By utilising the high-resolution 3D structure of an ion channel, researchers were able to develop peptidic positive allosteric modulators that can positively modulate the channel and exhibit long-lasting analgesic effects.
Pain is universal. From stubbing your toe on the corner of your bed to tearing a muscle when you overexert yourself, we grit our teeth in agony and cry out, but only for a while. Chronic pain, however, is ongoing and lasts for a prolonged period, usually more than six months. It can significantly lower a patient’s quality of life and bring about huge socio-economic costs. While analgesics like opioids and non-steroidal anti-inflammatory drugs are available, they are typically less effective against chronic pain, hence there is a need to look into the molecular mechanisms of pain and design safe and effective analgesic drugs.
With the rapid development of techniques in structural biology like single-particle cryo-electron microscopy, three-dimensional structures of many key proteins have been revealed. For example, the structure of at least one member of essentially every major ion channel family has been successfully resolved. As such, it is a step in the right direction to utilise numerous high-resolution 3D structures to aid in the development of drugs targeting specific proteins.
In collaboration with researchers at UC Davis and Qingdao University, the team led by Professor Yang Fan from the Department of Biophysics at the Zhejiang University School of Medicine utilised the high-resolution structure of an ion channel to develop peptidic positive allosteric modulators (PAMs) that were able to positively modulate the channel and exhibit long-lasting analgesic effects.
The transient receptor potential vanilloid 1 (TRPV1) ion channel is a prototypical sensor involved in nociception, or pain sensation, that facilitates the flow of calcium ions across cell membranes, converting pain and stimulus signals into meaningful neural electrical signals. Both the agonists and antagonists of TRPV1 have been found to effectively alleviate pain. Altogether, this makes TRPV1 a promising target for the development of analgesic drugs. However, as TRPV1 is heat-activated and involved in body temperature regulation, blocking the channel could result in hypothermia in clinical trials and thereby further hinder drug development.
To address this limitation, instead of using agonists and antagonists to regulate TRPV1 ion channel activity, PAMs that selectively fine-tune the high-activity population of TRPV1 could be used to exert analgesic effects. To this end, the researchers utilised a peptidic design approach, which took advantage of computational protein design systems and detailed information from structural and functional investigations in TRPV1. Through this approach, previous studies have reported that the ankyrin repeat-like domain (ARD) of the TRPV1 ion channel is crucial for ligand-induced desensitisation.
From there, the team first improved the optimised hotspot centric approach (OHCA) protein design strategy to increase the success rate of obtaining robust designed binders. Then, they applied the improved computational protein design approach to precisely target the specific domain of TRPV1, achieving positive allosteric modulation. In addition to that, both the crystal structure of the ARD and the cryo-electron microscopy structures of TRPV1 were established.
With a combination of their OHCA design, fluorescence resonance energy transfer imaging, protein chemistry, and a series of other tests, the team were able to demonstrate that two out of three of their designed PAMs were able to positively modulate the TRPV1 channel. Furthermore, they also reported longer-lasting analgesic effects in rats without inducing hypothermia.
This study demonstrates how high-resolution 3D structures allow for better rational drug design based on the structures of target proteins, effectively saving time, costs, and the number of failed attempts. “In this study, we made an attempt to design regulatory molecules targeting specific structural domains, which will provide theoretical support and new ideas for the development of analgesic drugs targeting the TRPV1 channel,” said Yang. “The OHCA computational design strategy can also be widely applied to the development of regulatory molecules for various protein drug targets with known 3D structures.”
Source: Xu et al. (2021). De Novo Design of Peptidic Positive Allosteric Modulators Targeting TRPV1 with Analgesic Effects. Advanced Science, 2101716.