel analysis to identify active sites.

The International Union of Basic and Clinical Pharmacology (IUPHAR) database provides information on human and rodent receptors (20).

There is a need for a specific resource for pain-relieving compounds targeting ion channels and their 3D homology models so researchers can identify targets and putative ligands.

MATERIALS AND METHODS

Here, we shortly describe our methods used. If you are interested in further details, please read the ‘About’ page on our Web site.

RESULTS

Docking

The docking of 6000 TRPV1, P2X, ASIC and hERG ligands in >1000 different binding poses revealed five binding poses for each ligand. Figure 1 shows capsaicin in the binding site of TRPV1 in an active interactive view. These binding poses were chosen regarding energetic conditions. The results are embedded into the database. Each ligand can be displayed in different manners, as well as the receptor itself (ball and stick, spacefill, etc.). Holding the left mouse button while moving the mouse leads to a rotation. A right click brings up a drop-down menu for zooming, measurements, color adjustments, etc. Safari or Tablet users can use their common gestures to navigate through the docking results. Each binding pose can be exported as a graphic (PNG) or file (MOL).

Figure 1.

Capsaicin in TRPV1. Capsaicin was put into the homology model of TRPV1 using a high-throughput docking algorithm. Each docked ligand is shown in the interactive view.

Usage of the database

There are different ways to use the database and browse through the data. Figure 2summarizes the main functionalities of the Web site.

Figure 2.

Main functionalities of ‘SuperPain’. The database provides information on pain-related ion channels, as well as 3D structures and interactive docking results. The ‘Compound’ search enables users to find ligands regarding…

‘Receptor’ holds information on pain-related ion channels. The homology model of TRPV1 and docking results can be found there.

There are two search boxes in the ‘Compounds’ section. Specific compounds can be found through a property search by typing in the name, PubChem ID, IUPAC or SMILES. It is also possible to search for a specific target such as TRPV1 or hERG or to select certain features like purchasability, IC50, EC50, molweight, rotatable bonds, etc. On the results page, information on compounds including vendors is listed in a table. This table can be used as a starting point for a similarity search or to compare structures directly by viewing the compound clusters. In the ‘Cluster’ section all clusters are listed with one compound of the cluster. A search box enables quick access to a distinct cluster. Clicking on a compound also enables browsing through different clusters. The heatmaps are diagonally divided to compare similarity (Tanimoto) and affinity (IC50). Mouseover shows the structure of the compared compounds. Clicking leads to a comparison page with information about (co-) affinities, as well as chemical information and vendors.

DISCUSSION

SuperPain aims at providing a comprehensive resource on ligands for pain-related ion channels.

Acid sensing ion channels (ASICs) belong to the degenerin-epithelial sodium channel superfamily and are voltage independent. They are activated by extracellular acidosis and are involved in different processes, such as taste, mechanosensation and nociception (27). Recently, it has been shown that mambalgin, a three-finger peptide from the venom of the black mamba, suppresses pain in mice without toxicity and fewer side effects than morphine (28). These findings show that ASICs are promising targets in the treatment of pain, especially to avoid addiction problems (29).

In traditional Chinese medicine, tetramethylprazine, sodium ferrulate and puerarin are used in the therapy of pain. It has been found that these compounds target some P2X receptors. These ligand-gated ion channels open in response to binding of adenosine 5′-triphosphaste (ATP). Advances in radiographic crystallography allow in silico ligand docking and P2X receptors are becoming therapeutically important drug targets (30).

Further potassium channels of interest are the TWIK-related spinal cord potassium channel (TRESK) and TREK-1. TRESK is a two-pore domain potassium channel that is mainly expressed in dorsal root and trigeminal ganglia (31). This channel is involved in acute and chronic pain and plays an important role in migraine pathogenesis, which makes it a promising target (32). TREK-1 is an interesting target because of its co-expression with TRPV1 and its involvement in polymodal pain perception (33). The present intensive research on 3D structures will improve the development of channel modulators. For example, there are different binding sites for agonists and antagonists (34). The binding sites of the ion channels are rather large, which allows binding of a variety of compounds if certain physiochemical property conditions are fulfilled. This is reflected by the great diversity of the pain-related compounds. They show a low mean similarity of 0.4 compared with other targets like PARP (0.6). It is also important to find out more about the interactions or co-inhibition of different receptors for pain. In the database, they can be found by choosing ‘MultiTarget’ from the ‘Compound Properties’ search box. For example, menthol is known to be an inhibitor of TRPM8 with a half maximal effective concentration (EC50) of 29 000 nM. At the same time, it has also inhibitory potency on TRPA1 with an EC50 of 28 400 nM. Cannabigerol is a compound that occurs naturally in hemp strains. In contrast to other cannabinoids, it is nonpsychoactive because it is not only a α2-adrenergic receptor agonist, but also a mild CB1 receptor antagonist (35). Although the compound is not well-studied, it has been found to lower the intraocular pressure (36) and there is some research on treating inflammatory bowel diseases with cannabigerol (37). ‘SuperPain’ stores affinities for TRPA1, TRPM8 and TRPV1 for the compound. These experimentally determined co-affinities suggest that these multi-target compounds might be promising for the development of pain therapeutics (38).

FUNDING

SynSys (EU Framework 7) and DKTK (BMBF). Funding for open access charge: SynSys (EU Framework 7).

Conflict of interest statement. None declared.

ACKNOWLEDGEMENTS

REFERENCES