key: cord-0308323-3pre6j89
authors: Dayer, Mohammad Reza
title: Old Drugs for JAK-STAT Pathway Inhibition in COVID-19
date: 2020-10-23
journal: nan
DOI: 10.13140/rg.2.2.33735.73122
sha: 055f5d7884c902014d88915b0a8fb66e7b26850c
doc_id: 308323
cord_uid: 3pre6j89

The pandemic threat of COVID-19 with more than 37 million cases in which about 5 percent entering critical stage characterized by cytokine storm and hyperinflammatory condition, the state more often leads to admission to intensive care unit with rapid mortality. Janus kinase enzymes of Jak-1, Jak-2, Jak-3, and Tyk2 seem to be good targets for inhibition by medications to control cytokine storm in this context. In the present work, the inhibitory properties of different analgesic drugs on these targets are studied to assess their ability for clinical application from different points of view. Our docking results indicated that naproxen, methadone, and amitriptyline considering their higher binding energy, lower energy variance, and higher hydrophobicity, seem to express more inhibitory effects on Janus kinase enzymes than thats for approved inhibitors i.e. baricitinib and ruxolitinib. Accordingly, we suggest our wide list of candidate drugs including indomethacin, etodolac, buprenorphine, rofecoxib, duloxetine, valdecoxib, naproxen, methadone, and amitriptilin for clinical assessments for their usefulness in COVID-19 treatment, especially taking into account that up to now, there is no approved cure for this disease.

Janus kinase (JAK) is a family of intracellular tyrosine kinase enzymes that participate in signal transduction through cytokine receptors in the JAK-STAT pathway. There are two types of cytokine receptors; type-1, and type-II. Both of these receptors have no kinase activities and so they dependent on JAK enzymes for phosphorylation and signal transduction. The family of JAK is comprised of tyrosine kinase-2 (Tyk2), JAK-1, JAK-2, and JAK-3 enzymes. This enzyme Tyk2 is the first described member of this family. The enzyme collaborates with cytoplasmic domains of cytokine receptors (type I and II) for signal transduction induced by IL-6, IL-11, IFN-α, IFN-β, and IFN-γ cytokines. The JAK-1 enzyme uses the gamma chain of type-I receptor and participates in signal transduction from IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21 cytokines and also mediates signals through type-II receptor posed by IFN-α, IFN-β and IFN-γ.

The JAK-2 enzyme facilitates signal transduction through a type-I receptor that is induced by IL-3, IL-5, IL-6, IL-11, GM-CSF, EPO, TPO, GH, G-CSF and also signals through type-II receptor exerted by TFN-α, IFN-β and IFN-γ cytokines [3] [4] [5] [6] . Unlike the other Janus kinase enzymes, JAK-3 only mediates signals through type-I receptor that is induced by IL-2, IL-4, IL-7, IL-9, IL-15, IL-21 cytokines [7] [8] [9] [10] [11] [12] . In contemporary medicine, Janus kinase inhibitors are used as medications to interfere with JAK-STAT signaling pathways and to manage and control hyperinflammatory states or cytokine storms in severe diseases such as cancer and autoimmune diseases [13] [14] . Among JAK inhibitors some are approved for clinical use including ruxolitinib, against JAK1/JAK2, oclacitinib, against JAK1, baricitinib, against JAK1/JAK2, peficitinib, against JAK3, fedratinib, against JAK2 inhibitor and upadacitinib, against JAK1 pathways [15] [16] [17] [18] . There are also some JAK inhibitors, e.g. filgotinib, cerdulatinib, gandotinib, lestaurtinib, momelotinib, pacritinib, and abrocitinib which are in clinical trials for future applications [19] [20] [21] .

The newly emerging disease of COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease causes a pandemic threat with more than 37 million cases and more than 1 million deaths by October 2020 [27] [28] . It is well documented that COVID-19 patients experience a dramatic increase in plasma levels of different kinds of inflammatory cytokines that in server cases lead to profound infiltration of immune cells in the lungs with ultimate alveolar damage and death [22] [23] [24] [25] [26] .

3 Increasing the cytokines of IL-2, IL-6, IL-7, IL-10, G-CSF, GM-CSF, and IFN-γ in accordance with increasing different chemokines comprises the main cause for COVID-19 mortality, the state primarily mediated by JAK-STAT pathway [28] [29] [30] .

There are increasing efforts performed to control hyperinflammatory state in COVID-19 by application of Janus kinase inhibitors. Ruxolitinib is one of the approved inhibitors used in the clinic for treatment of myelofibrosis and selectively inhibits JAK-1 and JAK-2 shows reasonable effects on mitigating hyperinflammatory state in COVID-19 patients [27] [28] [29] [30] [31] [32] . Baricitinib is the next example of JAK inhibitors that is prescribed as anti-rheumatic drug for rheumatoid arthritis and significantly blocks both JAK1 and JAK2 decreases fever, breathlessness, cough and improves pulmonary function in COVID-19 patients [33] [34] .

There are also miscellaneous reports indicating the benefits of JAK inhibitors in COVID-19 treatment that encouraged us to search for new candidates among old analgesic or pain relief drugs for their ability in this context from a bioinformatics point of view [35] [36] [37] .

Coordinate structures for JAK enzymes:

Coordinate structures of JAK-1, JAK-2, JAK-3, and TyK2 enzymes with PDB IDs' of 4I5C, 2W1I, 3LXK, and 4GVJ, respectively were retrieved from protein data bank (https://www.rcsb.org/). These structures were obtained by the X-ray diffraction and refined at the resolutions of 2.1Å, 2.60Å, 2Å, and 2.03Å, respectively.

These structures were energy minimized in separate rectangular boxes with dimensions of 9.79×9.98×6.84nm, 7.87×7.62×9.27nm, 5.62×5.73×6.87nm, and 5.67×7.18×6.18nm dimensions respectively. The boxes were filled with SPCE water. The algorithm of the steepest descent algorithm, neutral pH, 37°C temperature, 1atmosphere of pressure, and total energy of 200kj/mol was used as minimization criteria [38] [39] .

The coordinate structures of candidates drugs (selected from analgesics or pain relief drugs including almotriptan, amitriptyline, amlodipine, baricitinib, buprenorphine, celecoxib, diclofenac, duloxetine, ergotamine, esomeprazole, etodolac, famotidine, fentanyl, indomethacin, 4 lansoprazole, lasmiditan, methadone, nalbuphine, naloxone, naproxen, naratriptan, oxycodone, piroxicam, remifentanil, rimegepant, rofecoxib, ruxolitinib, sufentanil, sulindac, tofacitinib, ubrogepant and valdecoxib) in SDF format were retrieved from PubChem database (https://pubchem.ncbi.nlm.nih.gov/) and converted to PDB format with Open Babel software (http://openbabel.org/). The structures then were energy minimized in ArgusLab software (http://www.arguslab.com/) [40] . Results and Discussion: Figure 1 -a represents sequence alignment results for Janus kinase enzymes. As it is clear, there are high sequence similarities between these enzymes in such a way that the overall structures and their binding site motifs indicate structural similarities (Figure 1-b) . However, the ligand binding properties of the enzymes are somewhat different that lead to different results seen in our docking experiments. Table 1 represents the docking results obtained for the studied drugs used as ligands and Jak-1, Jak-2, Jak-3, and TyK2 as receptors. The drugs with higher binding energies, lower variances, higher logPs', and higher degree of binding site occupancies seem to be better candidates for enzyme inhibition. normalize absolute values in 0 to 1 range and then summate them in a total cumulative index for this purpose (Table 2 ). It is of prime importance to note that, in these calculations we take the same contribution effect for all variables on the total effects of drugs, the assumption that could be under question quantitatively. 8

Based on our finding and as indicated in table 2, indomethacin, etodolac, buprenorphine, rofecoxib, duloxetine, valdecoxib, naproxen, methadone, and amitriptyline with higher total effects seem to be good candidates for further studies in JAK-STAT pathway blockage and cytokine storm control in chronic and severe disease of cancer, autoimmune and COVID-19 disease via clinical trials assessments.

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The author would like to express his thanks to the vice chancellor of research and technology of Shahid