SARS-CoV-2 drug discovery: COVID-19 virus ion channels


10-05-2021
As well as the spike (S) protein which binds to human cells, there are other transmembrane proteins including the M class and the viroporin envelope protein (E) ion channel.

By Dr Marc Rogers, Chief Scientific Officer at Metrion Biosciences; an Ion Channel focused CRO.

The global pandemic of coronavirus disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) remains prevalent and a key target for novel medicines drug discovery.

This article offers background into ion channels as key (and often overlooked) drug discovery targets and explains how modulating SARS-CoV-2 Viroporin activity can potentially limit COVID-19 virus infectivity.  It is discussed that screening approved drugs against COVID-19 viroporins could also result in the identification of drug repurposing hits that can be used on patients, particularly those not able to receive vaccination due to compromised immune systems.

Introduction

Ion channels are well validated drug discovery targets based on their widespread distribution in the human body and involvement in many critical activities within the brain, heart, smooth muscle and endocrine organs. Additional validation is provided by channelopathy mutations associated with common diseases such as epilepsy and cardiac arrythmia as well as in many rare disease patient populations.1

In addition, ion channels are expressed in human disease vectors (e.g. malaria parasite) and infective agents such as bacteria and viruses, presenting new areas where ion channel drug discovery can deliver novel therapeutic approaches and agents to improve human health.2

The creation of novel therapeutics

The SARS-CoV-2 virus is a very topical example of where this second approach can be applied to the creation of novel therapeutics, as the sequencing of the COVID-19 genome in early 2020 revealed the presence of several envelope E protein and putative ion channel genes.3 Numerous academic groups have begun to target COVID-19 viral ion channels (viroporins) during the course of the pandemic to understand their structure–function and utility as anti-viral drug substrates, including a group from Massachusetts Institute of Technology (MIT) that recently published the NMR solution structure of the E ion channel protein that they used for initial ligand screening.4

This study from MIT illustrates some of the challenges of modern ion channel drug discovery techniques, which can affect the identification of novel ligands for both human and viral ion channel proteins. Firstly, having a novel gene sequence may allow homology mapping onto the structure of related and better characterised protein structures, but brings with it issues of evolutionary and functional diversification. For example, although the influenza virus M2 cation channel has been studied for many years,2 the MIT group found that the COVID-19 coronavirus E protein has a very different structure once expressed in a biological membrane, and thus inferences from homology modeling may be misleading.

Secondly, it is now possible to obtain high-fidelity protein structures, including that of SARS-CoV-2 viroporins,5 and use sophisticated computing software to implement structure-based drug design approaches whereby known drug structures are virtually bound to the target of interest. The MIT study provides an example of the risk in using such an approach for a novel protein, as the prediction that anandamide, a relatively potent inhibitor of the ‘flu M2 cation channel, could also efficaciously inhibit the COVID-19 ion channel was not borne out as only weak micromolar affinity was seen in their NMR binding experiments.

The way forward towards discovering effective inhibitors

This recent study does however point the way towards discovering effective inhibitors of SARS-CoV-2 viral ion channels with therapeutic potential. The MIT group managed to express a viral channel protein in lipid membranes, which will allow for functional screening of modulators that can affect channel biophysics and ionic flux through the pore. It is possible to screen for viroporin modulators using functional bacterial and yeast assays,6 but it is unclear at this stage if these hit compounds will deliver antiviral activity in human cells and patients.

Identifying drug re-purposing hits that can be used on patients

Nevertheless, identification of selective ligands will enable testing the hypothesis, that modulating SARS-CoV-2 viroporin activity can limit COVID-19 virus infectivity or replication in intact cellular systems, as shown for SARS CoV E protein. This COVID-19 viroporin target and mechanistic validation should also be done genetically, using RNA knockdown or CRISPR editing in human respiratory cell lines and patient lung samples, as it was for the original SARS viroporin. Finally, screening approved clinical drugs against COVID-19 viroporins could rapidly identify drug repurposing hits that can be used on patients, especially those not suited to vaccination owing to compromised immune systems.

Conclusion

The ultimate hope is that academic and industry groups can identify repurposed and novel drugs to inhibit a range of viral ion channels and thus offer an alternative strategy to treat both current endemic viral diseases as well as pandemic infections of the future.

Image:  As well as the spike (S) protein which binds to human cells, there are other transmembrane proteins including the M class and the viroporin envelope protein (E) ion channel.

References

1. Imbrici P, Liantonio, A, Camerino GM, et al. Therapeutic approaches to genetic ion channelopathies and perspectives in drug discovery. Front. Pharmacol. 2016. doi:10.3389/fphar.2016.00121
2. Charlton FW, Pearson HM, Hover S, et al. Ion channels as therapeutic targets for viral infections: Further discoveries and future perspectives. Viruses. 2020;12(8):844. doi:10.3390/v12080844
3. McClenaghan C, Hanson A, Lee S-J, Nichols CG. Coronavirus proteins as ion channels: Current and potential research. Front. Immunol. 2020. doi:10.3389/fimmu.2020.573339
4. Mandala VS, McKay MJ, Shcherbakov AA, et al. Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers. Nat Struct Mol Biol. 2020;27:1202-1208. doi:10.1038/s41594-020-00536-8
5. Kern DM, Sorum B, Hoel CM, et al. Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs. bioRxiv. 2020. doi:10.1101/2020.06.17.156554 (preprint)
6. Tomar and Arkin. SARS-CoV-2 E protein is a potential ion channel that can be inhibited by Gliclazide and Memantine. Biochem Biophys Res Commun. 2020;530(1):10-14. doi:10.1016/j.bbrc.2020.05.206

This article was originally published on Technology Networks

 

Dr Marc RogersDr Marc Rogers

Marc trained as a physiologist and neuroscientist in New Zealand and Australia before graduating with a PhD from the John Curtin School of Medical Research at the Australian National University in Canberra, Australia. He then embarked on an extensive postdoctoral career in the US which included fellowships at Baylor College in Houston, Texas, University of Hawaii in Honolulu, and finally UCSF in San Francisco. Marc then left academia to start a new career in ion channel drug discovery, beginning at Exelixis in the Bay Area before moving to the UK in 2005 to work at Xention on voltage- and ligand-gated ion channels involved in atrial fibrillation, immunology and pain. Marc then led the management buy-out of the biology group to create Metrion Biosciences in 2015, a specialist ion channel CRO that has steadily grown in size and value and worked on a wide variety of ion channel proteins brought to us by clients across the globe.

 

 

Metrion Biosciences is a UK-based pre-clinical Contract Research Organization (CRO) focused on delivering a range of high quality ion channel drug discovery services. We provide highly skilled electrophysiology screening services to support client medicinal chemistry optimisation programmes, CiPA compliant cardiac safety profiling assays, neuroscience assays and translational assays.

Metrion Biosciences