Our Technology

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Resistance mechanisms

There are several routes pathogens use to attain resistance against drugs that are meant to inhibit their spread. They may express enzymes that excrete or degrade the drugs. Conversely, the drug target in the virus may change. The latter route is widespread in viruses due to the low fidelity in replicating their genome.
Our work in the resistance mechanism aims to understand the resistance mechanism and, second, to attempt to determine the resistance options without any medical risk. 
Results from our group have uncovered the resistance mechanism of influenza against anti-viral agents. We have also been able to accurately predict all of the options that the virus may employ to evade such anti-viral drugs.

 

Selected publications:

  1. Assa D, Alhadeff R, Krugliak M, Arkin IT. Mapping the Resistance Potential of Influenza's H+ Channel against an Antiviral Blocker. J Mol Biol. 2016 Oct 9;428(20):4209-4217.

  2. Santner P, Martins JMDS, Laursen JS, Behrendt L, Riber L, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel. Biochemistry. 2018 Oct 16;57(41):5949-5956.

  3. Santner P, Martins JMDS, Kampmeyer C, Hartmann-Petersen R, Laursen JS, Stein A, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants. Biochemistry. 2018 Oct 16;57(41):5957-5968.

  4. Leonov H, Astrahan P, Krugliak M, Arkin IT. How do aminoadamantanes block the influenza M2 channel, and how does resistance develop? J Am Chem Soc. 2011 Jun 29;133(25):9903-11.

  5. Astrahan P, Flitman-Tene R, Bennett ER, Krugliak M, Gilon C, Arkin IT. Quantitative analysis of influenza M2 channel blockers. Biochim Biophys Acta. 2011 Jan;1808(1):394-8.

  6. Astrahan P, Arkin IT. Resistance characteristics of influenza to amino-adamantyls. Biochim Biophys Acta. 2011 Feb;1808(2):547-53.

  7. Astrahan P, Kass I, Cooper MA, Arkin IT. A novel method of resistance for influenza against a channel-blocking antiviral drug. Proteins. 2004 May 1;55(2):251-7.

DNA Strand

Genetic selections

Genetic selections are experiments in which a particular trait is examined based on its effect on viability. In particular, we have developed assays in which viral ion channels' activity is either essential or detrimental to bacterial growth. 
The first test examines if the viral channel activity can lead to membrane permeabilization, negatively impacting bacterial growth. As seen in numerous channels, channel activity hampers growth due to its deleterious impact on bacterial bioenergetics when expressed at increasing levels. Subsequently, one can identify channel-blocking drugs readily due to their ability to alleviate viral-driven growth retardation. 
The second experimental test that we perform examines potassium conductivity. Specifically, potassium-uptake deficient bacteria are incapable of growth unless the media is supplemented by potassium. However, when a channel capable of potassium transport is heterologously expressed, the bacteria can thrive even under low potassium media. Hence, the viral channel is essential to bacterial growth in this instance. 
When screening in the positive impact assay, a reciprocal picture is obtained for any blocker: potassium-uptake deficient bacteria experience growth enhancement due to the (low level) expression of the viral channel. Therefore, one can identify channel blockers since they result in growth retardation.

 

Selected publications:

  1. Singh Tomar PP, Arkin IT. SARS-CoV-2 E protein is a potential ion channel that can be inhibited by Gliclazide and Memantine. Biochem Biophys Res Commun. 2020 Sep 10;530(1):10-14.

  2. Tomar PPS, Oren R, Krugliak M, Arkin IT. Potential Viroporin Candidates From Pathogenic Viruses Using Bacteria-Based Bioassays. Viruses. 2019 Jul 9;11(7):632.

  3. Assa D, Alhadeff R, Krugliak M, Arkin IT. Mapping the Resistance Potential of Influenza's H+ Channel against an Antiviral Blocker. J Mol Biol. 2016 Oct 9;428(20):4209-4217.

  4. Taube R, Alhadeff R, Assa D, Krugliak M, Arkin IT. Bacteria-based analysis of HIV-1 Vpu channel activity. PLoS One. 2014 Oct 1;9(10):e105387.

  5. Astrahan P, Flitman-Tene R, Bennett ER, Krugliak M, Gilon C, Arkin IT. Quantitative analysis of influenza M2 channel blockers. Biochim Biophys Acta. 2011 Jan;1808(1):394-8.

Image by Fusion Medical Animation

Coronavirus channels

We have been studying viral membrane proteins from coronaviruses since the SARS pandemic's emergence in the winter of 2003/3. In particular, our focus has been on the E protein, which we characterized extensively in terms of its unique structure. More recently, in our studies of SARS-CoV-2, we have shown that its E protein is also a channel and, as such, an attractive drug target. Finally, screening efforts identified blocks of the E protein, which represent potential antiviral agents.

 

Selected publications:

  1. Singh Tomar PP, Krugliak M, Arkin IT. Identification of SARS-CoV-2 E Channel Blockers from a Repurposed Drug Library. Pharmaceuticals. 2021 14(7):604.

  2. Singh Tomar PP, Krugliak M, Arkin IT. Blockers of the SARS-CoV-2 3a Channel Identified by Targeted Drug Repurposing. Viruses 2021 13(3):532.

  3. Singh Tomar PP, Arkin IT. SARS-CoV-2 E protein is a potential ion channel that can be inhibited by Gliclazide and Memantine. Biochem Biophys Res Commun. 2020 Sep 10;530(1):10-14.

  4. Manor J, Arbely E, Beerlink A, Akkawi M, Arkin IT. Use of Isotope-Edited FTIR to Derive a Backbone Structure of a Transmembrane Protein. J Phys Chem Lett. 2014 Aug 7;5(15):2573-9.

  5. Arbely E, Granot Z, Kass I, Orly J, Arkin IT. A trimerizing GxxxG motif is uniquely inserted in the severe acute respiratory syndrome (SARS) coronavirus spike protein transmembrane domain. Biochemistry. 2006 Sep 26;45(38):11349-56.

  6. Khattari Z, Brotons G, Akkawi M, Arbely E, Arkin IT, Salditt T. SARS coronavirus E protein in phospholipid bilayers: an x-ray study. Biophys J. 2006 Mar 15;90(6):2038-50.

  7. Khattari Z, Brotons G, Arbely E, Arkin IT, Metzger TH, Salditt T. SARS E protein in phospholipid bilayers: an anomalous X-ray reflectivity study. Physica B Condens Matter. 2005 Feb 28;357(1):34-38.

  8. Arbely E, Khattari Z, Brotons G, Akkawi M, Salditt T, Arkin IT. A highly unusual palindromic transmembrane helical hairpin formed by SARS coronavirus E protein. J Mol Biol. 2004 Aug 13;341(3):769-79.

Image by Егор Камелев

Novel channels

Ion channels are proteins that enable salt and acid transport through membranes. They underpin neural conduction and numerous other processes in our body. Moreover, ion channels have traditionally been excellent drug targets. Viruses, too, have been shown to have ion channels, coined viroporins. Most importantly, in several instances, it was shown that the channel activity of the viroporin is critical for viral pathogenicity. Hence, viral ion channels represent excellent targets for pharmaceutical inhibition. 
Therefore, we have uncovered viral ion channels in other important human viruses, such as the dengue fever virus.

 

Selected publications:

  1. Singh Tomar PP., Krugliak, M., Singh, A., and Arkin, I.T. , Zika M - A Potential Viroporin: Mutational Study and Drug Repurposing. Biomedicines in press.

  2. Singh Tomar PP, Arkin IT. SARS-CoV-2 E protein is a potential ion channel that can be inhibited by Gliclazide and Memantine. Biochem Biophys Res Commun. 2020 Sep 10;530(1):10-14. 

  3. Tomar PPS, Oren R, Krugliak M, Arkin IT. Potential Viroporin Candidates From Pathogenic Viruses Using Bacteria-Based Bioassays. Viruses. 2019 Jul 9;11(7):632.